bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polyadenylated RNA sequencing analysis helps establish a reliable catalog of circular RNAs – a bovine example
Authors: Robic Annie , Hadlich Frieder , Monteiro Moreira Gabriel Costa , Clark Emily Louise , Plastow Graham , Charlier Carole , Kühn Christa 
Published: April 2024

AbstractThe aim of this study was to compare the circular transcriptome of divergent tissues in order to understand: i) the presence of circular RNAs (circRNAs) that are not exonic circRNAs, i.e. originated from backsplicing involving known exons and, ii) the origin of artificial circRNA (artif_circRNA), i.e. circRNA not generatedin-vivo. CircRNA identification is mostly anin-silicoprocess, and the analysis of data from the BovReg project (https://www.bovreg.eu/) provided an opportunity to explore new ways to identify reliable circRNAs. By considering 117 tissue samples, we characterized 23,926 exonic circRNAs, 337 circRNAs from 273 introns (191 ciRNAs, 146 intron circles), 108 circRNAs from small non-coding genes and nearly 36.6K circRNAs classified as other_circRNAs. We suggestedin-vivocopying of specific exonic circRNAs by an RNA-dependent RNA polymerase (RdRP) to explain the 20 identified circRNAs with reverse-complement exons. Furthermore, for 63 of those samples we analyzed in parallel data from total-RNAseq (ribosomal RNAs depleted prior to library preparation) with paired mRNAseq (library prepared with poly(A)-selected RNAs). The high number of circRNAs detected in mRNAseq, and the significant number of novel circRNAs, mainly other_circRNAs, led us to consider all circRNAs detected in mRNAseq as artificial. This study provided evidence that there were 189 false entries in the list of exonic circRNAs: 103 artif_circRNAs identified through comparison of total-RNAseq/mRNAseq using two circRNA tools, 26 probable artif_circRNAs, and 65 identified through deep annotation analysis. This study demonstrates the effectiveness of a panel of highly expressed exonic circRNAs (5-8%) in analyzing the diversity of the bovine circular transcriptome.
Crystallographic fragment screening and deep mutational scanning of Zika virus NS2B-NS3 protease enable development of resistance-resilient inhibitors
Authors: Ni Xiaomin , Richardson R. Blake , Godoy Andre Schutzer , Ferla Matteo P. , Kikawa Caroline , Scheen Jenke , Hannon William W , Capkin Eda , Lahav Noa , Balcomb Blake H , Marples Peter G , Fairhead Michael , Wang Siyi , Williams Eleanor P , Tomlinson Charlie W.E. , Aschenbrenner Jasmin Cara , Lithgo Ryan M , Winokan Max , Giroud Charline , Chandran Anu V , Walsh Martin , Thompson Warren , Bloom Jesse D , Barr Haim , Kirkegaard Karla , Koekemoer Lizbé , Fearon Daren , Evans Matthew J. , von Delft Frank 
Published: April 2024

AbstractThe Zika viral protease NS2B-NS3 is essential for the cleavage of viral polyprotein precursor into individual structural and non-structural (NS) proteins and is therefore an attractive drug target. Generation of a robust crystal system of co-expressed NS2B-NS3 protease has enabled us to perform a crystallographic fragment screening campaign with 1076 fragments. 47 fragments with diverse scaffolds were identified to bind in the active site of the protease, with another 6 fragments observed in a potential allosteric site. To identify binding sites that are intolerant to mutation and thus suppress the outgrowth of viruses resistant to inhibitors developed from bound fragments, we performed deep mutational scanning of NS2B-NS3 protease. Merging fragment hits yields an extensive set of ‘mergers’, defined as synthetically accessible compounds that recapitulate constellations of observed fragment-protein interactions. In addition, the highly sociable fragment hits enable rapid exploration of chemical space via algorithmic calculation and thus yield diverse possible starting points that maximally explore the binding opportunities to NS2B-NS3 protease, facilitating its resistance-resilient antiviral development.
Cryo- EM structure of ribosome from pathogenic protozoaEntamoeba histolytica,reveals unique features of its architecture
Authors: Sharma Shivani , Mishra Shalini , Gourinath Samudrala , Kaushal Prem S. 
Published: April 2024

