bluuebunny/crossref_metadata_2025_split huggingface dataset:
Terpenes fromCannabis sativaInduce Antinociception in Mouse Chronic Neuropathic Pain via Activation of Spinal Cord Adenosine A2AReceptors
Authors: Schwarz Abigail M. , Keresztes Attila , Bui Thai , Hecksel Ryan J. , Peña Adrian , Lent Brianna , Gao Zhan-Guo , Gamez-Rivera Martín , Seekins Caleb A. , Chou Kerry , Appel Taylor L. , Jacobson Kenneth A. , Al-Obeidi Fahad A. , Streicher John M. 
Published: March 2023

AbstractTerpenes are small hydrocarbon compounds that impart aroma and taste to many plants, includingCannabis sativa. A number of studies have shown that terpenes can produce pain relief in various pain states in both humans and animals. However, these studies were methodologically limited and few established mechanisms of action. In our previous work, we showed that the terpenes geraniol, linalool, β-pinene, α- humulene, and β-caryophyllene produced cannabimimetic behavioral effects via multiple receptor targets. We thus expanded this work to explore the efficacy and mechanism of theseCannabisterpenes in relieving chronic pain. We first tested for antinociceptive efficacy by injecting terpenes (200 mg/kg, IP) into male and female CD- 1 mice with chemotherapy-induced peripheral neuropathy (CIPN) or lipopolysaccharide-induced inflammatory pain, finding that the terpenes produced roughly equal efficacy to 10 mg/kg morphine or 3.2 mg/kg WIN55,212. We further found that none of the terpenes produced reward as measured by conditioned place preference, while low doses of terpene (100 mg/kg) combined with morphine (3.2 mg/kg) produced enhanced antinociception vs. either alone. We then used the adenosine A2Areceptor (A2AR) selective antagonist istradefylline (3.2 mg/kg, IP) and spinal cord-specific CRISPR knockdown of the A2AR to identify this receptor as the mechanism for terpene antinociception in CIPN.In vitrocAMP and binding studies andin silicomodeling studies further suggested that the terpenes act as A2AR agonists. Together these studies identifyCannabisterpenes as potential therapeutics for chronic neuropathic pain, and identify a receptor mechanism in the spinal cord for this activity.
Adaptable, Turn-On Monobody (ATOM) Fluorescent Biosensors for Multiplexed Detection in Cells
Authors: Sekhon Harsimranjit , Ha Jeung-Hoi , Presti Maria F. , Procopio Spencer B. , Mirsky Paige O. , John Anna M. , Loh Stewart N. 
Published: March 2023

AbstractA grand challenge in biosensor design is to develop a single molecule, fluorescent protein-based platform that can be easily adapted to recognize targets of choice. Conceptually, this can be achieved by fusing a small, antibody-like binding domain to a fluorescent protein in such a way that target binding activates fluorescence. Although this design is simple to envision, its execution is not obvious. Here, we created a family of adaptable, turn-on monobody (ATOM) biosensors consisting of a monobody, circularly permuted at one of two positions, inserted into a fluorescent protein at one of three surface loops. Multiplexed imaging of live human cells co-expressing cyan, yellow, and red ATOM sensors detected the biosensor targets (WDR5, SH2, and hRAS proteins) that were localized to the nucleus, cytoplasm, and plasma membrane, respectively, with high specificity. ER- and mitochondria-localized ATOM sensors also detected ligands that were targeted to those organelles. Fluorescence activation involved ligand-dependent chromophore maturation with fluorescence turn-on ratios of >20-fold in cells and up to 100-foldin vitro. The sensing mechanism was validated with three arbitrarily chosen monobodies inserted into jellyfish as well as anemone lineages of fluorescent proteins, suggesting that ATOM sensors with different binding specificities and additional colors can be generated relatively quickly.
Deep repertoire mining uncovers ultra-broad coronavirus neutralizing antibodies targeting multiple spike epitopes
Authors: Hurtado Jonathan , Rogers Thomas F. , Jaffe David B. , Adams Bruce A. , Bangaru Sandhya , Garcia Elijah , Capozzola Tazio , Messmer Terrence , Sharma Pragati , Song Ge , Beutler Nathan , He Wanting , Dueker Katharina , Musharrafieh Rami , Stubbington Michael J.T. , Burton Dennis R. , Andrabi Raiees , Ward Andrew B. , McDonnell Wyatt J. , Briney Bryan 
Published: March 2023

