bluuebunny/crossref_metadata_2025_split huggingface dataset:
The pan-epigenome of the symbiotic nitrogen fixing bacteriumSinorhizobium melilotiunravels unexpected variability of DNA-methylation profiles in closely related strains
Authors: Passeri Iacopo , Cangioli Lisa , Fondi Marco , Mengoni Alessio , Fagorzi Camilla 
Published: June 2023

AbstractIn prokaryotes, DNA methylation has been found to be involved in several mechanisms, such as DNA repair, DNA–protein interactions, gene expression, cell cycle progression and self-DNA recognition (the Restriction-Modification systems). Studies on representatives from the same bacterial species have found that genome-wide DNA methylation patterns can be highly variable and may affect phenotypic variation and gene transfer among closely related strains. However, broader evolutionary studies on such epigenomic variation in bacteria are still scarce.Here, we addressed this point by performing an epigenomic analysis on 21 strains of the facultative plant symbiotic nitrogen-fixing alphaproteobacteriumSinorhizobium meliloti. Strains of these species are characterized by a divided (multipartite) genome structure, including a chromosome, a chromid and a (more recently acquired) megaplasmid. Since these strains display extensive genomic and phenotypic variation, they are good models to test evolutionary hypotheses on the relationships among epigenomic signatures, genome structure evolution and phenotypic switches.Results showed the presence of a wide pan-epigenome with 16 DNA methylated motifs, including both 4mC and 6mA palindromic and nonpalindromic motifs. While 9 motifs have been found methylated by all strains, the remaining had differential methylation betweenS. melilotistrains, constituting a dispensable epigenome. Differences in frequency of methylation were found among replicons, with the megaplasmid and the additional plasmids displaying several motifs with different methylation frequency with respect to the chromosome and the chromid. Moreover, differences between coding, upstream and intergenic regions, were found, suggesting that DNA methylation at specific motifs may play a role in gene regulation and consequently in phenotypic variability among strains.Altogether, our data indicate the presence of a large epigenomic diversity inS. meliloti, with epigenome signatures differing between replicons, reflecting their timing of evolutionary acquisition inS. melilotigenomes and suggesting a role of DNA methylation in the variability of gene expression among strains.
Global patterns in gene content of soil microbiomes emerge from microbial interactions
Authors: Crocker Kyle , Lee Kiseok Keith , Chakraverti-Wuerthwein Milena , Li Zeqian , Tikhonov Mikhail , Mani Madhav , Gowda Karna , Kuehn Seppe 
Published: June 2023

AbstractMicrobial metabolism sustains life on Earth. Sequencing surveys of communities in hosts, oceans, and soils have revealed ubiquitous patterns linking the microbes present, the genes they possess, and local environmental conditions. One prominent explanation for these patterns is environmental filtering: local conditions select strains with particular traits. However, filtering assumes ecological interactions do not influence patterns, despite the fact that interactions can and do play an important role in structuring communities. Here, we demonstrate the insufficiency of the environmental filtering hypothesis for explaining global patterns in topsoil microbiomes. Using denitrification as a model system, we find that the abundances of two characteristic genotypes trade-off with pH;nargene abundances increase whilenapabundances decrease with declining pH. Contradicting the filtering hypothesis, we show that strains possessing the Nar genotype are enriched in low pH conditions but fail to grow alone. Instead, the dominance of Nar genotypes at low pH arises from an ecological interaction with Nap genotypes that alleviates nitrite toxicity. Our study provides a roadmap for dissecting how global associations between environmental variables and gene abundances arise from environmentally modulated community interactions.
Multiple E3 ligases control tankyrase stability and function
Authors: Perrard Jerome , Smith Susan 
Published: June 2023