AbstractEntamoeba histolytica, an anaerobic parasite protozoan, is the causative agent of amoebiasis, the bloody diarrhea, and liver abscesses in humans. Amoebiasis is more predominant in tropical areas with poor sanitation conditions, and it remains the fourth leading cause of death due to a protozoan infection.E. histolyticalife cycle spans between an infective ‘cyst stage’ and an active disease-causing ‘trophozoite stage’. We have determined cryo-EM structures ofE. histolyticaribosomes, large subunit (LSU), 53S ribosome at 2.8 Å resolution and associated, 75S ribosome at 3.3 Å resolution, isolated from its trophozoite stage. The overall core of the ribosome is conserved. However, the periphery has evolved withEntamoebaspecific unique features. The most notable features are, the presence of the rRNA triple helix near the peptide exit tunnel on LSU and the co-evolution of rRNA expansion segments and extensions in r-proteins. To the best of our knowledge, this structure reports the presence of RNA triple helix in the ribosome for the first time.
Uncovering the molecular interactions underlying MBD2 and MBD3 phase separation
Authors: Maurici Nicole , Phan Tien M. , Henty-Ridilla Jessica L. , Kim Young C. , Mittal Jeetain , Bah Alaji 
Published: April 2024

ABSTRACTChromatin organization controls DNA’s accessibility to regulatory factors to influence gene expression. Heterochromatin, or transcriptionally silent chromatin enriched in methylated DNA and methylated histone tails, self-assembles through multivalent interactions with its associated proteins into a condensed, but dynamic state. Liquid-liquid phase separation (LLPS) of key heterochromatin regulators, such as heterochromatin protein 1 (HP1), plays an essential role in heterochromatin assembly and function. Methyl-CpG-binding protein 2 (MeCP2), the most studied member of the methyl-CpG-binding domain (MBD) family of proteins, has been recently shown to undergo LLPS in the absence and presence of methylated DNA. These studies provide a new mechanistic framework for understanding the role of methylated DNA and its readers in heterochromatin formation. However, the details of the molecular interactions by which other MBD family members undergo LLPS to mediate genome organization and transcriptional regulation are not fully understood. Here, we focus on two MBD proteins, MBD2 and MBD3, that have distinct but interdependent roles in gene regulation. Using an integrated computational and experimental approach, we uncover the homotypic and heterotypic interactions governing MBD2 and MBD3 phase separation and DNA’s influence on this process. We show that despite sharing the highest sequence identity and structural homology among all the MBD protein family members, MBD2 and MBD3 exhibit differing residue patterns resulting in distinct phase separation mechanisms. Understanding the molecular underpinnings of MBD protein condensation offers insights into the higher-order, LLPS-mediated organization of heterochromatin.
The viscoelastic properties ofNicotiana tabacumBY-2 suspension cell lines adapted to high osmolarity
Authors: Skrzypczak Tomasz , Pochylski Mikołaj , Rapp Magdalena , Wojtaszek Przemysław , Kasprowicz-Maluśki Anna 
Published: April 2024

AbstractTo survive and grow, plant cells must regulate the properties of their cellular microenvironment in response to ever changing external factors. How the biomechanical balance across the cell’s internal structures is established and maintained during environmental variations remains a nurturing question. To provide insight into this issue we used two micro-mechanical imaging techniques, namely Brillouin light scattering and BODIPY-based molecular rotors Fluorescence Lifetime Imaging, to studyNicotiana tabacumsuspension BY-2 cells long-term adapted to high concentrations of NaCl and mannitol. We discuss our results in terms of molecular crowding in cytoplasm and vacuoles, as well as tension in plasma membrane. The viscoelastic behavior was elucidated relative to cells external environments revealing the difference between the responses of cytoplasm and vacuole in the adapted cells. To understand how sudden changes in osmolarity affect cellular mechanics, the response of control and already adapted cells to further short-term osmotic stimulus was also examined. The applied correlative approach provides evidence that adaptation to hyperosmotic stress leads to different ratios of protoplast and environmental qualities that help to maintain cell integrity. Presented results demonstrate that the viscoelastic properties of protoplasts are an element of plant cells adaptation to high osmolarity.
NAC-mediated ribosome localization regulates cell fate and metabolism in intestinal stem cells
Authors: Ramalho Sofia , Alkan Ferhat , Prekovic Stefan , Jastrzebski Katarzyna , Barberà Eric Pintó , Hoekman Liesbeth , Altelaar Maarten , van der Kammen Rob , Fedry Juliette , de Gooijer Mark C. , Faller William J. , Silva Joana 
Published: April 2024

