bluuebunny/crossref_metadata_2025 huggingface dataset:
Melanoma-specific mutation hotspots in distal, non-coding, promoter-interacting regions implicate novel candidate driver genes
Authors: Pudjihartono Michael , Pudjihartono Nicholas , O’Sullivan Justin M. , Schierding William
Published: May 2024

Investigations of the non-coding region are essential for uncovering the full spectrum of genetic drivers in melanoma. Here, we map distal, non-coding, promoter-interacting regulatory elements using Hi-C data from melanoma cells and integrating these with whole-genome sequence and gene expression data from the Pan Cancer Analysis of Whole Genomes. We identified eight recurrently mutated hotspots that are melanoma-specific, alter transcription factor binding motifs, and affect the expression of genes (e.g.HSPB7,CLDN1, ADCY9andFDXR) previously implicated as tumor suppressors/oncogenes. Our study integrates multiple levels of biological data to uncover novel melanoma-specific non-coding candidate drivers beyond the well-characterizedTERTpromoter.
Cellulose Rich Food Leads Anxiety through Gut-Brain Axis-mediated Amygdalar Dopamine Upregulation
Authors: Ito Kaede , Hosoki Haruka , Kasai Yuya , Sasaki Hiroyuki , Haraguchi Atsushi , Shibata Shigenobu , Nozaki Chihiro
Published: May 2024

It is widely said that healthy intestinal environment takes essential role for better mental condition. One of the known dietary nutrients which maintains intestinal environment is the dietary fiber. Recent study showed that maintaining intestinal environment by dietary fiber succeeded to alleviate the psychiatric disorder symptoms in animals. However, such effects have only been reported with soluble fiber, which is highly fermentable and promotes short-chain fatty acid (SCFA) production, and not with insoluble fiber. Therefore, we aimed to verify whether insoluble fiber, such as cellulose, can alter emotion via changes in the gut. We divided mice into two groups and fed either standard diet (SD, contains both insoluble and soluble dietary fibers) or cellulose rich diet (CRD, contains cellulose alone as the dietary fibers). The CRD-fed mice displayed 1) the increased the anxiety-like behavior accompanied with 2) the modified amygdalar dopamine signaling. We further found the decreased intestinal SCFA levels along with intestinal permeability, dysmotility and hypersensitivity in CRD-fed mice. These behavioral and physiological effect of CRD has been completely abolished in vagotomized mice, indicating the direct link between intestinal environment exacerbation to the emotion through gut-brain axis. Additionally, the opioid antagonist abolished the CRD-induced anxiety, suggesting the involvement of opioidergic system to the anxiety which may evoked by increased amygdalar dopamine levels. Altogether, our findings suggest that consumption of cellulose alone as the dietary fiber may evoke intestinal abnormalities which fires the vagus nerve then opiodergic system and amygdalar dopamine upregulation, resulting in the enhancement of anxiety.

Graphical Abstract: Possible mechanism of CRD-induced anxiety unveiled by current study

Our study clarified that long-consumption of cellulose-rich food (CRD) will lead decrease of SCFAs which may cause the intestinal disability, including decreased motility and increased intestinal permeability as well as upregulation of TRPA1 and SGLT1. These physiological modifications resulted as the intestinal hypersensitivity, which possibly overstimulate the vagal transmission which may activate endogenous opioidergic systems such as enkephalin (Enk) at the nucleus tractus solitarii (NTS). The activation of opioidergic system may suppress the GABAergic neuron in ventral tegmental area (VTA), resulting in the excess release of dopamine and further receptor modification in amygdala (Amyg), which might in the end cause the characteristic anxiety. The figure was created withBioRender.com.
Comparative genomics of three non-hematophagous leeches (Whitmaniaspp.): focusing on antithrombotic genes
Authors: Zhao Fang , Huang Zuhao , Tang Lizhou , He Bo , Liu Zichao , Lin Gonghua
Published: May 2024

Leeches are well known for their blood-feeding habits and are widely used for medicinal purposes as they secrete various antithrombotic substances. However, some leeches such asWhitmaniaspp. exhibit non-hematophagous feeding habits and their significance for medicinal use is debated. In this study, we provide chromosome-level genomes of two non-hematophagous leechesWhitmania acranulataandWhitmania laevis, and combined with our previous results ofWhitmania pigra, we systematically analyzed the similarities and differences on the genomes and especially their antithrombotic genes among the three non-hematophagousWhitmanialeeches. ForW. acranulata,W. laevis, andW. pigra, the genome size (181.72 Mb, 173.87 Mb, and 173.56), the percentage of repeat sites (29.55%, 28.28%, and 27.02%), and the number of protein-coding genes (27,068, 23,805, and 24,156) were close to each other, respectively. In contrast, both the total number of the antithrombotic genes (100, 63, and 79), and the detailed constitutes of different antithrombotic gene families were obviously different among the three leeches. There were also massive genetic variations among the members within each antithrombotic gene/protein family. RNA-Seq-based gene expression estimation showed that the expression profiles of the antithrombotic gene families were apparently different among the three leeches. This is the most comprehensive comparison of the genomes and antithrombic biomacromolecules for theWhitmanialeeches to date. Our results will greatly facilitate the evolutionary research and application of leech derivatives for medical and pharmaceutical purposes of thrombosis.
Extensive folding variability between homologous chromosomes in mammalian cells
Authors: Irastorza-Azcarate Ibai , Kukalev Alexander , Kempfer Rieke , Thieme Christoph J. , Mastrobuoni Guido , Markowski Julia , Loof Gesa , Sparks Thomas M. , Brookes Emily , Natarajan Kedar Nath , Sauer Stephan , Fisher Amanda G. , Nicodemi Mario , Ren Bing , Schwarz Roland F. , Kempa Stefan , Pombo Ana
Published: May 2024

