bluuebunny/crossref_metadata_2025 huggingface dataset:
Culture conditions greatly impact the levels of vesicular and extravesicular Ago2 and RNA in extracellular vesicle preparations
Authors: Jimenez Lizandra , Barman Bahnisikha , Jung Youn Jae , Cocozza Lauren , Krystofiak Evan , Saffold Cherie , Vickers Kasey C. , Wilson John T. , Dawson T. Renee , Weaver Alissa M.
Published: June 2023

Extracellular vesicle (EV)-carried miRNAs can influence gene expression and functional phenotypes in recipient cells. Argonaute 2 (Ago2) is a key miRNA-binding protein that has been identified in EVs and could influence RNA silencing. However, Ago2 is in a non-vesicular form in serum and can be an EV contaminant. In addition, RNA-binding proteins (RBPs), including Ago2, and RNAs are often minor EV components whose sorting into EVs may be regulated by cell signaling state. To determine the conditions that influence detection of RBPs and RNAs in EVs, we evaluated the effect of growth factors, oncogene signaling, serum, and cell density on the vesicular and nonvesicular content of Ago2, other RBPs, and RNA in small EV (SEV) preparations. Media components affected both the intravesicular and extravesicular levels of RBPs and miRNAs in EVs, with serum contributing strongly to extravesicular miRNA contamination. Furthermore, isolation of EVs from hollow fiber bioreactors revealed complex preparations, with multiple EV-containing peaks and a large amount of extravesicular Ago2/RBPs. Finally, KRAS mutation impacts the detection of intra- and extra-vesicular Ago2. These data indicate that multiple cell culture conditions and cell states impact the presence of RBPs in EV preparations, some of which can be attributed to serum contamination.
Purinergic Preconditioning Induces Epigenomic and Transcriptomic Changes Resembling Epilepsy-associated Microglial States
Authors: Martins-Ferreira Ricardo , Calafell-Segura Josep , Chaves João , Ciudad Laura , Martins da Silva António , Pinho e Costa Paulo , Leal Bárbara , Ballestar Esteban
Published: June 2023

Microglia, as the main immune effector cells in the central nervous system (CNS), play a crucial role in a diverse range of neuropathological conditions through their exacerbated activation. Microglial inflammatory responses can be influenced by prior exposures to noxious stimuli, such as increased levels of extracellular adenosine and ATP. These conditions are characteristic of brain insults like epileptic seizures and could potentially shape subsequent responses through epigenetic regulation. In this study, we investigated DNA methylation and expression changes in microglia-like cells differentiated from monocytes following ATP-mediated preconditioning. First, during differentiation, we demonstrate that microglia-like cells acquire standard microglial features, including whole transcriptomes and methylomes likein vivoprofiles. We show a predominant DNA demethylation in genomic sequences enriched in binding motifs of microglia lineage transcription factors like PU.1, consistent with the relevance of this factor inin vivomicroglia. TLR-mediated activation, after a first exposure to ATP, promotes exacerbated pro-inflammatory activation compared to cells not pre-exposed to ATP. These changes are accompanied by DNA methylation and transcriptional reprogramming associated with the acquisition of trained immunity and altered immune-related functions such as with antigen presentation, phagocytosis and cytokine signaling. Finally, the reprogramming associated with ATP-mediated preconditioning leads to profiles found in microglial subsets linked to epilepsy. Purine-driven microglia immune preconditioning drives epigenetic and transcriptional changes that could contribute to altered functions of microglia during seizure development and progression, particularly associated with neuroinflammation.
BrainProt(™) 3.0: Understanding Human Brain Diseases using comprehensively curated & Integrated OMICS datasets
Authors: Biswas Deeptarup , Shenoy Sanjyot Vinayak , Chauhan Aparna , Halder Ankit , Ghosh Biplab , Padhye Advait , Auromahima Shreeman , Yadav Deeksha , Sasmal Souvik , Dutta Sampurna , Kumari Neha , Bhavaskar Hiren , Mukherjee Ayan Prasad , Kumar Tunuguntla Rishi , Srivastava Sanjeeva
Published: June 2023

BrainProt 3.0 is an integrative and simplified omics-based knowledge base of the human brain and its associated diseases. The current version of BrainProt includes six domains, which provide simplified, robust, and comprehensive data visualization to understand the human brain and its diseases/disorders based on proteomics, transcriptomics, public data curation, and integration strategies. Firstly, the HBDA (Human Brain Disease Atlas), index and navigator of BrainProt provides a resource table for 56 brain diseases. Secondly, Brain Disease Marker Curator (BDMC) and Brain Disease Drug Finder (BDDF) include a total of 20,202 diseases associated genes, more than 1,30,000 Chemical Target interactions, and around 2,145 Clinical Trial Information for more than 50 Brain Diseases. Thirdly, Brain Disease Transcriptome Map (BDTM) and Brain Disease Proteome Map (BDPM) integrate multi-omics data for 11 and 6 alarming brain diseases respectively. Currently, these two domains feature an expressional profile of 52 datasets, information of 1,868 samples, 3,657 DEPs, and 6,256 DEGs. Lastly, BrainProt also modifies and integrates the proteome and phosphoproteome data of the Inter-hemispheric Brain Proteome Map (IBPM). Overall, BrainProt is the first knowledgebase that connects different omics level information of brain diseases and provides a powerful scoring-based ranking platform to select and identify brain disease-associated markers, along with exploration of clinical trials, and drugs/chemical compounds to accelerate the identification of new disease markers and novel therapeutic strategies. The objectives of BrainProt are to support and follow the footsteps of the HBPP (Human Brain Proteome Project) by integrating different datasets to unravel the complexity of Human Brain and its associated diseases.
Genome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities
Authors: Giordano Nils , Gaudin Marinna , Trottier Camille , Delage Erwan , Nef Charlotte , Bowler Chris , Chaffron Samuel
Published: June 2023