AbstractIntestinal stem cells (ISCs) face the challenge of integrating metabolic demands with unique regenerative functions. Studies have shown an intricate interplay between metabolism and stem cell capacity, however it is still not understood how this process is regulated. Combining ribosome profiling and CRISPR screening in intestinal organoids, we show that RNA translation is at the root of this interplay. We identify the nascent polypeptide-associated complex (NAC) as a key mediator of this process, and show that it regulates ISC metabolism by relocalizing ribosomes to the mitochondria. Upon NAC inhibition, intestinal cells show decreased import of mitochondrial proteins, which are needed for oxidative phosphorylation, and, consequently, enable the cell to maintain a stem cell identity. Furthermore, we show that overexpression of NACα is sufficient to drive mitochondrial respiration and promote ISC identity. Ultimately, our results reveal the pivotal role of ribosome localization in regulating mitochondrial metabolism and ISC function.TeaserThe location of ribosomes in cells is regulated, and defines the fate of intestinal stem cells.
Functional Biosynthetic Stereodivergence in a Gene Cluster via a DihydrosydnoneN-oxide
Authors: Ren Jiajun , Mathew Anugraha , Garcia Maria Rodriguez , Kohler Tobias , Blacque Olivier , Linden Anthony , Eberl Leo , Sieber Simon , Gademann Karl 
Published: April 2024

AbstractChirality features a critical role in the biochemistry of life and often only one enantiomeric series is observed (homochirality). Only few natural products have been obtained as racemates, e.g. the quorum-sensing signal valdiazen produced byBurkholderia cenocepaciaH111. In this study, we investigated its biosynthetic gene cluster and discovered that both the enantiomerically pure (R)–fragin and the racemic valdiazen are obtained from the same pathway. This stereodivergence is based on the unusual heterocycle dihydrosydnoneN-oxide intermediate, as evident from gene knockout, stable isotope feeding experiments, and mass spectrometry experiments. Both non-enzymatic racemisation via keto-enol tautomerisation and enzyme-mediated dynamic kinetic resolution were found to be crucial to this stereodivergent pathway. This novel mechanism underpins the production of configurationally and biologically distinct metabolites from a single gene cluster. Our findings highlight the intricate design of an intertwined biosynthesis pathway, providing a deeper understanding of microbial secondary metabolism related to microbial communication.Abstract Figure
The Unexpected Membrane Targeting of Marchantia Short PIN Auxin Exporters Illuminates Sequence Determinants and Evolutionary Significance
Authors: Tang Han , Smoljan Adrijana , Zou Minxia , Zhang Yuzhou , Lu Kuan-Ju , Friml Jiří 
Published: April 2024

SummaryThe plant hormone auxin and its directional transport are crucial for growth and development. PIN auxin transporters, on account of their polarized distribution, are instrumental in guiding auxin flow across tissues. Based on protein length and subcellular localization, thePINfamily is classified into two groups: plasma membrane (PM)-localized long PINs and endoplasmic reticulum (ER)-localized short PINs. The origin ofPINs was traced to the algaKlebsormidium, with a single PM-localized long KfPIN. Bryophytes, the earliest land plant clade, represent the initial clade harboring the short PINs. We tracked the evolutionary trajectory of the shortPINs and explored their function and localization in the model bryophyteMarchantia polymorpha, which carries four short and one long PIN. Our findings reveal that all short MpPINs can export auxin, and they are all PM-localized with MpPINX and MpPINW exhibiting asymmetric distribution. We identified a unique miniW domain within the MpPINW hydrophilic loop region, which is sufficient for its PM localization. Phosphorylation site mutations within the miniW domain abolish the PM localization. These findings not only identify the essential sequence determinant of PINs’ PM localization but also provide a unique insight into the evolution of ER-localized PINs. Short MpPINW, which is evolutionarily positioned between the ancestral long PINs and contemporary short PINs, still preserves the critical region essential for its PM localization. We propose that throughout land plant evolution, the unique miniW domain has been gradually lost thus converting the PM-localized short PINs in bryophytes to ER-localized short PINs in angiosperms.IMPORTANTManuscripts submitted to Review Commons are peer reviewed in a journal-agnostic way.Upon transfer of the peer reviewed preprint to a journal, the referee reports will be available in full to the handling editor.The identity of the referees will NOT be communicated to the authors unless the reviewers choose to sign their report.The identity of the referee will be confidentially disclosed to any affiliate journals to which the manuscript is transferred.GUIDELINESFor reviewers:https://www.reviewcommons.org/reviewersFor authors:https://www.reviewcommons.org/authorsCONTACTThe Review Commons office can be contacted directly at:office@reviewcommons.org
rarestR: An R package using rarefaction metrics to estimate α-diversity (species richness) and β-diversity (species shared) for incomplete samples
Authors: Zou Yi , Zhao Peng , Wu Naicheng , Lai Jiangshan , Peres-Neto Pedro R. , Axmacher Jan C. 
Published: April 2024

