bluuebunny/crossref_metadata_2025 huggingface dataset:
Mechanistic basis of staphylococcal interspecies competition for skin colonization
Authors: Maciag Joseph J. , Chantraine Constance , Mills Krista B. , Yadav Rahul , Yarawsky Alexander E. , Chaton Catherine T. , Vinod Divya , Fitzkee Nicholas C. , Mathelié-Guinlet Marion , Dufrêne Yves F. , Fey Paul D. , Horswill Alexander R. , Herr Andrew B.
Published: January 2023

Staphylococci, whether beneficial commensals or pathogens, often colonize human skin, potentially leading to competition for the same niche. In this multidisciplinary study we investigate the structure, binding specificity, and mechanism of adhesion of the Aap lectin domain required forStaphylococcus epidermidisskin colonization and compare its characteristics to the lectin domain from the orthologousStaphylococcus aureusadhesin SasG. The Aap structure reveals a legume lectin-like fold with atypical architecture, showing specificity for N-acetyllactosamine and sialyllactosamine. Bacterial adhesion assays using human corneocytes confirmed the biological relevance of these Aap-glycan interactions. Single-cell force spectroscopy experiments measured individual binding events between Aap and corneocytes, revealing an extraordinarily tight adhesion force of nearly 900 nN and a high density of receptors at the corneocyte surface. The SasG lectin domain shares similar structural features, glycan specificity, and corneocyte adhesion behavior. We observe cross-inhibition of Aap- and SasG-mediated staphylococcal adhesion to corneocytes. Together, these data provide insights into staphylococcal interspecies competition for skin colonization and suggest potential avenues for inhibition ofS. aureuscolonization.
Neural substrates of parallel devaluation-sensitive and devaluation-insensitive Pavlovian learning in humans
Authors: Pool Eva R. , Pauli Wolfgang M. , Cross Logan , O’Doherty John P.
Published: January 2023

Pavlovian learning depends on multiple and parallel associations leading to distinct classes of conditioned responses that vary in their flexibility following changes in the value of an associated outcome. Here, we aimed to differentiate brain areas involved in learning and encoding associations that are sensitive to changes in the value of an outcome from those that are not sensitive to such changes. To address this question, we combined a Pavlovian learning task with outcome devaluation, eye–tracking and functional magnetic resonance imaging. We used computational modeling to identify brain regions involved in learning stimulus-reward associations and stimulus–stimulus associations, by testing for brain areas correlating with reward–prediction errors and state-prediction errors, respectively. We found that, contrary to theoretical predictions about reward prediction errors being exclusively model–free, voxels correlating with reward prediction errors in the ventral striatum and subgenual anterior cingulate cortex were sensitive to devaluation. On the other hand, brain areas correlating with state prediction errors were found to be devaluation insensitive. In a supplementary analysis, we distinguished brain regions encoding predictions about outcome taste identity from those involved in encoding predictions about its expected spatial location. A subset of regions involved in taste identity predictions were devaluation sensitive while those involved in encoding predictions about spatial location were devaluation insensitive. These findings provide insights into the role of multiple associative mechanisms in the brain in mediating Pavlovian conditioned behavior – illustrating how distinct neural pathways can in parallel produce both devaluation sensitive and devaluation insensitive behaviors.
Excitation energy transfer between higher excited states of photosynthetic pigments: 2. Chlorophyllbis a B band energy trap
Authors: Götze Jan P. , Lokstein Heiko
Published: January 2023

Chlorophylls (Chls) are known for fast, sub-picosecond internal conversion (IC) from ultraviolet/blue absorbing (“B” or “Soret” states) to the energetically lower, red light-absorbing Q states. Consequently, excitation energy transfer (EET) in photosynthetic pigment-protein complexes involving the B states has so far not been considered. We present, for the first time, a theoretical framework for the existence of B-B EET in tightly coupled Chl aggregates, such as photosynthetic pigment-protein complexes. We show that according to a simple Förster resonance energy transport (FRET) scheme, unmodulated B-B EET likely poses an existential threat, in particular the photochemical reaction centers (RCs). This insight leads to so-far undescribed roles for carotenoids (Crts, cf. previous article in this series) and Chlb(this article) of possibly primary importance.

It is demonstrated how pigments in a photosynthetic antenna pigment-protein complex (CP29) undergo FRET. Here, the focus is on the role of Chlbfor EET in the Q and B bands. Further, the initial excited pigment distribution in the B band is computed for relevant solar irradiation and wavelength-centered laser pulses. It is found that both accessory pigment classes compete efficiently with Chlaabsorption in the B band, leaving only 40% of B band excitations for Chla. B state population is preferentially relocated to Chlbafter excitation of any Chls, due to a near-perfect match of ChlbB band absorption with ChlaB state emission spectra. This results in an efficient depletion of the Chlapopulation (0.66 per IC/EET step, as compared to 0.21 in a Chla-only system). Since Chlbonly occurs in the peripheral antenna complexes, and RCs contain only Chla, this would automatically trap potentially dangerous B state population distantly from the RCs.
Genetic diversity of the eastern black rhinoceros (Diceros bicornis michaeli) in Tanzania; implications for future conservation
Authors: Mellya Ronald. V. K. , Hopcraft J. Grant C. , Eblate Ernest M. , Otiende Moses , Chuma Idrissa S. , Macha Emmanuel S. , Wambura Dickson , Kilbride Elizabeth , Mable Barbara K.
Published: January 2023

