bluuebunny/crossref_metadata_2025 huggingface dataset:
Bradykinin release following trauma and hemorrhagic shock causes pulmonary alveolar leak in a rodent model
Authors: Eitel Andrew , Moore Ernest E. , Kelher Marguerite R. , Cohen Mitchell J. , Kissau Daniel , Hadley Jamie B. , Debot Margot , Banerjee Anirban , Silliman Christopher C.
Published: June 2023

BACKGROUND

Hemorrhage accounts for 40% of the preventable death following severe injury. Activation of systemic coagulation produces bradykinin (BK), which may cause leak from the plasma to the extravascular space and to the tissues, which is part of the complex pathophysiology of trauma-induced end-organ injury. We hypothesize that BK, released during activation of coagulation in severe injury, induces pulmonary alveolar leak.

METHODS

Isolated neutrophils (PMNs) were pretreated with a specific BK receptor B2 antagonist HOE-140/icatibant and BK priming of the PMN oxidase was completed. Rats underwent tissue injury/hemorrhagic shock (TI/HS), TI/icatibant/HS, and controls (no injury). Evans blue dye was instilled, and the percentage leak from the plasma to the lung was calculated from the bronchoalveolar lavage fluid (BALF). CINC-1 and total protein were measured in the BALF, and myeloperoxidase was quantified in lung tissue.

RESULTS

The BK receptor B2 antagonist HOE140/icatibant inhibited (85.0 ± 5.3%) BK priming of the PMN oxidase (p < 0.05). The TI/HS model caused activation of coagulation by increasing plasma thrombin-antithrombin complexes (p < 0.05). Versus controls, the TI/HS rats had significant pulmonary alveolar leak: 1.46 ± 0.21% versus 0.36 ± 0.10% (p = 0.001) and increased total protein and CINC-1 in the BALF (p < 0.05). Icatibant given after the TI significantly inhibited lung leak and the increase in CINC-1 in the BALF from TI/icatibant/HS rats versus TI/HS (p < 0.002 and p < 0.05) but not the total protein. There was no PMN sequestration in the lungs. Conclusions: This mixed injury model caused systemic activation of hemostasis and pulmonary alveolar leak likely due to BK release.

CONCLUSION

This mixed injury model caused systemic activation of hemostasis and pulmonary alveolar leak likely due to BK release.

LEVEL OF EVIDENCE

Original Article, Basic Science
Early venous thromboembolism prophylaxis in patients with trauma intracranial hemorrhage: Analysis of the prospective multicenter Consortium of Leaders in Traumatic Thromboembolism study
Authors: Wu Yu-Tung , Chien Chih-Ying , Matsushima Kazuhide , Schellenberg Morgan , Inaba Kenji , Moore Ernest E. , Sauaia Angela , Knudson M. Margaret , Martin Matthew J. ,   the CLOTT Study Group
Published: June 2023

BACKGROUND

The optimal time to initiate venous thromboembolism prophylaxis (VTEp) for patients with intracranial hemorrhage (ICH) is controversial and must balance the risks of VTE with potential progression of ICH. We sought to evaluate the efficacy and safety of early VTEp initiation after traumatic ICH.

METHODS

This is a secondary analysis of the prospective multicenter Consortium of Leaders in the Study of Thromboembolism study. Patients with head Abbreviated Injury Scale score of > 2 and with immediate VTEp held because of ICH were included. Patients were divided into VTEp ≤ or >48 hours and compared. Outcome variables included overall VTE, deep vein thrombosis (DVT), pulmonary embolism, progression of intracranial hemorrhage (pICH), or other bleeding events. Univariate and multivariate logistic regressions were performed.