Marine microorganisms form complex communities of interacting organisms that influence central ecosystem functions in the ocean such as primary production and nutrient cycling. Identifying the mechanisms controlling their assembly and activities is a major challenge in microbial ecology. Here, we integratedTaraOceans meta-omics data to predict genome-scale community interactions within prokaryotic assemblages in the euphotic ocean. A global genome-resolved co-activity network revealed a significant number of inter-lineage associations across large phylogenetic distances. Identified co-active communities included species displaying smaller genomes but encoding a higher potential for quorum sensing, biofilm formation, and secondary metabolism. Community metabolic modelling revealed a higher potential for interaction within co-active communities and pointed towards conserved metabolic cross-feedings, in particular of specific amino acids and group B vitamins. Our integrated ecological and metabolic modelling approach indicates genome streamlining and metabolic auxotrophies as central joint mechanisms shaping bacterioplankton community assembly in the surface global ocean.
Co-linear Chaining on Pangenome Graphs
Authors: Rajput Jyotshna , Chandra Ghanshyam , Jain Chirag
Published: June 2023

Pangenome reference graphs are useful in genomics because they compactly represent the genetic diversity within a species, a capability that linear references lack. However, efficiently aligning sequences to these graphs with complex topology and cycles can be challenging. The seed-chain-extend based alignment algorithms use co-linear chaining as a standard technique to identify a good cluster of exact seed matches that can be combined to form an alignment. Recent works show how the co-linear chaining problem can be efficiently solved for acyclic pangenome graphs by exploiting their small width [Makinenet al., TALG’19] and how incorporating gap cost in the scoring function improves alignment accuracy [Chandra and Jain, RECOMB’23]. However, it remains open on how to effectively generalize these techniques for general pangenome graphs which contain cycles. Here we present the first practical formulation and an exact algorithm for co-linear chaining on cyclic pangenome graphs. We rigorously prove the correctness and computational complexity of the proposed algorithm. We evaluate the empirical performance of our algorithm by aligning simulated long reads from the human genome to a cyclic pangenome graph constructed from 95 publicly available haplotype-resolved human genome assemblies. While the existing heuristic-based algorithms are faster, the proposed algorithm provides a significant advantage in terms of accuracy.

Implementation

https://github.com/at-cg/PanAligner
TRPML1 activation ameliorates lysosomal phenotypes in CLN3 deficient retinal pigment epithelial cells
Authors: Wünkhaus D. , Tang R. , Nyame K. , Laqtom N. N. , Schweizer M. , Rosato A. Scotto , Krogsæter E. K. , Wollnik C. , Abu-Remaileh M. , Grimm C. , Hermey G. , Kuhn R. , Gruber-Schoffnegger D. , Markmann S.
Published: June 2023

Mutations in the lysosomal membrane protein CLN3 cause Juvenile Neuronal Ceroid Lipofuscinosis (JNCL). Activation of the lysosomal ion channel TRPML1 has previously been shown to be beneficial in several neurodegenerative disease models. Here, we tested whether TRPML1 activation rescues disease-associated phenotypes in CLN3-deficient retinal pigment epithelial (ARPE-19 CLN3-KO) cells. ARPE-19 CLN3-KO cells accumulate LAMP1 positive organelles and show lysosomal storage of mitochondrial ATPase subunit C (SubC), globotriaosylceramide (Gb3), and glycerophosphodiesters (GPDs), whereas lysosomal bis(monoacylglycero)phosphate (BMP/LBPA) lipid levels were significantly decreased. Activation of TRPML1 reduced lysosomal storage of Gb3 and SubC but failed to restore BMP levels in CLN3-KO cells. TRPML1-mediated decrease of storage was TFEB-independent, and we identified TRPML1-mediated enhanced lysosomal exocytosis as a likely mechanism for clearing storage including GPDs. Therefore, ARPE-19 CLN3-KO cells represent a human cell model for CLN3 disease showing many of the described core lysosomal deficits, some of which can be improved using TRPML1 agonists.
Targeting the conserved active site of splicing machines with specific and selective small molecule modulators
Authors: Silvestri Ilaria , Manigrasso Jacopo , Andreani Alessandro , Brindani Nicoletta , Vivo Marco De , Marcia Marco
Published: June 2023

