bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of B values obtained by two methodologies that use soil as a substrate and their influence on the estimation of the proportion of nitrogen fixed by legumes
Authors: Berriel Verónica , Monza Jorge , Perdomo Carlos 
Published: June 2022

AbstractThe B value is required to quantify the nitrogen derived from the atmosphere (%Ndfa) in the Rhizobium-legume symbiosis using the 15N natural abundance method. When the B value of a particular specie is not known, one possibility Is to use as a proxy the B value of a specie from the same genus, but this can cause the estimate of %Ndfa to be inaccurate. In this work, we compared two methodologies for determining the B value of Crotalaria juncea, C. spectabilis, C. ochroleuca and Cajanus cajan, using soil as the substrate. One method involvedgrowing plants in soil and averaging the lowest δ15N values of plant shoots (B-minimum), while the other consisted in adding sucrose to soil to immobilize the mineral nitrogen (N-immobilized), and then averaging the shoot δ15N values of all plants. Results showed that B values of C. cajan and C. ochroleuca obtained using the N-immobilized method were up to 1‰ lower than those reported in the literature for these species. Therefore, we propose that, at least in these species, B values determined with the N-immobilized method should be used to estimate the%Ndfa.
Shared enhancer gene regulatory networks between wound and oncogenic programs
Authors: Floc’hlay Swann , Balaji Ramya , Christiaens Valerie , González-Blas Carmen Bravo , De Winter Seppe , Hulselmans Gert , De Waegeneer Maxime , Quan Xiaojiang , Koldere Duygu , Atkins Mardelle , Halder Georg , Classen Anne , Aerts Stein 
Published: June 2022

AbstractWound response programs are often activated during neoplastic growth in tumors. In both wound repair and tumor growth, cells respond to acute stress and balance the activation of multiple programs including apoptosis, proliferation, and cell migration. Central to those responses are the activation of the JNK/MAPK and JAK/STAT signaling pathways. Yet, to what extent these signaling cascades interact at the cis-regulatory level, and how they orchestrate different regulatory and phenotypic responses is still unclear. Here, we aim to characterize the regulatory states that emerge and cooperate in the wound response, using the Drosophila melanogaster wing disc as a model system, and compare these with cancer cell states induced by rasV12scrib-/- in the eye disc. We used single-cell multiome profiling to derive enhancer Gene Regulatory Networks (eGRNs) by integrating chromatin accessibility and gene expression signals. We identify a “proliferative” eGRN, active in the majority of wounded cells and controlled by AP-1 and STAT. In a smaller, but distinct population of wound cells, a “senescent” eGRN is activated and driven by C/EBP-like transcription factors (Irbp18, Xrp1, Slow border, and Vrille) and Scalloped. In tumor cells on the other hand, both eGRN signatures are simultaneously active within the same cell. Our single-cell multiome and eGRNs resource offers an in-depth characterisation of the senescence markers, together with a new perspective on the shared gene regulatory programs acting during wound response and oncogenesis.
GCN2 eIF2 kinase promotes prostate cancer by maintaining amino acid homeostasis
Authors: Cordova Ricardo A. , Misra Jagannath , Amin Parth H. , Klunk Angela J. , Damayanti Nur P. , Carlson Kenneth R. , Elmendorf Andrew J. , Kim Hyeong-Geug , Mirek Emily T. , Elzey Bennet D. , Miller Marcus J. , Dong X. Charlie , Cheng Liang , Anthony Tracy G. , Pili Roberto , Wek Ronald C. , Staschke Kirk A. 
Published: June 2022