RESULTS

There were 881 patients in total; 378 (43%) started VTEp ≤48 hours (early). Patients starting VTEp >48 hours (late) had higher VTE (12.4% vs. 7.2%, p = 0.01) and DVT (11.0% vs. 6.1%, p = 0.01) rates than the early group. The incidence of pulmonary embolism (2.1% vs. 2.2%, p = 0.94), pICH (1.9% vs. 1.8%, p = 0.95), or any other bleeding event (1.9% vs. 3.0%, p = 0.28) was equivalent between early and late VTEp groups. On multivariate logistic regression analysis, VTEp >48 hours (odds ratio [OR], 1.86), ventilator days >3 (OR, 2.00), and risk assessment profile score of ≥5 (OR, 6.70) were independent risk factors for VTE (all p < 0.05), while VTEp with enoxaparin was associated with decreased VTE (OR, 0.54, p < 0.05). Importantly, VTEp ≤48 hours was not associated with pICH (OR, 0.75) or risk of other bleeding events (OR, 1.28) (both p = NS).

CONCLUSION

Early initiation of VTEp (≤48 hours) for patients with ICH was associated with decreased VTE/DVT rates without increased risk of pICH or other significant bleeding events. Enoxaparin is superior to unfractionated heparin as VTE prophylaxis in patients with severe TBI.

LEVEL OF EVIDENCE

Therapeutic/Care Management; Level IV.
American Association for the Surgery of Trauma/American College of Surgeons Committee on Trauma clinical protocol for management of acute respiratory distress syndrome and severe hypoxemia
Authors: Fawley Jason A. , Tignanelli Christopher J. , Werner Nicole L. , Kasotakis George , Mandell Samuel P. , Glass Nina E. , Dries David J. , Costantini Todd W. , Napolitano Lena M.
Published: June 2023

LEVEL OF EVIDENCE

Therapeutic/Care Management: Level V.
Visual versus visual-inertial guidance in hawks pursuing terrestrial targets
Authors: Kempton James A. , Brighton Caroline H. , France Lydia A. , KleinHeerenbrink Marco , Miñano Sofia , Shelton James , Taylor Graham K.
Published: June 2023

The aerial interception behaviour of falcons is well modelled by a guidance law called proportional navigation, which commands steering at a rate proportional to the angular rate of the line-of-sight from predator to prey. Because the line-of-sight rate is defined in an inertial frame of reference, proportional navigation must be implemented using visual-inertial sensor fusion. By contrast, the aerial pursuit behaviour of hawks chasing terrestrial targets is better modelled by a mixed guidance law combining information on the line-of-sight rate with information on the deviation angle between the attacker’s velocity and the line-of-sight. Here we ask whether this behaviour may be controlled using visual information alone. We use high-speed motion capture to record
n
= 228 flights from
N
= 4 Harris’ hawks
Parabuteo unicinctus
, and show that proportional navigation and mixed guidance both model their trajectories well. The mixed guidance law also models the data closely when visual-inertial information on the line-of-sight rate is replaced by visual information on the motion of the target relative to its background. Although the visual-inertial form of the mixed guidance law provides the closest fit, all three guidance laws provide an adequate phenomenological model of the behavioural data, whilst making different predictions on the physiological pathways involved.
Homogenization of thin-structured surfaces for acoustics in the presence of a two-dimensional low Mach potential flow
Authors: Mercier Jean-François
Published: June 2023

A surface homogenization method for acoustic waves over thin microstructured surfaces in the presence of a fluid in a potential flow is presented. Sound hard surfaces are considered, the flow is considered two-dimensional and slow and a low Mach approximation is introduced. We consider acoustic waves with a typical wavelength

1

/

k

much larger than the array spacing

h

and thickness

e

. Owing to the small parameter

ε
=
k
h

, with

e

/

h
=
O
(
1
)

, a matched asymptotic expansion technique is applied to the low Mach potential wave equation in the frequency domain. A boundary condition is obtained on an equivalent flat wall, which links the acoustic velocity to its normal and tangential derivatives (of the Myers type). The accuracy of the effective model is tested numerically for various periodic shapes and the accuracy of the model in

O
(

ε
2

)

is validated.
Diacammaants adjust liquid foraging strategies in response to biophysical constraints
Authors: Fujioka Haruna , Marchand Manon , LeBoeuf Adria C.
Published: June 2023

