bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lipid nanoparticle-mediated delivery of mRNA into the mouse and human retina and other ocular tissues
Authors: Chambers Cheri Z. , Soo Gillian L. , Engel Abbi L. ,   Birth Defects Research Laboratory (BDRL), Glass Ian A. , Frassetto Andrea , Martini Paolo G. V. , Cherry Timothy J. 
Published: July 2023

Structured AbstractPurposeLipid nanoparticles (LNPs) show promise in their ability to introduce mRNA to drive protein expression in specific cell types of the mammalian eye. Here, we examined the ability of mRNA encapsulated in lipid nanoparticles (LNPs) with two distinct formulations to drive gene expression in mouse and human retina and other ocular tissues.MethodsWe introduced mRNA carrying LNPs into two biological systems. Intravitreal injections were tested to deliver LNPs into the mouse eye. Human retinal pigment epithelium (RPE) and retinal explants were used to assess mRNA expression in human tissue. We analyzed specificity of expression using histology, immunofluorescence, and imaging.ResultsIn mice, mRNAs encoding GFP and ciliary neurotrophic factor (CNTF) were specifically expressed by Müller glia and retinal pigment epithelium (RPE). Acute inflammatory changes measured by microglia distribution (Iba-1) or interleukin-6 (IL-6) expression were not observed 6 hours post-injection. Human RPE also expressed high levels of GFP. Human retinal explants expressed GFP in cells with apical and basal processes consistent with Müller glia and in perivascular cells consistent with macrophages.ConclusionsWe demonstrated the ability to reliably transfect subpopulations of retinal cells in mice eye tissuesin vivoand in human ocular tissues. Of significance, intravitreal injections were sufficient to transfect the RPE in mice. To our knowledge we demonstrate delivery of mRNA using LNPs in human ocular tissues for the first time.Translational RelevanceOcular gene-replacement therapies using non-viral vector methods are of interest as alternatives to adeno-associated virus (AAV) vectors. Our studies show that mRNA LNP delivery can be used to transfect retinal cells in both mouse and human tissues without inducing significant inflammation. This promising methodology could be used to transfect retinal cell lines, tissue explants, mice, or potentially as gene-replacement therapy in a clinical setting in the future.
Four-dimensional omics data reveals ribosome heterogeneity, regulation of translation efficacy, and nonsense-mediated decay in the differentiation of spermatocyte to round spermatid
Authors: Lee Szu-Shuo , Kung Ying-Chih , Jou Yuh-Shan 
Published: July 2023

AbstractA protein expression is regulated by transcription, translation, and sequential processing. However, well correlated RNA and protein abundance just only proportionate 40%, and even poorer when cell was stressed, differentiated, or tumorigenic transformed. Here, we discovered spermatocyte (SP) differentiated to round spermatid (RS) had equal regulation extent which may related to ribosomal behavior alteration. The change of ribosome occupancy was related to SP and RS specific function in spermatogenesis. Interactome of functional ribosome in SP and RS revealed the activated ribosome in SP but stalled and nonsense-mediated decay (NMD) associated ribosome in RS. Functional ribosomes of RS occupied 5’untranslated regions (5’UTR) of SP specific transcripts and correlated its’ RNA and protein downregulation. These findings suggested a branched NMD pathway was activated in RS to eliminate SP specific transcripts and keep them from being translated. Our discovery suggested the heterogeneity of ribosomal interactome may play an important role in spermatogenesis.
Chronic cisplatin exposure does not affect epimutations inC. elegansbut induces fluctuations in tRNA-derived small non-coding RNAs
Authors: Fallet Manon , Wilson Rachel , Sarkies Peter 
Published: July 2023

