Nanoscale profiling of evolving intermolecular interactions in ageing FUS condensates DOI Creative Commons
Alyssa Miller, Zenon Toprakcioglu, Seema Qamar

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 23, 2023

Abstract In addition to the native state, proteins can form liquid-like condensates, viscoelastic such as gels, well solid-like amyloid fibrils, crystals and amorphous materials. The material properties of these condensates play important roles in their cellular functions, with aberrant liquid-to-solid phase transitions having been implicated neurodegenerative diseases. However, molecular changes resultant across whole space are complex yet be fully understood. extreme sensitivity environment, which enables biological function, is also what makes protein particularly challenging experimental targets. Here, we provide a characterisation ageing behaviour full-length fused sarcoma (FUS) protein. We achieve this goal by using microfluidic sample deposition technology enable application surface-based techniques study condensates. first demonstrate that maintain relevant structural features physiologically-relevant conditions on surfaces. Then, combination atomic force microscopy vibrational spectroscopy, characterise spatio-temporal structure mechanical reveal local individual observe initially dynamic, fluid-like undergo global increase elastic response conferred an density cation-π intermolecular interactions. Solid-like structures at condensate-solvent interfaces, before heterogeneously propagating throughout aged fluid core. These solid composed heterogenous, non-amyloid β-sheets, stabilised hydrogen-bonding interactions not observed state. Overall, identifies conformations associated different physical states FUS establishing platform understand role condensate function dysfunction.

Language: Английский

Efficient inference of large pangenomes with PanTA DOI Creative Commons
Duc Quang Le, Nguyễn Anh Tiến, Son Hoang Nguyen

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: July 3, 2023

Abstract Pangenome analysis is an indispensable step in bacterial genomics to address the high variability of bacteria genomes. However, speed and scalability remain a challenge for pangenome inference software tools cope with fast-growing genomic collections. We present PanTA, package constructing pangenomes large show that PanTA exhibits unprecedented multiple times more efficient than current state-of-the-arts while maintaining similar accuracy. In addition, introduces novel mechanism construct progressively where new samples are added into existing without rebuilding accumulated collection from scratch. progressive mode, demonstrated consume orders magnitude less computational resource solutions managing growing microbial datasets. further can build entire >28000 Escherichia coli genomes RefSeq database on laptop computer 32 hours, highlighting practicality PanTA.The open source publicly available at https://github.com/amromics/panta under MIT license.

Language: Английский

Citations

7
Forest growth resistance and resilience to the 2018-2020 drought depend on tree diversity and mycorrhizal type DOI Creative Commons
Lena Sachsenmaier, Florian Schnabel, Peter Dietrich

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 25, 2024

Abstract The frequency of consecutive drought years is predicted to increase due climate change. These droughts have strong negative impacts on forest ecosystems. Mixing tree species proposed the resistance and resilience communities. However, this promising diversity effect has not yet been investigated under extreme conditions in context complementary mycorrhizal associations their potential role enhancing water uptake. Here, we investigate whether promotes growth responses are modulated by associations. We used inventory data (2015 – 2021) a young experiment Germany, manipulating richness (1, 2, 4 species) type (communities containing arbuscular (AM) or ectomycorrhizal (EM) species, both). For all communities, calculated basal area increment (BAI) periods before, during, after concepts quantify drought. found declines during 2018-2020 for most Contrary our hypothesis, did find that per se can buffer growth. while EM resistance, decreased with richness, they increased AM communities comprising both types. highlight among various mixtures, only those mixed types outperformed respective monocultures Further, drought, community tends segregate into “winner” “loser” terms diversity, indicating intensification competition. While cannot disentangle underlying mechanisms, clarify mycorrhiza findings suggest mixtures within could help safeguard forests against increasing frequency. Synthesis : Drought depend association diverse holds promise restoration face

Language: Английский

Citations

2
Insights into cyanobacterial blooms through the lens of omics DOI Creative Commons
Ve Van Le, Quynh-Giao Tran, So-Ra Ko

et al.