Ant foragers provide food to the rest of the colony, often requiring transport over long distances. Foraging for liquid is challenging because it is difficult to transport and share. Many social insects store liquids inside the crop to transport them to the nest, and then regurgitate to distribute to nest-mates through a behaviour called trophallaxis. Some ants instead transport fluids with a riskier behaviour called pseudotrophallaxis—holding a drop of liquid between the mandibles through surface tension. Ants share this droplet with nest-mates without ingestion or regurgitation. We hypothesised that ants optimize their liquid-collection approach depending on viscosity. Using an ant that employs both trophallaxis and pseudotrophallaxis, we investigated the conditions where each liquid-collection behaviour is favoured by measuring biophysical properties, collection time and reaction to food quality for typical and viscosity-altered sucrose solutions. We found that ants collected more liquid per unit time by mandibular grabbing than by drinking. At high viscosities ants switched liquid collection method to mandibular grabbing in response to viscosity and not to sweetness. Our results demonstrate that ants change transport and sharing methods according to viscosity–a natural proxy for sugar concentration–thus increasing the mass of sugar returned to the nest per trip.
Directing polymorph specific calcium carbonate formation with de novo protein templates
Authors: Davila-Hernandez Fatima A. , Jin Biao , Pyles Harley , Zhang Shuai , Wang Zheming , Huddy Timothy F. , Chen Chun-Long , De Yoreo James J. , Baker David
Published: June 2023

Biomolecules modulate inorganic crystallization to generate hierarchically structured biominerals1–5, but the atomic structure of the organic-inorganic interfaces that regulate mineralization remain unknown6–8. We hypothesized that heterogeneous nucleation of calcium carbonate could be achieved by a structured flat molecular template that pre-organizes calcium ions on its surface. To test this hypothesis, we designed helical repeat proteins (DHRs) displaying regularly spaced carboxylate arrays on their surfaces and found that both protein monomers and protein-Ca2+assemblies directly nucleate nano-calcite with non-natural (110) or (202) faces while vaterite, which forms first absent the proteins, is bypassed. The nanocrystals then assemble by oriented attachment into calcite mesocrystals. We find further that nanocrystal size and polymorph can be tuned by varying the length and surface chemistry of the designed protein templates. Thus, bio-mineralization can be programmed using de novo protein design, providing a route to next-generation hybrid materials.

One sentence summary

De novo designed protein templates promote nucleation of nano-calcite and direct its growth by oriented particle attachment.
Single Cell Track and Trace: live cell labelling and temporal transcriptomics via nanobiopsy
Authors: Marcuccio Fabio , Chau Chalmers C. , Tanner Georgette , Elpidorou Marilena , Finetti Martina A. , Ajaib Shoaib , Taylor Morag , Lascelles Carolina , Carr Ian , Macaulay Iain , Stead Lucy F. , Actis Paolo
Published: June 2023

Single-cell RNA sequencing has revolutionised our understanding of cellular heterogeneity, but whether using isolated cells or more recent spatial transcriptomics approaches, these methods require isolation and lysis of the cell under investigation. This provides a snapshot of the cell transcriptome from which dynamic trajectories, such as those that trigger cell state transitions, can only be inferred. Here, we present cellular nanobiopsy: a platform that enables simultaneous labelling and sampling from a single cell without killing it. The technique is based on scanning ion conductance microscopy (SICM) and uses a double-barrel nanopipette to inject a fluorescent dye and to extract femtolitre-volumes of cytosol. We used the nanobiopsy to longitudinally profile the transcriptome of single glioblastoma (GBM) brain tumour cells in vitro over 72hrs with and without standard treatment. Our results suggest that treatment either induces or selects for more transcriptionally stable cells. We envision the nanobiopsy will transform standard single-cell transcriptomics from a static analysis into a dynamic and temporal assay.
Homeostasis of a representational map in the neocortex
Authors: Noda Takahiro , Kienle Eike , Eppler Jens-Bastian , Aschauer Dominik F. , Kaschube Matthias , Loewenstein Yonatan , Rumpel Simon
Published: June 2023