AbstractThe individual lifestyle and environment of an organism can influence its phenotype and potentially the phenotype of its offspring. The different genetic and non-genetic components of the inheritance system and their mutual interactions are key mechanisms to generate inherited phenotypic changes. Epigenetic changes can be transmitted between generations independently from changes in DNA sequence. InC. elegans, epigenetic differences, i.e., epimutations, mediated by small non-coding RNAs, particularly 22G-RNAs, as well as chromatin have been identified and their average persistence is 3 to 5 generations. In addition, previous research showed that some epimutations had a longer duration and concerned genes that were enriched for multiple components of xenobiotic response pathways. These results raise the possibility that environmental stresses might change the rate at which epimutations occur, with potential significance for adaptation. In this work, we explore this question by propagatingC. eleganslines either in control conditions or in moderate or high doses of cisplatin, which introduces genotoxic stress by damaging DNA. Our results show that cisplatin has a limited effect on global small non-coding RNAs epimutations and epimutations in gene expression levels. However, cisplatin exposure leads to increased fluctuations in the levels of small non-coding RNAs derived from tRNA cleavage. We show that changes in tRNA-derived small RNAs may be associated with gene expression changes. Our work shows that epimutations are not substantially altered by cisplatin exposure but identifies transient changes in tRNA-derived small RNAs as a potential source of transcriptional variation induced by genotoxic stress.
Peptriever: A Bi-Encoder approach for large-scale protein-peptide binding search
Authors: Gurvich Roni , Markel Gal , Tanoli Ziaurrehman , Meirson Tomer 
Published: July 2023

AbstractMotivationIn peptide therapeutics, the successful interaction between a designed peptide and a specific receptor is crucial, while minimizing interactions with other receptors is equally essential. Current computational methods excel at estimating the probability of the former but estimating the latter requires excessive computational resources, making it challenging.ResultsIn this study, we propose transformers-based protein embeddings that can quickly identify and rank millions of interacting proteins. Furthermore, the proposed approach outperforms existing sequence- and structure-based methods, with a mean AUC-ROC and AUC-PR of 0.73.AvailabilityTraining data, scripts, and fine-tuned parameters are available athttps://github.com/RoniGurvich/Peptriever. A live demonstration of the application can be found athttps://peptriever.app/.Contacttomermrsn@gmail.comandzia.rehman@helsinki.fi
Inconsistencies of empirical ecological network inference are governed by considerations of statistical approaches and dimensions of input data
Authors: Kusch Erik , Bimler Malyon D. , Blanchet F. Guillaume , Lutz James A. , Ordonez Alejandro 
Published: July 2023

AbstractIdentifying the most suitable method of ecological network inference in line with individual research considerations is a non-trivial task, which significantly hinders adoption of network approaches to forest management applications. To advance the study of ecological networks and better guide their use in managing forest ecosystems, we propose a framework that aligns pairwise species-association inference methods with specific research questions, biological interaction types, data availability, and spatial scales of study. We motivate the adoption of this framework through an empirical comparison of multiple inference methods, highlighting substantial inconsistencies that arise across scales and methodologies. Using data on species distributions and attributes at local, regional, and continental scales for temperate conifer forests in North America, we show that network inference varies significantly depending on whether occurrence, abundance, or performance data are used and the degree to which confounding factors are accounted for. Across four widely used and/or cutting-edge inference methods (COOCCUR, NETASSOC, HMSC, NDD-RIM), we find notable disparities in both whole-network metrics and pairwise species associations, particularly at continental scales. These findings underscore that no single method is likely to universally outperforms others across scales, emphasizing the importance of choosing an inference approach that aligns with specific ecological and spatial contexts. Our framework aids in interpreting network topologies and interactions in light of these method- and datatype-driven variances, providing a structured approach to more reliably infer ecological associations and address complex network dynamics in forest management practices.
Geomagnetic orientation in subterranean mole crickets during burrowing
Authors: Endo Tsubasa , Ando Noriyasu 
Published: July 2023