SummaryDevelopment of vaccines and therapeutics that are broadly effective against known and emergent coronaviruses is an urgent priority. Current strategies for developing pan-coronavirus countermeasures have largely focused on the receptor binding domain (RBD) and S2 regions of the coronavirus Spike protein; it has been unclear whether the N-terminal domain (NTD) is a viable target for universal vaccines and broadly neutralizing antibodies (Abs). Additionally, many RBD-targeting Abs have proven susceptible to viral escape. We screened the circulating B cell repertoires of COVID-19 survivors and vaccinees using multiplexed panels of uniquely barcoded antigens in a high-throughput single cell workflow to isolate over 9,000 SARS-CoV-2-specific monoclonal Abs (mAbs), providing an expansive view of the SARS-CoV-2-specific Ab repertoire. We observed many instances of clonal coalescence between individuals, suggesting that Ab responses frequently converge independently on similar genetic solutions. Among the recovered antibodies was TXG-0078, a public neutralizing mAb that binds the NTD supersite region of the coronavirus Spike protein and recognizes a diverse collection of alpha- and beta-coronaviruses. TXG-0078 achieves its exceptional binding breadth while utilizing the same VH1-24 variable gene signature and heavy chain-dominant binding pattern seen in other NTD supersite-specific neutralizing Abs with much narrower specificity. We also report the discovery of CC24.2, a pan-sarbecovirus neutralizing mAb that targets a novel RBD epitope and shows similar neutralization potency against all tested SARS-CoV-2 variants, including BQ.1.1 and XBB.1.5. A cocktail of TXG-0078 and CC24.2 provides protection againstin vivochallenge with SARS-CoV-2, suggesting potential future use in variant-resistant therapeutic Ab cocktails and as templates for pan-coronavirus vaccine design.
Conserved satellite DNA motif and lack of interstitial telomeric sites in highly rearranged AfricanNothobranchiuskillifish karyotypes
Authors: Lukšíková Karolína , Pavlica Tomáš , Altmanová Marie , Štundlová Jana , Pelikánová Šárka , Simanovsky Sergey A. , Krysanov Eugene Yu. , Jankásek Marek , Hiřman Matyáš , Reichard Martin , Ráb Petr , Sember Alexandr 
Published: March 2023

AbstractRepetitive DNA may have significant impact on genome evolution. African annual killifishes of the genusNothobranchius(Teleostei: Nothobranchiidae), which has adapted to temporary water pools in African savannahs, possess genomes with high repeat content. They are also characterized by rapid karyotype and sex chromosome evolution but the role of genome repeats in these processes remains largely unknown. Here, we analyzed the distribution of telomeric (TTAGGG)nrepeat and Nfu-SatC satellite DNA (isolated formerly fromN. furzeri) by fluorescencein situhybridization in representatives across theNothobranchiusphylogeny (15 species), and withFundulosoma thierryias an outgroup. All analyzed taxa shared the presence of Nfu-SatC repeat but with diverse organization and distribution on chromosomes (from small clusters scattered genome-wide, to large localized accumulations, or a combined pattern). Nfu-SatC landscape was similar in conspecific populations ofN. guentheriandN. melanospilusbut slightly-to-moderately differed between populations ofN. pienaari, and between closely relatedN. kuhntaeandN. orthonotus. Inter-individual variability in Nfu-SatC patterns was found inN. orthonotusandN. krysanovi, including distinct segments present often in heterozygous condition. We revealed mostly no sex-linked patterns of studied repeat’s distribution in any of the sampled species including those with known sex chromosomes. Only inN. brieni(having an X1X2Y multiple sex chromosome system), Nfu-SatC probe covered substantial portion of the Y chromosome, similarly as formerly found inN. furzeriandN. kadleci(XY sex chromosomes), sister species not closely related toN. brieni. All studied species further shared patterns of telomeric FISH, with expected signals at the ends of all chromosomes and no additional interstitial telomeric sites. In summary, we revealed i) the presence of conserved satDNA class inNothobranchiusclade (a rare pattern among ray-finned fishes), ii) independent trajectories ofNothobranchiussex chromosome diferentiation, with recurrent and convergent accumulation of Nfu-SatC on the Y chromosome in some species, and iii) genus-wide shared propensity to loss of telomeric repeats during the mechanism of interchromosomal rearrangements. Collectively, our findings advance our understanding of genome structure, mechanisms of karyotype reshuffling and sex chromosome differentiation inNothobranchiuskillifishes from the genus-wide perspective.
k-mer-based GWAS enhances the discovery of causal variants and candidate genes in soybean
Authors: Lemay Marc-André , de Ronne Maxime , Bélanger Richard , Belzile François 
Published: March 2023