AbstractTankyrase 1 and 2 are ADP-ribosyltransferases that use NAD+as a substrate to catalyze polyADP-Ribose (PAR) onto themselves and their protein binding partners. Tankyrases have diverse cellular functions, ranging from resolution of telomere cohesion to activation of the Wnt/β-catenin signaling pathway. Robust and specific small molecule tankyrase inhibitors have been developed and are being investigated for cancer therapies. Tankyrase is regulated by the PAR-binding E3 ligase RNF146, which promotes K48-linked polyubiquitylation and proteasomal degradation of PARylated tankyrases and their PARylated partners. We have identified a novel interaction between tankyrase and a distinct class of E3 ligases: the RING-UIM (Ubiquitin-Interacting Motif) family. We show that RING-UIM E3 ligases (specifically RNF114 and RNF166) bind and stabilize monoubiquitylated tankyrase and promote K11-linked diubiquitylation. This action competes with RNF146-mediated K48-linked polyubiquitylation and degradation, leading to stabilization of tankyrase and to a subset of its binding partners, including Angiomotin, a protein that functions in cancer signaling pathways. Moreover, we identify multiple PAR-binding E3 ligases (in addition to RNF146) that promote ubiquitylation of tankyrase and induce stabilization or degradation. Discovery of this novel K11 ubiquitylation of tankyrase that opposes K48-mediated degradation along with identification of multiple PAR-binding E3 ligases that ubiquitylate tankyrase, provide new insights into mechanisms of tankyrase regulation and may offer new uses for tankyrase inhibitors in cancer therapy.
NIRis: A low-cost, versatile imaging system for NIR fluorescence detection of phototrophic cell colonies used in science and education
Authors: Franz Ole , Häkkänen Heikki , Kovanen Salla , Heikkilä-Huhta Kati , Nissinen Riitta , Ihalainen Janne A. 
Published: June 2023

AbstractA variety of costly research-grade imaging devices are available for the detection of spectroscopic features. Here we present an affordable, open-source and versatile device, suitable for a range of applications. We provide the files to print the imaging chamber with commonly available 3D printers and instructions to assemble it with easily available hardware. The imager is suitable for rapid sample screening in research, as well as for educational purposes. We provide details and results for an already proven set-up which suits the needs of a research group and students interested in UV-induced near-infrared fluorescence detection of microbial colonies grown on Petri dishes. The fluorescence signal confirms the presence of bacteriochlorophyllain aerobic anoxygenic phototrophic bacteria (AAPB). The imager allows for the rapid detection and subsequent isolation of AAPB colonies on Petri dishes with diverse environmental samples. To this date, 15 devices have been build and more than 7000 Petri dishes have been analyzed for AAPB, leading to over 1000 new AAPB isolates. Parts can be modified depending on needs and budget. The latest version with automated switches and double band pass filters costs around 350€ in materials and resolves bacterial colonies with diameters of 0.5 mm and larger. The low cost and modular build allow for the integration in high school classes to educate students on light properties, fluorescence and microbiology. Computer-aided design of 3D-printed parts and programming of the employed Raspberry Pi computer could be incorporated in computer sciences classes. Students have been also inspired to do agar art with microbes. The device is currently used in seven different high schools in Finland. Additionally, a science education network of Finnish universities has incorporated it in its program for high school students. Video guides have been produced to facilitate easy operation and accessibility of the device.Abstract Figure
TERRA R-loops connect and protect sister telomeres in mitosis
Authors: Sze Samantha , Bhardwaj Amit , Fnu Priyanka , Azarm Kameron , Mund Rachel , Ring Katherine , Smith Susan 
Published: June 2023

