bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic robustness to growth temperature of a cold adapted bacterium
Authors: Riccardi Christopher , Calvanese Marzia , Ghini Veronica , Alonso-Vásquez Tania , Perrin Elena , Turano Paola , Giurato Giorgio , Weisz Alessandro , Parrilli Ermenegilda , Tutino Maria Luisa , Fondi Marco 
Published: October 2022

AbstractMicrobial communities experience continuous environmental changes, among which temperature fluctuations are arguably the most impacting. This is particularly important considering the ongoing global warming but also in the “simpler” context of seasonal variability of sea-surface temperature. Understanding how microorganisms react at the cellular level can improve our understanding of possible adaptations of microbial communities to a changing environment. In this work, we investigated which are the mechanisms through which metabolic homeostasis is maintained in a cold-adapted bacterium during growth at temperatures that differ widely (15 and 0°C). We have quantified its intracellular and extracellular central metabolomes together with changes occurring at the transcriptomic level in the same growth conditions. This information was then used to contextualize a genome-scale metabolic reconstruction and to provide a systemic understanding of cellular adaptation to growth at two different temperatures. Our findings indicate a strong metabolic robustness at the level of the main central metabolites, counteracted by a relatively deep transcriptomic reprogramming that includes changes in gene expression of hundreds of metabolic genes. We interpret this as a transcriptomic buffering of cellular metabolism, able to produce overlapping metabolic phenotypes despite the wide temperature gap. Moreover, we show that metabolic adaptation seems to be mostly played at the level of few key intermediates (e.g. phosphoenolpyruvate) and in the cross-talk between the main central metabolic pathways. Overall, our findings reveal a complex interplay at gene expression level that contributes to the robustness/resilience of core metabolism, also promoting the leveraging of state-of-the-art multi-disciplinary approaches to fully comprehend molecular adaptations to environmental fluctuations.
Ribozyme-phenotype coupling in peptide-based coacervate protocells
Authors: Vay Kristian Le , Salibi Elia , Ghosh Basusree , Dora Tang T-Y , Mutschler Hannes 
Published: October 2022

AbstractCondensed coacervate phases are now understood to be important features of modern cell biology, as well as valuable protocellular models in origin of life studies and synthetic biology. In each of these fields, the development of model systems with varied and tuneable material properties is of great importance for replicating properties of life. Here, we develop a ligase ribozyme system capable of concatenating short RNA fragments into extremely long chains. Our results show that formation of coacervate microdroplets with the ligase ribozyme and poly(L-lysine) enhances ribozyme rate and yield, which in turn increases the length of the anionic polymer component of the system and imparts specific physical properties to the droplets. Droplets containing active ribozyme sequences resist growth, do not wet or spread on unpassivated surfaces, and exhibit reduced transfer of RNA between droplets when compared to controls containing inactive sequences. These altered behaviours, which stem from RNA sequence and catalytic activity, constitute a specific phenotype and potential fitness advantage, opening the door to selection and evolution experiments based on a genotype – phenotype linkage.
HSPB1 facilitates chemoresistance through inhibiting ferroptotic cancer cell death and regulating NF-κB signaling pathway in breast cancer
Authors: Liang Yiran , Wang Yajie , Zhang Yan , Ye Fangzhou , Luo Dan , Li Yaming , Jin Yuhan , Han Dianwen , Wang Zekun , Chen Bing , Zhao Wenjing , Wang Lijuan , Chen Xi , Ma Tingting , Kong Xiaoli , Yang Qifeng 
Published: October 2022

AbstractChemoresistance is one of the major causes of therapeutic failure and poor prognosis for breast cancer patients, especially for triple-negative breast cancer patients. However, the underlying mechanism remains elusive. Here, we identified novel functional roles of heat shock protein beta-1 (HSPB1), regulating the chemoresistance and ferroptotic cell death in breast cancer. Based on TCGA and GEO databases, HSPB1 expression was upregulated in breast cancer tissues and associated with poor prognosis of breast cancer patients, which was considered as an independent prognostic factor for breast cancer. Functional assays revealed that HSPB1 could promote cancer growth and metastasis in vitro and in vivo. Furthermore, HSPB1 facilitated doxorubicin resistance through protecting breast cancer cells from drug-induced ferroptosis. Mechanistically, HSPB1 could bind with Ikβ-α and promote its ubiquitination-mediated degradation, leading to increased nuclear translocation and activation of NF-κB signaling. In addition, HSPB1 overexpression led to enhanced secretion of IL6, which further facilitated breast cancer progression. These findings revealed that HSPB1 upregulation might be a key driver to progression and chemoresistance through regulating ferroptosis in breast cancer, while targeting HSPB1 could be an effective strategy against breast cancer.
On the genetic consequences of habitat contraction: edge effects and habitat loss
Authors: Sgarlata Gabriele Maria , Maié Tiago , de Zoeten Tiago , Rasteiro Rita , Chikhi Lounès 
Published: October 2022