AbstractGenome-wide association studies (GWAS) are powerful statistical methods that detect associations between genotype and phenotype at genome scale. Despite their power, GWAS frequently fail to pinpoint the causal variant or the gene controlling a trait at a given locus in crop species. Assessing genetic variants beyond single-nucleotide polymorphisms (SNPs) could alleviate this problem, for example by including structural variants (SVs). In this study, we tested the potential of SV-andk-mer-based GWAS in soybean by applying these methods to 13 traits. We also performed conventional GWAS analysis based on SNPs and small indels for comparison. We assessed the performance of each GWAS approach based on results at loci for which the causal genes or variants were known from previous genetic studies. We found thatk-mer-based GWAS was the most versatile approach and the best at pinpointing causal variants or candidate genes based on the most significantly associatedk-mers. Moreover,k-mer-based analyses identified promising candidate genes for loci related to pod color, pubescence form, and resistance to the oomycetePhytophthora sojae. In our dataset, SV-based GWAS did not add value compared tok-mer-based GWAS and may not be worth the time and computational resources required to genotype SVs at population scale. Despite promising results, significant challenges remain regarding the downstream analysis ofk-mer-based GWAS. Notably, better methods are needed to associate significantk-mers with sequence variation. Together, our results suggest that couplingk-mer-and SNP/indel-based GWAS is a powerful approach for discovering candidate genes in crop species.
The amino acid composition of a protein influences its expression
Authors: Thompson Reece , Simon Pickard Benjamin 
Published: March 2023

AbstractThe quantity of each protein in a cell only is only partially correlated with its gene transcription rate. Independent influences on protein synthesis levels include mRNA sequence motifs, amino acyl-tRNA synthesis levels, elongation factor action, and protein susceptibility to degradation. Here we report two novel forms of interaction between the amino acid composition of a protein and its expression level.In animals, the differing origins of amino acids define a nutritional classification system and indicate their potential for scarcity – essential amino acids (EAA) are solely obtained from dietary supply, non-essential amino acids (NEAA) from biosynthetic supply, and conditionally essential amino acids (CEAA) from both. Accessing public proteomic datasets, we demonstrate that CEAA sequence composition is inversely correlated with expression – a rule of supply that is further magnified by rapid cellular proliferation. Similarly, proteins with the most extreme compositions of EAA are reduced in abundance. Homeostatic responses to malnutrition may result from the reductions in expression of extreme composition proteins participating in biological systems such as taste and food-seeking behaviour, oxidative phosphorylation, and chemokine function. The rule can also influence general human phenotypes and disease susceptibility: stature proteins are enriched in CEAAs, and a curated dataset of over 700 cancer proteins is significantly under-represented in EAAs.A second rule, whereby individual amino acids influence protein expression is also described. This rule is shared across all kingdoms of life and rooted in the immutable structural and encoding parameters of each amino acid. Species-specific environmental survival pathways are shown to be enriched in proteins with amino acid compositions favouring higher expression according to this rule.These two rules of protein expression regulation promise new insights into systems biology, evolutionary studies, experimental research design, and public health intervention.
Integrative multi-omic sequencing reveals the MMTV-Myc mouse model mimics human breast cancer heterogeneity
Authors: Broeker Carson D. , Ortiz Mylena M. O. , Murillo Michael S. , Andrechek Eran R. 
Published: March 2023