In the past decade, there has been a drastic decline in the number of Eastern Black rhinoceros (black rhinoceros) (Diceros bicornis michaeli), primarily because of poaching across their natural habitats, leaving few individuals in small, isolated populations that are vulnerable to demographic extinction, disease epidemics, genetic drift and inbreeding. However, genetic consequences of the demographic decline on the remaining populations have not been investigated. Using the mitochondrial control region, this study investigated how current levels of genetic diversity relate to historical patterns, quantified genetic differentiation between extant populations and assessed the impacts of previous translocations on genetic diversity across populations. A total of 74 individual eastern black rhinoceroses were sampled from five extant populations in Tanzania and one neighbouring cross-border population in the Maasai Mara in Kenya. Six maternal haplotypes were identified, with an overall haplotype diversity of h=0.7 but low overall nucleotide diversity within populations (π = 0.017) compared to historical populations from Tanzania (π = 0.021). There was extensive variation in haplotype distribution between populations, with more variation exists within (65.5 %) than among the populations (35.5%), which may indicate lack of migration between populations. Specifically, some geographically close populations with different histories of introductions didn’t share any haplotypes, suggesting that gene flow is currently restricted. The haplotypes were distributed among three east African haplogroups (CV, CE and EA) that have been described in previous studies, suggesting that multiple lineages have been preserved despite loss of haplotypes. One of the haplotypes was highly divergent and matched sequences previously classified as a subspecies that has not been recognised in recent years (D. b. ladoensis). We recommend that current levels of diversity be maintained by allowing natural movements of rhinoceroses between the populations, with the possibility of introducing additional variations by translocation of individuals between sites.
Population genomics of the mostly thelytokousDiplolepis rosae(Linnaeus, 1758) (Hymenoptera: Cynipidae) reveals population-specific selection for sex
Authors: Mozhaitseva Ksenia , Tourrain Zoé , Branca Antoine
Published: January 2023

In Hymenoptera, arrhenotokous parthenogenesis (arrhenotoky) is a common reproductive mode. Thelytokous parthenogenesis (thelytoky), when virgin females produce only females, is less common and is found in several taxa. In our study, we assessed the efficacy of recombination and the effect of thelytoky on the genome structure ofDiplolepis rosae, a gall wasp producing bedeguars in dog roses. We assembled a high-quality reference genome using Oxford Nanopore long-read technology and sequenced 17 samples collected in France with high-coverage Illumina reads. We found twoD.rosaeperipatric lineages that differed in the level of recombination and homozygosity. The firstD.rosaelineage showed a recombination rate that was 13.2 times higher and a per-individual heterozygosity that was 1.6 times higher. We inferred that genes under negative selection were enriched in functions related to male traits (‘sperm competition’, ‘insemination’, and ‘copulation’ gene ontology terms) in the more recombining lineage, while in the less recombining form, the same lineage genes showed traces pointing towards balancing or relaxed selection. Thus, althoughD.rosaereproduces mainly by thelytoky, selection may act to maintain sexual reproduction.

Significance

Many organisms can alternate between sexual and asexual reproduction in different ways. Sexual reproduction is essential to creating genetic diversity for adaptation to changing environments, whereas asexual reproduction is important in the short term and in stable environments. Using genomic data, we demonstrated the existence of two lineages in the rose bedeguar waspDiplolepis rosaepreviously shown to reproduce mainly by thelytokous parthenogenesis, giving almost only females. One of the lineages showed higher recombination, higher heterozygosity, and genes involved in male traits under negative selection. This could be linked to the expected advantages of maintaining sexual reproduction in natural populations.
Somatic mutation rates scale with time not growth rate in long-lived tropical trees
Authors: Satake Akiko , Imai Ryosuke , Fujino Takeshi , Tomimoto Sou , Ohta Kayoko , Na’iem Mohammad , Indrioko Sapto , Widiyatno  , Purnomo Susilo , Mollá–Morales Almudena , Nizhynska Viktoria , Tani Naoki , Suyama Yoshihisa , Sasaki Eriko , Kasahara Masahiro
Published: January 2023

The rates of appearance of new mutations play a central role in evolution. However, mutational processes in natural environments and their relationship with growth rates are largely unknown, particular in tropical ecosystems with high biodiversity. Here, we examined the somatic mutation landscapes of two tropical trees,Shorea laevis(slow-growing) andS. leprosula(fast-growing), in central Borneo, Indonesia. Using newly-constructed genomes, we identified a greater number of somatic mutations in tropical trees than in temperate trees. In both species, we observed a linear increase in the number of somatic mutations with physical distance between branches. However, we found that the rate of somatic mutation accumulation per meter of growth was 3.7-fold higher inS. laevisthan inS. leprosula. This difference in the somatic mutation rate was scaled with the slower growth rate ofS. laeviscompared toS. leprosula,resulting in a constant somatic mutation rate per year between the two species. We also found that somatic mutations are neutral within an individual, but those mutations transmitted to the next generation are subject to purifying selection. These findings suggest that somatic mutations accumulate with absolute time and older trees have a greater contribution towards generating genetic variation.

