bluuebunny/crossref_metadata_2025_split huggingface dataset:
A GID E3 ligase assembly ubiquitinates an Rsp5 E3 adaptor and regulates plasma membrane transporters
Authors: Langlois Christine R. , Beier Viola , Karayel Ozge , Chrustowicz Jakub , Sherpa Dawafuti , Mann Matthias , Schulman Brenda A. 
Published: September 2021

AbstractCells rapidly remodel their proteomes to align their cellular metabolism to environmental conditions. Ubiquitin E3 ligases enable this response, by facilitating rapid and reversible changes to protein stability, localization, or interaction partners. In S. cerevisiae, the GID E3 ligase regulates the switch from gluconeogenic to glycolytic conditions through induction and incorporation of the substrate receptor subunit Gid4, which promotes the degradation of gluconeogenic enzymes. Here, we show an alternative substrate receptor, Gid10, which is induced in response to changes in temperature, osmolarity and nutrient availability, and regulates the ART-Rsp5 pathway. Art2 levels are elevated upon GID10 deletion, a crystal structure shows the basis for Gid10-Art2 interactions, and Gid10 directs a GID E3 ligase complex to ubiquitinate Art2. We also find that the GID E3 ligase affects the flux of plasma membrane nutrient transporters during heat stress. The data reveal GID as a system of E3 ligases with metabolic regulatory functions outside of glycolysis and gluconeogenesis, controlled by distinct stress-specific substrate receptors.
Macrophages induce inflammation by efferocytosis of apoptotic prostate cancer cells via HIF-1α stabilization
Authors: Mendoza-Reinoso Veronica , Schnepp Patricia M. , Baek Dah Youn , Rubin John R. , Schipani Ernestina , Keller Evan T. , McCauley Laurie K. , Roca Hernan 
Published: September 2021

AbstractClearance of apoptotic cancer cells by macrophages, known as efferocytosis, fuels the bone-metastatic growth of prostate cancer cells via pro-inflammatory and immunosuppressive processes. However, the exact molecular mechanisms remain unclear. In this study, single-cell transcriptomics of bone marrow macrophages undergoing efferocytosis of apoptotic prostate cancer cells revealed a significant enrichment of a cellular response to hypoxia. Here we show that efferocytic macrophages promote HIF-1α stabilization under normoxic conditions through interaction with phosphorylated STAT3. Inflammatory cytokine gene expression analysis of efferocytic HIF-1α-mutant macrophages revealed a reduced expression of the pro-tumorigenic Mif. Furthermore, stabilization of HIF-1α using the HIF-prolyl-hydroxylase inhibitor, Roxadustat, enhanced MIF expression in macrophages. Finally, macrophages treated with recombinant MIF protein activated NF-κB (p65) signaling and increased the expression of pro-inflammatory cytokines. Altogether, these findings suggest that the clearance of apoptotic cancer cells by tumor-associated macrophages triggers p-STAT3/HIF-1α/MIF signaling to enhance tumor-promoting inflammation in bone, suggesting this axis as a target for metastatic prostate cancer.
Diffusion MRI Anisotropy in the Cerebral Cortex is Determined by Unmyelinated Tissue Features
Authors: Reveley Colin , Ye Frank Q , Mars Rogier B , Matrov Denis , Chudasama Yogita , Leopold David A 
Published: September 2021

AbstractDiffusion magnetic resonance imaging (dMRI) is commonly used to assess the tissue and cellular substructure of the human brain. In the white matter, myelinated axons are the principal neural elements that shape dMRI through the restriction of water diffusion; however, in the gray matter the relative contributions of myelinated axons and other tissue features to dMRI are poorly understood. Here we investigate the determinants of diffusion in the cerebral cortex. Specifically, we ask whether myelinated axons significantly shape dMRI fractional anisotropy (dMRI-FA), a measure commonly used to characterize tissue properties in humans. We compared ultra-high resolution ex vivo dMRI data from the brain of a marmoset monkey with both myelin- and Nissl-stained histological sections obtained from the same brain after scanning. We found that cortical diffusion was only minimally related to the density and arrangement of myelinated fibers. Instead, the spatial pattern of dMRI-FA in the cortex was more closely related to anisotropy of tissue features indicated in the Nissl stained sections. Our results suggest that unmyelinated neurites such as large caliber apical dendrites are the primary features shaping dMRI measures in the cerebral cortex.
Tracking transitional probabilities and segmenting auditory sequences are dissociable processes in adults and neonates
Authors: Benjamin Lucas , Fló Ana , Palu Marie , Naik Shruit , Melloni Lucia , Dehane-Lambertz Ghislaine 
Published: September 2021