AbstractResolution of cohesion between sister telomeres in human cells depends on TRF1-mediated recruitment of the polyADP-ribosyltransferase, tankyrase to telomeres. In cells where tankyrase is deleted or the tankyrase binding site in TRF1 is mutated, sister telomeres remain cohered in mitosis. Human aged cells and ALT cancer cells naturally exhibit persistent telomere cohesion due to shortened telomeres that do not recruit sufficient TRF1/tankyrase for resolution. Persistent cohesion plays a protective role, but the mechanism by which sister telomeres remain cohered is not well understood. Here we show that telomere repeat containing RNA (TERRA) holds sister telomeres together through RNA-DNA hybrid (R-loop) structures. We show that a tankyrase-interacting partner, the RNA-binding protein C19orf43 is required for resolution of telomere cohesion and for repression of TERRA R-loops. Depletion of C19orf43 led to persistent telomere cohesion and an increase in TERRA R-loops. Overexpression of RNaseH1 counteracted persistent cohesion in C19orf43-depleted cells, as well as in aged and ALT cells. In fact, treatment of cohered telomeres in mitotic cells with RNaseH1 in situ, was sufficient to resolve sister telomere cohesion, confirming that RNA-DNA hybrids hold sister telomeres together. Consistent with a protective role for persistent telomere cohesion, depletion of C19orf43 in aged cells reduced DNA damage and significantly delayed replicative senescence. We propose that the inherent inability of shortened telomeres to recruit R-loop repressing machinery permits a controlled onset of senescence.
Developmental Alterations in Brain Network Asymmetry in 3- to 9-Month Infants with Congenital Sensorineural Hearing Loss
Authors: Liu Guangfang , Zhou Xin , Hu Zhenyan , Liu Yidi , Huo Endi , Bortfeld Heather , Dong Qi , Liu Haihong , Niu Haijing 
Published: June 2023

AbstractAuditory exposure plays crucial roles in shaping healthy brain development and generating lateralization of functional network organization. However, little is known about whether and how an initial lack of auditory exposure in early infancy may disrupt development of functional network lateralization. We addressed this issue by recruiting 55 infants with congenital sensorineural hearing loss (SNHL) and 60 typically developing (TD) controls. Resting-state fNIRS imaging data were acquired to construct hemispheric cerebral networks, and graph theory was applied to quantify the topological characteristics of hemispheric networks. The infants with SNHL exhibited efficient small-world characteristic within each hemispheric network, however, the lateralization of functional network efficiency was substantially disrupted. Compared with TD infants with significantly increased network efficiency lateralized toward left hemisphere with age, the SNHL infants did not exhibit the emergence and development of such cerebral lateralization. Furthermore, the increased leftward asymmetry in nodal efficiency with age was found in TD but not in SNHL infants. Interestingly, the degree of hearing loss had no correlation with lateralization strength in the SNHL group. These results suggest that SNHL infants exhibited disrupted development of cortical lateralization in functional network organization, and highlight the importance of auditory stimulation-promoted multisensory functional integration in early infancy.
How NINJ1 mediates plasma membrane rupture and why NINJ2 cannot
Authors: Sahoo Bibekananda , Mou Zongjun , Liu Wei , Dubyak George , Dai Xinghong 
Published: June 2023

SummaryNINJ1 is a recently identified active executioner of plasma membrane rupture (PMR), a process previously thought to be a passive osmotic lysis event in lytic cell death. NINJ2 is a close paralog of NINJ1 but it failed to mediate PMR. By cryoEM, we found that both NINJ1 and NINJ2 were able to assemble into linear filament that binds strongly to lipids on one side but is water-soluble on the other side. The more-or-less straight NINJ1 filament was able to wrap around a membrane bleb and solubilize it from the plasma membrane to induce PMR; however, the intrinsically curved NINJ2 filament failed to do so, explaining its incapability of mediating PMR. We further demonstrated that binding to cholesterol at the inner leaflet of the lipid bilayer was responsible for the curving of the NINJ2 filament, while strong lipid binding at the outer leaflet was contributing to NINJ1’s capability of mediating PMR.
SPARCS, a platform for genome-scale CRISPR screening for spatial cellular phenotypes
Authors: Schmacke Niklas A. , Mädler Sophia C. , Wallmann Georg , Metousis Andreas , Bérouti Marleen , Harz Hartmann , Leonhardt Heinrich , Mann Matthias , Hornung Veit 
Published: June 2023