AbstractA stress adaptation pathway termed the integrated stress response has been suggested to be active in many cancers including prostate cancer (PCa). Here, we demonstrate that the eIF2 kinase GCN2 is required for sustained growth in androgen-sensitive and castration-resistant models of PCa both in vitro and in vivo, and is active in PCa patient samples. Using RNA-seq transcriptome analysis and a CRISPR-based phenotypic screen, GCN2 was shown to regulate expression of over 60 solute-carrier (SLC) genes, including those involved in amino acid transport and loss of GCN2 function reduces amino acid import and levels. Addition of essential amino acids or expression of 4F2 (SLC3A2) partially restored growth following loss of GCN2, suggesting that GCN2 targeting of SLC transporters is required for amino acid homeostasis needed to sustain tumor growth. A small molecule inhibitor of GCN2 showed robust in vivo efficacy in androgen-sensitive and castration-resistant mouse models of PCa, supporting its therapeutic potential for the treatment of PCa.SignificanceThe ISR kinase GCN2 is critical for maintaining tumor amino acid levels to facilitate growth, suggesting a novel therapeutic strategy for the treatment of prostate cancer by inducing starvation for essential amino acids.
IMPPAT 2.0: an enhanced and expanded phytochemical atlas of Indian medicinal plants
Authors: Vivek-Ananth R. P. , Mohanraj Karthikeyan , Sahoo Ajaya Kumar , Samal Areejit 
Published: June 2022

AbstractCompilation, curation, digitization and exploration of the phytochemical space of Indian medicinal plants can expedite ongoing efforts toward natural product and traditional knowledge based drug discovery. To this end, we present IMPPAT 2.0, an enhanced and expanded database, compiling manually curated information on 4010 Indian medicinal plants, 17967 phytochemicals, 1095 therapeutic uses and 1133 traditional Indian medicinal formulations. Notably, IMPPAT 2.0 compiles associations at the level of plant parts, and provides a FAIR compliant non-redundant in silico stereo-aware library of 17967 phytochemicals from Indian medicinal plants. The phytochemical library has been annotated with several useful properties to enable easier exploration of the chemical space. We also filtered a subset of 1335 drug-like phytochemicals of which majority have no similarity to existing approved drugs. Using cheminformatics, we have characterized the molecular complexity and molecular scaffold based structural diversity of the phytochemical space of Indian medicinal plants, and performed a comparative analysis with other chemical libraries. Altogether, IMPPAT is the largest phytochemical atlas of Indian medicinal plants which is accessible at: https://cb.imsc.res.in/imppat/.
Generating New Musical Preferences from Multi-level Mapping of Predictions to Reward
Authors: Kathios Nicholas , Sachs Matthew E. , Zhang Euan , Ou Yongtian , Loui Psyche 
Published: June 2022

AbstractMuch of what we know and love about music hinges on our ability to make successful predictions, which appears to be an intrinsically rewarding process. Yet the exact process by which learned predictions become pleasurable is unclear. Here, we created novel melodies in an alternative scale different from any established musical culture, to show how musical preference is generatedde novo. Across nine studies (n=1185), participants learned to like more frequently-presented items that adhered to this rapidly-learned structure, suggesting that exposure and prediction errors both affected self-report liking ratings. Learning trajectories varied by music reward sensitivity, but were similar for USA and Chinese participants. Furthermore, fMRI activity in auditory areas reflected prediction errors whereas functional connectivity between auditory and medial prefrontal regions reflected both exposure and prediction errors. Collectively, results support predictive coding as a cognitive mechanism by which new musical sounds become rewarding.
GAVISUNK: Genome assembly validation via inter-SUNK distances in Oxford Nanopore reads
Authors: Dishuck Philip C. , Rozanski Allison N. , Logsdon Glennis A. , Eichler Evan E. 
Published: June 2022

AbstractMotivationHighly contiguous de novo genome assemblies are now feasible for large numbers of species and individuals. Methods are needed to validate assembly accuracy and detect misassemblies with orthologous sequencing data to allow for confident downstream analyses.ResultsWe developed GAVISUNK, an open-source pipeline that detects misassemblies and produces a set of reliable regions genome-wide by assessing concordance of distances between unique k-mers in Pacific Biosciences high-fidelity (HiFi) assemblies and raw Oxford Nanopore Technologies reads.AvailabilityGAVISUNK is available at https://github.com/pdishuck/GAVISUNK.Contacteee@gs.washington.edu
Limited role of generation time changes in driving the evolution of mutation spectrum in humans
Authors: Gao Ziyue , Zhang Yulin , Cramer Nathan , Przeworski Molly , Moorjani Priya 
Published: June 2022