Significance Statement

The significance of our study lies in the discovery of an absolute time-dependent accumulation of somatic mutations in long-lived tropical trees, independent of growth rate. Through a comparative analysis of somatic mutation landscapes in slow- and fast-growing species, we observed a clock-like accumulation of somatic mutations in both species, regardless of their growth rates. Although the majority of somatic mutations were restricted to a single branch, we also identified mutations present in multiple branches, likely transmitted during growth. Our findings suggest that older trees make a greater contribution towards generating genetic variation.
Environmental DNA Reveals Patterns of Biological Invasion in an Inland Sea
Authors: Duprey Joe , Gallego Ramón , Klinger Terrie , Kelly Ryan P.
Published: January 2023

Non-native species have the potential to cause ecological and economic harm to coastal and estuarine ecosystems. Understanding which habitat types are most vulnerable to biological invasions, where invasions originate, and the vectors by which they arrive can help direct limited resources to prevent or mitigate ecological and socio-economic harm. Information about the occurrence of non-native species can help guide interventions at all stages of invasion, from first introduction, to naturalization and invasion. However, monitoring at relevant scales requires considerable investment of time, resources, and taxonomic expertise. Environmental DNA (eDNA) metabarcoding methods sample coastal ecosystems at broad spatial and temporal scales to augment established monitoring methods. We use COI mtDNA eDNA sampling to survey a diverse assemblage of species across distinct habitats in the Salish Sea in Washington State, USA, and classify each as non-native, native, or indeterminate in origin. The non-native species detected include both well-documented invaders and species not previously reported within the Salish Sea. We find a non-native assemblage dominated by shellfish and algae with native ranges in the temperate western Pacific, and find more-retentive estuarine habitats to be invaded at far higher levels than better-flushed rocky shores. Furthermore, we find an increase in invasion level with higher water temperatures in spring and summer across habitat types. This analysis contributes to a growing understanding of the biotic and abiotic factors that influence invasion level, and underscores the utility of eDNA surveys to monitor biological invasions and to better understand the factors that drive these invasions.
Species-aware DNA language models capture regulatory elements and their evolution
Authors: Karollus Alexander , Hingerl Johannes , Gankin Dennis , Grosshauser Martin , Klemon Kristian , Gagneur Julien
Published: January 2023

The rise of large-scale multi-species genome sequencing projects promises to shed new light on how genomes encode gene regulatory instructions. To this end, new algorithms are needed that can leverage conservation to capture regulatory elements while accounting for their evolution. Here we introduce species-aware DNA language models (LMs), which we trained on more than 800 species spanning over 500 million years of evolution. Investigating their ability to predict masked nucleotides from context, we show that DNA LMs distinguish transcription factor and RNA-binding protein motifs from background non-coding sequence. Owing to their flexibility, DNA LMs capture conserved regulatory elements over much further evolutionary distances than sequence alignment would allow. Remarkably, DNA LMs reconstruct motif instances bound in vivo better than unbound ones and account for the evolution of motif sequences and their positional constraints, showing that these models capture functional high-order sequence and evolutionary context. We further show that species-aware training yields improved sequence representations for endogenous and MPRA-based gene expression prediction, as well as motif discovery. Collectively, these results demonstrate that species-aware DNA language models are a powerful, flexible, and scalable tool to integrate information from large compendia of highly diverged genomes.
macrosyntR : Drawing automatically ordered Oxford Grids from standard genomic files in R
Authors: El Hilali Sami , Copley Richard R.
Published: January 2023

Macrosynteny refers to the conservation of chromosomal to sub-chromosomal domains across species and its conservation can provide insight on the evolution of animal genomes. Pairwise comparison of de-novo assembled genomes based on predicted protein sequences often use a graphical visualization called an Oxford grid. We implemented an R package to draw Oxford grids from standard genomic file formats. The package can automatically order the chromosomes, to improve interpretability, and is thus helpful for both exploratory data analysis and production of publication quality graphics.
Reprogramming Intrahepatic Cholangiocarcinoma Immune Microenvironment by Chemotherapy and CTLA-4 Blockade Enhances Anti-PD1 Therapy
Authors: Chen Jiang , Amoozgar Zohreh , Liu Xin , Aoki Shuichi , Liu Zelong , Shin Sarah , Matsui Aya , Pu Zhangya , Lei Pin-Ji , Datta Meenal , Zhu Lingling , Ruan Zhiping , Shi Lei , Staiculescu Daniel , Inoue Koetsu , Munn Lance L. , Fukumura Dai , Huang Peigen , Bardeesy Nabeel , Ho Won Jin , Jain Rakesh. K. , Duda Dan G.
Published: January 2023