Genetic variation and 3D chromatin structure have major roles in gene regulation. Due to challenges in mapping chromatin conformation with haplotype-specific resolution, the effects of genetic sequence variation on 3D genome structure and gene expression imbalance remain understudied. Here, we applied Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (mESC) line with high density of single nucleotide polymorphisms (SNPs). GAM resolved haplotype-specific 3D genome structures with high sensitivity, revealing extensive allelic differences in chromatin compartments, topologically associating domains (TADs), long-range enhancer-promoter contacts, and CTCF loops. Architectural differences often coincide with allele-specific differences in gene expression, mediated by Polycomb repression. We show that histone genes are expressed with allelic imbalance in mESCs, are involved in haplotype-specific chromatin contact marked by H3K27me3, and are targets of Polycomb repression through conditional knockouts of Ezh2 or Ring1b. Our work reveals highly distinct 3D folding structures between homologous chromosomes, and highlights their intricate connections with allelic gene expression.
Activation loop phosphorylation of Cdk11 is restrained by PNUTS-PP1 and regulates Cdk11 activity and function
Authors: Campbell Amy E , Aljabri Abdulrahman A , Hesketh Andrew , Byrne Dominic P , Bennett Hayley , Patel Sanjai , Brownridge Philip , Zacharchenko Thomas , Bucca Giselda , Eyers Patrick A , Betancourt Andrea J , Eyers Claire E , Bennett Daimark
Published: May 2024

Organisation of the transcription cycle is facilitated by the reversible phosphorylation of the C-terminal domain of RNA Polymerase II (RNAPII-CTD) and its accessory factors. The PNUTS-PP1 protein phosphatase is crucial for mRNA synthesis and processing, yet the complete spectrum of its physiological targets in these processes remain elusive. Here, using quantitative phosphoproteomics, we discover that Cdk11, in addition to various spliceosomal and RNA processing factors, associates with PNUTS, and that disruption of PP1-binding results in hyperphosphorylation of Cdk11 at an evolutionarily conserved Serine residue, seven amino acid residues C-terminal to DFG residues in the activation loop.In vitroexperiments reveal a role for Ser DFG+7 in modulating Cdk11 kinase activity towards RNAPII-CTD Ser5. Making use of a novel technique to conditionally disrupt PP1 binding, we show that PNUTS-PP1 normally serves to restrain Cdk11 phosphorylationin vivo. Mutational analysis shows thatcdk11is not only essential for survival but also plays a widespread role in regulating normal mRNA expression and splicing. Notably, we find that a phosphomimetic mutation incdk11exhibits distinct biological effects compared to loss ofcdk11function, including defective processing of intronic small nucleolar RNAs, diminished intronic RNA Pol II velocity, and a decrease in intergenic transcription. These findings underscore physiologically significant roles of Cdk11 dephosphorylation by PNUTS-PP1 in the regulation of mRNA transcription and processing.
Thetis cells induce food-specific Treg cell differentiation and oral tolerance
Authors: Parisotto Yollanda Franco , Cabric Vanja , Park Tyler , Akagbosu Blossom , Zhao Zihan , Lo Yun , Fisher Logan , Shibu Gayathri , Paucar Iza Yoselin A. , Leslie Christina , Brown Chrysothemis C.
Published: May 2024

The intestinal immune system must establish tolerance to food antigens to prevent onset of allergic and inflammatory diseases. Peripherally generated regulatory T (pTreg) cells play an essential role in suppressing inflammatory responses to allergens; however, the antigen-presenting cell (APC) that instructs food-specific pTreg cells is not known. Here, we show that antigen presentation and TGF-β activation by a subset of RORγt+antigen-presenting cells (APC), Thetis cells IV (TC IV), is required for food-induced pTreg cell differentiation and oral tolerance. By contrast, antigen presentation by dendritic cells (DCs) was dispensable for pTreg induction but required for TH1 effector responses, highlighting a division of labor between tolerogenic TCs and pro-inflammatory DCs. While antigen presentation by TCs was required for food-specific pTreg generation both in early life and adulthood, the increased abundance of TCs in the peri-weaning period was associated with a window of opportunity for enhanced pTreg differentiation. These findings establish a critical role for TCs in oral tolerance and suggest that these cells may represent a key therapeutic target for the treatment of food-associated allergic and inflammatory diseases.
Light regulates widespread plant alternative polyadenylation through the chloroplast
Authors: Guillermina Kubaczka M. , Godoy Herz Micaela A. , Chen Wei-Chun , Zheng Dinghai , Petrillo Ezequiel , Tian Bin , Kornblihtt Alberto R.
Published: May 2024