The self-splicing group II introns are bacterial and organellar ancestors of the nuclear spliceosome and retro-transposable elements of pharmacological and biotechnological importance. Integrating enzymatic, crystallographic, and simulation studies, we demonstrate how these introns recognize small molecules through their conserved active site. These RNA-binding small molecules selectively inhibit the two steps of splicing by adopting distinctive poses at different stages of catalysis, and by preventing crucial active site conformational changes that are essential for splicing progression. Our data exemplify the enormous power of RNA binders to mechanistically probe vital cellular pathways. Most importantly, by proving that the evolutionarily-conserved RNA core of splicing machines can recognize small molecules specifically, our work puts solid bases for the rational design of splicing modulators not only against bacterial and organellar introns, but also against the human spliceosome, which is a validated drug target for the treatment of congenital diseases and cancers.
The Chicken Chorioallantoic Membrane as a Low-Cost, High-Throughput Model for Cancer Imaging
Authors: Smith Lydia M. , Greenwood Hannah E. , Tyrrell Will E. , Edwards Richard S. , Santis Vittorio de , Baark Friedrich , Firth George , Tanc Muhammet , Terry Samantha Y.A. , Herrmann Anne , Southworth Richard , Witney Timothy H.
Published: June 2023

Purpose

Mouse models are invaluable tools for radiotracer development and validation. They are, however, expensive, low throughput, and are constrained by animal welfare considerations. Here, we assessed the chicken chorioallantoic membrane (CAM) as an alternative to mice for preclinical cancer imaging studies.

Methods

Growth of NCI-H460 Fluc tumors on the CAM was optimized using a range of physical and chemical supports. Tumor-bearing eggs were imaged by dynamic18F-2-fluoro-2-deoxy-D-glucose (18F-FDG) or (4S)-4-(3-18F-fluoropropyl)-L-glutamate (18F-FSPG) PET/CT following intravenous injection, with mice bearing subcutaneous NCI-H460 Fluc xenografts imaged with18F-FDG for comparison. The dependence of the transporter system xc-onin ovo18F-FSPG tumor uptake was determined through treatment with imidazole ketone erastin. Additionally,18F-FSPG PET/CT was used to monitor treatment responsein ovo24 h following external beam radiotherapy.

Results

NCI-H460 Fluc cells grown in Matrigel formed vascularized tumors of reproducible size without compromising embryo viability. By designing a simple method for cannulation it was possible to perform dynamic PET imagingin ovo, producing high tumor-to-background signal for both18F-FDG and18F-FSPG.18F-FDG tumor uptake kinetics were similarin ovoandin vivo, with18F-FSPG providing an early marker of both treatment response and target inhibition in CAM-grown tumors.

Conclusions

The CAM provides a low-cost alternative to tumor xenograft mouse models which may broaden access to PET and SPECT imaging. Rapid tumor growth and high-quality PET images that can be obtained with this model suggest its potential use for early radiotracer screening, pharmacological studies, and monitoring response to therapy.
Separation-of-function mutants reveal the NF-κB-independent involvement of IκBα in the regulation of stem cell and oncogenic programs
Authors: Álvarez-Villanueva Daniel , Galán-Palma Luis , Bertran Joan , Floor Martin , Solé Laura , Lobo-Jarne Teresa , Maqueda María , Rajbhandari Rajani , Marruecos Laura , Villà-Freixa Jordi , Bredel Markus , Bigas Anna , Espinosa Lluís
Published: June 2023

We previously demonstrated that the NF-κB inhibitor IκBα binds the chromatin together with PRC2 to regulate a subset of developmental- and stem cell-related genes. This alternative function has been elusive in both physiological and disease conditions because of the predominant role of IκBα as a negative regulator of NF-κB.

We here uniquely characterize specific residues of IκBα that allow the generation of separation-of-function (SOF) mutants that are defective for either NF-κB-related (SOFΔNF-κB) or chromatin-related (SOFΔH2A,H4) activities. Expression of IκBα SOFΔNF-κB, but not SOFΔH2A/H4, is sufficient to negatively regulate a specific stemness program in intestinal cells, thus rescuing the differentiation blockage imposed by IκBα deficiency. In contrast, full IκBα activity is required for regulating clonogenic/tumor-initiating activity of colorectal cancer cells.

Our data indicate that SOF mutants represent an exclusive tool for studying IκBα functions in physiology and disease, and identified IκBα as a robust prognosis biomarker for human cancer.
A systematic approach identifies p53-DREAM target genes associated with blood or brain abnormalities
Authors: Rakotopare Jeanne , Lejour Vincent , Duval Carla , Eldawra Eliana , Escoffier Hugues , Toledo Franck
Published: June 2023

p53 is mainly known as a tumor suppressor, but mouse models revealed that increased p53 activity may cause bone marrow failure, through mechanisms that likely include gene repression mediated by the p53-DREAM pathway. Here we designed a systematic approach to identify p53-DREAM targets whose repression might contribute to abnormal hematopoiesis. We used gene ontology to analyze transcriptomic changes associated with bone marrow cell differentiation and p53 activation, then ChIP-seq data to find promoters bound by the DREAM complex. We next created positional frequency matrices to identify evolutionary conserved sequence elements potentially bound by DREAM. The same approach was developed to find p53-DREAM targets associated with brain abnormalities, also observed in mice with increased p53 activity. Putative DREAM binding sites were found for 151 candidate p53-DREAM target genes, of which 106 are mutated in a blood or brain genetic disorder. Twenty-one DREAM binding sites were tested and found to impact on gene expression in luciferase reporter assays, notably regulating genes mutated in dyskeratosis congenita (Rtel1), Fanconi anemia (Fanca), Diamond-Blackfan anemia (Tsr2), primary microcephaly (Casc5,Ncaph,Wdr62) or pontocerebellar hypoplasia (Toe1). These results provide clues on the role of the p53-DREAM pathway in regulating hematopoiesis and brain development, with implications for tumorigenesis.