Intrahepatic cholangiocarcinoma (ICC) has limited therapeutic options and a dismal prognosis. Anti-PD-L1 immunotherapy combined with gemcitabine/cisplatin chemotherapy has recently shown efficacy in biliary tract cancers, but responses are seen only in a minority of patients. Here, we studied the roles of anti-PD1 and anti-CTLA-4 immune checkpoint blockade (ICB) therapies when combined with gemcitabine/cisplatin and the mechanisms of treatment benefit in orthotopic murine ICC models. We evaluated the effects of the combined treatments on ICC vasculature and immune microenvironment using flow cytometry analysis, immunofluorescence, imaging mass cytometry, RNA-sequencing, qPCR, andin vivoT-cell depletion and CD8+T-cell transfer using orthotopic ICC models and transgenic mice. Combining gemcitabine/cisplatin with anti-PD1 and anti-CTLA-4 antibodies led to substantial survival benefits and reduction of morbidity in two aggressive ICC models, which were ICB-resistant. Gemcitabine/cisplatin treatment increased the frequency of tumor-infiltrating lymphocytes and normalized the ICC vessels, and when combined with dual CTLA-4/PD1 blockade, increased the number of activated CD8+Cxcr3+IFN-γ+T-cells. Depletion of CD8+but not CD4+T-cells compromised efficacy. Conversely, CD8+T-cell transfer fromCxcr3−/−versusCxcr3+/+mice intoRag1−/−immunodeficient mice restored the anti-tumor effect of gemcitabine/cisplatin/ICB combination therapy. Finally, rational scheduling of the ICBs (anti-CTLA-4 “priming”) with chemotherapy and anti-PD1 therapy achieved equivalent efficacy with continuous dosing while reducing overall drug exposure. In summary, gemcitabine/cisplatin chemotherapy normalizes vessel structure, increases activated T-cell infiltration, and enhances anti-PD1/CTLA-4 immunotherapy efficacy in aggressive murine ICC. This combination approach should be clinically tested to overcome resistance to current therapies in ICC patients.

One Sentence Summary

Immune microenvironment reprogramming by chemotherapy and priming using CTLA-4 blockade render ICCs responsive to anti-PD-1 immunotherapy.
Decoupling of transcript and protein concentrations ensures budding yeast histone homeostasis in different nutrient conditions
Authors: Chatzitheodoridou Dimitra , Bureik Daniela , Padovani Francesco , Nadimpalli Kalyan Varma , Schmoller Kurt M.
Published: January 2023

To maintain protein homeostasis in changing nutrient environments, cells must precisely control the amount of their proteins, despite the accompanying changes in cell growth and biosynthetic capacity. As nutrients are major regulators of cell cycle length and progression, a particular challenge arises for the nutrient-dependent regulation of ‘cell cycle genes’, which are periodically expressed during the cell cycle. One important example are histones, which are needed at a constant histone-to-DNA stoichiometry. Here we show that budding yeast achieves histone homeostasis in different nutrients through a decoupling of transcript and protein abundance. We find that cells downregulate histone transcripts in poor nutrients to avoid toxic histone overexpression, but produce constant amounts of histone proteins through nutrient-specific regulation of translation efficiency. Our findings suggest that this allows cells to balance the need for rapid histone production under fast growth conditions with the tight regulation required to avoid toxic overexpression in poor nutrients.
Integration of genetic fine-mapping and multi-omics data reveals candidate effector genes for hypertension
Authors: van Duijvenboden Stefan , Ramírez Julia , Young William J. , Olczak Kaya J. , Ahmed Farah , Alhammadi Mohammed J.A.Y. ,   International Consortium of Blood Pressure, Bell Christopher G. , Morris Andrew P. , Munroe Patricia B.
Published: January 2023

Genome-wide association studies of blood pressure (BP) have identified >1000 loci but the effector genes and biological pathways at these loci are mostly unknown. Using published meta-analysis summary statistics, we conducted annotation-informed fine-mapping incorporating tissue-specific chromatin segmentation to identify causal variants and candidate effector genes for systolic BP, diastolic BP, and pulse pressure. We observed 532 distinct signals associated with ≥2 BP traits and 84 with all three. For >20% of signals, a single variant accounted for >75% posterior probability, 65 were missense variants in known (SLC39A8, ADRB2, DBH) and previously unreported BP candidate genes (NRIP1, MMP14). In disease-relevant tissues, we colocalized >80 and >400 distinct signals for each BP trait withcis-eQTLs, and regulatory regions from promoter capture Hi-C, respectively. Integrating mouse, human disorder, tissue expression data and literature review, we provide consolidated evidence for 394 BP candidate genes for future functional validation and identifies several new drug targets.
Acinar-ductal cell rearrangement drives pancreas branching morphogenesis in an IGF/PI3K-dependent manner
Authors: Darrigrand Jean-Francois , Salowka Anna , Spagnoli Francesca M.
Published: January 2023

During organ formation, progenitor cells need to acquire the diversity of cell identities found in the organ as well as organize themselves into distinct structural units. How these processes are coordinated, and how tissue architecture(s) are preserved despite the dramatic cell rearrangements occurring in developing organs remain unclear. Here, we identified cellular rearrangements between acinar and ductal progenitors as a mechanism to drive branching morphogenesis in the pancreas while preserving the integrity of the acinar-ductal functional unit.