Transcription of eukaryotic protein-coding genes generates immature mRNAs that are subjected to a series of processing events, including capping, splicing, cleavage and polyadenylation (CPA) and chemical modifications of bases. Alternative polyadenylation (APA) greatly contributes to mRNA diversity in the cell. By determining the length of the 3’ untranslated region, APA generates transcripts with different regulatory elements, such as miRNA and RBP binding sites, which can influence mRNA stability, turnover and translation. In the model plantArabidopsis thaliana, APA is involved in the control of seed dormancy and flowering. In view of the physiological importance of APA in plants, we decided to investigate the effects of light/dark conditions and compare the underlying mechanisms to those elucidated for alternative splicing (AS). We found that light controls APA in approximately 30% ofArabidopsisgenes. Similar to AS, the effect of light on APA requires functional chloroplasts, is not affected in mutants of the phytochrome and cryptochrome photoreceptor pathways and is observed in roots only when the communication with the photosynthetic tissues is not interrupted. Furthermore, mitochondrial activity is necessary for the effect of light in roots but not in shoots. However, unlike AS, coupling with transcriptional elongation does not seem to be involved since light-dependent APA regulation is neither abolished in mutants of the TFIIS transcript elongation factor nor universally affected by chromatin relaxation caused by the histone deacetylase inhibition. Instead, regulation seems to be linked to light-elicited changes in the abundance of constitutive CPA factors, also mediated by the chloroplast.
Advancing chloroplast synthetic biology through high-throughput plastome engineering ofChlamydomonas reinhardtii
Authors: Inckemann René , Chotel Tanguy , Brinkmann Cedric K. , Burgis Michael , Andreas Laura , Baumann Jessica , Sharma Priyati , Klose Melanie , Barrett James , Ries Fabian , Paczia Nicole , Glatter Timo , Willmund Felix , Mackinder Luke C. M. , Erb Tobias J.
Published: May 2024

Chloroplast synthetic biology holds promise for developing improved crops through improving the function of plastids. However, chloroplast engineering efforts face limitations due to the scarcity of genetic tools and the low throughput of plant-based systems. To address these challenges, we here establishedChlamydomonas reinhardtiias a prototyping chassis for chloroplast synthetic biology. We developed an automation workflow that enables the generation, handling, and analysis of thousands of transplastomic strains in parallel, expanded the repertoire of selection markers for chloroplast transformation, established new reporter genes, and characterized over 140 regulatory parts, including native and synthetic promoters, UTRs, and intercistronic expression elements. We integrated the system within the Phytobrick cloning standard and demonstrate several applications, including a library-based approach to develop synthetic promoter designs in plastids. Finally, we provide a proof-of-concept for prototyping novel traits in plastids by introducing a chloroplast-based synthetic photorespiration pathway and demonstrating a twofold increase in biomass production. Overall, our study advances chloroplast engineering, and provides a promising platform to rapidly prototype chloroplast manipulations before their transfer into higher plants and crops.
Network Analyses of Brain Tumor Patients’ Multiomic Data Reveals Pharmacological Opportunities to Alter Cell State Transitions
Authors: Bumbaca Brandon , Birtwistle Marc R. , Gallo James M.
Published: May 2024

Glioblastoma Multiforme (GBM) remains a particularly difficult cancer to treat, and survival outcomes remain poor. In addition to the lack of dedicated drug discovery programs for GBM, extensive intratumor heterogeneity and epigenetic plasticity related to cell-state transitions are major roadblocks to successful drug therapy in GBM. To study these phenomenon, publicly available snRNAseq and bulk RNAseq data from patient samples were used to categorize cells from patients into four cell states (i.e. phenotypes), namely: (i) neural progenitor-like (NPC-like), (ii) oligodendrocyte progenitor-like (OPC-like), (iii) astrocyte-like (AC-like), and (iv) mesenchymal-like (MES-like). Patients were subsequently grouped into subpopulations based on which cell-state was the most dominant in their respective tumor. By incorporating phosphoproteomic measurements from the same patients, a protein-protein interaction network (PPIN) was constructed for each cell state. These four-cell state PPINs were pooled to form a single Boolean network that was used forin silicoprotein knockout simulations to investigate mechanisms that either promote or prevent cell state transitions. Simulation results were input into a boosted tree machine learning model which predicted the cell states or phenotypes of GBM patients from an independent public data source, the Glioma Longitudinal Analysis (GLASS) Consortium. Combining the simulation results and the machine learning predictions, we generated hypotheses for clinically relevant causal mechanisms of cell state transitions. For example, the transcription factor TFAP2A can be seen to promote a transition from the NPC-like to the MES-like state. Such protein nodes and the associated signaling pathways provide potential drug targets that can be further testedin vitroand support cell state-directed (CSD) therapy.
High-throughput protein characterization by complementation using DNA barcoded fragment libraries
Authors: Biggs Bradley W. , Price Morgan N. , Lai Dexter , Escobedo Jasmine , Fortanel Luis , Huang Yolanda Y. , Kim Kyoungmin , Trotter Valentine V. , Kuehl Jennifer V. , Lui Lauren M. , Chakraborty Romy , Deutschbauer Adam M. , Arkin Adam P.
Published: May 2024

Our ability to predict, control, or design biological function is fundamentally limited by poorly annotated gene function. This can be particularly challenging in non-model systems. Accordingly, there is motivation for new high-throughput methods for accurate functional annotation. Here, we usecomplementation ofauxotrophs and DNA barcodesequencing (Coaux-Seq) to enable high-throughput characterization of protein function. Fragment libraries from eleven genetically diverse bacteria were tested in twenty different auxotrophic strains ofEscherichia colito identify genes that complement missing biochemical activity. Although assay effectiveness ranged with respect to source genome, with 41% of expected enzymes recovered, even distantE. colirelatives likeBacillus subtilisandBacteroides thetaiotaomicronshowed success. Coaux-Seq provided the first experimental validation for 53 proteins, of which 11 are less than 40% identical to an experimentally characterized protein on an amino acid basis. Among unexpected function identified was a sulfate uptake transporter, an O-succinylhomoserine sulfhydrylase for methionine synthesis, and an aminotransferase. We also identified instances of cross-feeding wherein protein overexpression and nearby non-auxotrophic strains enabled growth. Altogether, Coaux-Seq’s utility is demonstrated, with future applications in ecology, health, and engineering.
Adhesive and mechanical properties of the glue produced by 25 Drosophila species
Authors: Monier Manon , Lorenzi Jean-Noël , Narasimha Sunitha , Borne Flora , Contremoulins Vincent , Mevel Louis , Petit Romane , El Hachem Youssef , Graner François , Courtier-Orgogozo Virginie
Published: May 2024

