bluuebunny/crossref_metadata_2025_split huggingface dataset:
Camera trap methods and drone thermal surveillance provide reliable, comparable density estimates of large, free-ranging ungulates
Authors: Baldwin Robert W. , Beaver Jared T. , Messinger Max , Muday Jeffrey , Windsor Matt , Larsen Gregory D. , Silman Miles , Anderson T. Michael 
Published: April 2023

AbstractCamera traps and drone surveys both leverage advancing technologies to study dynamic wildlife populations with little disturbance. Both techniques entail strengths and weaknesses, and common camera trap methods can be confounded by unrealistic assumptions and prerequisite conditions. We compared three methods to estimate the population density of white-tailed deer (Odocoileus virgnianus) at a section of Pilot Mountain State Park, NC, USA: (1) camera trapping using mark-resight ratios or (2) N-mixture modelling, and (3) aerial thermal videography from a drone platform. All three methods yielded similar density estimates, suggesting that they converged on an accurate estimate. We also included environmental covariates in N-mixture modeling to explore spatial habitat use, and we fit models for each season to understand temporal changes in population density. Deer occurred in greater densities on warmer, south-facing slopes in the fall and winter, and on cooler north-facing slopes and in areas with flatter terrain in the summer. Seasonal density estimates over two years suggested an annual cycle of higher densities in fall and winter than in summer, suggesting that the region may function as a refuge during the hunting season.Simple SummaryWildlife researchers and managers can choose from several techniques to estimate the number of animals in a population. Camera traps and drones are increasingly common and cost-effective options that can estimate the number and density of wildlife. We compared three simple methods that are used to estimate the number and density of deer in Pilot Mountain State Park: (1) mark-resighting and (2) N-mixture modeling, both using camera trap data, and (3) extrapolating transect counts from thermal videos collected from an aerial drone. We found that all three methods provided similar estimates of the population’s density, with complementary strengths and weaknesses: drone surveys collected data quickly and precisely, mark-resight ratios provided estimates of different demographic groups, and N-mixture modeling revealed changes in density across different habitat qualities and seasons.
A core NRF2 gene set defined through comprehensive transcriptomic analysis predicts selective drug resistance and poor multi-cancer prognosis
Authors: Luo George , Kumar Harshita , Aldridge Kristin , Rieger Stevie , Jiang Ethan , Chan Ernest R. , Soliman Ahmed , Mahdi Haider , Letterio John J. 
Published: April 2023

ABSTRACTThe NRF2-KEAP1 pathway plays an important role in the cellular response to oxidative stress but may also contribute to metabolic changes and drug resistance in cancer. We investigated the activation of NRF2 in human cancers and fibroblast cells through KEAP1 inhibition and cancer associated KEAP1/NRF2 mutations. We define a core set of 14 upregulated NRF2 target genes from seven RNA-Sequencing databases that we generated and analyzed, which we validated this gene set through analyses of published databases and gene sets. An NRF2 activity score based on expression of these core target genes correlates with resistance to drugs such as PX-12 and necrosulfonamide but not to paclitaxel or bardoxolone methyl. We validated these findings and also found NRF2 activation led to radioresistance in cancer cell lines. Finally, our NRF2 score is prognostic for cancer survival and validated in additional independent cohorts for novel cancers types not associated with NRF2-KEAP1 mutations. These analyses define a core NRF2 gene set that is robust, versatile, and useful as a NRF2 biomarker and for predicting drug resistance and cancer prognosis.
Unsaturated fatty acid synthesis is associated with poor prognosis and differentially regulated byMYCNand tumor suppressor microRNAs in neuroblastoma
Authors: Sheeter Dennis A. , Garza Secilia , Park Hui Gyu , Badi Niharika R. , Espinosa Erika C. , Kothapalli Kumar , Brenna J. Thomas , Powers John T. 
Published: April 2023