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 934, P. 173028 - 173028

Published: May 7, 2024

Cyanobacteria are oxygen-producing photosynthetic bacteria that convert carbon dioxide into biomass upon exposure to sunlight. However, favorable conditions cause harmful cyanobacterial blooms (HCBs), which the dense accumulation of at water surface or subsurface, posing threats freshwater ecosystems and human health. Understanding mechanisms underlying bloom formation is crucial for effective management. In this regard, recent advancements in omics technologies have provided valuable insights HCBs, raised expectations develop more control methods near future. This systematic literature review aims present genomic architecture, adaptive mechanisms, microbial interactions, ecological impacts HCBs through lens omics. Genomic analysis indicates genome plasticity cyanobacteria has enabled their resilience adaptation environmental changes. Transcriptomic investigations revealed use various strategies adapting stress. Additionally, metagenomic metatranscriptomic analyses emphasized significant role community regulating HCBs. Finally, we offer perspectives on potential opportunities further research field.

Language: Английский

Citations

2
Changes in Mean Seasonal Carbon Cycle Due to Climate Change DOI Creative Commons
Mauro Morichetti, Elia Vangi, Alessio Collalti

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 21, 2024

Abstract Through photosynthesis, forests absorb annually large amounts of atmospheric CO 2 . However, they also release back through respiration. These two, opposite in sign, fluxes determine, much the carbon that is stored or released to atmosphere. The mean seasonal cycle (MSC) an interesting metric associates phenology and (C) partitioning-allocation analysis within forest stands. Here we applied 3D-CMCC-FEM model analyzed its capability represent main C-fluxes, by validating against observed data, questioning if sink/source seasonality influenced under two scenarios climate change, five contrasting European sites. We found has, current conditions, robust predictive abilities estimating NEE. Model results predict a consistent reduction forest’s capabilities act as C-sink change stand-ageing at all Such predicted despite number annual days evergreen increasing over years, indicating downward trend. Similarly, deciduous forests, maintaining relatively stable throughout year century, show their overall capacity. Overall, both types sites future mitigating potential.

Language: Английский

Citations

2
A novel hybrid high speed mass spectrometer allows rapid translation from biomarker candidates to targeted clinical tests using 15N labeled proteins DOI Creative Commons
Maria Wahle, Philip M. Remes, Vincent Albrecht

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 2, 2024

Abstract Recent developments in affinity binder or mass spectrometry (MS)-based plasma proteomics are now producing panels of potential biomarker candidates for diagnosis prognosis. However, clinical validation and implementation these biomarkers remain limited by the reliance on dated triple quadrupole MS technology. Here, we evaluate a novel hybrid high-speed spectrometer, Stellar MS, which integrates robustness quadrupoles with enhanced capabilities an advanced linear ion trap analyzer. This instrument allows extremely rapid sensitive parallel reaction monitoring (PRM) MS3 targeting. The allowed targeting thousands peptides originally measured Orbitrap Astral achieving high reproducibility low coefficients variation (CV) as well sensitivity specificity sufficient more than top 1000 proteins. Furthermore, developed targeted assays alcohol-related liver disease (ALD) biomarkers, showcasing applications. Absolute quantification is typically requirement explore use 15 N labeled protein standards rapid, streamlined generic manner. Our results indicate that can bridge gap between discovery routine testing, enhancing diagnostic prognostic utility biomarkers.

Language: Английский

Citations

2
TREM2 expression level is critical for microglial state, metabolic capacity and efficacy of TREM2 agonism DOI
Astrid Feiten,

Kilian Dahm,

Bettina van Lengerich

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 22, 2024

Abstract Triggering receptor expressed on myeloid cells 2 (TREM2) is a central regulator of microglial activity and sequence variants are major risk factors for late onset Alzheimer’s disease (LOAD). To better understand the molecular functional changes associated with TREM2 signalling, we generated reporter mouse model observed gradual upregulation expression increasing plaque proximity. Isolated microglia were sorted based their transcriptomic profiles acquired in both wildtype APP transgenic animals, allowing us to disentangle versus pathology-specific effects. Bulk RNA-sequencing highlighted level-dependent immunometabolic pathways, enrichment genes oxidative phosphorylation cholesterol metabolism increased expression. confirm these findings, next analysed uptake fluorodeoxyglucose (FDG) examined metabolomic lipidomic profiles. Again, independent Aβ pathology, correlated FDG as well cellular redox, energetics, homeostasis. Finally, performed chronic treatment brain penetrant agonist identified window where most responsive. Thus, our data provide novel insights into TREM2-mediated regulation metabolic function informs current efforts bring agonists clinical application.

Language: Английский

Citations

2
Efficient inference of large prokaryotic pangenomes with PanTA DOI Creative Commons
Duc Quang Le, Nguyễn Anh Tiến, Son Hoang Nguyen

et al.