AbstractWhile many terrestrial animals use celestial and terrestrial cues for orientation, subterranean animals lack access to these cues. The geomagnetic field serves as a reliable alternative cue for underground navigation. Subterranean mammals use the geomagnetic field to burrow and navigate within their nests; however, whether subterranean insects possess magnetoreception remains unclear. Here, we investigated the influence of magnetic fields on burrowing directions in subterranean mole crickets (Gryllotalpa orientalis). Under an intact magnetic field, mole crickets predominantly burrow in the north-south direction. However, when the magnetic field was rotated by 90°, the preferred burrowing direction shifted to the east-west axis. Notably, when the horizontal component of the geomagnetic field was reduced to near 0 µT, no preferred direction was observed. These results suggest that mole crickets have a magnetic sense and they align the direction at the beginning of burrowing. The study enhances our comprehension of underground orientation mechanisms in subterranean insects and reveals convergent evolution between insects and mammals in utilizing the geomagnetic field as a navigational cue.
Enhancing sensitivity and versatility of Tn5-based single cell omics
Authors: Seufert Isabelle , Sant Pooja , Bauer Katharina , Syed Afzal P. , Rippe Karsten , Mallm Jan-Philipp 
Published: July 2023

AbstractThe analysis of chromatin features in single cells centers around Tn5 transposase and exploits its activity to simultaneously fragment target DNA and integrate adapter sequences of choice. This reaction provides a direct readout in the assay for transposase-accessible chromatin in single cells (scATAC-seq) to map open chromatin regions. However, a current limitation is the sparse coverage of open chromatin loci that are detected in a given single cell by droplet-based methods. Thus, enhancing Tn5 activity to improve genomic coverage of scATAC-seq or facilitating multi-omics readouts of chromatin features via Tn5 together with the transcriptome is of great interest. Here, we address these issues by optimizing scATAC-seq for an increased number of integrations per cell. In addition, we provide a protocol that combines mapping of histone modification with scRNA-seq from the same cell by targeting Tn5 to antibody-bound chromatin epitopes. Our experimental workflows improve the results obtained from the downstream data analysis and serve to better resolve epigenetic heterogeneity and transcription regulation in single cells.
Spatiotemporal dynamics and emergent ordering in a mixture of morphologically distinct bacteria having different cell motility
Authors: Mondal Kaustav , Bera Palash , Ghosh Pushpita 
Published: July 2023

AbstractMicrobial communities exhibit complex behaviors driven by species interactions and individual characteristics. In this study, we delve into the dynamics of a mixed bacterial population comprising two distinct species with different morphology and motility aspects. Employing agent-based modeling and computer simulations, we analyze the impacts of size ratios and packing fractions on dispersal patterns, aggregate formation, clustering, and spatial ordering. Notably, we find that motility and anisotropy of elongated bacteria significantly influence the distribution and spatial organization of nonmotile spherical species. Passive spherical cells display superdiffusive behavior, particularly at smaller size ratios, while active rod-like cells exhibit normal diffusive behavior in the diffusion regime. As the size ratio increases, clustering of passive cells is observed, accompanied by enhanced alignment and closer packing of active cells in the presence of higher passive cell area fractions. As the size ratio increases, clustering of passive cells is observed, accompanied by enhanced alignment and closer packing of active cells in the presence of higher passive cell area fractions. Additionally, we identify the pivotal role of passive cell area fraction in influencing the response of active cells toward nematicity, with its dependence on size ratio. These findings shed light on the significance of morphology and motility in shaping the collective behavior of microbial communities, providing valuable insights into complex microbial behaviors with implications for ecology, biotechnology, and bioengineering.
Effect size of delayed freezing, diurnal variation, and hindgut location on the mouse fecal microbiome relative to a standardized biological variable
Authors: Gustafson K.L. , McAdams Z.L. , Russell A.L. , Dorfmeyer R.A. , Turner G.M. , Ericsson A.C. 
Published: July 2023