Cortical function in general and the processing of sensory stimuli in particular are remarkably robust against the continuous loss of neurons during aging, and even the accelerated loss during prodromal stages of neurodegeneration1,2. Population activity of neurons in sensory cortices represents the environment in form of a map, which is structured in an informative way for guiding behavior. Here, we used the mouse auditory cortex as a model and tested in how far the structure of the representational map is protected by homeostatic network mechanisms against the removal of neurons. We combined longitudinal two-photon calcium imaging of population responses evoked by a diverse set of sound stimuli with a targeted microablation of functionally characterized neurons. Unilateral microablation of 30 - 40 selected highly sound-responsive neurons in layer 2/3 led to a temporary disturbance of the representational map in the spared population that, however, recovered in subsequent days. At the level of individual neurons, we observed that the recovery of the spared network was predominantly driven by neurons unresponsive to the sounds before microablation which strengthened the correlation structure of the local network after gaining responsiveness. In contrast, selective microablation of inhibitory neurons induced a prolonged disturbance of the representational map that was primarily characterized by a destabilization of sound responses across trials. Together, our findings provide a link between the tuning and plasticity of individual neurons and the structure of a representational map at the population level which reveals homeostatic network mechanisms safeguarding sensory processing in neocortical circuits.
Coordinated regulation of photosynthesis and translation via NIK1/RPL10/LIMYB signaling module in response to biotic and abiotic stresses
Authors: Teixeira Ruan M. , Ferreira Marco Aurélio , Brustolini Otávio J.B. , Saia Thainá F.F. , Jean-Baptiste James , Breves Samera S. , Soares Igor N. , Ribeiro Nathalia G.A. , Duarte Christiane E. M. , Lima Lucas L. , Oliveira Leandro Licursi , Ramos Humberto J.O. , Reis Pedro A.B. , Fontes Elizabeth P. B.
Published: June 2023

Photosynthesis and translation are targets of metabolic control and development in plants, yet, how stress signals coordinately regulate these opposing energy-producing and consuming processes remains enigmatic. Here, we described a growth control circuit that ties the photosynthetic function to translational control in response to biotic and abiotic signals. We showed first that the downstream component of the NIK1/RPL10 antiviral signaling module, LIMYB, which represses translational machinery-related gene expression and translation, also suppresses photosynthetic apparatus-related genes leading to inhibition of the photosynthetic function. The repressing transcriptional activity of LIMYB, which was regulated by phosphorylation, was the primary determinant for the decrease in electron transport rate, exchange gas parameters, quantum efficiency, and water-use efficiency in the LIMYB-overexpressing lines. The decreased photosynthetic activity was linked to the NIK1 antiviral signaling and stunted growth. NIK1 activation by viral or bacterial PAMPs, or expressing a constitutively activated NIK1 mutant, T474D, repressed the photosynthesis-related marker genes and inhibited the photosynthetic function in control lines but not inlymyb. We also showed that heat and osmotic stress activate the NIK1/RPL10/LIMYB signaling circuit readouts in wild- type lines. Conversely, inlimyb-32knockout, heat and osmotic stress induced NIK1 phosphorylation but did not cause repression of the marker genes, indicating that LIMYB links NIK1 activation to the stress-mediated downregulation of translation- and photosynthesis-related genes. The coordinated repression of photosynthesis and translation via the stress-activated NIK1/RPL10/LIMYB signaling module may adjust the plant growth pattern in response to the changing environment.

Short summary

The receptor-like kinase NIK1 (NSP-Interacting Kinase 1) undergoes phosphorylation under multiple biotic and abiotic signals activating the NIK1/RPL10/LIMYB signaling circuit, which coordinately downregulates translation and photosynthesis in response to the changing environment.
Longitudinal characterization of the captive adult and tadpole Wyoming toad (Anaxyrus baxteri) microbiome
Authors: Scarberry Nicole , McAdams Zachary L. , Benson Derek , Herrick Jason , Moore Brandon , Ericsson Aaron C.
Published: June 2023