Author Summary

The capacity of p53 to activate the transcription of genes important for cell cycle arrest, apoptosis or cellular metabolism has been recognized for decades. By contrast, the potential importance of p53-dependent transcriptional repression emerged more recently. Although p53 frequently appears to repress genes indirectly via the DREAM repressor complex, only a few studies attempted to define p53-DREAM target gene repertoires, often by analyzing cell cycle regulation in fibroblasts. Here we aimed to gain a better appreciation of the clinical relevance of the p53-DREAM pathway by designing a systematic approach for the identification of p53-DREAM targets. Because mouse models with increased p53 activity suffer from bone marrow failure or brain hypoplasia, we relied on transcriptomic changes associated with bone marrow cell differentiation, blood- and brain-related gene ontology terms and RNAseq data from hematopoietic or neural progenitor cells to identify p53-DREAM targets, then created positional frequency matrices to find putative DREAM binding sites. Our study provides a resource of predicted DREAM binding sites for 151 genes associated with blood and/or brain abnormalities, many of which were not previously known to be DREAM targets. Furthermore, our analysis suggests that p53-DREAM alterations may contribute to phenotypic variations in glioblastoma cells.
Extensive profiling of transcription factors in postmortem brains defines genomic occupancy in disease-relevant cell types and links TF activities to neuropsychiatric disorders
Authors: Loupe Jacob M. , Anderson Ashlyn G. , Rizzardi Lindsay F. , Rodriguez-Nunez Ivan , Moyers Belle , Trausch-Lowther Katie , Jain Rashmi , Bunney William E. , Bunney Blynn G. , Cartagena Preston , Sequeira Adolfo , Watson Stanley J. , Akil Huda , Cooper Gregory M. , Myers Richard M.
Published: June 2023

Transcription factors (TFs) orchestrate gene expression programs crucial for cell physiology, but our knowledge of their function in the brain is limited. Using bulk tissues and sorted nuclei from multiple human post-mortem brain regions, we generated a multi-omic resource (1121 total experiments) that includes binding maps for more than 100 TFs. We demonstrate improved measurements of TF activity, including motif recognition and gene expression modeling, upon identification and removal of regions of high TF occupancy. Further, we find that predictive TF binding models demonstrate a bias for these high occupancy sites. Neuronal TFs SATB2 and TBR1 bind unique regions depleted for such sites and promote neuronal gene expression. Several TFs, including TBR1 and PKNOX1, are enriched for risk variants associated with neuropsychiatric disorders, predominantly in neurons. These data are a powerful resource for future studies seeking to understand the role of TFs in epigenetic regulation in the human brain.
Coordinated wound responses in a regenerative animal-algal photosymbiotic metaorganism
Authors: Sarfati Dania Nanes , Xue Yuan , Song Eun Sun , Byrne Ashley , Le Daniel , Darmanis Spyros , Quake Stephen R. , Burlacot Adrien , Sikes James , Wang Bo
Published: June 2023

Animal regeneration requires coordinated responses of many cell types throughout the animal body. In animals carrying endosymbionts, cells from the other species may also participate in regeneration, but how cellular responses are integrated across species is yet to be unraveled. Here, we study the acoelConvolutriloba longifissura, which hosts symbioticTetraselmisgreen algae and can regenerate entire bodies from small tissue fragments. We show that animal injury leads to a decline in the photosynthetic efficiency of the symbiotic algae and concurrently induces upregulation of a cohort of photosynthesis-related genes. A deeply conserved animal transcription factor,runt, is induced after injury and required for the acoel regeneration. Knockdown ofruntalso dampens algal transcriptional responses to the host injury, particularly in photosynthesis related pathways, and results in further reduction of photosynthetic efficiency post-injury. Our results suggest that therunt-dependent animal regeneration program coordinates wound responses across the symbiotic partners and regulates photosynthetic carbon assimilation in this metaorganism.
Ex vivoquantification of anti-tumor T-cell activity upon anti-PD-1 treatment in patient-derived lung tumor-on-chip
Authors: Veith Irina , Mencattini Arianna , Nurmik Martin , Damei Isabelle , Lansche Christine , Brosseau Solenn , Gropplero Giacomo , Corgnac Stéphanie , Filippi Joanna , Poté Nicolas , Mordant Pierre , Tosello Jimela , Sedlik Christine , Piaggio Eliane , Girard Nicolas , Camonis Jacques , Shirvani Hamasseh , Mami-Chouaib Fathia , Mechta-Grigoriou Fatima , Descroix Stéphanie , Martinelli Eugenio , Zalcman Gérard , Parrini Maria Carla
Published: June 2023