Usingex vivoandin vivomouse models, we found that pancreatic ductal cells form clefts by protruding and pulling on the acinar basement membrane, which lead to acini splitting. Newly formed acini remain connected to bifurcated branches generated by ductal cell rearrangement. IGF/PI3K pathway regulates this process by controlling ductal cell fluidity. If components of the pathway are genetically or chemically dysregulated, ductal cell fluidity prevents branching and affects pancreatic cell fates. Hence, our results explain how acinar multiplication and branch bifurcation are synchronized during pancreas organogenesis.
Single fluorogen imaging reveals distinct environmental and structural features of biomolecular condensates
Authors: Wu Tingting , King Matthew R. , Qiu Yuanxin , Farag Mina , Pappu Rohit V. , Lew Matthew D.
Published: January 2023

Biomolecular condensates are viscoelastic materials. Simulations predict that fluid-like condensations are defined by spatially inhomogeneous organization of the underlying molecules. Here, we test these predictions using single-fluorogen tracking and super-resolution imaging. Specifically, we leverage the localization and orientational preferences of freely diffusing fluorogens and the solvatochromic effect whereby specific fluorogens are turned on in response to condensate microenvironments. We deployed three different fluorogens to probe the microenvironments and molecular organization of different protein-based condensates. The spatiotemporal resolution and environmental sensitivity afforded by single-fluorogen imaging shows that the internal environments of condensates are more hydrophobic than coexisting dilute phases. Molecules within condensates are organized in a spatially inhomogeneous manner, and this gives rise to slow-moving nanoscale molecular clusters that coexist with fast-moving molecules. Fluorogens that localize preferentially to the interface help us map their distinct features. Our findings provide a structural and dynamical basis for the viscoelasticity of condensates.
Evaluating Retention Index Score Assumptions to Refine GC-MS Metabolite Identification
Authors: Degnan David J. , Bramer Lisa M. , Flores Javier E. , Paurus Vanessa L. , Corilo Yuri E. , Clendinen Chaevien S.
Published: January 2023

As metabolomics grows into a high-throughput and high demand research field, current metrics for the identification of small molecules in GC-MS still require manual verification. Though steps have been taken to improve scoring metrics by combining spectral similarity (SS) and retention index (RI), the problem persists. A large body of literature has analyzed and refined SS scores, but few studies have explicitly studied improvements to RI scores. Here, we examined whether uninvestigated assumptions of the RI score are valid and propose ways to improve them. Query RI were matched to library RI with a generous window of +/-35 to avoid unintentional removal of valid compound identifications. Each match was manually verified as a true positive, true negative or unknown. Metabolites with at least 30 true positive identifications were included in downstream analyses, resulting in a total of 87 metabolites from samples of varying complexity and type (e.g., amino acid mixtures, human urine, fungal species, etc.). Our results showed that the RI score assumptions of normality, consistent variance across metabolites, and a mean error centered at 0 are often violated. We demonstrated through a cross-validation analysis that modifying these underlying assumptions according to empirical, metabolite-specific distributions improved the true positive and negative rankings. Further, we statistically determined the minimum number of samples required to estimate distributional parameters for scoring metrics. Overall, this work proposes a robust statistical pipeline to reduce the time bottleneck of metabolite identification by improving RI scores and thus minimizes the effort to complete manual verification.
Improved gene regulatory network inference from single cell data with dropout augmentation
Authors: Zhu Hao , Slonim Donna K.
Published: January 2023

A major challenge in working with single-cell RNA sequencing data is the prevalence of “dropout,” when some transcripts’ expression values are erroneously not captured. Addressing this issue, which produces zero-inflated count data, is crucial for many downstream data analyses including the inference of gene regulatory networks (GRNs). In this paper, we introduce two novel contributions. First, we propose Dropout Augmentation (DA), a simple but effective model regularization method to address the zero inflation problem in single-cell data by augmenting the data with synthetic dropout events. DA offers a new perspective to solve the “dropout” problem beyond imputation. Second, we present DAZZLE, a stabilized and robust version of the autoencoder-based structure equation model for GRN inference using the DA concept. Benchmark experiments illustrate the improved performance and increased stability of the proposed DAZZLE model over existing approaches. The practical application of the DAZZLE model on a longitudinal mouse microglia dataset containing over 15,000 genes illustrates its ability to handle real-world single cell data with minimal gene filtration. The improved robustness and stability of DAZZLE make it a practical and valuable addition to the toolkit for GRN inference from single-cell data. Finally, we propose that Dropout Augmentation may have wider applications beyond the GRN-inference problem. Project website:https://bcb.cs.tufts.edu/DAZZLE.

Author summary

The prevalence of false zeros in single-cell data, or “dropout,” affects many downstream analyses. A common approach is to eliminate these zeros through data imputation. We propose an alternative solution that focuses on regularizing the model and increasing model robustness against dropout noise. Counter-intuitively, this is done by augmenting the input data with a small number of zeros to simulate additional dropout noise. Validation is performed on the task of gene regulatory network inference. Our proposed model, DAZZLE, which uses the dropout augmentation idea, shows improved performance and robustness.
A computational model of chemically and mechanically induced platelet plug formation
Authors: Cardillo Giulia , Barakat Abdul I.
Published: January 2023

Objectives

Thrombotic deposition is a major consideration in the development of implantable cardiovascular devices. Recently, it has been experimentally demonstrated that localized changes in the blood shear rate -i.e. shear gradients-play a critical role in thrombogenesis. The goal of the present work is to develop a predictive computational model of platelet plug formation that can be used to assess the thrombotic burden of cardiovascular devices, introducing for the first time the role of shear gradients. We have developed a comprehensive model of platelet-mediated thrombogenesis which includes platelet transport in the blood flow, platelet activation and aggregation induced by both biochemical and mechanical factors, kinetics and mechanics of platelet adhesion, and changes in the local fluid dynamics due to the thrombus growth.