ABSTRACTMYCNamplification and disruption of tumor suppressor microRNA (TSmiR) function are central drivers of poor outcomes in neuroblastoma (NB). MYC, MYCN, and TSmiRs regulate glucose metabolism; however, their role in unsaturated fatty acid synthesis (UFAS) remains poorly understood. Here we show thatde novoand UFAS pathway genesFASN,ELOVL6,SCD,FADS2, andFADS1are upregulated in high-risk NB and are associated with poor prognosis. RNA-Seq analysis of eight human NB cell lines revealed parallel UFAS gene expression patterns. Consistent with this, we found that NB-related TSmiRs were predicted to extensively target these genes. In addition, we observed that both MYC and MYCN upregulated UFAS pathway genes while suppressing TSmiR host gene expression, thereby creating a possible UFAS regulatory network betweenMYCNand TSmiRs in NB. Furthermore, NB cells are high in omega 9 (ω9) unsaturated fatty acids that can be synthesizedde novoand low in both ω6 and ω3, providing a plausible means for NB to limit cell-autonomous immune stimulation and reactive oxygen species (ROS)-driven apoptosis from ω6 and ω3 unsaturated fatty acid derivatives, respectively. We propose a model in which the UFAS pathway, through novel regulation byMYCNand TSmiRs, plays a key role in neuroblastoma pathology with implications for otherMYC-driven cancers.
Transcript Assembly and Annotations: Bias and Adjustment
Authors: Zhang Qimin , Shao Mingfu 
Published: April 2023

AbstractMotivationTranscript annotations play a critical role in gene expression analysis as they serve as a reference for quantifying isoform-level expression. The two main sources of annotations are RefSeq and Ensembl/GENCODE, but discrepancies between their methodologies and information resources can lead to significant differences. It has been demonstrated that the choice of annotation can have a significant impact on gene expression analysis. Furthermore, transcript assembly is closely linked to annotations, as assembling large-scale available RNA-seq data is an effective data-driven way to construct annotations, and annotations are often served as benchmarks to evaluate the accuracy of assembly methods. However, the influence of different annotations on transcript assembly is not yet fully understood.ResultsWe investigate the impact of annotations on transcript assembly. We observe that conflicting conclusions can arise when evaluating assemblers with different annotations. To understand this striking phenomenon, we compare the structural similarity of annotations at various levels and find that the primary structural difference across annotations occurs at the intron-chain level. Next, we examine the biotypes of annotated and assembled transcripts and uncover a significant bias towards annotating and assembling transcripts with intron retentions, which explains above the contradictory conclusions. We develop a standalone tool, available athttps://github.com/Shao-Group/irtool, that can be combined with an assembler to generate an assembly without intron retentions. We evaluate the performance of such a pipeline and offer guidance to select appropriate assembling tools for different application scenarios.
Hold out the genome: A roadmap to solving the cis-regulatory code
Authors: de Boer Carl G. , Taipale Jussi 
Published: April 2023

AbstractGene expression is regulated by transcription factors that work together to read cis-regulatory DNA sequences. The “cis-regulatory code” - the rules that cells use to determine when, where, and how much genes should be expressed - has proven to be exceedingly complex, but recent advances in the scale and resolution of functional genomics assays and Machine Learning have enabled significant progress towards deciphering this code. However, we will likely never solve the cis-regulatory code if we restrict ourselves to models trained only on genomic sequences; regions of homology can easily lead to overestimation of predictive performance, and there is insufficient sequence diversity in our genomes to learn all relevant parameters. Fortunately, randomly synthesized DNA sequences enable us to test a far larger sequence space than exists in our genomes in each experiment, and designed DNA sequences enable a targeted query of the sequence space to maximally improve the models. Since cells use the same biochemical principles to interpret DNA regardless of its source, models that are trained on these synthetic data can predict genomic activity, often better than genome-trained models. Here, we provide an outlook on the field, and propose a roadmap towards solving the cis-regulatory code by training models exclusively on non-genomic DNA sequences, and using genomic sequences solely for evaluating the resulting models.
Extreme structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programs
Authors: Xie Ting , Danieli-Mackay Adi , Buccarelli Mariachiara , Barbieri Mariano , Papadionysiou Ioanna , Giorgio D’Alessandris Q. , Übelmesser Nadine , Vinchure Omkar Suhas , Lauretti Liverana , Fotia Giorgio , Wang Xiaotao , Ricci-Vitiani Lucia , Gopalakrishnan Jay , Pallini Roberto , Papantonis Argyris 
Published: April 2023