There is a compelling need for new approaches to predict efficacy of immunotherapy drugs. Tumor-on-chip technology exploits microfluidics to generate 3D cell co-cultures embedded in hydrogels that recapitulate immune and stromal characteristics of a simplified tumor ecosystem. Here, we present the development and validation of lung-tumor-on-chip platforms to quickly and precisely measureex vivothe effects of immune check-point inhibitors on T-cell-mediated cancer cell death, by exploiting the power of live imaging and advanced image analysis algorithms. These tumor-on-chips were generated with patient-derived autologous primary cells isolated from fresh lung cancer samples, opening the path for applications in personalized medicine. Moreover, cancer-associated fibroblasts were shown to impair the response to anti-PD-1, indicating that tumor-on-chips are capable of recapitulating stroma-dependent mechanisms of immunotherapy resistance. This interdisciplinary combination of microfluidic devices, clinically-relevant cell models, and advanced computational methods, can innovatively improve both the fundamental understanding and clinical efficacy of immuno-oncology drugs.
SCFFBXW11complex targets interleukin-17 receptor A for ubiquitin-proteasome-mediated degradation
Authors: Jin Ben , Moududee Sayed Ala , Ge Dongxia , Zhou Pengbo , Wang Alun R. , Liu Yao-Zhong , You Zongbing
Published: June 2023

Interleukin-17 (IL-17) is a pro-inflammatory cytokine, participating in innate and adaptive immune responses, that plays an important role in host defense, autoimmune diseases, tissue regeneration, metabolic regulation, and tumor progression. Post-translational modifications (PTMs) are crucial for protein function, stability, cellular localization, cellular transduction, and cell death. However, PTMs of IL-17 receptor A (IL-17RA) have not been investigated. Here, we showed that human IL-17RA was targeted by F-box and WD repeats domain containing 11 (FBXW11) for ubiquitination, followed by proteasome-mediated degradation. We used bioinformatics tools and biochemical techniques to determine that FBXW11 ubiquitinated IL-17RA through a lysine 27-linked polyubiquitin chain, targeting IL-17RA for proteasomal degradation. Domain 665-804 of IL-17RA was critical for interaction with FBXW11 and subsequent ubiquitination. Our study demonstrates that FBXW11 regulates IL-17 signaling pathways at IL-17RA level.
Genetic disruption of dopamine β-hydroxylase dysregulates innate responses to predator odor in mice
Authors: Liu Joyce , Lustberg Daniel J. , Galvez Abigail , Liles L. Cameron , McCann Katharine E. , Weinshenker David
Published: June 2023

In rodents, exposure to predator odors such as cat urine acts as a severe stressor that engages innate defensive behaviors critical for survival in the wild. The neurotransmitters norepinephrine (NE) and dopamine (DA) modulate anxiety and predator odor responses, and we have shown previously that dopamine β-hydroxylase knockout (Dbh -/-), which reduces NE and increases DA in mouse noradrenergic neurons, disrupts innate behaviors in response to mild stressors such as novelty. We examined the consequences ofDbhknockout (Dbh -/-) on responses to predator odor (bobcat urine) and compared them to Dbh-competent littermate controls. Over the first 10 min of predator odor exposure, controls exhibited robust defensive burying behavior, whereasDbh -/-mice showed high levels of grooming. Defensive burying was potently suppressed in controls by drugs that reduce NE transmission, while excessive grooming inDbh -/-mice was blocked by DA receptor antagonism. In response to a cotton square scented with a novel “neutral” odor (lavender), most control mice shredded the material, built a nest, and fell asleep within 90 min.Dbh -/-mice failed to shred the lavender-scented nestlet, but still fell asleep. In contrast, controls sustained high levels of arousal throughout the predator odor test and did not build nests, whileDbh -/-mice were asleep by the 90-min time point, often in shredded bobcat urine-soaked nesting material. Compared with controls exposed to predator odor,Dbh -/-mice demonstrated decreased c-fos induction in the anterior cingulate cortex, lateral septum, periaqueductal gray, and bed nucleus of the stria terminalis, but increased c-fos in the locus coeruleus and medial amygdala. These data indicate that relative ratios of central NE and DA signaling coordinate the type and valence of responses to predator odor.
Scalable phylogenetic Gaussian process models improve the detectability of environmental signals on extinction risks for many Red List species
Authors: Matsuba Misako , Fukasawa Keita , Aoki Satoshi , Akasaka Munemitsu , Ishihama Fumiko
Published: June 2023

1. Conservation biologists have a daunting task of understanding the causes of species decline associated with anthropogenic factors and predicting the extinction risk of a growing number of endangered species. By stabilising estimates with information on closely related species, phylogenetic information among species can bridge gaps in information on species with small sample sizes when modelling large numbers of endangered species. However, modelling many species with the Gaussian process (GP), which underlies the evolutionary process of phylogenetic random effects, remains a challenge owing to the computational burden in estimating the large variance–covariance matrix.

2. Here, we applied a phylogenetic generalised mixed model with random slopes and random intercepts to 1,010 endangered vascular plant taxa in Japan following phylogenetic GPs implemented by nearest neighbour GP (NNGP) approximation. NNGP enables flexibility in changing the proximity on the phylogenetic tree of species from which information is borrowed to stabilise parameter estimates with a realistic computational burden. We evaluated the effectiveness of phylogenetic models by comparing the predictive performance and descriptive power of phylogenetic and non-phylogenetic models and identified the anthropogenic factors contributing to the decline of each of the studied endangered species.

3. We found that the model with phylogenetic information had better prediction performance than the model without phylogenetic information. The results showed that across all explanatory variables, the phylogenetic model could detect interspecific differences in response to environmental factors in a number of species more clearly. Combined with the phylogenetic signal results, we could also detect a phylogenetic bias in the species that could benefit from the positive effects of protected areas but reduce the extinction risk of 95% of all studied taxa.