AbstractNatural climate change and recent anthropogenic activities have largely contributed to habitat loss and fragmentation across the world, leading to 70% of worldwide remaining forests to be within 1 km of forest’s edges (Haddad et al., 2015). Ecological studies have shown that edge-effect influences ecological communities, species richness and abundance across many taxa, contributing to worldwide decline in biodiversity. Since edge-effect reduces species abundance and connectivity, it is also expected to negatively influence species genetic variation. In fact, previous theoretical studies had showed that populations closer to the edges of a finite stepping-stone model tends to have shorter coalescence times, and therefore, lower genetic diversity, than central populations. However, predicting the impact of edge effect on local genetic diversity remains challenging in realistic and more complex habitat fragments, where the additive effect of multiple edges is expected to take place. In the present study we explore the genetic consequence of habitat loss at the scale of a habitat fragment (patch-scale), looking at the interplay betweenpatch-sizeandedge-effecton spatial genetic diversity. We propose a statistical approach to estimate ‘edge-impacted effective population size’ from habitat cover information and use this measure to predict spatial genetic diversity in both equilibrium and non-equilibrium populations. We address these questions using spatially-explicit simulations and propose a spatially-explicit analytical framework able to model spatio-temporal changes in genetic diversity due to edge-effect and habitat loss.
Echolocating bats prefer a high risk-high gain foraging strategy to increase prey profitability
Authors: Stidsholt Laura , Hubancheva Antoniya , Greif Stefan , Goerlitz Holger R. , Johnson Mark , Yovel Yossi , Madsen Peter T. 
Published: October 2022

AbstractMost bats catch nocturnal prey during active flight guided by echolocation but some species depart from this ancestral behaviour to capture ground prey using passive listening. Here, we explore the costs and benefits of these hunting transitions by combining high-resolution biologging data and DNA metabarcoding to quantify the relative contributions of aerial and ground prey to the total food intake of wild greater mouse-eared bats. We show that these bats use both foraging strategies with similar average nightly captures of 25 small, aerial insects and 30 large, ground-dwelling insects per bat, but with higher capture success in air (78 % in air vs 30 % on ground). However, owing to the 3 to 20 times heavier ground prey, 85 % of the estimated nightly food acquisition comes from ground prey despite the 2.5 times higher failure rates. Further, we find that most bats use the same foraging strategy on a given night suggesting that bats adapt their hunting behaviour to weather and ground conditions. We conclude that prey switching matched to environmental dynamics plays a key role in covering the energy intake even in specialised predators.
Technical report on best practices for hybrid and long readde novoassembly of bacterial genomes utilizing Illumina and Oxford Nanopore Technologies reads
Authors: Hackl Simon T. , Harbig Theresa A. , Nieselt Kay 
Published: October 2022

AbstractThe emergence of commercial long read sequencing technologies in the 2010s and the concomitant development of new bioinformatics tools bears the potential ofde novogenome assemblies of unprecedented contiguity and quality. However, until today these novel technologies suffer from high rates of sequencing errors. These may be overcome by using long and short reads in combination, in so called hybrid approaches, or by increasing the through-put and thereby the coverage of sequencing runs. In particular the latter will thereby increase the cost of the assembly inevitably. Herein, to-date long read and hybrid assemblers were tested on real whole genome sequencing Illumina and Oxford Nanopore Technologies read data sets and sub samples of these in order to elaborate a best practice forde novoassembly. The findings suggest that although long reads alone can be used to reconstruct complete and contiguous genomes, in particular the single-nucleotide and indel error rate remains high compared to hybrid approaches and that this can impact downstream applications such as variation discovery and gene prediction negatively.
The role of hydrodynamic flow in the self-assembly of dragline spider silk proteins
Authors: Herrera-Rodríguez Ana M. , Dasanna Anil Kumar , Daday Csaba , Cruz-Chú Eduardo R. , Aponte-Santamaría Camilo , Schwarz Ulrich S. , Gräter Frauke 
Published: October 2022