AbstractSince speech is a continuous stream with no systematic boundaries between words, how do pre-verbal infants manage to discover words? A proposed solution is that they might use the transitional probability between adjacent syllables, which drops at word boundaries. Here, we tested the limits of this mechanism by increasing the size of the word-unit to 4 syllables, and its automaticity by testing asleep neonates. Using markers of statistical learning in neonates’ EEG, compared to adult’ behavioral performances in the same task, we confirmed that statistical learning is automatic enough to be efficient even in sleeping neonates. But we also revealed that: 1) Successfully tracking transition probabilities in a sequence is not sufficient to segment it 2) Prosodic cues, as subtle as subliminal pauses, enable to recover segmenting capacities 3) Adults’ and neonates’ capacities are remarkably similar despite the difference of maturation and expertise. Finally, we observed that learning increased the similarity of neural responses across infants, providing a new neural marker to monitor learning. Thus, from birth, infants are equipped with adult-like tools, allowing to extract small coherent word-like units within auditory streams, based on the combination of statistical analyses and prosodic cues.
A cerebellar-prepontine circuit for tonic immobility triggered by inescapable threat
Authors: Bhandiwad Ashwin A , Chu Nickolas , Semenova Svetlana A , Burgess Harold A 
Published: September 2021

AbstractSudden changes in the sensory environment are frequently perceived as threats and may provoke defensive behavioral states. One such state is tonic immobility, a conserved defensive strategy characterized by a powerful suppression of movement and motor reflexes. Tonic immobility has been associated with multiple brainstem regions and cell types, but the underlying circuit is not known. Here, we demonstrate that a strong vibratory stimulus evokes tonic immobility in larval zebrafish defined by suppression of exploratory locomotion and sensorimotor responses. Using a circuit-breaking screen and targeted neuron ablations, we show that cerebellar granule cells and a cluster of glutamatergic ventral prepontine neurons (vPPNs) that express key stress-associated neuropeptides are critical components of the circuit that suppresses movement. The complete sensorimotor circuit transmits information from primary sensory neurons through the cerebellum to vPPNs to regulate reticulospinal premotor neurons. These results show that cerebellar regulation of a neuropeptide-rich prepontine structure governs a conserved and ancestral defensive behavior that is triggered by inescapable threat.
The serine/threonine kinase MINK1 directly regulates the function of promigratory proteins
Authors: Daulat Avais M. , Wagner Mônica S. , Audebert Stéphane , Kowalczewska Malgorzata , Ariey-Bonnet Jeremy , Finetti Pascal , Bertucci François , Camoin Luc , Borg Jean-Paul 
Published: September 2021

AbstractUpregulation of the developmental Wnt/planar cell polarity pathway is observed in many cancers and is associated with cancer development at early and late stages. We recently showed that PRICKLE1 and VANGL2, two core Wnt/PCP components, are overexpressed in triple negative breast cancer and associated with poor prognosis. PRICKLE1 is a cytoplasmic protein phosphorylated by the poorly described serine/threonine kinase MINK1 which triggers its localization at the plasma membrane, a key step for its function. Knockdown experiments have demonstrated that MINK1 and PRICKLE1 contribute to TNBC cell motility and spreading in vitro and in vivo. However, the identity of MINK1 substrates and the role of MINK1 enzymatic activity in this process have not yet been addressed issues.We carried out a phosphoproteomic strategy and identified novel MINK1 substrates including LL5β. LL5β is a membrane scaffold molecule that anchors microtubules at the cell cortex through its association with the plus-end MT proteins CLASPs to trigger focal adhesion disassembly. LL5β is a prominent member of the MINK1-PRICKLE1 protein complex and is directly phosphorylated by MINK1 that promotes its interaction with CLASP. Using a kinase inhibitor, we demonstrate that the enzymatic activity of MINK1 is involved in the protein complex assembly and localization, and cell migration. Analysis of gene expression data show that the concomitant up-regulation of PRICKLE1 and LL5β mRNA levels encoding MINK1 substrates is associated with a poor metastasis-free survival for TNBC patients. Altogether, our results suggest that MINK1 may represent a potential target in TNBC.
Characterising sex differences of autosomal DNA methylation in whole blood using the Illumina EPIC array
Authors: Grant Olivia A , Wang Yucheng , Kumari Meena , Zabet Nicolae Radu , Schalkwyk Leonard 
Published: September 2021