AbstractRecent studies have suggested that the human germline mutation rate and spectrum evolve rapidly. Variation in generation time has been linked to these changes, though its contribution remains unclear. We develop a framework to characterize temporal changes in polymorphisms within and between populations, while controlling for the effects of natural selection and biased gene conversion. Application to the 1000 Genomes Project dataset reveals multiple independent changes that arose after the split of continental groups, including a previously reported, transient elevation in TCC>TTC mutations in Europeans and novel signals of divergence in C>G and T>A mutation rates among population samples. We also find a significant difference between groups sampled in and outside of Africa, in old T>C polymorphisms that predate the out-of-Africa migration. This surprising signal is driven by TpG>CpG mutations, and stems in part from mis-polarized CpG transitions, which are more likely to undergo recurrent mutations. Finally, by relating the mutation spectrum of polymorphisms to parental age effects onde novomutations, we show that plausible changes in the generation time cannot explain the patterns observed for different mutation types jointly. Thus, other factors--genetic modifiers or environmental exposures--must have had a non-negligible impact on the human mutation landscape.
Sparse-spectral microendoscopy for real-time visualization of tumor cell phenotype and microenvironment spatial heterogeneity in vivo
Authors: Spring Bryan Q. , Palanisami Akilan , Saad Mohammad Ahsan , Kercher Eric M. , Lang Ryan T. , Harman Rebecca C. , Sutin Jason , Mai Zhiming , Hasan Tayyaba 
Published: June 2022

AbstractCancer heterogeneity and its transformation with time propels treatment resistance and confounds patient outcomes. The inability to monitor in vivo the low abundance, heterocellular phenotypes that resist treatment and ultimately lead to patient death limits the ability to design precision therapies. Here we overcome limitations in multiplexed fluorescence phenotyping to introduce real-time, cellular resolution visualization of tumor heterogeneity in vivo. This method was performed to simultaneously map for the first time 5 individual biomarkers of stemness, proliferation, metabolism, leukocytes and angiogenesis deep within the peritoneal cavities of micrometastatic cancer mouse models at 17 frames per second (fps). The newly developed imaging system revealed distinct cancer cell phenotype–immune cell spatial correlations and clearly visualized the dynamic spatial response of resistant cancer cell niches following treatment. Furthermore, wide-field datasets were generated to facilitate derivation of a mathematical framework for quantifying biomarker spatial variation and thereby overcoming the area restrictions of conventional tumor biopsy. These results pave the way for real-time identification of cancer cell phenotypes in a clinical setting, on which optimized treatment regimens can be based for personalized treatment and precision therapy e.g., tumor margin determination during surgical resection. Additionally, this modality can be used to obtain more fundamental insights into tumor heterogeneity and how treatments affect the molecular and cellular responses of patient-specific disease.
Adjuvant Discovery via a High Throughput Screen using Human Primary Mononuclear Cells
Authors: Chew Katherine , Lee Branden , van Haren Simon D. , Nanishi Etsuro , O’Meara Timothy , Splaine Jennifer B. , DeLeon Maria , Soni Dheeraj , Seo Hyuk-Soo , Dhe-Paganon Sirano , Ozonoff Al , Smith Jennifer A. , Levy Ofer , Dowling David J. 
Published: June 2022

SummaryWe describe a methodology utilizing high-throughput and high-content screening for novel adjuvant candidates that was used to screen a library of ∼2,500 small molecules via a 384-well quantitative combined cytokine and flow cytometry immunoassay in primary human peripheral blood mononuclear cells (PBMCs) from 4 healthy adult study participants. Hits were identified based on their induction of soluble cytokine (TNF, IFNγ and IL-10) secretion and PBMC maturation (CD 80/86, Ox40, and HLA-DR) in at least two of the four donors screened. From an initial set of 197 compounds identified using these biomarkers—an 8.6% hit rate—we downselected to five scaffolds that demonstrated robust efficacy and potencyin vitroand evaluated the top hit, vinblastine sulfate, for adjuvanticityin vivo. Vinblastine sulfate significantly enhanced murine humoral responses to recombinant SARS-CoV-2 spike protein, including a four-fold enhancement of IgG titer production when compared to treatment with the spike antigen alone. Overall, we outline a methodology for discovering immunomodulators with adjuvant potential via high-throughput screening of PBMCsin vitrothat yielded a lead compound within vivoadjuvanticity.MotivationVaccines are a key biomedical intervention to prevent the spread of infectious diseases, but their efficacy can be limited by insufficient immunogenicity and nonuniform reactogenic profiles. Adjuvants are molecules that potentiate vaccine responses by inducing innate immune activation. However, there are a limited number of adjuvants in approved vaccines, and current approaches for preclinical adjuvant discovery and development are inefficient. To enhance adjuvant identification, we developed a protocol based onin vitroscreening of human primary leukocytes.
Steric accessibility of the N-terminus improves the titer and quality of recombinant proteins secreted from Komagataella phaffii
Authors: Dalvie Neil C. , Naranjo Christopher A. , Rodriguez-Aponte Sergio A. , Johnston Ryan S. , Love J. Christopher 
Published: June 2022