Genome biology, Journal Year: 2024, Volume and Issue: 25(1)

Published: Aug. 6, 2024

Pangenome inference is an indispensable step in bacterial genomics, yet its scalability poses a challenge due to the rapid growth of genomic collections. This paper presents PanTA, software package designed for constructing pangenomes large datasets, showing unprecedented efficiency levels multiple times higher than existing tools. PanTA introduces novel mechanism construct pangenome progressively without rebuilding accumulated collection from scratch. The progressive mode shown consume orders magnitude less computational resources solutions managing growing datasets. open source and publicly available at https://github.com/amromics/panta 10.6084/m9.figshare.23724705 .

Language: Английский

Citations

2
Spatiotemporal dynamics of cyanobacterium Dolichospermum lemmermannii populations in a bloom-prone region of Lake Superior DOI Creative Commons
Andrew W. Wood, Jake D. Callaghan,

Reane Loiselle

et al.

Journal of Great Lakes Research, Journal Year: 2024, Volume and Issue: unknown, P. 102455 - 102455

Published: Oct. 1, 2024

Language: Английский

Citations

2
Expression of Microcystis Biosynthetic Gene Clusters in Natural Populations Suggests Temporally Dynamic Synthesis of Novel and Known Secondary Metabolites in Western Lake Erie DOI
Colleen E. Yancey,

Fengan Yu,

Ashootosh Tripathi

et al.

Applied and Environmental Microbiology, Journal Year: 2023, Volume and Issue: 89(5)

Published: April 18, 2023

Microcystis spp. produce diverse secondary metabolites within freshwater cyanobacterial harmful algal blooms (cyanoHABs) around the world. In addition to biosynthetic gene clusters (BGCs) encoding known compounds, genomes harbor numerous BGCs of unknown function, indicating a poorly understood chemical repertoire. While recent studies show that produces several in lab and field, little work has focused on analyzing abundance expression its broader suite during cyanoHAB events. Here, we use metagenomic metatranscriptomic approaches track relative their transcripts throughout 2014 western Lake Erie cyanoHAB. The results indicate presence transcriptionally active are predicted synthesize both novel metabolites. these shifted bloom, with transcript levels correlating temperature, nitrate, phosphorus concentrations co-occurring predatory competitive eukaryotic microorganisms, suggesting importance abiotic biotic controls regulating expression. This highlights need for understanding ecology potential risks human environmental health posed by produced but often unmonitored. It also indicates prospects identifying pharmaceutical-like molecules from cyanoHAB-derived BGCs. IMPORTANCEMicrocystis dominate worldwide pose significant threats water quality through production metabolites, many which toxic. toxicity biochemistry microcystins other compounds have been studied, remains understood, leaving gaps our impacts ecosystem health. We used community DNA RNA sequences diversity genes synthesis natural populations assess patterns transcription cyanoHABs. Our reveal encode toxic as well ones may cryptic compounds. research targeted metabolite Erie, vital source United States Canada.

Language: Английский

Citations

5
Description of Pseudocalidococcus azoricus gen. sp. nov. (Thermosynechococcaceae, Cyanobacteria), a Rare but Widely Distributed Coccoid Cyanobacteria DOI Creative Commons
Rúben Luz, Rita Cordeiro, Jan Kaštovský

et al.

Diversity, Journal Year: 2023, Volume and Issue: 15(12), P. 1157 - 1157

Published: Nov. 21, 2023

Coccoid cyanobacteria represent an important part of cyanobacterial freshwater diversity, with many studied strains in public databases identified as Synechococcus. This is a diverse genus, both morphologically and ecologically, global distribution. However, the so-called Synechococcus-like could several independent genera that require further studies. In this work, four isolated from lakes terrestrial atmophytic habitats on São Miguel Flores Islands (Azores archipelago) were genetically using 16S rRNA 16S–23S ITS, light transmission electron microscopy, ecologically. A draft genome was produced reference strain by Illumina sequencing, which allowed more complete phylogenetic study deeper taxonomic analysis, revealing divergent evolution low ANI AAI values (69.4% 66.3%, respectively) to Thermosynechococcus, closest genus. Although similar Synechococcus, analysis placed clade sister inside Thermosynechococcaceae. Thus, Pseudocalidococcus azoricus gen. sp. nov. described new coccoid genus species Azores archipelago. detailed comparison morphological taxa provided, supporting separation The high genetic similarity other continents Synechococcus suggests probably has worldwide Future studies should be performed clarify identity those strains.

Language: Английский

Citations

4