AbstractHydrodynamic flow in the spider duct induces conformational changes in dragline spider silk proteins (spidroins) and drives their assembly, but the underlying physical mechanisms are still elusive. Here we address this challenging multiscale problem with a complementary strategy of atomistic and coarse-grained Molecular Dynamics (MD) simulations with uniform flow. The conformational changes at the molecular level were analyzed for single tethered spider silk peptides. Uniform flow leads to coiled-to-stretch transitions and pushes alanine residues intoβ-sheet and Poly-Proline II (PPII) conformations. Coarse-grained simulations of the assembly process of multiple semi-flexible block copolymers using multi-particle collision dynamics reveal that the spidroins aggregate faster but into low-order assemblies when they are less extended. At medium-to-large peptide extensions (50%-80%), assembly slows down and becomes reversible with frequent association and dissociation events, while spidroin alignment increases and alanine repeats form ordered regions. Our work highlights the role of flow in guiding silk self-assembly into tough fibers by enhancing alignment and kinetic reversibility, a mechanism likely relevant for other proteins whose function depends on hydrodynamic flow.
Overproduction of Native and Click-able Colanic Acid Slime from EngineeredEscherichia coli
Authors: Sadler Joanna C. , Brewster Richard C. , González Alba F. , Nirkko Jessica S. , Varzandeh Simon , Wallace Stephen 
Published: October 2022

ABSTRACTThe fundamental biology and application of bacterial exopolysaccharides is gaining increasing attention. However, current synthetic biology efforts to produce the major component ofEscherichia sp. slime, colanic acid, and functional derivatives thereof have been limited. Herein, we report the overproduction of colanic acid (up to 1.32 g/L) from D-glucose in an engineered strain ofE. coliJM109. Furthermore, we report that chemically-synthesized L-fucose analogues containing an azide motif can be metabolically incorporated into the slime layer via a heterologous fucose salvage pathway fromBacteroides sp. and used in a click reaction to attach an organic cargo to the cell surface. This molecular engineered bio-polymer possesses enormous potential as a new tool for use in chemical, biological and materials research.
Rugged fitness landscapes minimize promiscuity in the evolution of transcriptional repressors
Authors: Meger Anthony T. , Spence Matthew A. , Sandhu Mahakaran , Jackson Colin J. , Raman Srivatsan 
Published: October 2022

ABSTRACTHow a protein’s function influences the shape of its fitness landscape, smooth or rugged, is a fundamental question in evolutionary biochemistry. Smooth landscapes arise when incremental mutational steps lead to a progressive change in function, as commonly seen in enzymes and binding proteins. On the other hand, rugged landscapes are poorly understood because of the inherent unpredictability of how sequence changes affect function. Here, we experimentally characterize the entire sequence phylogeny, comprising 1158 extant and ancestral sequences, of the DNA-binding domain (DBD) of the LacI/GalR transcriptional repressor family. Our analysis revealed an extremely rugged landscape with rapid switching of specificity even between adjacent nodes. Further, the ruggedness arises due to the necessity of the repressor to simultaneously evolve specificity for asymmetric operators and disfavors potentially adverse regulatory crosstalk. Our study provides fundamental insight into evolutionary, molecular, and biophysical rules of genetic regulation through the lens of fitness landscapes.
SETD2 safeguards the genome against isochromosome formation
Authors: Mason Frank M. , Kounlavong Emily S. , Tebeje Anteneh T. , Dahiya Rashmi , Guess Tiffany , Vlach Logan , Norris Stephen R. , Lovejoy Courtney A. , Dere Ruhee , Ohi Ryoma , Ly Peter , Walker Cheryl L. , Rathmell W. Kimryn 
Published: October 2022