AbstractBackgroundKomagataella phaffii is a commonly used alternative host for manufacturing therapeutic proteins, in part because of its ability to secrete recombinant proteins into the extracellular space. Incorrect processing of secreted proteins by cells can, however, cause non-functional product-related variants, which are expensive to remove in purification and lower overall process yields. The secretion signal peptide, attached to the N-terminus of the recombinant protein, is a major determinant of the quality of the protein sequence and yield. In K. phaffii, the signal peptide from the Saccharomyces cerevisiae alpha mating factor often yields the highest secreted titer of recombinant proteins, but the quality of secreted protein can vary highly.ResultsWe determined that an aggregated product-related variant of the SARS-CoV-2 receptor binding domain is caused by N-terminal extension from incomplete cleavage of the signal peptide. We eliminated this variant and improved secreted protein titer up to 76% by extension of the N-terminus with a short, functional peptide moiety or with the EAEA residues from the native signal peptide. We then applied this strategy to three other recombinant subunit vaccine antigens and observed consistent elimination of the same aggregated product-related variant. Finally, we demonstrated that this benefit in quality and secreted titer can be achieved with addition of a single amino acid to the N-terminus of the recombinant protein.ConclusionsOur observations suggest that steric hindrance of proteases in the Golgi that cleave the signal peptide can cause unwanted N-terminal extension and related product variants. We demonstrated that this phenomenon occurs for multiple recombinant proteins, and can be addressed by minimal modification of the N-terminus to improve steric accessibility. This strategy will enable consistent secretion of a broad range of recombinant proteins with the highly productive alpha mating factor secretion signal peptide.
Compensatory epistasis maintains ACE2 affinity in SARS-CoV-2 Omicron BA.1
Authors: Moulana Alief , Dupic Thomas , Phillips Angela M. , Chang Jeffrey , Nieves Serafina , Roffler Anne A. , Greaney Allison J. , Starr Tyler N. , Bloom Jesse D. , Desai Michael M. 
Published: June 2022

AbstractThe Omicron BA.1 variant emerged in late 2021 and quickly spread across the world. Compared to the ancestral Wuhan Hu-1 strain and other pre-Omicron SARS-CoV-2 variants, BA.1 has many mutations, a number of which are known to enable antibody escape 1–3. Many of these antibody-escape mutations individually decrease the spike receptor-binding domain (RBD) affinity for ACE2 in the background of early SARS-CoV-2 variants 4, but BA.1 still binds ACE2 with high affinity 5,6. The fitness and evolution of the BA.1 lineage is therefore driven by the combined effects of numerous mutations. Here, we systematically map the epistatic interactions between the 15 mutations in the RBD of BA.1 relative to the Wuhan Hu-1 strain. Specifically, we measure the ACE2 affinity of all possible combinations of these 15 mutations (2 15 = 32,768 genotypes), spanning all possible evolutionary intermediates from the ancestral Wuhan Hu-1 strain to BA.1. We find that immune escape mutations in BA.1 individually reduce ACE2 affinity but are compensated by epistatic interactions with other affinity-enhancing mutations, including Q498R and N501Y. Thus, the ability of BA.1 to evade immunity while maintaining ACE2 affinity is contingent on acquiring multiple interacting mutations. Our results implicate compensatory epistasis as a key factor driving substantial evolutionary change for SARS-CoV-2 and are consistent with Omicron BA.1 arising from a chronic infection.
EWSR1 prevents the induction of aneuploidy by regulating the localization of Aurora B at inner centromere
Authors: Kim Haeyoung , Park Hyewon , Schulz Evan T. , Azuma Yoshiaki , Azuma Mizuki 
Published: June 2022