ABSTRACTSex differences are known to play a role in disease etiology, progression and outcome. Previous studies have revealed autosomal epigenetic differences between males and females in some tissues, including differences in DNA methylation patterns. Here, we report for the first time an analysis of autosomal sex differences in DNAme using the Illumina EPIC array in human whole blood (n=1171). We identified 554 sex-associated differentially methylated CpG sites (saDMPs) with the majority found to be hypermethylated in females (70%). These saDMP’s are enriched in CpG islands and CpG shores and located preferentially at 5’UTRs, 3’UTRs and enhancers. Additionally, we identified 311 significant sex associated differentially methylated regions (saDMRs). Transcription factor binding site enrichment revealed enrichment of transcription factors related to critical developmental processes and sex determination such as SRY and SOX9. Our study reports a reliable catalogue of sex associated CpG sites and elucidates several characteristics of these sites.
Glial TGFβ activity promotes axon survival in peripheral nerves
Authors: Lassetter Alexandria P. , Corty Megan M. , Barria Romina , Sheehan Amy E. , Hill Jo , Aicher Sue A. , Fox A. Nicole , Freeman Marc R. 
Published: September 2021

AbstractAxons can represent the majority of the volume of a neuron and are energetically very demanding. Specialized glia ensheathe axons and are believed to support axon function and maintenance throughout life, but molecular details of glia-neuron support mechanisms remain poorly defined. Here we identify a collection of secreted and transmembrane genes that are required in glia for long-term axon survival in vivo. We show that key components of the TGFβ superfamily are required cell-autonomously in glia for peripheral nerve maintenance, although their loss does not disrupt glial morphology. We observe age-dependent neurodegeneration in the absence of glial TGFβ signaling that can be rescued by genetic blockade of Wallerian degeneration. Our data argue that glial TGFβ signaling normally acts to promote axon survival and suppress neurodegeneration.Significance StatementAxon maintenance is critical to preserving the functional integrity of the nervous system across animal lifespan. Glia contribute to axon maintenance, but their precise roles remain to be fully characterized. We identify glial genes that regulate axon support and provide new molecular insight into the means by which glia promote axon survival, which may help explain why neurodegeneration occurs when glia are lost in disease. We show that TGFβ signaling in mature glia is essential for long-term maintenance of axons, and that loss of TGFβ signaling activates an axon death signaling pathway.
Extensive germline-somatic interplay drives prostate cancer through HNF1B co-option of TMPRSS2-ERG
Authors: Giannareas Nikolaos , Zhang Qin , Yang Xiayun , Tian Yijun , Zhang Peng , Yang Yuehong , Manninen Aki , Wang Liang , Wei Gong-Hong 
Published: September 2021

AbstractGenome-wide association studies have identified 270 loci conferring risk for prostate cancer (PCa), yet the underlying biology and clinical impact remain to be investigated. Here we observe an enrichment of transcription factor genes including HNF1B within PCa risk-associated regions. While focused on the 17q12/HNF1B locus, we find a strong eQTL for HNF1B and multiple potential causal variants involved in the regulation of HNF1B expression in PCa. An unbiased genome-wide co-expression analysis reveals PCa-specific somatic TMPRSS2-ERG fusion as a transcriptional mediator of this locus and the HNF1B eQTL signal is ERG fusion status dependent. We investigate the role of HNF1B and find its involvement in several pathways related to cell cycle progression and PCa severity. Furthermore, HNF1B interacts with TMPRSS2-ERG to co-occupy large proportion of genomic regions with a remarkable enrichment of additional PCa risk alleles. We finally show that HNF1B co-opts ERG fusion to mediate mechanistic and biological effects of the PCa risk-associated locus 17p13.3/VPS53/FAM57A/GEMIN4. Taken together, we report an extensive germline-somatic interaction between TMPRSS2-ERG fusion and genetic variations underpinning PCa risk association and progression.
In vitro antimicrobial and cytotoxic activity of Lippia origanoides essential oil against bacteria of potential health concern
Authors: Quiguanás-Guarín Edwin Stiven , Agudelo Juan Pablo Bedoya , López-Carvajal Jhon Esteban , Tabares Yuly Andrea Ramírez , Sanabria Leonardo Padilla , Castaño-Osorio Jhon Carlos 
Published: September 2021