AbstractGlioblastoma multiforme (GBM) encompasses brain malignancies marked by phenotypic and transcriptional heterogeneity thought to render these tumors aggressive, resistant to therapy, and inevitably recurrent. However, little is known about how the spatial organization of GBM genomes underlies this heterogeneity and its effects. Here, we compiled a cohort of 28 patient-derived glioblastoma stem cell-like lines (GSCs) known to reflect the properties of their tumor-of-origin; six of these were primary-relapse tumor pairs from the same patient. We generated and analyzed kbp-resolution chromosome conformation capture (Hi-C) data from all GSCs to systematically map >3,100 standalone and complex structural variants (SVs) and the >6,300 neoloops arising as a result. By combining Hi-C, histone modification, and gene expression data with chromatin folding simulations, we explain how the pervasive, uneven, and idiosyncratic occurrence of neoloops sustains tumor-specific transcriptional programs via the formation of new enhancer-promoter contacts. We also show how even moderately recurrent neoloops can help us infer patient-specific vulnerabilities. Together, our data provide a resource for dissecting GBM biology and heterogeneity, as well as for informing therapeutic approaches.
Influence of Alzheimer’s disease related neuropathology on local microenvironment gene expression in the human inferior temporal cortex
Authors: Kwon Sang Ho , Parthiban Sowmya , Tippani Madhavi , Divecha Heena R. , Eagles Nicholas J. , Lobana Jashandeep S. , Williams Stephen R. , Mak Michelle , Bharadwaj Rahul A. , Kleinman Joel E. , Hyde Thomas M. , Page Stephanie C. , Hicks Stephanie C. , Martinowich Keri , Maynard Kristen R. , Collado-Torres Leonardo 
Published: April 2023

AbstractNeuropathological lesions in the brains of individuals affected with neurodegenerative disorders are hypothesized to trigger molecular and cellular processes that disturb homeostasis of local microenvironments. Here, we applied the 10x Genomics Visium Spatial Proteogenomics (Visium-SPG) platform, which measures spatial gene expression coupled with immunofluorescence protein co-detection, in post-mortem human brain tissue from individuals with late-stage Alzheimer’s disease (AD) to investigate changes in spatial gene expression with respect to amyloid-β (Aβ) and hyperphosphorylated tau (pTau) pathology. We identified Aβ-associated transcriptomic signatures in the human inferior temporal cortex (ITC) during late-stage AD, which we further investigated at cellular resolution with combined immunofluorescence and single molecule fluorescent in situ hybridization (smFISH) co-detection technology. We present a workflow for analysis of Visium-SPG data and demonstrate the power of multi-omic profiling to identify spatially-localized changes in molecular dynamics that are linked to pathology in human brain disease. We provide the scientific community with web-based, interactive resources to access the datasets of the spatially resolved AD-related transcriptomes athttps://research.libd.org/Visium_SPG_AD/.
Actin polymerization drives lumen formation in a human epiblast model
Authors: Indana Dhiraj , Zakharov Andrei , Lim Youngbin , Dunn Alexander R. , Bhutani Nidhi , Shenoy Vivek B. , Chaudhuri Ovijit 
Published: April 2023

SummaryLumens or fluid-filled cavities are a ubiquitous feature of mammals and are often evolutionarily linked to the origin of body-plan complexity. Post-implantation, the pluripotent epiblast in a human embryo forms a central lumen, paving the way for gastrulation. While osmotic pressure gradients drive lumen formation in many developmental contexts, mechanisms of human epiblast lumenogenesis are unknown. Here, we study lumenogenesis in a pluripotent-stem-cell-based model of the epiblast using engineered hydrogels that model the confinement faced by the epiblast in the blastocyst. Actin polymerization into a dense mesh-like network at the apical surface generates forces to drive early lumen expansion, as leaky junctions prevent osmotic pressure gradients. Theoretical modeling reveals that apical actin polymerization into a stiff network drives lumen opening, but predicts that a switch to pressure driven lumen growth at larger lumen sizes is required to avoid buckling of the cell layer. Consistent with this prediction, once the lumen reaches a radius of around 12 μm, tight junctions mature, and osmotic pressure gradients develop to drive further lumen growth. Human epiblasts show a transcriptional signature of actin polymerization during early lumenogenesis. Thus, actin polymerization drives lumen opening in the human epiblast, and may serve as a general mechanism of lumenogenesis.
Simultaneous tracking of near-isogenic bacterial strains in syntheticArabidopsismicrobiota by chromosomally-integrated barcodes
Authors: Ordon Jana , Thouin Julien , Nakano Ryohei Thomas , Ma Ka-Wai , Zhang Pengfan , Huettel Bruno , Garrido-Oter Ruben , Schulze-Lefert Paul 
Published: April 2023