ABSTRACTEWSR1 (Ewing sarcoma breakpoint region 1) was originally identified as a part of an aberrant EWSR1/FLI1 fusion gene in Ewing sarcoma, the second most common pediatric bone cancer. Due to formation of the EWSR1/FLI1 fusion gene in the tumor genome, the cell loses one wild type EWSR1 allele. Our previous study demonstrated that the loss of ewsr1a (homologue of human EWSR1) in zebrafish leads to the high incidence of mitotic dysfunction, of aneuploidy, and of tumorigenesis in the tp53 mutant background. To dissect the molecular function of EWSR1, we successfully established a stable DLD-1 cell line that enables a conditional knockdown of EWSR1 using Auxin Inducible Degron (AID) system. When both EWSR1 genes of DLD-1 cell were tagged with mini-AID at its 5’-end using CRISPR/Cas9 system, treatment of the (AID-EWSR1/AID-EWSR1) DLD-1 cells with a plant-based Auxin (AUX) led to the significant levels of degradation of AID-EWSR1 proteins. During anaphase, the EWSR1 knockdown (AUX+) cells displayed higher incidence of lagging chromosomes compared to the control (AUX-) cells. This defect was proceeded by a lower incidence of the localization of Aurora B at inner centromeres, and by a higher incidence of the protein at kinetochores compared to the control cells during pro/metaphase. Despite these defects, the EWSR1 knockdown cells did not undergo mitotic arrest, suggesting that the cell lacks the error correction mechanism. Significantly, the EWSR1 knockdown (AUX+) cells induced higher incidence of aneuploidy compared to the control (AUX-) cells. Since our previous study demonstrated that EWSR1 interacts with the key mitotic kinase, Aurora B, we generated replacement lines of EWSR1-mCherry and EWSR1:R565A-mCherry (a mutant that has low affinity for Aurora B) in the (AID-EWSR1/AID-EWSR1) DLD-1 cells. The EWSR1-mCherry rescued the high incidence of aneuploidy of EWSR1 knockdown cells, whereas EWSR1-mCherry:R565A failed to rescue the phenotype. Together, we demonstrate that EWSR1 is essential to prevent aneuploidy through interaction with Aurora B, most likely by regulating the localization of Aurora B at centromere.
Transcriptome analysis of FOXO-dependent hypoxia gene expression identifies Hipk as a regulator of low oxygen tolerance in Drosophila
Authors: Ding Kate , Barretto Elizabeth C , Johnston Michael , Lee Byoungchun , Gallo Marco , Grewal Savraj S 
Published: June 2022

SummaryWhen exposed to low oxygen or hypoxia, animals must alter their metabolism and physiology to ensure proper cell-, tissue- and whole-body level adaptations to their hypoxic environment. These alterations often involve changes in gene expression. While extensive work has emphasized the importance of the HIF-1 alpha transcription factor on controlling hypoxia gene expression, less is known about other transcriptional mechanisms. We previously identified the transcription factor FOXO as a regulator of hypoxia tolerance in Drosophila larvae and adults. Here we use an RNA-sequencing approach to identify FOXO-dependent changes in gene expression that are associated with these tolerance effects. We found that hypoxia altered the expression of over 2000 genes and that approximately 40% of these gene expression changes required FOXO. We discovered that hypoxia exposure led to a FOXO-dependent increase in genes involved in cell signaling, such as kinases, GTPase regulators, and regulators of the Hippo/Yorkie pathway. Among these, we identified homeodomain-interacting protein kinase (Hipk) as being required for hypoxia survival. We also found that hypoxia suppresses the expression of genes involved in ribosome synthesis and egg production, and we showed that hypoxia suppresses tRNA synthesis and mRNA translation and reduces female fecundity. Among the downregulated genes, we discovered that FOXO was required for suppression of many ribosomal protein genes and genes involved in oxidative phosphorylation, pointing to a role for FOXO in limiting energetically costly processes such as protein synthesis and mitochondrial activity upon hypoxic stress. This work uncovers a widespread role for FOXO in mediating hypoxia changes in gene expression.