AbstractDue to the growing resistance they develop of bacteria to drugs, the search for alternatives in natural products is considered important such as Lippia origanoides essential oil. Here, the antibacterial activity of the oil and two of its major chemical components were tested against bacteria of potential health concern. The cytotoxicity of these compounds was evaluated in human erythrocytes and Vero cells. 51 compounds were identified in the LOEO, being terpinen-4-ol, γ-Terpinene, citronellal and thymol the main. LOEO and thymol showed antibacterial activity from 904 μg/mL and 200 μg/mL, respectively. γ-Terpinene did not show activity any concentration tested. LOEO showed hemolysis at concentration of 3000 μg/mL and thymol at 100 μg/mL. LOEO and thymol showed cytotoxicity in the evaluated cell lines at 250 μg/mL and 100 μg/mL, respectively. These compounds have a moderate cytotoxicity so it’s considered necessary to study alternatives to reduce the in vitro cytotoxicity of these compounds.Abstract Figure
Structural and Biochemical Rationale for Enhanced Spike Protein Fitness in Delta and Kappa SARS-CoV-2 Variants
Authors: Saville James W. , Mannar Dhiraj , Zhu Xing , Srivastava Shanti S. , Berezuk Alison M. , Demers Jean-Philippe , Zhou Steven , Tuttle Katharine S. , Sekirov Inna , Kim Andrew , Li Wei , Dimitrov Dimiter S. , Subramaniam Sriram 
Published: September 2021

AbstractThe Delta and Kappa variants of SARS-CoV-2 co-emerged in India in late 2020, with the Delta variant underlying the resurgence of COVID-19, even in countries with high vaccination rates. In this study, we assess structural and biochemical aspects of viral fitness for these two variants using cryo-electron microscopy (cryo-EM), ACE2-binding and antibody neutralization analyses. Both variants demonstrate escape of antibodies targeting the N-terminal domain, an important immune hotspot for neutralizing epitopes. Compared to wild-type and Kappa lineages, Delta variant spike proteins show modest increase in ACE2 affinity, likely due to enhanced electrostatic complementarity at the RBD-ACE2 interface, which we characterize by cryo-EM. Unexpectedly, Kappa variant spike trimers form a novel head-to-head dimer-of-trimers assembly, which we demonstrate is a result of the E484Q mutation. The combination of increased antibody escape and enhanced ACE2 binding provides an explanation, in part, for the rapid global dominance of the Delta variant.
Changes to the mtDNA copy number during yeast culture growth
Authors: Galeota-Sprung Ben , Fernandez Amy , Sniegowski Paul 
Published: September 2021

AbstractWe show that the mtDNA copy number in growing cultures of the yeast Saccharomyces cerevisiae increases by a factor of up to 4, being lowest (∼10 per haploid genome) and stable during rapid fermentative growth, and highest at the end of the respiratory phase. When yeast are grown on glucose, the onset of the mtDNA copy number increase coincides with the early stages of the diauxic shift, and the increase continues through respiration. A lesser yet still substantial copy number increase occurs when yeast are grown on a nonfermentable carbon source, i.e. when there is no diauxic shift. The mtDNA copy number increase during and for some time after the diauxic shift is not driven by an increase in cell size. The copy number increase occurs in both haploid and diploid strains, but is markedly attenuated in a diploid wild isolate that is a ready sporulator. Strain-to-strain differences in mtDNA copy number are least apparent in fermentation and most apparent in late respiration or stationary phase. While changes in mitochondrial morphology and function were previously known to accompany changes in physiological state, it had not been previously shown that the mtDNA copy number changes substantially over time in a clonal growing culture. The mtDNA copy number in yeast is therefore a highly dynamic phenotype.
Signatures of plant defense response specificity mediated by herbivore-associated molecular patterns in legumes
Authors: Steinbrenner Adam D. , Saldivar Evan , Hodges Nile , Chaparro Antonio F. , Schmelz Eric A. 
Published: September 2021