AbstractDNA amplicon-based microbiota profiling currently relies on polymorphisms in microbial marker genes to estimate species diversity and abundance. However, this technique cannot resolve genetic differences among microbial individuals of the same species. We report here the development of modular bacterial tags (MoBacTags) encoding DNA barcodes. These tags facilitate tracking of near-isogenic bacterial commensals in synthetic communities (SynComs), which allow assessment of the contributions of individual bacterial genes to root microbiota establishment inArabidopsis thaliana. Chromosomally-integrated DNA barcodes are co-amplified with endogenous marker genes of the community by integrating corresponding primer binding sites into the barcode. We generated MoBacTag-labeled strains of wild-typePseudomonas capeferrumWCS358 and of pqqF and cyoB mutants with known defects in gluconic acid-mediated host immunosuppression and validated reduced root colonization of both mutants in a 15-member synthetic microbiota. We detected a reduced SynCom load on roots in the presence of the WCS358:pqqF mutant, but not WCS358:cyoB, revealing distinctpqqFandcyoBactivities in a community context. Using MoBacTags, we also show that WCS358 pqqF mutant-specific colonization and community establishment is nottrans-complemented by wild-type WCS358. Given that gluconic acid production inP. capeferrumis indirectly abolished in the pqqF mutant by disruption of pyrroloquinoline quinone (PQQ) biosynthesis, we propose that drastic changes in the root-associated community result from depletion of the cofactor PQQ, which might serve as a common good during root microbiota establishment. Our proof-of-principle experiments illustrate how MoBacTags can be applied to assess scaling of individual bacterial genetic determinants in the plant microbiota.
Antagonistic nanobodies reveal mechanism of GSDMD pore formation and unexpected therapeutic potential
Authors: Schiffelers Lisa D.J. , Normann Sabine , Binder Sophie C. , Hagelauer Elena , Kopp Anja , Alon Assaf , Geyer Matthias , Ploegh Hidde L. , Schmidt Florian I. 
Published: April 2023

AbstractActivation of various inflammasomes converges on the cleavage of gasdermin D (GSDMD) by pro-inflammatory caspases, followed by oligomerization of the N-terminal domain (GSDMDNT) and the assembly of pores penetrating target membranes. Yet, it remained unclear what triggers the conformational changes that allow membrane insertion, as methods to study pore formation in living cells were limited. We raised nanobodies specific for human GSDMD and found two nanobodies that prevent pyroptosis and IL-1β release when expressed in the cytosol of human macrophages. Nanobody binding to GSDMDNTblocked its oligomerization, while inflammasome assembly and GSDMD processing itself were not affected. The nanobody-stabilized monomers of GSDMDNTpartitioned into the plasma membrane, suggesting that pore formation is initiated by insertion of monomers, followed by oligomerization in the target membrane. When GSDMD pore formation was inhibited, cells still underwent caspase-1-dependent apoptosis, likely due to the substantially augmented caspase-1 activity. This hints at a novel layer of regulation of caspase-1 activity by GSDMD pores. Moreover, we revealed the unexpected therapeutic potential of antagonistic GSDMD nanobodies, as recombinant nanobodies added to the medium prevented cell death by pyroptosis, likely by entering through GSDMD pores and curtailing the assembly of additional pores. GSDMD nanobodies may thus be suitable to treat the ever-growing list of diseases caused by activation of the (non-) canonical inflammasomes.
Assessment of the Glycan-Binding Profile ofPseudomonas aeruginosaPAO1
Authors: Sanchez Hector , O’Toole George A. , Berwin Brent 
Published: April 2023