SummaryFactors governing the faithful replication of chromosomes are essential for cellular and genomic integrity. While a variety of mechanisms to manage breaks and promote repair of DNA are widely recognized, epigenetic landmarks that preserve telomere-to-telomere replication fidelity and prevent genome instability are not well-understood. SETD2 is the histone methyltransferase responsible for trimethylation on histone H3 lysine 36 and is newly recognized as a tumor suppressor that acts to maintain genome stability. Importantly, SETD2 is frequently lost in cancers that exhibit extensive intratumoral heterogeneity. Here, we demonstrate that loss ofSETD2and H3K36me3 promotes chromosome segregation errors and DNA bridging during mitosis, and that these bridges are driven by the formation of dicentric chromosomes. Cytogenetic analyses revealed that these chromosomes were comprised of mirror-imaged isochromosomes and isodicentric chromosomes that contain two active centromeres. These data demonstrate that the SETD2 histone methyltransferase is essential to prevent a palindromic replication intermediate, whose loss precipitates the formation of a mutable chromatin structure known to initiate a cascade of genomic instability in cancer.
Gating interactions steer loop conformational changes in the active site of the L1 metallo-β-lactamase
Authors: Zhao Zhuoran , Shen Xiayu , Chen Shuang , Gu Jing , Wang Huan , Mojica Maria F. , Samanta Moumita , Bhowmik Debsindhu , Vila Alejandro J. , Bonomo Robert A. , Haider Shozeb 
Published: October 2022

Abstractβ-lactam antibiotics are the most important and widely used antibacterial agents across the world. However, the widespread dissemination of β-lactamases among pathogenic bacteria limits the efficacy of β-lactam antibiotics. This has created a major public health crisis. The use of β-lactamase inhibitors has proven useful in restoring the activity of β-lactam antibiotics, yet, effective clinically approved inhibitors against class B metallo-β-lactamases (MBLs) are not available. L1, a class B3 enzyme expressed byStenotrophomonas maltophilia, is a significant contributor to the β-lactam resistance displayed by this opportunistic pathogen. Structurally, L1 is a tetramer with two elongated loops, α3-β7 and β12-α5, present around the active site of each monomer. Residues in these two loops influence substrate/inhibitor binding. To study how the conformational changes of the elongated loops affect the active site in each monomer, enhanced sampling molecular dynamics (MD) simulations were performed, Markov State Models (MSM) were built, and convolutional variational autoencoder (CVAE)-based deep learning was applied. The key identified residues (D150a, H151, P225, Y227, R236) were mutated and the activity of the generated L1 variants was evaluated in cell-based experiments. The results demonstrate that there are extremely significant gating interactions between α3-β7 and β12-α5 loops. Taken together, the gating interactions with the conformational changes of the key residues play an important role in the structural remodeling of the active site. These observations offer insights into the potential for novel drug development exploiting these gating interactions.
Characterization and utility of novel monoclonal antibodies to cholera toxin B subunit
Authors: Garcia Noel Verjan , Celis Ian Carlosalberto Santisteban , Dent Matthew , Matoba Nobuyuki 
Published: October 2022

ABSTRACTCholera toxin B subunit (CTB) is a potent immunomodulator exploitable in mucosal vaccine and immunotherapeutic development. To aid in the characterization of pleiotropic biological functions of CTB and its variants, we generated a panel of anti-CTB monoclonal antibodies (mAbs). By ELISA and surface plasmon resonance, two mAbs, 7A12B3 and 9F9C7, were analyzed for their binding affinities to cholera holotoxin (CTX), CTB, and EPICERTIN: a recombinant CTB variant possessing mucosal healing activity. Both 7A12B3 and 9F9C7 bound efficiently to CTX, CTB, and EPICERTIN with equilibrium dissociation constants at low to sub-nanomolar concentrations but bound weakly, if at all, toEscherichia coliheat-labile enterotoxin B subunit. In a cyclic adenosine monophosphate (cAMP) assay using Caco2 human colon epithelial cells, the 7A12B3 mAb was found to be a potent inhibitor of CTX, whereas 9F9C7 had relatively weak inhibitory activity. Meanwhile, the 9F9C7 mAb effectively detected CTB and EPICERTIN bound to the surface of Caco2 cells and mouse spleen leukocytes by flow cytometry. Using 9F9C7 in immunohistochemistry, we confirmed the preferential localization of EPICERTIN in colon crypts following oral administration of the protein in mice. Collectively, these mAbs provide valuable tools to investigate the biological functions and preclinical development of CTB variants.
Time in allopatry does not predict the outcome of secondary contact in lowland Panamanian birds
Authors: Mclaughlin Jessica F. , Miller Matthew J. 
Published: October 2022