Drosophila glue, a bioadhesive produced by fly larvae to attach themselves to a substrate for several days, has recently gained attention for its peculiar adhesive and mechanical properties. Although Drosophila glue production was described more than 50 years ago, a general survey of the adhesive and mechanical properties of this proteinaceous gel across Drosophila species is lacking. To measure adhesion, we present here a protocol that is robust to variations in protocol parameters, pupal age and calculation methods. We find that the glue, which covers the entire pupal surface, increases the animal rigidity and plasticity when bound to a glass slide. Our survey of pupal adhesion in 25 Drosophilidae species reveals la wide range of phenotypes, from species that produce no or little glue and adhere little, to species that produce high amounts of glue and adhere strongly. One species,D. hydei, stands out from the rest and emerges as a promising model for the development of future bioadhesives, as it has the highest detachment force per glue area and produces relatively large amounts of glue relative to its size. We also observe that species that invest more in glue tend to live in more windy and less rainy climates, suggesting that differences in pupal adhesion properties across species are shaped by ecological factors. Our present survey provides a basis for future biomimetic studies based on Drosophila glue.
N-Myc and STAT Interactor is an endometriosis suppressor
Authors: Park Yuri , Guan Xiaoming , Han Sang Jun
Published: May 2024

In patients with endometriosis, refluxed endometrial fragments evade host immunosurveillance, developing into endometriotic lesions. However, the mechanisms underlying this evasion have not been fully elucidated. N-Myc and STAT Interactor (NMI) have been identified as key players in host immunosurveillance, including interferon (IFN)-induced cell death signaling pathways. NMI levels are markedly reduced in the stromal cells of human endometriotic lesions due to modulation by the Estrogen Receptor beta/Histone Deacetylase 8 axis. Knocking down NMI in immortalized human endometrial stromal cells (IHESCs) led to elevated RNA levels of genes involved in cell-to-cell adhesion and extracellular matrix signaling following IFNA treatment. Furthermore, NMI knockdown inhibited IFN-regulated canonical signaling pathways, such as apoptosis mediated by Interferon Stimulated Gene Factor 3, and necroptosis upon IFNA treatment. In contrast, NMI knockdown with IFNA treatment activated non-canonical IFN-regulated signaling pathways that promote proliferation, including β-Catenin and AKT signaling. Moreover, NMI knockdown in IHESCs stimulated ectopic lesions’ growth in mouse endometriosis models. Therefore, NMI is a novel endometriosis suppressor, enhancing apoptosis and inhibiting proliferation and cell adhesion of endometrial cells upon IFN exposure.
The large GTPase Guanylate-Binding Protein-1 (GBP-1) promotes mitochondrial fission in glioblastoma
Authors: Kalb Ryan C. , Nyabuto Geoffrey O. , Morran Michael P. , Maity Swagata , Justinger Jacob S. , Nestor-Kalinoski Andrea L. , Vestal Deborah J.
Published: May 2024

Glioblastomas (aka Glioblastoma multiforme (GBMs)) are the most deadly of the adult brain tumors. Even with aggressive treatment, the prognosis is extremely poor. The large GTPase Guanylate-Binding Protein-1 (GBP-1) contributes to the poor prognosis of GBM by promoting migration and invasion. GBP-1 is substantially localized to the cytosolic side of the outer membrane of mitochondria in GBM cells. Because mitochondrial dynamics, particularly mitochondrial fission, can drive cell migration and invasion, the potential interactions between GBP-1 and mitochondrial dynamin-related protein 1 (Drp1) were explored. Drp1 is the major driver of mitochondrial fission. While GBP-1 and Drp1 both had punctate distributions within the cytoplasm and localized to regions of the cytoplasmic side of the plasma membrane of GBM cells, the proteins were only molecularly co-localized at the mitochondria. Subcellular fractionation showed that the presence of elevated GBP-1 promoted the movement of Drp1 from the cytosol to the mitochondria. Migration of U251 cells treated with the Drp1 inhibitor, Mdivi-1, was less inhibited in the cells with elevated GBP-1. Elevated GBP-1 in GBM cells resulted in shorter and wider mitochondria, most likely from mitochondrial fission. Mitochondrial fission can drive a number of important cellular processes, including cell migration, invasion, and metastasis.