AbstractSpecies abundance data is commonly used to study biodiversity patterns. In this context, estimating α- and β-diversity based on incomplete samples can lead to ‘undersampling biases’. It is therefore essential to employ methods that enable accurate comparisons of α- and β-diversity across varying sample sizes. This involves relying on biodiversity measures that are focused on accurately estimating the total number of species within a community, as well as the total number of species shared by two communities. Rarefaction offers such a method, where α-diversity is estimated for standardized sample sizes. Rarefaction methods can also be used as a basis for β-diversity calculations for standardized sample sizes. In this application note, we introduce a new R package,rarestR, designed to estimate abundance-based α- and β-diversity measures for inconsistent samples using rarefaction metrics. Additionally, the package offers parametric extrapolations to estimate the total expected number of species within a single community and the total expected number of species shared between two communities. Furthermore, it provides visualization for the curve fitting associated with these estimators. Overall, therarestRpackage is useful in estimating α- and β-diversity values for incomplete samples, for example in studies involving highly mobile or species-rich taxa. These species estimators offer a complementary approach to non-parametric methods, such as the Chao series of estimators.
Subcellular visualization of the distribution of atmospheric dinitrogen fixed byGluconacetobacter diazotrophicusbacteria in maize
Authors: McMahon G. , Rey S. , Moore K. , Greenidge G. , Patel D. , Murchie E.H. , Dent D. , Cocking E. 
Published: April 2024

AbstractPlants normally obtain the nitrogen required for growth through their roots, often after application of synthetic fertilizer to the soil, at great cost to the environment and climate. Inoculation of plant seeds with nitrogen-fixing bacteria is a promising alternative means of supplying plants the nitrogen they require in an environmentally friendly manner. When maize seeds inoculated with nitrogen-fixingGluconacetobacter diazotrophicus (Gd)are grown for two weeks in a15N2air environment, nanoscale secondary ion mass spectrometry (NanoSIMS) imaging shows the distribution of fixed nitrogen with subcellular resolution, with the majority being incorporated heterogeneously into chloroplasts. Chloroplasts, as the chief energy source that drives plant growth via photosynthesis, are vital for healthy plant growth and these results help explain the observations of enhanced growth rates in plants containing this nitrogen fixing bacteria. The methodology provides a template upon which more powerful, correlative studies combining genomic and/or spatial transcriptomic methods may be based.
A noncanonical polyamine from bacteria antagonizes animal mitochondrial function
Authors: Nauta Kelsie M. , Gates Darrick R. , Weiland Matthew , Mechan-Llontop Marco E. , Wang Xiao , Nguyen Kim P. , Isaguirre Christine , Genjdar Megan R. , Sheldon Ryan D. , Krawczyk Connie M. , Burton Nicholas O. 
Published: April 2024