Methods

A 2D computational model was developed using the multi-physics finite element solver COMSOL 5.6. The model can be described by a coupled set of convection-diffusion-reaction equations. Platelet adhesion at the surface was modeled via flux boundary conditions. Using a moving mesh for the surface, thrombus growth and consequent alterations in blood flow were modeled. In the case of a stenosis, the notions of shear stress induced platelet activation in the contraction zone and shear gradients induced platelet deposition in the expansion zone downstream of the stenosis were studied.

Results

The model provides the spatial and temporal evolution of platelet plug in the flow field. The computed platelet plug size evolution was validated against literature data. The results confirm the importance of considering both mechanical and chemical aggregation of platelets.

Conclusions

The developed model represents a potentially useful tool for the optimization of the design of the cardiovascular device flow path.
The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences
Authors: Stefancsik Ray , Balhoff James P. , Balk Meghan A. , Ball Robyn , Bello Susan M. , Caron Anita R. , Chessler Elissa , de Souza Vinicius , Gehrke Sarah , Haendel Melissa , Harris Laura W. , Harris Nomi L. , Ibrahim Arwa , Koehler Sebastian , Matentzoglu Nicolas , McMurry Julie A. , Mungall Christopher J. , Munoz-Torres Monica C. , Putman Tim , Robinson Peter , Smedley Damian , Sollis Elliot , Thessen Anne E , Vasilevsky Nicole , Walton David O. , Osumi-Sutherland David
Published: January 2023

Existing phenotype ontologies were originally developed to represent phenotypes that manifest as a character state in relation to a wild-type or other reference. However, these do not include the phenotypic trait or attribute categories required for the annotation of genome-wide association studies (GWAS), Quantitative Trait Loci (QTL) mappings or any population-focused measurable trait data. Moreover, variations in gene expression in response to environmental disturbances even without any genetic alterations can also be associated with particular biological attributes. The integration of trait and biological attribute information with an ever increasing body of chemical, environmental and biological data greatly facilitates computational analyses and it is also highly relevant to biomedical and clinical applications.

The Ontology of Biological Attributes (OBA) is a formalised, species-independent collection of interoperable phenotypic trait categories that is intended to fulfil a data integration role. OBA is a standardised representational framework for observable attributes that are characteristics of biological entities, organisms, or parts of organisms. OBA has a modular design which provides several benefits for users and data integrators, including an automated and meaningful classification of trait terms computed on the basis of logical inferences drawn from domain-specific ontologies for cells, anatomical and other relevant entities. The logical axioms in OBA also provide a previously missing bridge that can computationally link Mendelian phenotypes with GWAS and quantitative traits. The term components in OBA provide semantic links and enable knowledge and data integration across specialised research community boundaries, thereby breaking silos.
How PTEN mutations degrade function at the membrane and life expectancy of carriers of mutations in the human brain
Authors: Jang Hyunbum , Chen Jiaye , Iakoucheva Lilia M , Nussinov Ruth
Published: January 2023

PTEN dysfunction, caused by loss of lipid phosphatase activity or deletion, promotes pathologies, cancer, benign tumors, and neurodevelopmental disorders (NDDs). Despite efforts, exactly how the mutations trigger distinct phenotypic outcomes, cancer or NDD, has been puzzling. It has also been unclear how to distinguish between mutations harbored by isoforms, are they cancer or NDDs-related. Here we address both. We demonstrate that PTEN mutations differentially allosterically bias P-loop dynamics and its connection to the catalytic site, affecting catalytic activity. NDD-related mutations are likely to sample conformations present in the wild-type, while sampled conformations sheltering cancer-related hotspots favor catalysis-prone conformations, suggesting that NDD mutations are weaker. Analysis of isoform expression data indicates that if the transcript has NDD-related mutations, alone or in combination with cancer hotspots, there is high prenatal expression. If no mutations within the measured days, low expression levels. Cancer mutations promote stronger signaling and cell proliferation; NDDs’ are weaker, influencing brain cell differentiation. Further, exon 5 is impacted by NDD or non-NDD mutations, while exon 7 is exclusively impacted by NDD mutations. Our comprehensive conformational and genomic analysis helps discover how same allele mutations can foster different clinical manifestations and uncovers correlations of splicing isoform expression to life expectancy.
Analysis of NIH K99/R00 Awards and the Career Progression of Awardees
Authors: Woitowich Nicole C , Hengel Sarah R , Solis Christopher , Vilgalys Tauras P , Babdor Joel , Tyrrell Daniel J
Published: January 2023