Simple Summary

Glioblastomas are the most common and most aggressive adult brain tumors arising from astrocytes. Up to 60% of glioblastomas are promoted by either amplification and/or mutation of the Epidermal Growth Factor Receptor (EGFR). The large GTPase Guanylate-Binding Protein-1 (GBP-1) is one of the most robustly induced proteins following EGFR signaling in glioblastomas. How GBP-1 promotes tumor progression in glioblastomas is still under investigation. This study shows that GBP-1 promotes tumor progression by associating with Drp1 at glioblastoma mitochondria and enhancing their fission. Specifically, increased mitochondrial fission can promote tumor cell migration, invasion, and metastasis.
Genome-Wide Identification and Expression Pattern of theN-acetylserotonin deacetylase (ASDAC) Gene Family in Orchidaceae
Authors: Sun Enda , Zhao Erqiang , Li Qianqian , lu wenxiu , Jin JiaQI , Li Yingjia , Yang Chen , Chen Tingying , Mou Zongmin , Zhao Dake
Published: May 2024

Orchids are a kind of horticultural plant with highly ornamental and medical value.N-acetylserotonin deacetylase (ASDAC) is the only reverse enzyme of the melatonin biosynthesis pathway, and plays an important role in regulating the balance of melatonin. Melatonin as a multifunctional molecule, is typically involved in plant growth and development regulation, as well as abiotic stress tolerance. Here, we aimed at identifyingASDACgenes from the orchid genome to provide valuable information for further study of the role of melatonin in orchids.

In this study, a total of 7ASDACgenes were identified from the 7 orchid genome with one member in each species. The 7 orchidASDACshave an HDAC functional domain, and cluster together with functionally confirmedOsHDAC10andAtHDAC14, it shows that these members may have function ofN-acetylserotonin deacetylase. Furthermore, based on the phylogenetic, motif, and gene structure analysis, the same cluster’s orchidASDACorASDAC-like genes generally contained similar introns and motifs, suggesting the distribution pattern of exons/introns and motifs were strongly related to phylogeny on an evolutionary basis. Interestingly, homologous genes ofOsHDAC10andAtHDAC14inGastrodia elatahave low homology and not cluster together with rice andA.thaliana ASDACs, showing thatASDACgene family may lost in the holomycoheterotrophic orchids. The Ka/Ks ratios ofASDACgene pairs from lower plant to higher plant were less than one, suggested thatASDACgenes have undergone purifying selection during the evolution process.Cis-acting element analysis results showed that the promoter regions of orchidASDACgenes contained plant growth and development, phytohormone, and stress-responsive elements. Moreover, most orchidASDACswere expressed in the roots, stems, leaves, flowers, and seeds. Combinedcis-acting element and tissue expression analysis, indicating orchidASDACgenes are involved in melatonin regulation of growth and development, as well as melatonin responding to various stresses in orchids. These findings of orchidASDACgenes may provide valuable information for further study of the role of melatonin in orchids.
Genetic variation in trophic avoidance shows fruit flies are generally attracted to bacterial pathogens
Authors: Monteith Katy M. , Thornhill Phoebe , Vale Pedro F.
Published: May 2024

Pathogen avoidance behaviours are often assumed to be an adaptive host defence from infection. However, there is limited experimental data on the prerequisite for this assumption: heritable, intrapopulation phenotypic variation for avoidance. We investigated trophic pathogen avoidance in 122 inbredDrosophila melanogasterlines, and in a derived outbred population. Using the FlyPAD system, we tracked the feeding choice that flies made between substrates that were either clean or contained a bacterial pathogen. We uncovered significant, but weakly heritable variation in the preference index among fly lines. However, instead of avoidance, most lines demonstrated a preference for several bacterial pathogens, showing avoidance only for extremely high bacterial concentrations. Bacterial preference was not associated with susceptibility to infection and was retained in flies with disrupted immune signalling. Phenotype-genotype association analysis indicated several novel genes (CG2321, CG2006, ptp99A) associated with increased preference for the bacterial substrate, while the amino-acid transportersobremesawas associated with greater aversion. Together with previous work showing fitness benefits of consuming high-protein diets, our results suggest that bacterial attraction may instead reflect a dietary preference for protein over carbohydrate. More work quantifying intrapopulation variation in avoidance behaviours is needed to fully assess its importance in host-pathogen evolutionary ecology.
Closely related facultative and constitutive CAM phenotypes activate different transcriptional responses upon water withholding in the subgenus Tillandsia
Authors: Crego Clara Groot , Saadain Sarah , de La Harpe Marylaure , Hess Jaqueline , Barfuss Michael H.J. , Till Walter , Lexer Christian , Paun Ovidiu
Published: May 2024

2.

The evolutionary trajectory and genetic architecture of crassulacean acid metabolism (CAM), a water-efficient form of photosynthesis that has evolved repeatedly in the plant kingdom, remains elusive. The extent to which different CAM phenotypes share a genetic basis, forming a continuum through varying degrees of expression, or exhibit divergence and redundancy of employed genes and their expression, is still debated. The subgenusTillandsiaprovides an excellent opportunity to compare the genetic basis of different CAM forms, given its broad range of photosynthetic phenotypes. Through physiological and transcriptomic analyses of well-watered and water-limited accessions of a closely related species pair, we comprehensively characterized facultative and constitutive CAM inTillandsia. By comparing orthologous gene expression and orthogroup recruitment, we found that while both species performed CAM upon water-withholding, transcriptional modulation of orthogroups related to stomatal movement, sugar/malate transport, aquaporins and starch metabolism showed little similarity. Enzymes of the CAM (de)carboxylation modules exhibited shared expression patterns, though distinct orthologs of PEPC were upregulated at night in each species. Our study reveals that, while the expression of certain core CAM enzymes is shared, these species exhibit substantial divergence of CAM-related transcriptomic modulation, revealing CAM’s polygenic nature and providing a possible hypothesis for its evolvability.

1.