AbstractGeographic speciation models assume that time in allopatry should result in greater reproductive isolation between populations. Here we test the prediction that greater time in allopatry results in greater reproductive isolation using comparative ultraconserved element (UCE) data from ten bird lineages in secondary contact in Panama, measuring both genome-wide divergence and the geographic extent of hybridization. The best-fit models for the proportion of fixed Z-linked and autosomal loci to our data includes a combination of both time (as measured by mtDNA divergence) and hand-wing index, emphasizing that the role of time is tempered by dispersal capability. Furthermore, time does not predict the extent of genome-wide introgression as measured by the median width of diagnostic loci clines or the degree of variation in cline centers or widths. These metrics of the outcome of secondary contact were best predicted by ecological and genomic factors, including diet, hand-wing index, and genome-wideFSTrespectively, that are understood to serve as proxies for dispersal, the variability of population size, and overall genomic divergence. We find a primary role for ecological factors instead of isolation time in determining secondary contact outcomes for a lineage, highlighting how ecology shapes the development of reproductive isolation.
Dissecting the effects of GTPase and kinase domain mutations on LRRK2 endosomal localization and activity
Authors: Rinaldi Capria , Waters Christopher S. , Kumbier Karl , Rao Lee , Nichols R. Jeremy , Jacobson Matthew P. , Wu Lani F. , Altschuler Steven J. 
Published: October 2022

AbstractParkinson’s disease-causing LRRK2 mutations lead to varying degrees of Rab GTPase hyperphosphorylation. Puzzlingly, LRRK2 GTPase-inactivating mutations—which do not affect intrinsic kinase activity—lead to higher levels of cellular Rab phosphorylation than kinase-activating mutations. Here, we investigated whether mutation-dependent differences in LRRK2 cellular localization could explain this discrepancy. We discovered that blocking endosomal maturation leads to the rapid formation of mutant LRRK2+endosomes on which LRRK2 phosphorylates substrate Rabs. LRRK2+endosomes are maintained through positive feedback, which mutually reinforces membrane localization of LRRK2 and phosphorylated Rab substrates. Furthermore, across a panel of mutants, cells expressing GTPase-inactivating mutants formed strikingly more LRRK2+endosomes than cells expressing kinase-activating mutants, resulting in higher total cellular levels of phosphorylated Rabs. Our study suggests that an increased probability of LRRK2 GTPase-inactivating mutants to be retained on intracellular membranes over the kinase-activating mutants leads to higher substrate phosphorylation.
Lymph node expansion predicts magnitude of vaccine immune response
Authors: Najibi Alexander J. , Lane Ryan S. , Sobral Miguel C. , Freedman Benjamin R. , Estupinan Joel Gutierrez , Elosegui-Artola Alberto , Tringides Christina M. , Dellacherie Maxence O. , Williams Katherine , Müller Sören , Turley Shannon J. , Mooney David J. 
Published: October 2022

AbstractLymph nodes (LNs) dynamically expand in response to immunization, but the relationship between LN expansion and the accompanying adaptive immune response is unclear. Here, we first characterized the LN response across time and length scales to vaccines of distinct strengths. High-frequency ultrasound revealed that a bolus ‘weak’ vaccine induced a short-lived, 2-fold volume expansion, while a biomaterial-based ‘strong’ vaccine elicited an ∼7-fold LN expansion, which was maintained several weeks after vaccination. This latter expansion was associated with altered matrix and mechanical properties of the LN microarchitecture. Strong vaccination resulted in massive immune and stromal cell engagement, dependent on antigen presence in the vaccine, and conventional dendritic cells and inflammatory monocytes upregulated genes involved in antigen presentation and LN enlargement. The degree of LN expansion following therapeutic cancer vaccination strongly correlated with vaccine efficacy, even 100 days post-vaccination, and direct manipulation of LN expansion demonstrated a causative role in immunization outcomes.