ABSTRACTPseudomonas aeruginosais an opportunistic pathogen that can establish acute and chronic infections in individuals that lack fully functional innate immunity. In particular, phagocytosis by neutrophils and macrophages is a key mechanism that modulates host control and clearance ofP. aeruginosa. Individuals with neutropenia or cystic fibrosis are highly susceptible toP. aeruginosainfection thus underscoring the importance of the host innate immune response. Cell-to-cell contact between host innate immune cells and the pathogen, a first step in phagocytic uptake, is facilitated by simple and complex glycan structures present at the host cell surface. We have previously shown that endogenous polyanionic N-linked glycans localized to the cell surface of phagocytes mediate binding and subsequent phagocytosis ofP. aeruginosa. However, the suite of glycans thatP. aeruginosabinds to on host phagocytic cells remains poorly characterized. Here we demonstrate, with the use of exogenous N-linked glycans and a glycan array, thatP. aeruginosaPAO1 preferentially attaches to a subset of glycans, including a bias towards monosaccharide versus more complex glycan structures. Consistent with these findings, we were able to competitively inhibit bacterial adherence and uptake by the addition of exogenous N-linked mono- and di-saccharide glycans. We discuss of findings in the context of previous reports ofP. aeruginosaglycan binding.IMPORTANCEP. aeruginosabinds to a variety of glycans as part of its interaction with host cells, and a number ofP. aeruginosa-encoded receptors and target ligands have been described that allow this microbe to bind to such glycans. Here we extend this work by studying the glycans used byP. aeruginosaPAO1 to bind to phagocytic cells and by using a glycan array to characterize the suite of such molecules that could facilitate host cell-binding by this microbe. This study provides an increased understanding of the glycans bound byP. aeruginosa, and furthermore, provides a useful dataset for future studies ofP. aeruginosa-glycan interactions.
Feature-Based 3D+t Descriptors of Hyperactivated Human Sperm Beat Patterns
Authors: Hernández Haydee O. , Montoya Fernando , Hernández-Herrera Paul , Díaz-Guerrero Dan S. , Olveres Jimena , Darszon Alberto , Escalante-Ramírez Boris , Corkidi Gabriel 
Published: April 2023

AbstractThe flagellar movement of the mammalian sperm is essential for male fertility as it enables this cell to reach and fertilize an egg. In the female reproductive tract, human spermatozoa undergo a process called capacitation which promotes changes in their motility. Only those spermatozoa that change to hyperactivated (HA) motility are capable of fertilizing the egg; this type of motility is characterized by asymmetric flagellar bends of greater amplitude and lower frequency. Historically, clinical fertilization studies have used two-dimensional analysis to classify sperm motility, although, sperm motility is three-dimensional (3D). Recent studies have described several 3D beating features of sperm flagella, including curvature, torsion, and asymmetries. However, the 3D motility pattern of hyperactivated spermatozoa has not yet been characterized. One of the main difficulties in classifying these patterns in 3D is the lack of a ground-truth reference, as it can be difficult to visually assess differences in flagellar beat patterns. Additionally, only about 10 − 20% of sperm that have been induced to capacitate are truly capacitated (i.e., hyperactivated). In this work, we used an image acquisition system that can acquire, segment, and track sperm flagella in 3D+t. We developed a feature-based vector that describes the spatio-temporal flagellar sperm motility patterns by an envelope of ellipses. Our results demonstrate that the proposed descriptors can effectively be used to distinguish between hyperactivated and nonhyperactivated spermatozoa, providing a tool to characterize the 3D sperm flagellar beat motility patterns without prior training or supervision. We demonstrated the effectiveness of the descriptors by applying them to a dataset of human sperm cells and showing that they can accurately classify the motility patterns of the sperm cells. This work is potentially useful for assessing male fertility or for diagnosing.
Efficient protein tagging andcis-regulatory element engineering via precise and directional oligonucleotide-based targeted insertion in plants
Authors: Kumar Jitesh , Char Si Nian , Weiss Trevor , Liu Hua , Liu Bo , Yang Bing , Zhang Feng 
Published: April 2023

AbstractEfficient and precise targeted insertion holds great promise but remains challenging in plant genome editing. An efficient NHEJ-mediated targeted insertion method was recently developed by combining CRISPR-Cas9 with phosphorothioate modified double-stranded oligodeoxynucleotides (dsODNs). Yet this approach often led to imprecise insertions with no control over the insertion direction. In this study, we first quantitatively compared the impact of the chemical protection on efficiency of targeted insertion. With the observation that CRISPR-SpCas9 could frequently induce staggered cleavages with 5′ 1-nucleotide overhangs, we then evaluated the impact of the donor end structures on the direction and preciseness of targeted insertions. Our study demonstrated that the chemically protected dsODNs with 5′ 1-nt overhangs could significantly improve the precision and direction control of target insertions in all tested CRIPSR targeting sites. Lastly, we applied this method to endogenous gene tagging inSetaria viridis, andcis-regulatory element engineering for disease resistance in rice. Two distinct TAL effector binding elements were directionally inserted into the promoter region of a recessive rice bacterial blight resistance gene at up to 24.4% efficiency. The resulting rice lines with heritable insertions exhibited strong resistance to the infection ofXanthomonas oryzaepv.oryzaepathogen in an inducible and strain-specific manner.