AbstractCanonical polyamines such as agmatine, putrescine, and spermidine are evolutionarily conserved metabolites found in nearly all forms of life ranging from bacteria to humans. Recently, interactions between polyamines produced by gut bacteria and human intestinal cells have been proposed to contribute to both Irritable Bowel Syndrome with Diarrhea (IBS-D) and inflammatory bowel diseases. However, the molecular mechanisms that underlie these effects are often unclear due in part to limitations in the methods used to manipulate and study polyamine functionsin vivo.Here, we developed aCaenorhabditis elegansbased screening platform and a modified LC-MS approach for profiling polyamine metabolites. We combined these methods to make the unexpected discovery that dysfunctional polyamine metabolism in both Gram-negative (E. coli) and Gram-positive (B. subtilis) bacteria can result in the accumulation of a noncanonical polyamine intermediate, N1-Aminopropylagmatine (N1-APA). We further find that N1-APA is produced via spermidine synthase (SpeE) and that it is bioactive when encountered by animals. Specifically, we find that when N1-APA is produced by bacteria in animal intestines it can be transported into intestinal cells via the polyamine transporter CATP-5 where it antagonizes both animal development and mitochondrial function across diverse animal species. Lastly, we find that N1-APA functions analogously to the deoxyhypusine synthase inhibitor GC7. For example, like GC7, N1-APA antagonizes eIF5A hypusination and inhibits the alternative activation of mammalian macrophages. To our knowledge, these findings are the first to demonstrate that N1-APA is a bioactive metabolite and that bacteria can produce a small molecule that functions similarly to existing deoxyhypusine synthase inhibitors. Furthermore, these results suggest an exciting new mechanistic hypothesis for why the loss ofspeBin gut microbes, includingE. coli,has been both linked to inflammatory bowel disease (IBD) in humans and found to drive IBD in germ free mice.
Comparative single cell analysis of transcriptional bursting reveals the role of genome organization onde novotranscript origination
Authors: Lee UnJin , Li Cong , Langer Christopher B. , Svetec Nicolas , Zhao Li 
Published: April 2024

AbstractSpermatogenesis is a key developmental process underlying the origination of newly evolved genes. However, rapid cell type-specific transcriptomic divergence of theDrosophilagermline has posed a significant technical barrier for comparative single-cell RNA-sequencing (scRNA-Seq) studies. By quantifying a surprisingly strong correlation between species- and cell type-specific divergence in three closely relatedDrosophilaspecies, we apply a new statistical procedure to identify a core set of 198 genes that are highly predictive of cell type identity while remaining robust to species-specific differences that span over 25-30 million years of evolution. We then utilize cell type classifications based on the 198-gene set to show how transcriptional divergence in cell type increases throughout spermatogenic developmental time. After validating these cross-species cell type classifications using RNA fluorescence in situ hybridization (FISH) and imaging, we then investigate the influence of genome organization on the molecular evolution of spermatogenesis vis-a-vis transcriptional bursting. We first demonstrate how mechanistic control of pre-meiotic transcription is achieved by altering transcriptional burst size while post-meiotic control is exerted via altered bursting frequency. We then report how global differences in autosomal vs. X chromosomal transcription likely arise in a developmental stage preceding full testis organogenesis by showing evolutionarily conserved decreases in X-linked transcription bursting kinetics in all examined somatic and germline cell types. Finally, we provide evidence supporting the cultivator model ofde novogene origination by demonstrating how the appearance of newly evolved testis-specific transcripts potentially provides short-range regulation of neighboring genes’ transcriptional bursting properties during key stages of spermatogenesis.Significance StatementUnderstanding the divergence and evolution of novel genes and expression is essential in evolutionary biology. The testis is a hotspot for gene origination and diversification, partly because of strong sexual selection on male reproduction. However, rapid transcriptomic divergence in the germline has significantly hindered comparative single-cell RNA-seq studies and understanding of the rapidly evolving components of the cell types. Our novel strategy, which does not rely on preexisting marker genes for cell type identity, overcame the challenge. We provide evidence supporting the cultivator model of de novo gene origination—a model we recently proposed to emphasize the genomic environment in shaping novel gene origination—by illustrating how newly evolved transcripts are regulated by the transcriptional bursting of neighboring genes.
Lithic bacterial communities: ecological aspects focusing onTintenstrich communities
Authors: Pittino Francesca , Fink Sabine , Oliveira Juliana , Janssen Elisabeth M.-L. , Scheidegger Christoph 
Published: April 2024

ABSTRACTTintenstrichcommunities (TC) are mainly composed by Cyanobacteria developing on the rock substrate and forming physical structures strictly connected to the rock itself. Endolithic and epilithic bacterial communities are important because they contribute to nutrients release within run-off waters flowing on the rock surface. Despite them being ubiquitous, little information about their ecology and main characteristics is available. In this paper, we characterized the bacterial communities of rock surfaces ofTCin Switzerland through Illumina sequencing and investigated their bacterial community composition on two substrate types (silicious and limestone rocks) through multivariate models. Our results show that Cyanobacteria and Proteobacteria are the predominant phyla in this environment. Bacterial alpha diversity was higher on limestone than on siliceous rock, and beta diversity of siliceous rock varied with changes in rock surface structure. Here we provide novel insights into the bacterial community composition ofTC, their differences from other lithic communities, and the effects of the rock substrate and structure.