Highlight

We comprehensively characterized and compared facultative and constitutive CAM phenotypes inTillandsiabromeliads on a physiological and transcriptomic level. We found substantial divergence in CAM-related transcriptomic modulation between phenotypes, highlighting the polygenic nature of the CAM continuum.
Analyzing the Involvement of Cholinesterases in the Immune Landscape of Lung Adenocarcinoma and Their Prognostic Values
Authors: Zhang Fengyu , Zhu Zhouhai , Guan Ying , Li Meng , Pan Zhenhua , Wang Ju
Published: May 2024

Lung adenocarcinoma (LUAD) is the most common subtype of lung cancer and its prognosis is poor. The cholinergic system is involved in the development of lung cancer but its role is still unclear. In this study, we collected 231 cholinergic-related genes, and examined their expression in LUAD samples and normal tissues, from which 37 differentially expressed genes were screened. Then, by survival analysis, we identified 7 genes related to the prognosis of LUAD, among which acetylcholinesterase (ACHE) and butyrylcholinesterase (BCHE) were included. The expression of AChE was upregulated in LUAD samples, and its expression had a significant positive correlation with the prognosis of male patients. But the expression of BChE was down-regulated in LUAD samples, and the elevated BChE expression was associated with a good prognosis in women and non-smoking patients. We also observed a close relationship between the two genes and immune landscape of LUAD. The AChE high expression patients had a higher ratio of tumor-infiltrating immune cells than the low expression patients, while the BChE high expression group had higher ratios of both tumor-infiltrating immune cells and stromal cells. We collected a total of 113 immunomodulatory genes associated with AChE and BChE to build an immunoregulatory network, which comprised several gene clusters. We also found that the expression of AChE and BChE was associated with immune escape in LUAD. Our results showed that AChE and BChE may play an important role in the development of LUAD, and could be promising biomarkers and targets for its diagnosis and treatment.
Imaging the extracellular matrix in live tissues and organisms with a glycan-binding fluorophore
Authors: Fiore Antonio , Yu Guoqiang , Northey Jason J. , Patel Ronak , Ravenscroft Thomas A. , Ikegami Richard , Kolkman Wiert , Kumar Pratik , Grimm Jonathan B. , Dilan Tanya L. , Ruetten Virginia M.S. , Ahrens Misha B. , Shroff Hari , Lavis Luke D. , Wang Shaohe , Weaver Valerie M. , Pedram Kayvon
Published: May 2024

All multicellular systems produce and dynamically regulate extracellular matrices (ECM) that play important roles in both biochemical and mechanical signaling. Though the spatial arrangement of these extracellular assemblies is critical to their biological functions, visualization of ECM structure is challenging, in part because the biomolecules that compose the ECM are difficult to fluorescently label individually and collectively. Here, we present a cell-impermeable small molecule fluorophore, termed Rhobo6, that turns on and red shifts upon reversible binding to glycans. Given that most ECM components are densely glycosylated, the dye enables wash-free visualization of ECM, in systems ranging fromin vitrosubstrates toin vivomouse mammary tumors. Relative to existing techniques, Rhobo6 provides a broad substrate profile, superior tissue penetration, nonperturbative labeling, and negligible photobleaching. This work establishes a straightforward method for imaging the distribution of ECM in live tissues and organisms, lowering barriers for investigation of extracellular biology.
Red Blood Cell-Derived Exosomal Oncogenic MicroRNA Promote Cancer Development and Progression
Authors: Li Jin , Dhilipkannah Pushpa , Holden Van K , Sachdeva Ashutosh , Jiang Feng
Published: May 2024

The role of red blood cells (RBCs) in tumorigenesis is poorly understood. We previously identified RBC-microRNAs with aberrations linked to lung cancer, including miR-93-5p. Here we find that miR-93-5p levels are elevated in RBC-derived exosomes among lung cancer patients and are associated with their shorter survivals. RBC-derived miR-93-5p transfers to cancer cells primarily through the exosomal pathway. The transferred RBC-miR-93-5p can target PTEN in cancer cells, and hence increase cell proliferation, invasion, and migration. RBC-derived miR-93-5p accelerates, whereas targeting miR-93-5p diminishes tumor growth in xenograft models. These findings reveal a novel biological function of RBCs in tumorigenesis, where they facilitate cancer progression by transferring the oncomiR via exosomes, thereby offering new diagnostic and treatment strategies for lung cancer.
Neuron Derived Cytokine Interleukin-34 Controls Developmental Microglia Function
Authors: Devlin Benjamin A. , Nguyen Dang M. , Grullon Gabriel , Clark Madeline J. , Ceasrine Alexis M. , Deja Martha , Shah Ashka , Ati Shomik , Finn Amelie , Ribeiro Diogo , Schaefer Anne , Bilbo Staci D.
Published: May 2024