4. In conclusion, our model, considering phylogenetic information with NNGP, allows the elucidation of factors causing the decline of many endangered species. In future analyses, the estimation of extinction probability linked to environmental change using such modelling might be applied to future climate–land use scenarios, advancing the comprehensive assessment of biodiversity degradation and threats to species at multiple scales.
The role of relatedness within a neighborhood in plant-to-plant interaction: effect on height growth and rust damage inPopulus nigra
Authors: Tiret Mathieu , Sánchez Leopoldo , Lascoux Martin
Published: June 2023

The competitive ability of domesticated plants, which may have conferred a fitness advantage in the wild, may result in a reduction of yield in agricultural and forestry contexts, as what matters is the group rather than the individual performance. Traits related to competitive ability can be affected by the presence or absence of related individuals in their neighborhood. Consequently, local relatedness might reveal plant-to-plant interaction that can enhance the predictive abilities of genomic models when accounted for, though it remains difficult to measure. To overcome this difficulty, we analyzed data from the French breeding program ofPopulus nigraL., where 1,452 genotypes were replicated six to eight times, each time encountering a different neighborhood. We assessed local relatedness and investigated genomic estimated breeding values on tree height and vulnerability to rust with a single-step GBLUP incorporating local relatedness as a covariate. The results indicate that incorporating local relatedness as an additional factor in GBLUP models has a significantly greater influence on resistance to rust than on tree height, though its overall effect on genomic predictions themselves was limited. The influence of local relatedness is small but likely trait-specific, and the genetic architecture of the trait under selection could attenuate or improve the efficacy of breeding for group performance.
CRISPR/Cas9 generatedMeSWEET10amutants show reduced susceptibility to cassava bacterial blight and produce viable seed
Authors: Elliott Kiona , Veley Kira M. , Jensen Greg , Gilbert Kerrigan B. , Norton Joanna , Kambic Lukas , Yoder Marisa , Weil Alex , Motomura-Wages Sharon , Bart Rebecca S.
Published: June 2023

Bacteria from the genusXanthomonasare prolific phytopathogens that elicit disease in over 400 plant species. Xanthomonads carry a repertoire of specialized proteins called transcription activator-like (TAL) effectors that promote disease and pathogen virulence by inducing expression of host susceptibility (S) genes.Xanthomonas phaseolipv.manihotis(Xpm) causes bacterial blight on the staple food crop, cassava. The Xpm effector, TAL20, induces ectopic expression of the S gene,MeSWEET10a, a sugar transporter that contributes to cassava bacterial blight susceptibility. We used CRISPR/Cas9 to generate multiple cassava lines with edits to theMeSWEET10aTAL20 effector binding site and/or coding sequence. In several of the regenerated lines,MeSWEET10aexpression was no longer induced byXpmand in these cases, we observed reduced cassava bacterial blight disease symptoms post Xpm infection.MeSWEET10ais expressed in cassava flowers. Therefore, we investigated flower development and reproductive function in anMeSWEET10amutant line. We found that theMeSWEET10amutant produced phenotypically wildtype cassava flowers and viable F1 seed. Thus, blockingMeSWEET10ainduction is a viable strategy for decreasing cassava susceptibility to CBB.
Omics Scale Quantitative Mass Spectrometry Imaging of Lipids in Brain Tissue using a Multi-Class Internal Standard Mixture
Authors: Vandenbosch Michiel , Mutuku Shadrack M. , Mantas Maria José Q. , Patterson Nathan H. , Hallmark Tucker , Claesen Marc , Heeren Ron M. A. , Hatcher Nathan G. , Verbeeck Nico , Ekroos Kim , Ellis Shane R.
Published: June 2023

Mass spectrometry imaging (MSI) has accelerated the understanding of lipid metabolism and spatial distribution in tissues and cells. However, few MSI studies have approached lipid imaging quantitatively and those that have focus on a single lipid class. Herein, we overcome limitation of quantitative MSI (Q-MSI) by using a multi-class internal standard lipid mixture that is sprayed homogenously over the tissue surface with analytical concentrations that reflects endogenous brain lipid levels. Using this approach we have performed Q-MSI for 13 lipid classes representing >200 sum-composition lipid species. This was carried out using both MALDI (negative ion mode) and MALDI-2 (positive ion mode) and pixel-wise normalisation of each lipid species signal to the corresponding class-specific IS an approach analogous to that widely used for shotgun lipidomics from biological extracts. This approach allows pixel concentrations of lipids to be reported in pmol/mm2. Q-MSI of lipids covered 3 orders of magnitude in dynamic range and revealed subtle change sin in distribution compared to conventional total-ion-current normalisation approaches. The robustness of the method was evaluated by repeating experiments in two laboratories on biological replicates using both timsTOF and Orbitrap mass spectrometers operated with a ~4-fold difference in mass resolution power. There was a strong overall correlation in the Q-MSI result obtained using the two approaches with outliers mostly rationalised by isobaric interferences that are only resolved with the Orbitrap system or the higher sensitivity of one instrument for particular lipid species, particularly for lipids detected at low intensity. These data provide insight into how mass resolving power can affect Q-MSI data. This approach opens up the possibility of performing large-scale Q-MSI studies across numerous lipid classes and reveal how absolute lipid concentrations vary throughout and between biological tissues.
Design and Evaluation of an Affordable Hypoxic Chamber with Comprehensive Environmental Control for Research Applications
Authors: Roshan Syed Aasish , Jayachandran Swaminathan K , Kandasamy Mahesh , Anusuyadevi Muthuswamy
Published: June 2023

Purpose

In-vivo Hypoxia chamber is sought after for research on sleep apnea, among others. Recently hypoxia chambers are utilized to create intermittent hypoxia, thereby utilizing it as a treatment strategy. The commonly used Invivo hypoxic chambers only monitor oxygen levels and fail to read up on vital factors like CO2 buildup, and humidity among others. In addition, these devices are expensive and make them unaffordable for many labs.