AbstractForward genetic screening associates phenotypes with genotypes by randomly inducing mutations and then identifying those that result in phenotypic changes of interest. Here we presentspatiallyresolvedCRISPRscreening (SPARCS), a platform for microscopy-based genetic screening for spatial cellular phenotypes. SPARCS uses automated high-speed laser microdissection to physically isolate phenotypic variantsin situfrom virtually unlimited library sizes. We demonstrate the potential of SPARCS in a genome-wide CRISPR-KO screen on autophagosome formation in 40 million cells. Coupled to deep learning image analysis, SPARCS recovered almost all known macroautophagy genes in a single experiment and discovered a role for the ER-resident protein EI24 in autophagosome biogenesis. Harnessing the full power of advanced imaging technologies, SPARCS enables genome-wide forward genetic screening for diverse spatial phenotypesin situ.
Microstructured silk-fiber scaffolds with enhanced stretchability
Authors: Viola Martina , Cedillo-Servin Gerardo , van Genderen Anne Metje , Imhof Isabelle , Vena Paula , Mihajlovic Marko , Piluso Susanna , Malda Jos , Vermonden Tina , Castilho Miguel 
Published: June 2023

AbstractDespite extensive research, current methods for creating three-dimensional (3D) silk fibroin (SF) scaffolds lack control over molecular rearrangement, particularly in the formation of β-sheet nanocrystals, as well as hierarchical fiber organization at both micro- and macroscale. In this study, we introduce a fabrication process based on electrowriting of aqueous SF-based solutions followed by post-processing using an aqueous solution of sodium dihydrogen phosphate (NaH2PO4). This approach enables hierarchical assembly of SF chains via β-sheet and α-helix formation. Moreover, this process allows for precise control over micro- and macro-architectures in microfiber scaffolds, enabling the creation of 3D flat and tubular macrogeometries with square-based and crosshatch microarchitectures, featuring inter-fiber distances of 400 µm and approximately 97% open porosity. Remarkably, the printed structures demonstrated restored β-sheet and α-helix structures, which imparted an elastic response of up to 20% deformation and the ability to support cyclic loading without plastic deformation. Furthermore, the printed constructs supportedin vitroadherence and growth of human conditionally immortalized proximal tubular epithelial cells and glomerular endothelial cells, with cell viability above 95%. These cells formed uniform, aligned monolayers that deposited their own extracellular matrix. These findings represent a significant development in fabricating organized SF scaffolds with unique fiber structures, mechanical and biological properties, making them highly promising for regenerative medicine applications.
The actin cytoskeleton plays multiple roles in structural color formation in butterfly wing scales
Authors: Lloyd Victoria J. , Burg Stephanie L. , Harizanova Jana , Hill Olivia , Enciso-Romero Juan , Cooper Rory L. , Flenner Silja , Longo Elena , Greving Imke , Nadeau Nicola J. , Parnell Andrew J. 
Published: June 2023

AbstractVivid structural colors in butterflies are caused by photonic nanostructures scattering light. Structural colors evolved for numerous biological signaling functions and have technological applications. Optically, such structures are well understood, however their developmentin vivoremains obscure. We show that actin is intimately involved in structural color formation in the butterflyHeliconius sara. Using comparisons between iridescent (structurally colored) and non-iridescent scales in adult and developingH. sara, we show that iridescent scales have more densely packed actin bundles leading to an increased density of reflective ridges. Super-resolution microscopy revealed that actin is repeatedly re-arranged in later development, when optical nanostructures are forming. Furthermore, actin perturbation experiments at these later developmental stages resulted in near total loss of structural color. Overall, this shows that actin plays vital templating roles during structural color formation in butterfly scales, with mechanisms potentially universal across lepidoptera.TeaserThe actin cytoskeleton is essential for templating the optical nanostructures responsible for structural color production in butterfly scales.Actin templates the reflective ridges on butterfly scales and is directly involved in forming the color-producing nanostructures within these
Molecular determinants of avoidance and inhibition ofPseudomonas aeruginosaMexB efflux pump
Authors: Gervasoni Silvia , Mehla Jitender , Bergen Charles , Leus Inga V. , Margiotta Enrico , Malloci Giuliano , Bosin Andrea , Vargiu Attilio V. , Lomovskaya Olga , Rybenkov Valentin V. , Ruggerone Paolo , Zgurskaya Helen I. 
Published: June 2023