I.SummaryChewing herbivores activate plant defense responses through a combination of mechanical wounding and elicitation by herbivore associated molecular patterns (HAMPs). HAMPs are wound response amplifiers; however, specific defense outputs may also exist that strictly require HAMP-mediated defense signaling. To investigate HAMP-mediated signaling and defense responses, we characterized cowpea transcriptome changes following elicitation by inceptin, a peptide HAMP common in Lepidoptera larvae oral secretions. Following inceptin treatment, we observed large-scale reprogramming of the transcriptome consistent with 3 different response categories: 1) amplification of mechanical wound responses, 2) temporal extension through accelerated or prolonged responses, and 3) examples of inceptin-specific elicitation and suppression. At both early and late timepoints, namely 1 and 6 hours, large sets of transcripts specifically accumulated following inceptin elicitation but not wounding alone. Further inceptin-regulated transcripts were classified as reversing changes induced by wounding alone. Within key signaling and defense related gene families, inceptin-elicited responses commonly targeted select subsets of wound-induced transcripts. Transcripts displaying the largest inceptin-elicited fold-changes included terpene synthases (TPS) and peroxidases (POX) that correspond with induced volatile production and increased peroxidase activity in cowpea. Characterization of inceptin-elicited cowpea defenses via heterologous expression in Nicotiana benthamiana demonstrated that specific cowpea TPS and POX were able to confer terpene emission and the reduced growth of beet armyworm (Spodoptera exigua) herbivores, respectively. Collectively, our present findings in cowpea support a model where HAMP-elicitation both amplifies concurrent wound responses and specifically contributes to the activation of selective outputs associated with direct and indirect anti-herbivore defenses.II.Significance StatementPlants recognize herbivore-associated molecular patterns (HAMPs) to induce defenses, but interactions with the more general wound response are not well-understood. We leveraged a known HAMP-receptor interaction to characterize transcriptomic modulation of the wound response by the peptide HAMP, inceptin. Inceptin not only amplifies wound responses, but can specifically induce or suppress transcripts with demonstrated functions in direct and indirect defense against herbivores. The plant immune system thus recognizes HAMPs to fine-tune wound responses against herbivory.
Biosynthesis of linear protein nanoarrays using the flagellar axoneme
Authors: Ishikawa Hiroaki , Tian Jie L. , Yu Jefer E. , Marshall Wallace F. , Qin Hongmin 
Published: September 2021

ABSTRACTApplications in biotechnology and synthetic biology often make use of soluble proteins, but there are many potential advantages to anchoring enzymes to a stable substrate, including stability and the possibility for substrate channeling. To avoid the necessity of protein purification and chemical immobilization, there has been growing interest in bio-assembly of protein-containing nanoparticles, exploiting the self-assembly of viral capsid proteins or other proteins that form polyhedral structures. But these nanoparticle are limited in size which constrains the packaging and the accessibility of the proteins. The axoneme, the insoluble protein core of the eukaryotic flagellum or cilium, is a highly ordered protein structure that can be several microns in length, orders of magnitude larger than other types of nanoparticles. We show that when proteins of interest are fused to specific axonemal proteins and expressed in living cells, they become incorporated into linear arrays which have the advantages of high protein loading capacity, high stability, and single-step purification with retention of biomass. The arrays can be isolated as membrane enclosed vesicle or as exposed protein arrays. The approach is demonstrated for both fluorescent proteins and enzymes, and in the latter case it is found that incorporation into axoneme arrays provides increased stability for the enzyme.
Mpe1 senses the polyadenylation signal in pre-mRNA to control cleavage and polyadenylation
Authors: Rodríguez-Molina Juan B. , O’Reilly Francis J. , Sheekey Eleanor , Maslen Sarah , Skehel J. Mark , Rappsilber Juri , Passmore Lori A. 
Published: September 2021

AbstractMost eukaryotic messenger RNAs (mRNAs) are processed at their 3’-end by the cleavage and polyadenylation factor (CPF/CPSF). CPF mediates endonucleolytic cleavage of the pre-mRNA and addition of a polyadenosine (poly(A)) tail, which together define the 3’-end of the mature transcript. Activation of CPF is highly regulated to maintain fidelity of RNA processing. Here, using cryoEM of yeast CPF, we show that the Mpe1 subunit directly contacts the polyadenylation signal sequence in nascent pre- mRNA. This RNA-mediated link between the nuclease and polymerase modules promotes activation of the CPF endonuclease and controls polyadenylation. Mpe1 rearrangement is antagonized by another subunit, Cft2.In vivo, depletion of Mpe1 leads to widespread defects in transcription termination by RNA Polymerase II, resulting in transcription interference on neighboring genes. Together, our data suggest that Mpe1 plays a major role in selecting the cleavage site, activating CPF and ensuring timely transcription termination.