Many postdoctoral fellows and scholars who hope to secure tenure-track faculty positions in the United States apply to the National Institutes of Health (NIH) for a Pathway to Independence Award. This award has two phases (K99 and R00) and provides funding for up to five years. Using NIH data for the period 2006-2022, we report that ∼230 K99 awards were made every year, representing up to ∼$250 million annual investment. About 40% of K99 awardees were women and ∼89% of K99 awardees went on to receive an R00 award annually. Institutions with the most NIH funding produced the most recipients of K99 awards and recruited the most recipients of R00 awards. The time between a researcher starting an R00 award and receiving a major NIH award (such as an R01) ranged between 4.6 and 7.4 years, and was significantly longer for women, for those who remained at their home institution, and for those hired by an institution that was not one of the 25 institutions with the most NIH funding. Shockingly, there has yet to be a K99 awardee at a historically Black college or university. We go on to show how K99 awardees flow to faculty positions, and to identify various factors that influence the future success of individual researchers and, therefore, also influence the composition of biomedical faculty at universities in the US.
Loss of the endocytic tumor suppressor HD-PTP phenocopies LKB1 and promotes RAS-driven oncogenesis
Authors: Seong Chang-Soo , Huang Chunzi , Boese Austin C. , Hou Yuning , Koo Junghui , Mouw Janna K. , Rupji Manali , Joseph Greg , Johnston H. Richard , Claussen Henry , Switchenko Jeffrey M. , Behera Madhusmita , Churchman Michelle , Kolesar Jill M. , Arnold Susanne M. , Kerrigan Katie , Akerley Wallace , Colman Howard , Johns Margaret A. , Arciero Cletus , Zhou Wei , Marcus Adam I. , Ramalingam Suresh S. , Fu Haian , Gilbert-Ross Melissa
Published: January 2023

Abstract/Summary

Oncogenic RAS mutations drive aggressive cancers that are difficult to treat in the clinic, and while direct inhibition of the most common KRAS variant in lung adenocarcinoma (G12C) is undergoing clinical evaluation, a wide spectrum of oncogenic RAS variants together make up a large percentage of untargetable lung and GI cancers. Here we report that loss-of-function alterations (mutations and deep deletions) in the gene that encodes HD-PTP (PTPN23) occur in up to 14% of lung cancers in the ORIEN Avatar lung cancer cohort, associate with adenosquamous histology, and occur alongside an altered spectrum of KRAS alleles. Furthermore, we show that in publicly available early-stage NSCLC studies loss of HD-PTP is mutually exclusive with loss of LKB1, which suggests they restrict a common oncogenic pathway in early lung tumorigenesis. In support of this, knockdown of HD-PTP in RAS-transformed lung cancer cells is sufficient to promote FAK-dependent invasion. Lastly, knockdown of the Drosophila homolog of HD-PTP (dHD-PTP/Myopic) synergizes to promote RAS-dependent neoplastic progression. Our findings highlight a novel tumor suppressor that can restrict RAS-driven lung cancer oncogenesis and identify a targetable pathway for personalized therapeutic approaches for adenosquamous lung cancer.
Understanding Painful versus Non-Painful Dental Pain in Male and Female Patients: A Transcriptomic Analysis of Human Biopsies
Authors: Patel Biraj , Eskander Michael Andrew , Fang-Mei Chang , Chapa Brett , Shivani Ruparel , Lai Zhao , Chen Yidong , Armen Akopian , Ruparel Nikita B.
Published: January 2023

Dental pain from apical periodontitis is an infection induced-orofacial pain condition that presents with diversity in pain phenotypes among patients. While 60% of patients with a full-blown disease present with the hallmark symptom of mechanical allodynia, nearly 40% of patients experience no pain. Furthermore, a sexual dichotomy exists, with females exhibiting lower mechanical thresholds under basal and diseased states. Finally, the prevalence of post-treatment pain refractory to commonly used analgesics ranges from 7-19% (~2 million patients), which warrants a thorough investigation of the cellular changes occurring in different patient cohorts. We, therefore, conducted a transcriptomic assessment of periapical biopsies (peripheral diseased tissue) from patients with persistent apical periodontitis. Surgical biopsies from symptomatic male (SM), asymptomatic male (AM), symptomatic female (SF), and asymptomatic female (AF) patients were collected and processed for bulk RNA sequencing. Using strict selection criteria, our study found several unique differentially regulated genes (DEGs) between symptomatic and asymptomatic patients, as well as novel candidate genes between sexes within the same pain group. Specifically, we found the role of cells of the innate and adaptive immune system in mediating nociception in symptomatic patients and the role of genes involved in tissue homeostasis in potentially inhibiting nociception in asymptomatic patients. Furthermore, sex-related differences appear to be tightly regulated by macrophage activity, its secretome, and/or migration. Collectively, we present, for the first time, a comprehensive assessment of peripherally diseased human tissue after a microbial insult and shed important insights into the regulation of the trigeminal system in female and male patients.