AbstractTransporters of the Resistance-Nodulation-cell Division (RND) superfamily of proteins are the dominant multidrug efflux power of Gram-negative bacteria. The major RND efflux pump ofPseudomonas aeruginosais MexAB-OprM, in which the inner membrane transporter MexB is responsible for recognition and binding of compounds. The high importance of this pump in clinical antibiotic resistance made it a subject of intense investigations and a promising target for the discovery of efflux pump inhibitors. This study is focused on a series of peptidomimetic compounds developed as effective inhibitors of MexAB-OprM. Previous analyses of antibacterial and biochemical activities showed that these compounds vary broadly in their efficiency as inhibitors or substrates of MexAB and can be categorized into different functional classes. Here, we performed multi-copy molecular dynamics simulations, machine learning analyses and site-directed mutagenesis of MexB to investigate interactions of MexB with representatives of the various classes. The analysis of both direct and water-mediated protein-ligand interactions revealed characteristic patterns for each class, highlighting significant differences between them. We found that efflux avoiders poorly interact with the access binding site of MexB, and inhibition engages amino acid residues that are not directly involved in binding and transport of substrates. In agreement, machine learning models selected different residues predictive of MexB substrates and inhibitors. The differences in interactions were further validated by site-directed mutagenesis. We conclude that the substrate translocation and inhibition pathways of MexB split at the interface (between the main putative binding sites) and at the deep binding pocket, and that interactions outside of the hydrophobic patch contribute to the inhibition of MexB. This molecular-level information could help in the rational design of new inhibitors and antibiotics less susceptible to the efflux mechanism.ImportanceMultidrug transporters recognize and expel from cells a broad range of ligands including their own inhibitors. The difference between the substrate translocation and inhibition routes remains unclear. In this study, machine learning, computational and experimental approaches were used to understand dynamics of MexB interactions with its ligands. Our results show that some ligands engage a certain combination of polar and charged residues in MexB binding sites to be effectively expelled into the exit funnel, whereas others engage aromatic and hydrophobic residues that slow down or hinder the next step in the transporter cycle. These findings suggest that all MexB ligands fit into this substrate-inhibitor spectrum depending on their physico-chemical structures and properties.
Phage anti-CBASS protein simultaneously sequesters cyclic trinucleotides and dinucleotides
Authors: Cao Xueli , Xiao Yu , Huiting Erin , Cao Xujun , Li Dong , Ren Jie , Guan Linlin , Wang Yu , Li Lingyin , Bondy-Denomy Joseph , Feng Yue 
Published: June 2023

SummaryCBASS is a common anti-phage immune system that uses cyclic oligonucleotide signals to activate effectors and limit phage replication. In turn, phages encode anti-CBASS (Acb) proteins. We recently uncovered a widespread phage anti-CBASS protein Acb2 that acts as a “sponge” by forming a hexamer complex with three cGAMP molecules. Here, we identified that Acb2 binds and sequesters many CBASS and cGAS-produced cyclic dinucleotidesin vitroand inhibits cGAMP-mediated STING activity in human cells. Surprisingly, Acb2 also binds CBASS cyclic trinucleotides 3’3’3’-cyclic AMP-AMP-AMP (cA3) and 3’3’3’-cAAG with high affinity. Structural characterization identified a distinct binding pocket within the Acb2 hexamer that binds two cyclic trinucleotide molecules and another binding pocket that binds to cyclic dinucleotides. Binding in one pocket does not allosterically alter the other, such that one Acb2 hexamer can simultaneously bind two cyclic trinucleotides and three cyclic dinucleotides. Phage-encoded Acb2 provides protection from Type III-C CBASS that uses cA3 signaling moleculesin vivoand blocks cA3-mediated activation of the endonuclease effectorin vitro. Altogether, Acb2 sequesters nearly all known CBASS signaling molecules through two distinct binding pockets and therefore serves as a broad-spectrum inhibitor of cGAS-based immunity.