Methods

Here we report a lab-designed and assembled Arduino microcontroller-based hypoxic chamber with automatic maintenance of O2 level, CO2 level, and Humidity. The entire 650$ setup is inclusive of an Arduino module with sensors for oxygen, CO2, humidity, pressure, and temperature. A detailed software program was also written to help efficiently carry out the parameters set out for use.

Results

The equipment is capable of automatically regulating the inner environment based on the set parameters. The combined cluster of regulators, efficiently controlled the oxygen levels, CO2 levels, and humidity levels within the experimental parameters.

Conclusion

This equipment thus acts as one of the easily reproducible simple assembly units with the integration of complex parameters, thus monitoring and controlling the inner environment with high precision.
PROTOCOL OF A SYSTEMATIC REVIEW AND METAANALYSIS OF CASE-SERIES AND CASE-REPORTS INVOLVING GLUCAGON IN BETA-BLOCKER OVERDOSE
Authors: Domene Ramón Aranda , Esteban-Blanes Alberto
Published: June 2023

The utility of glucagon in human myocardium remains controversial. In the past, some articles have reported inotropic and chronotropic effects of glucagon on the heart, but other studies have found no significant effects. The main cardiovascular indication for glucagon is beta-blocker toxicity (BB), which is listed as recommendation IIb in some guidelines on the basis of some experimental studies and case reports. To our knowledge, no systematic review has been published analyzing the outcomes of glucagon in reports of overdose. This study will attempt to incorporate findings from case series and reports to fill the gap on a topic where experimental and comparative studies have already been conducted. A protocol to the development of this work is provided.
Patient-centered approaches for family planning counseling and support: A systematic review
Authors: Meekers Dominique , Elkins Aaron , Obozekhai Vivian
Published: June 2023

Background

This paper identifies how patient-centered family planning care has been defined, conceptualized, and measured, describes tools to make family planning care more patient-centered, and discusses their impact on patient satisfaction and family planning outcomes.

Methods

We systematically searched PubMed and SCOPUS for documents on “patient-centered family planning counseling or support” published between 2013 and 2022. Eligibility criteria included discussion of 1) a strategy for providing patient-centered care, 2) an intervention that used a patient- centered approach, or 3) evidence of the impact of patient-centered approaches. We excluded documents that only recommended using patient-centered approaches. To assess how studies conceptualized patient-centered care, we reviewed how the concept was measured. We identified tools for patient-centered care, and mapped them against the main domains of patient-centered care. We reported the available evidence of the impact on those tools without further statistical analysis.

Results

Our review is based on 33 documents, including three theoretical articles and three systematic reviews. Nine studies addressed women’s experiences with family planning counseling, five discussed instruments for measuring the patient-centeredness of care, ten discussed tools for patient-centered family planning, and three discussed broader counseling programs.

We identified important differences in how patient-centered family planning care was defined and measured, although most studies emphasized patients’ needs and preferences, respect for the patient, and informed decision-making. We identified six tools for increasing the patient-centeredness of family planning counseling. None of the tools addressed all domains of patient-centered care. Evidence about the impact of these tools is scarce. Overall, the tools appeared well accepted by both providers and patients. There was some evidence that the tools improved patients’ perception about the quality of care, but no evidence that the tools improved family planning outcomes.

Discussion

Limitations of our study include that our search was restricted to two databases, and that the studies predominantly focused on Western countries which may limit the generalizability of the findings. Wider use of existing scales to measure patient-centered family planning care may help standardize the definition of patient-centered care and strengthen the evidence base. Although tools for patient-centered care improve the patient experience, there is a need to identify strategies for translating this into improved family planning outcomes. In addition, there is a need to test patient- centered approaches in a wider range of settings.
Cryptic bacterial pathogens of diatoms peak during senescence of a winter diatom bloom
Authors: Branscombe Laura , Harrison Ellen L. , Daniel Choong Zhi Yi , Keys Matthew , Widdicombe Claire , Wilson William H. , Cunliffe Michael , Helliwell Katherine
Published: June 2023