AbstractBackgroundWhile murine fecal collection is central to microbiome research, there are a number of practical considerations that may vary during fecal sample collection, including time to sample storage, time of day the sample is collected, and position within the colon during terminal collections. While the need to control these factors is recognized, the relative effect on microbial community of duration at room temperature, time of day, and hindgut position, in the context of a known biological variable, is unclear. To answer these questions, and assess reproducibility of results across different microbiome compositions, parallel experiments were performed to investigate the effect of those factors on the microbiome of age- and sex-matched isogenic mice colonized with two different vendor-origin microbiomes.Results16S rRNA amplicon sequencing data from flash-frozen fecal samples showed no statistical difference in alpha or beta diversity compared to samples incubated for 1, 2, 3, 4, 6, and 9 hours at room temperature. Overall, samples collected in the AM period showed greater richness and alpha-diversity compared to samples collected in the PM period. While a significant effect of time was detected in all hindgut regions, the effect increased from cecum to distal colon. When using two vendor-origin microbiomes as a biological variable, its effect size vastly outweighed the effect size of the time samples spent at room temperature, the time of day samples were collected, and the position within the colon from which samples were collected.ConclusionsThis study has highlighted multiple scenarios encountered in microbiome research that may affect outcome measures of microbial diversity and composition. Unexpectedly, delayed time to sample cold storage up to nine hours did not affect the alpha or global beta diversity of fecal sample. We then presented evidence of location- and time-dependent effects within the hindgut on microbial richness, diversity, and composition. We finally demonstrated a relatively low effect size of these technical factors when compared to a primary experimental factor with large intergroup variability.
Chromatin states contribute to coordinated allelic transcriptional bursting to drive iPSC reprogramming
Authors: Parichitran A , Naik HC , Naskar AJ , Bammidi LS , Gayen S 
Published: July 2023

AbstractMolecular mechanisms behind the reprogramming of somatic cells to induced pluripotent stem cells (iPSC) remain poorly understood. While dynamic changes in gene expression are considered to drive reprogramming, the contribution of individual alleles of genes to reprogramming remains unexplored. It is thought that two alleles of a gene can transcribe independently or coordinatedly, which in turn can lead to temporal expression heterogeneity with potentially distinct impacts on cell fate. Here, we profiled genome-wide transcriptional burst kinetics with an allelic resolution during the reprogramming of mouse embryonic fibroblast (MEF) to iPSC. We show that many genes involved in iPSC reprogramming pathways exhibit bursty expression and contribute to dynamic autosomal random monoallelic expression (aRME). Moreover, we find that the degree of coordination of allelic bursting differs among genes and changes dynamically during iPSC reprogramming. Importantly, we show that alleles of many reprogramming-related genes burst in a highly coordinated fashion. ATAC-seq analysis revealed that coordination of allelic bursting is linked to allelic chromatin accessibility. Consistently, we show that highly coordinated genes are enriched with chromatin accessibility regulators such as H3K36me3, H3K27ac, histone variant H3.3 and BRD4. Collectively, our study demonstrates that chromatin states contribute to coordinated allelic bursting to fine-tune the expression of genes involved in iPSC reprogramming and provides insights into the implications of allelic bursting coordination in cell fate specification.Abstract Figure
A singular PpaA/AerR-like protein inRhodospirillum rubrumrules beyond the boundaries of photosynthesis in response to the intracellular redox state
Authors: Godoy Manuel S. , de Miguel Santiago R. , Prieto M. Auxiliadora 
Published: July 2023