AbstractBackgroundBreast cancer is a complex and heterogeneous disease with distinct subtypes and molecular profiles corresponding to different clinical outcomes. Mouse models of breast cancer are widely used, but their relevance in capturing the heterogeneity of human disease is unclear. Previous studies have shown the heterogeneity at the gene expression level for the MMTV-Myc model, but have only speculated on the underlying genetics.ResultsHerein, we examine three common histological subtypes of the MMTV-Myc model through whole genome sequencing and have integrated these results with gene expression data. Significantly, key genomic alterations driving cell signaling pathways were well conserved within histological subtypes. Genomic changes included frequent, co-occurring mutations in KIT and RARA in the microacinar histological subtype as well as SCRIB mutations in the EMT subtype. EMT tumors additionally displayed strong KRAS activation signatures downstream of genetic activating events primarily ascribed to KRAS activating mutations, but also FGFR2 amplification. Analogous genetic events in human breast cancer showed stark decreases in overall survival. In further analyzing transcriptional heterogeneity of the MMTV-Myc model, we report a supervised machine learning model that classifies MMTV-Myc histological subtypes and other mouse models as being representative of different human intrinsic breast cancer subtypes.ConclusionsWe conclude the well-established MMTV-Myc mouse model presents further opportunities for investigation of human breast cancer heterogeneity.
A Universal Method for Crossing Molecular and Atlas Modalities using Simplex-Based Image Varifolds and Quadratic Programming
Authors: Stouffer Kaitlin M. , Trouvé Alain , Younes Laurent , Kunst Michael , Ng Lydia , Zeng Hongkui , Anant Manjari , Fan Jean , Kim Yongsoo , Miller Michael I. 
Published: March 2023

AbstractThis paper explicates a solution to the problem of building correspondences between molecular-scale transcriptomics and tissue-scale atlases. The central model represents spatial transcriptomics as generalized functions encoding molecular position and high-dimensional transcriptomic-based (gene, cell type) identity. We map onto low-dimensional atlas ontologies by modeling each atlas compartment as a homogeneous random field with unknown transcriptomic feature distribution. The algorithm presented solves simultaneously for the minimizing geodesic diffeomorphism of coordinates and latent atlas transcriptomic feature fractions by alternating LDDMM optimization for coordinate transformations and quadratic programming for the latent transcriptomic variables. We demonstrate the universality of the algorithm in mapping tissue atlases to gene-based and cell-based MERFISH datasets as well as to other tissue scale atlases. The joint estimation of diffeomorphisms and latent feature distributions allows integration of diverse molecular and cellular datasets into a single coordinate system and creates an avenue of comparison amongst atlas ontologies for continued future development.
Phylobone: A comprehensive database of bone extracellular matrix proteins in human and model organisms
Authors: Fontcuberta-Rigo Margalida , Nakamura Miho , Puigbò Pere 
Published: March 2023