Diatoms are globally abundant algae that form extensive blooms in aquatic ecosystems. Certain bacteria behave antagonistically towards diatoms, killing or inhibiting their growth. Despite their crucial implications to diatom health and bloom control, insight of the prevalence and dynamics of antagonistic bacteria in nature is lacking. We report an ecosystem assessment of the diversity and seasonal patterns of bacterial antagonists of diatoms via regular plaque-assay sampling in the Western English Channel (WEC), where diatoms frequently bloom. Unexpectedly, peaks in antagonist detection did not occur during characteristic spring blooms, but coincided with a winter bloom ofCoscinodiscus, suggesting bacterial pathogens likely influence distinct diatom host populations. We isolated multiple antagonists, spanning 4 classes and 10 bacterial orders. Many species had no prior reports of pathogenicity towards diatoms, and we verified diatom growth inhibitory effects of 8 isolates. In all cases tested, pathogenicity was activated by pre-exposure to diatom organic matter. Discovery of widespread ‘cryptic’ antagonistic activity evident under specific conditions, indicates that bacterial pathogenicity towards diatoms is more prevalent than previously recognised. Finally, miningTaraOceans data revealed the global biogeography of WEC antagonists and co-occurrence patterns with diatom hosts. Our study indicates that multiple, diverse antagonistic bacteria have potential to impact diatom growth and bloom dynamics in marine waters globally.
Collagen type VI regulates TGFβ bioavailability in skeletal muscle
Authors: Mohassel Payam , Rooney Jachinta , Zou Yaqun , Johnson Kory , Norato Gina , Hearn Hailey , Nalls Matthew A , Yun Pomi , Ogata Tracy , Silverstein Sarah , Sleboda David A , Roberts Thomas J , Rifkin Daniel B , Bönnemann Carsten G
Published: June 2023

Collagen VI-related disorders (COL6-RDs) are a group of rare muscular dystrophies caused by pathogenic variants in collagen VI genes (COL6A1, COL6A2,andCOL6A3). Collagen type VI is a heterotrimeric, microfibrillar component of the muscle extracellular matrix (ECM), predominantly secreted by resident fibroadipogenic precursor cells in skeletal muscle. The absence or mislocalizatoion of collagen VI in the ECM underlies the non-cell autonomous dysfunction and dystrophic changes in skeletal muscle with an as of yet elusive direct mechanistic link between the ECM and myofiber dysfunction. Here, we conduct a comprehensive natural history and outcome study in a novel mouse model ofCOL6-RDs (Col6a2-/-mice) using standardized (Treat-NMD) functional, histological, and physiologic parameter. Notably, we identify a conspicuous dysregulation of the TGFβ pathway early in the disease process and propose that the collagen VI deficient matrix is not capable of regulating the dynamic TGFβ bioavailability at baseline and also in response to muscle injury. Thus, we propose a new mechanism for pathogenesis of the disease that links the ECM regulation of TGFβ with downstream skeletal muscle abnormalities, paving the way for developing and validating therapeutics that target this pathway.
Genetic characterization of a captive marmoset colony using genotype-by-sequencing
Authors: Cole SA , Lyke MM , Christensen C , Newman D , Bagwell A , Galindo S , Glenn J , Layne-Colon D , Sayers K , Tardif SD , Cox LA , Ross CN , Cheeseman IH
Published: June 2023

The marmoset is a fundamental non-human primate model for the study of aging, neurobiology, and many other topics. Genetic management of captive marmoset colonies is complicated by frequent chimerism in the blood and other tissues, a lack of tools to enable cost-effective, genome-wide interrogation of variation, and historic mergers and migrations of animals between colonies. We implemented genotype-by-sequencing (GBS) of hair follicle derived DNA (a minimally chimeric DNA source) of 82 marmosets housed at the Southwest National Primate Research Center (SNPRC). Our primary goals were the genetic characterization of our marmoset population for pedigree verification and colony management and to inform the scientific community of the functional genetic makeup of this valuable resource. We used the GBS data to reconstruct the genetic legacy of recent mergers between colonies, to identify genetically related animals whose relationships were previously unknown due to incomplete pedigree information, and to show that animals in the SNPRC colony appear to exhibit low levels of inbreeding. Of the >99,000 single-nucleotide variants (SNVs) that we characterized, >9,800 are located within gene regions known to harbor pathogenic variants of clinical significance in humans. Overall, we show the combination of low-resolution (sparse) genotyping using hair follicle DNA is a powerful strategy for the genetic management of captive marmoset colonies and for identifying potential SNVs for the development of biomedical research models.
Multichannel joint image reconstruction allows for artifact-free focused small field of view magnetic particle imaging
Authors: Gevaert Julia J. , Konkle Justin , Goodwill Patrick , Foster Paula J.
Published: June 2023

Magnetic Particle Imaging (MPI) directly detects superparamagnetic iron oxide (SPIO) labeled cells. We have used MPI to detect SPIO-labeled dendritic cells (DC) migrated to the popliteal lymph nodes (pLN) after injection into the hind footpads. However, in some cases the low pLN signal could not be resolved from nearby higher footpad signal where window leveling to pLN signal oversaturated the footpad signal. The same limitation occurs when SPIO is injected intravenously, accumulates in the liver, and prevents isolation of regions of interest with lower signals. Previous studies have reported on the issue of resolving a wide range of differing iron concentration. A small focused field of view (FOV), to exclude high sources of nearby signal cannot be performed with the standard reconstruction algorithm equipped on the MomentumTM MPI scanner because it is assumed that there is no signal at the edge of the FOV and these values are set to zero for each line along the transmit axis. However, when there is signal at the FOV edge, an inverted negative artifact is created. The multichannel joint reconstruction method uses an iterative reconstruction technique to recover edge information using information from an orthogonal axis, preventing this artifact and allowing the user to prescribe a small FOV on the region of interest. Here we describe the implementation of this method to isolate and quantify low regions of MPI signal from higher regions.