Neuron-microglia interactions dictate the development of neuronal circuits in the brain. However, the factors that support and broadly regulate these processes across developmental stages are largely unknown. Here, we find that IL34, a neuron-derived cytokine, is upregulated in development and plays a critical role in supporting and maintaining neuroprotective, mature microglia in the anterior cingulate cortex (ACC) of mice. We show that IL34 mRNA and protein is upregulated in neurons in the second week of postnatal life and that this increase coincides with increases in microglia number and expression of mature, homeostatic markers, e.g., TMEM119. We also found that IL34 mRNA is higher in more active neurons, and higher in excitatory (compared to inhibitory) neurons. Genetic KO of IL34 prevents the functional maturation of microglia and results in an anxiolytic phenotype in these mice by adulthood. Acute, low dose blocking of IL34 at postnatal day (P)15 in mice decreased microglial TMEM119 expression and increased aberrant microglial phagocytosis of thalamocortical synapses within the ACC. In contrast, viral overexpression of IL34 early in life (P1-P8) caused early maturation of microglia and prevented microglial phagocytosis of thalamocortical synapses during the appropriate neurodevelopmental refinement window. Taken together, these findings establish IL34 as a key regulator of neuron-microglia crosstalk in postnatal brain development, controlling both microglial maturation and synapse engulfment.
UPF1 is required for gene expression in mitochondria and paternal mtDNA clearance during spermatogenesis
Authors: Wright Matthew T , Singh Anand K , Dixon Hannah L , Price Emily M , Connolly Elizabeth , Maio Alessandro Di , Barlow Jonathon , Catoni Marco , Fan Yun , Brogna Saverio
Published: May 2024

UPF1 is a conserved RNA helicase in eukaryotes which is crucial for the correct expression of nuclear genes. This study presents ChIP-seq evidence indicating its RNA-dependent interaction with mtDNA transcription sites inDrosophilaS2 cells. Mitochondrial and frequent co-localisation with nucleoids were validated by immunostaining and GFP-tagging of UPF1 in various fly tissues and cell types. Depletion of UPF1, but not other NMD factors, during spermatogenesis, causes severe meiosis and cytokinesis defects, leading to sterility. RNA-seq indicates that these phenotypes could be primarily due to the reduced expression of genes essential for chromosome segregation. Yet also shows that spermatids depleted of UPF1 exhibit a widespread downregulation of mtDNA transcription and, unlike in wild type, fail to eliminate their mtDNA at the elongation stage. Cumulatively, this study indicates a crucial requirement of UPF1 in the expression of both nuclear and mtDNA genes during spermatogenesis.
Task-specific topographical maps of neural activity in the primate lateral prefrontal cortex
Authors: Xiang Jinkang Derrick , Roussy Megan , Corrigan Benjamin , Gulli Roberto A. , Luna Rogelio , Mofrad Maryam Hasanzadeh , Muller Lyle , Diedrichsen Jörn , Schmitz Taylor W. , Martinez-Trujillo Julio , Mur Marieke
Published: May 2024

Neurons in the primate lateral prefrontal cortex (LPFC) flexibly adapt their activity to support a wide range of cognitive tasks. Whether and how the topography of LPFC neural activity changes as a function of task is unclear. In the present study, we address this issue by characterizing the functional topography of LPFC neural activity in awake behaving macaques performing three distinct cognitive tasks. We recorded from chronically implanted multi-electrode arrays and show that the topography of LPFC activity is stable within a task, but adaptive across tasks. The topography of neural activity exhibits a spatial scale compatible with that of cortical columns and prior anatomical tracing work on afferent LPFC inputs. Our findings show that LPFC maps of neural population activity are stable for a specific task, providing robust neural codes that support task specialization. Moreover, the variability in functional topographies across tasks indicates activity landscapes can adapt, providing flexibility to LPFC neural codes.
Unraveling Morphogenesis, Starvation, and Light Responses in a Mushroom-Forming Fungus,Coprinopsis cinerea, Using Long Read Sequencing and Extensive Expression Profiling
Authors: Hegedüs Botond , Sahu Neha , Bálint Balázs , Haridas Sajeet , Bense Viktória , Merényi Zsolt , Virágh Máté , Wu Hongli , Liu Xiao-Bin , Riley Robert , Lipzen Anna , Koriabine Maxim , Savage Emily , Guo Jie , Barry Kerrie , Ng Vivian , Urbán Péter , Gyenesei Attila , Freitag Michael , Grigoriev Igor V. , Nagy László G.
Published: May 2024

Mushroom-forming fungi (Agaricomycetes) are emerging as pivotal players in several fields, as drivers of nutrient cycling, sources of novel applications, and the group includes some of the most morphologically complex multicellular fungi. Genomic data for Agaricomycetes are accumulating at a steady pace, however, this is not paralleled by improvements in the quality of genome sequence and associated functional gene annotations, which leaves gene function notoriously poorly understood in comparison with other fungi and model eukaryotes. We set out to improve our functional understanding of the model mushroomCoprinopsis cinereaby integrating a new, chromosome-level assembly with high-quality gene predictions and functional information derived from gene-expression profiling data across 67 developmental, stress, and light conditions. The new annotation has considerably improved quality metrics and includes 5’- and 3’-untranslated regions (UTRs), polyadenylation sites (PAS), upstream ORFs (uORFs), splicing isoforms, conserved sequence motifs (e.g., TATA and Kozak boxes) and microexons. We found that alternative polyadenylation is widespread inC. cinerea, but that it is not specifically regulated across the various conditions used here. Transcriptome profiling allowed us to delineate core gene sets corresponding to carbon starvation, light-response, and hyphal differentiation, and uncover new aspects of the light-regulated phases of life cycle. As a result, the genome ofC. cinereahas now become the most comprehensively annotated genome among mushroom-forming fungi, which will contribute to multiple rapidly expanding fields, including research on their life history, light and stress responses, as well as multicellular development.
Human Substantia Nigra Neurons Encode Reward Expectations
Authors: Imtiaz Zarghona , Kato Ayaka , Kopell Brian H. , Qasim Salman E. , Davis Arianna Neal , Martinez Lizbeth Nunez , Heflin Matt , Kulkarni Kaustubh , Morsi Amr , Gu Xiaosi , Saez Ignacio
Published: May 2024