Clinical diversity paves the way for translational research. We conducted a comprehensive transcriptomic assessment of peripherally diseased human tissue from patients with apical periodontitis to understand better clinical diversity observed in pain phenotypes between patients as well as perform in-depth analyses of sex-related dimorphism in patients with apical periodontitis.
TRPV1 Opening is Stabilized Equally by Its Four Subunits
Authors: Li Shisheng , Nguyen Phuong Tran , Vu Simon , Yarov-Yarovoy Vladimir , Zheng Jie
Published: January 2023

Capsaicin receptor TRPV1 is a nociceptor for vanilloid molecules such as capsaicin and resiniferatoxin (RTX). Even though cryo-EM structures of TRPV1 in complex with these molecules are available, how their binding energetically favors the open conformation is not known. Here we report an approach to control the number of bound RTX molecules (0-to-4) in functional mouse TRPV1. The approach allowed direct measurements of each of the intermediate open states under equilibrium conditions at both macroscopic and single-molecule levels. We found that RTX binding to each of the four subunits contributes virtually the same activation energy, which we estimated to be 1.86 kcal/mol and found to arise predominately from destabilizing the closed conformation. We further showed that sequential bindings of RTX increase open probability without altering single-channel conductance, confirming that there is likely a single open-pore conformation for TRPV1 activated by RTX.
Molecular mechanisms of coronary artery disease risk at thePDGFDlocus
Authors: Kim Hyun-Jung , Cheng Paul , Travisano Stanislao , Weldy Chad , Monteiro João P. , Kundu Ramendra , Nguyen Trieu , Sharma Disha , Shi Huitong , Lin Yi , Liu Boxiang , Haldar Saptarsi , Jackson Simon , Quertermous Thomas
Published: January 2023

Platelet derived growth factor (PDGF) signaling has been extensively studied in the context of vascular disease, but the genetics of this pathway remain to be established. Genome wide association studies (GWAS) for coronary artery disease (CAD) have identified a risk locus at 11q22.3, and we have verified with fine mapping approaches that the regulatory variant rs2019090 andPDGFDrepresent the functional variant and putative functional gene. Further, FOXC1/C2 transcription factor (TF) binding at rs2019090 was found to promotePDGFDtranscription through the CAD promoting allele. Employing a constitutivePdgfdknockout allele along with SMC lineage tracing in a male atherosclerosis mouse model we mapped single cell transcriptomic, cell state, and lesion anatomical changes associated with gene loss. These studies revealed that Pdgfd promotes expansion, migration, and transition of SMC lineage cells to the chondromyocyte phenotype and vascular calcification. This is in contrast to protective CAD genesTCF21,ZEB2, andSMAD3which we have shown to promote the fibroblast-like cell transition or perturb the pattern or extent of transition to the chondromyocyte phenotype. Further,Pdgfdexpressing fibroblasts and pericytes exhibited greater expression of chemokines and leukocyte adhesion molecules, consistent with observed increased macrophage recruitment to the plaque. Despite these changes there was no effect ofPdgfddeletion on SMC contribution to the fibrous cap or overall lesion burden. These findings suggest thatPDGFDmediates CAD risk through promoting SMC expansion and migration, in conjunction with deleterious phenotypic changes, and through promoting an inflammatory response that is primarily focused in the adventitia where it contributes to leukocyte trafficking to the diseased vessel wall.
Glutathionylation of Pyruvate Dehydrogenase Complex E2 and Inflammatory Cytokine Production During Acute Inflammation Are Magnified By Mitochondrial Oxidative Stress
Authors: Long David L. , McCall Charles E. , Poole Leslie B.
Published: January 2023

Lipopolysaccharide (LPS) is a known inducer of inflammatory signaling which triggers generation of reactive oxygen species (ROS) and cell death in responsive cells like THP-1 promonocytes and freshly isolated human monocytes. A key LPS-responsive metabolic pivot point is the 9 megadalton mitochondrial pyruvate dehydrogenase complex (PDC), which provides pyruvate dehydrogenase (E1), lipoamide-linked transacetylase (E2) and lipoamide dehydrogenase (E3) activities to produce acetyl-CoA from pyruvate. While phosphorylation-dependent decreases in PDC activity following LPS treatment or sepsis have been deeply investigated, redox-linked processes have received less attention. Data presented here demonstrate that LPS-induced reversible oxidation within PDC occurs in PDCE2 in both THP-1 cells and primary human monocytes. Knockout of PDCE2 by CRISPR and expression of FLAG-tagged PDCE2 in THP-1 cells demonstrated that LPS-induced glutathionylation is associated with wild type PDCE2 but not mutant protein lacking the lipoamide-linking lysine residues. Moreover, the mitochondrially-targeted electrophile MitoCDNB, which impairs both glutathione-and thioredoxin-based reductase systems, elevates ROS similar to LPS but does not cause PDCE2 glutathionylation. However, LPS and MitoCDNB together are highly synergistic for PDCE2 glutathionylation, ROS production, and cell death. Surprisingly, the two treatments together had differential effects on cytokine production; pro-inflammatory IL-1β production was enhanced by the co-treatment, while IL-10, an important anti-inflammatory cytokine, dropped precipitously compared to LPS treatment alone. This new information may expand opportunities to understand and modulate PDC redox status and activity and improve the outcomes of pathological inflammation.

Highlights

PDCE2 is glutathionylated (-SSG) during acute inflammation in monocytes

Lipopolysaccharide-induced PDCE2-SSG occurs in THP1 cells and human monocytes.

Lipoamide-deficient PDCE2 lowers LPS-induced PDCE2-SSG and ROS production.

MitoCDNB leads to ROS production without PDCE2-SSG, but is synergistic with LPS

MitoCDNB causes the LPS-stimulated cytokine profile to become more proinflammatory

Graphical Abstract