ABSTRACTThe bone extracellular matrix (ECM) contains minerals deposited on highly crosslinked collagen fibrils and hundreds of non-collagenous proteins. Some of these proteins are key to the regulation of bone formation and regenerationviasignaling pathways, and play important regulatory and structural roles. However, the complete list of bone extracellular matrix proteins, their roles, and the extent of individual and cross-species variations have not been fully captured in both humans and model organisms. Here, we introduce the most comprehensive resource of bone extracellular matrix (ECM) proteins that can be used in research fields such as bone regeneration, osteoporosis, and mechanobiology. The Phylobone database (available athttps://phylobone.com) includes 255 proteins potentially expressed in the bone extracellular matrix (ECM) of humans and 30 species of vertebrates. A bioinformatics pipeline was used to identify the evolutionary relationships of bone ECM proteins. The analysis facilitated the identification of potential model organisms to study the molecular mechanisms of bone regeneration. A network analysis showed high connectivity of bone ECM proteins. A total of 214 functional protein domains were identified, including collagen and the domains involved in bone formation and resorption. Information from public drug repositories was used to identify potential repurposing of existing drugs. The Phylobone database provides a platform to study bone regeneration and osteoporosis in light of (biological) evolution, and will substantially contribute to the identification of molecular mechanisms and drug targets.
De novodesign of stable proteins that efficaciously inhibit oncogenic G proteins
Authors: Cummins Matthew C. , Tripathy Ashutosh , Sondek John , Kuhlman Brian 
Published: March 2023

AbstractMany protein therapeutics are competitive inhibitors that function by binding to endogenous proteins and preventing them from interacting with native partners. One effective strategy for engineering competitive inhibitors is to graft structural motifs from a native partner into a host protein. Here, we develop and experimentally test a computational protocol for embedding binding motifs in de novo designed proteins. The protocol uses an “inside-out” approach: Starting with a structural model of the binding motif docked against the target protein, the de novo protein is built by growing new structural elements off the termini of the binding motif. During backbone assembly, a score function favors backbones that introduce new tertiary contacts within the designed protein and do not introduce clashes with the target binding partner. Final sequences are designed and optimized using the molecular modeling program Rosetta. To test our protocol, we designed small helical proteins to inhibit the interaction between Gαqand its effector PLC-β isozymes. Several of the designed proteins remain folded above 90°C and bind to Gαqwith equilibrium dissociation constants tighter than 80 nM. In cellular assays with oncogenic variants of Gαq, the designed proteins inhibit activation of PLC-β isozymes and Dbl-family RhoGEFs. Our results demonstrate that computational protein design, in combination with motif grafting, can be used to directly generate potent inhibitors without further optimization via high throughput screening or selection.statement for broader audienceEngineered proteins that bind to specific target proteins are useful as research reagents, diagnostics, and therapeutics. We used computational protein design to engineer de novo proteins that bind and competitively inhibit the G protein, Gαq, which is an oncogene for uveal melanomas. This computational method is a general approach that should be useful for designing competitive inhibitors against other proteins of interest.
Intraspecies genomic divergence of coral algal symbionts shaped by gene duplication
Authors: Shah Sarah , Dougan Katherine E. , Chen Yibi , Bhattacharya Debashish , Chan Cheong Xin 
Published: March 2023

AbstractDinoflagellates of Order Suessiales include the diverse Family Symbiodiniaceae known for their role as essential coral reef symbionts, and the cold-adaptedPolarella glacialis. These taxa inhabit a broad range of ecological niches and exhibit extensive genomic divergence, although their genomes are in the smaller size ranges (haploid size < 3 Gbp) compared to most other dinoflagellates. Different isolates of a species are known to form symbiosis with distinct hosts and exhibit different regimes of gene expression, but intraspecies whole-genome divergence remains little known. Focusing on three Symbiodiniaceae species (the free-livingEffrenium voratum, and the symbioticSymbiodinium microadriaticumandDurusdinium trenchii) and the free-living outgroupP. glacialis, all for which whole-genome data from multiple isolates are available, we assessed intraspecies genomic divergence at sequence and structural levels. Our analysis based on alignment and alignment-free methods revealed greater extent of intraspecies sequence divergence in symbiodiniacean species than inP. glacialis. Our results also reveal the implications of gene duplication in generating functional innovation and diversification of Symbiodiniaceae, particularly inD. trenchiifor which whole-genome duplication was involved. Interestingly, tandem duplication of single-exon genes was found to be more prevalent in genomes of free-living species than in those of symbiotic species. These results in combination demonstrate the remarkable intraspecies genomic divergence in dinoflagellates under the constraint of reduced genome sizes, shaped by genetic duplications and symbiogenesis events during diversification of Symbiodiniaceae.