Dopamine (DA) signals originating from substantia nigra (SN) neurons are centrally involved in the regulation of motor and reward processing. DA signals behaviorally relevant events where reward outcomes differ from expectations (reward prediction errors, RPEs). RPEs play a crucial role in learning optimal courses of action and in determining response vigor when an agent expects rewards. Nevertheless, how reward expectations, crucial for RPE calculations, are conveyed to and represented in the dopaminergic system is not fully understood, especially in the human brain where the activity of DA neurons is difficult to study. One possibility, suggested by evidence from animal models, is that DA neurons explicitly encode reward expectations. Alternatively, they may receive RPE information directly from upstream brain regions. To address whether SN neuron activity directly reflects reward expectation information, we directly examined the encoding of reward expectation signals in human putative DA neurons by performing single-unit recordings from the SN of patients undergoing neurosurgery. Patients played a two-armed bandit decision- making task in which they attempted to maximize reward. We show that neuronal firing rates (FR) of putative DA neurons during the reward expectation period explicitly encode reward expectations. First, activity in these neurons was modulated by previous trial outcomes, such that FR were greater after positive outcomes than after neutral or negative outcome trials. Second, this increase in FR was associated with shorter reaction times, consistent with an invigorating effect of DA neuron activity during expectation. These results suggest that human DA neurons explicitly encode reward expectations, providing a neurophysiological substrate for a signal critical for reward learning.
Polyamines promote disordered protein phase separation
Authors: Percival Matthew , Pantoja Christian F. , Cima-Omori Maria-Sol , Becker Stefan , Zweckstetter Markus
Published: May 2024

Abstact

Membrane-less organelles are spatially heterogenous deposits of interacting macromolecules, often intrinsically disordered proteins and RNA, that form and dissolve in response to cellular stimuli. How membraneless organelles control composition while maintaining stimuli-responsiveness in an environment with competitive interactions is not well understood. Here we demonstrate that natural polyamines, which are found in all living organisms and help in many biological processes, promote protein phase separation via attractive interactions with acidic disordered domains. We show that the abundant polyamine spermine promotes phase separation of the stress-granule associated protein G3BP1 and modulates together with RNA the phase separation and amyloid formation of the Parkinson’s disease-related protein α-synuclein. Polyamine-promoted phase separation is controllable via polyamine acetylation and RNA-mediated competitive interactions. The results suggest that cellular polyamines may serve diverse roles in biomolecular condensation and the regulation of membraneless organelles.
Laboratoryin vitroreplication of Ostreid Herpes Virus (OsHV-1) using Pacific oyster tissue explants
Authors: Potts Robert W.A. , Regan Tim , Ross Stuart , Bateman Kelly , Hooper Chantelle , Paley Richard , Houston Ross D. , Bean Tim P.
Published: May 2024

Pacific oysters (CrassostreaorMagallana gigas) are one of the most economically important aquaculture species globally. Over the past two decades, ostreid herpesvirus (OsHV-1), has become a major pathogen of cultured Pacific oysters resulting in widespread mortality with a global distribution. Experimental use of OsHV-1 is challenging for many reasons, including both complexity and relative obscurity of host pathogen dynamics, and a lack of functioning model systems. The goal of this study was to improve the tools available for working with OsHV-1 in both whole animals and in tissue explants establishedex vivofrom oysters and maintained in controlled laboratory conditions. Tissue explants were taken from oysters originating from two different sources that have different levels of mortality in OsHV-1 challenges and were used in disease challenges alongside whole animals for comparison. Quantitative PCR, histology and electron microscopy were used to confirm that the explants were capable of replicating OsHV-1. Furthermore, the quantitative PCR results suggests that the source of the oysters was significant in determining the outcome of infection in the explants, supporting the validity of the explant model for OsHV-1 infection. This approach for studying OsHV-1 allows for the control of confounding factors in disease outcome that is not possible in whole animal challenges, providing a new tool for studying OsHV-1 in Pacific oysters.
Encoding of interdependent features of head direction and angular head velocity in navigation
Authors: Cai Dongqin , Liu Tao , Liu Jia
Published: May 2024

To comprehend the complex world around us, our brains are tasked with the remarkable job of integrating multiple features into a cohesive whole. While previous studies have primarily focused on the processing and integration of independent features, here we investigated the simultaneous encoding of the interdependent features, specifically head direction (HD) and its temporal derivative, angular head velocity (AHV), by first employing computational modeling on HD systems to explore emergent algorithms and then validated its biological plausibility with empirical data from mice’s HD systems. Our analysis revealed two distinct neuron populations: those with multiphasic tuning curves for HD compromised their HD encoding capacity to better capture AHV dynamics, while those with monophasic tuning curves primarily encoded HD. This pattern of functional dissociation was observed in both artificial HD systems and the cortical and subcortical regions upstream of biological HD systems, suggesting a general principle for encoding interdependent features. Further, exploration of the underlying mechanisms involved examining neural manifolds embedded within the representational space constructed by these neurons. We found that the manifold by neurons with multiphasic tuning curves was locally jagged and complex, which effectively expanded the dimensionality of the neural representation space and in turn facilitated a high-precision representation of AHV. Therefore, the encoding strategy for HD and AHV likely integrates characteristics of both dense and sparse coding schemes to achieve a balance between preserving specificity for individual features and maintaining their interdependency nature, marking a significant departure from the encoding of independent features and thus advocating future research delving into the encoding strategies of interdependent features.