ABSTRACTPhotosynthesis (PS) in Purple Non-Sulphur Bacteria (PNSB) is strictly controlled to avoid energy consumption and to prevent oxidative stress when oxygen is present. PpsR, a transcriptional repressor codified in the Photosynthetic Gene Cluster (PGC), is one of the main players in the regulation of PS related genes. In some cases, PpsR do not sense the environmental cue by itself but delegates this task to another protein like PpaA/AerR anti-repressors, which can ultimately affect PpsR affinity to some promoter regions. In this work, the effects of locus Rru_A0625 product (HP1) on PS regulation ofRhodospirillum rubrum, were studied by mutation/complementation and transcriptomic strategies. Rru_A0625 is located next toppsRgene, just like other PpaA/AerR members, and its deletion annuls pigment synthesis in dark micro/anaerobic growth conditions. HP1 shows similarity to PpaA/AerR anti-repressors family, although it does not possess their typical cobalamin binding domain. A transcriptomic analysis of Rru_A0625 deletion mutant showed that HP1 not only has effects on bacterioclorophyll and carotenoid biosynthesis, but also many other biological processes in the cell. The most notorious is the impact on the transcription of the nitrogenase complex components and some accessory proteins. Our results suggest that this new member of the PpaA/AerR family has evolved losing the canonical cobalamin binding domain, but not the redox sensing capability, conserving a not fully understood mechanism of PS regulation.IMPORTANCERhodospirillum rubrumvast metabolic versatility places it as a remarkable model bacterium and an excellent biotechnological chassis. The key component of PS studied in this work (HP1) stands out among the other members of PpaA/AerR anti-repressors family since it lacks the most conserved motif they all share: the cobalamin B-12 binding motif. Even with a minimized and barely recognizable aminoacidic sequence, HP1 stills controls PS as the other members of the family, allowing a fast response to changes in the redox state of the cell. This work also shows that HP1 absence affects genes form relevant biological processes other than PS, including nitrogen fixation and stress response. From a biotechnological perspective, HP1 could be manipulated in approaches where PS is not necessary, such hydrogen or polyhydroxyalkanoates production, to suppress unnecessary energy burden.
Intracellular sphingolipid sorting drives membrane phase separation in the yeast vacuole
Authors: Kim Hyesoo , Budin Itay 
Published: July 2023

AbstractThe yeast vacuole membrane can phase separate into ordered and disordered domains, a phenomenon that is required for micro-lipophagy under nutrient limitation. Here we report that sorting of sphingolipids (SLs) into the vacuole membrane controls this process. We first developed a vacuole isolation method to identify lipidome changes during the onset of phase separation in early stationary stage cells. We found that phase separated vacuoles are characterized by increases in lipid raft-forming components not found in the whole cell, including a dramatic change in SL composition. Sorting of both SLs and ergosterol into the vacuole membrane is dependent on Npc2, the yeast homologue of the Niemann-Pick Type C2 lipid transporter. Genetic dissection of SL biosynthesis revealed that the composition of vacuole SLs modulates membrane phase separation and micro-lipophagy under glucose restriction. These results show that lipid trafficking can drive membrane phase separationin vivoand identify SLs as key mediators of this process in yeast.
Monitoring integrated stress response in liveDrosophila
Authors: Lidsky Peter V. , Yuan Jing , Lashkevich Kseniya A. , Dmitriev Sergey E. , Andino Raul 
Published: July 2023

SummaryCells exhibit stress responses to various environmental changes. Among these responses, the integrated stress response (ISR) plays a pivotal role as a crucial stress signaling pathway. While extensive ISR research has been conducted on cultured cells, our understanding of its implications in multicellular organisms remains limited, largely due to the constraints of current techniques that hinder our ability to track and manipulate the ISR in vivo. To overcome these limitations, we have successfully developed an internal ribosome entry site (IRES)-based fluorescent reporter system. This innovative reporter enables us to label Drosophila cells, within the context of a living organism, that exhibit eIF2 phosphorylation-dependent translational shutoff – a characteristic feature of the ISR and viral infections. Through this methodology, we have unveiled tissue- and cell-specific regulation of stress response in Drosophila flies and have even been able to detect stressed tissues in vivo during virus and bacterial infections. To further validate the specificity of our reporter, we have engineered ISR-null eIF2αS50A mutant flies for stress response analysis. Our results shed light on the tremendous potential of this technique for investigating a broad range of developmental, stress, and infection-related experimental conditions. Combining the reporter tool with ISR-null mutants establishes Drosophila as an exceptionally powerful model for studying the ISR in the context of multicellular organisms.