At one time thought to be extinct in the wild, the Wyoming toad (Anaxyrus baxteri) is one of the most critically endangered North American amphibian species. Despite approximately 20 years ofex situbreeding and reintroduction programs, these animals remain functionally extinct in the wild. There is concern among those working in these programs that individuals bred in captivity fail to develop the proper microbiome to withstand the stressors of their native habitat following release. In related species, the skin microbiome has been shown to have a defensive function against common pathogens affecting these animals. However, the early-life microbiome of developing tadpoles in this species remains unknown and therefore this defensive function is unexplored in the Wyoming toad. This study employed 16S rRNA amplicon sequencing to document the baseline microbiome of tadpoles bred for release and captive adult breeder populations. To characterize microbiome development, multiple rounds of skin mucosal and cloacal swabs were obtained concurrently from adult Wyoming toads bred at Omaha’s Henry Doorly Zoo and Aquarium. Our results revealed significant differences between tadpole and adult microbiomes, as well as significant sex-dependent differences within the adult Wyoming toads, in terms of richness and composition. Thus, these findings have identified the baseline microbiome of this endangered species, and variables significantly influencing its composition. Ongoing studies of the only extant wild population are expected to identify taxa not present in captive toads, and potentially help design husbandry modifications to maximize survivability following reintroduction to the wild.
Development of anin situcell-type specific proteome analysis method using antibody-mediated biotinylation
Authors: Ryu Taekyung , Kim Seok-Young , Thuraisamy Thujitha , Jang Yura , Na Chan Hyun
Published: June 2023

Since proteins are essential molecules exerting cellular functions, decoding proteome changes is the key to understanding the normal physiology and pathogenesis mechanism of various diseases. However, conventional proteomic studies are often conducted on tissue lumps, in which multiple cell types are entangled, presenting challenges in interpreting the biological dynamics among diverse cell types. While recent cell-specific proteome analysis techniques, like BONCAT, TurboID, and APEX, have emerged, their necessity for genetic modifications limits their usage. The alternative, laser capture microdissection (LCM), although it does not require genetic alterations, is labor-intensive, time-consuming, and requires specialized expertise, making it less suitable for large-scale studies. In this study, we develop the method forin situcell-type specific proteome analysis usingantibody-mediatedbiotinylation (iCAB), in which we combined immunohistochemistry (IHC) with the biotin-tyramide signal amplification approach. Poly-horseradish peroxidase (HRP) conjugated to the secondary antibody will be localized at a target cell type via a primary antibody specific to the target cell type and biotin-tyramide activated by HRP will biotinylate the nearby proteins. Therefore, the iCAB method can be applied to any tissues that can be used for IHC. As a proof-of-concept, we employed iCAB for mouse brain tissue enriching proteins for neuronal cell bodies, astrocytes, and microglia, followed by identifying the enriched proteins using 16-plex TMT-based proteomics. In total, we identified ∼8,400 and ∼6,200 proteins from enriched and non-enriched samples. Most proteins from the enriched samples showed differential expressions when we compared different cell type data, while there were no differentially expressed proteins from non-enriched samples. The cell type enrichment analysis with the increased proteins in respective cell types using Azimuth showed that neuronal cell bodies, astrocytes, and microglia data exhibited Glutamatergic Neuron, Astrocyte and Microglia/Perivascular Macrophage as the representative cell types, respectively. The proteome data of the enriched proteins showed similar subcellular distribution as non-enriched proteins, indicating that the iCAB-proteome is not biased toward any subcellular compartment. To our best knowledge, this study represents the first implementation of a cell-type-specific proteome analysis method using an antibody-mediated biotinylation approach. This development paves the way for the routine and widespread use of cell-type-specific proteome analysis. Ultimately, this could accelerate our understanding of biological and pathological phenomena.
Regional estimates of gross primary production applying the Process-Based Model 3D-CMCC-FEM vs. multiple Remote-Sensing datasets
Authors: Dalmonech D. , Vangi E. , Chiesi M. , Chirici G. , Fibbi L. , Giannetti F. , Marano G. , Massari C. , Nolè A. , Xiao J. , Collalti A.
Published: June 2023

Process-based Forest Models (PBFMs) offer the possibility to capture important spatial and temporal patterns of both carbon fluxes and stocks in forests, accounting for ecophysiological, climate and geographical variability. Yet, their predictive capacity should be demonstrated not only at the stand-level but also in the context of large spatial and temporal heterogeneity. For the first time, we apply a stand scale process-based model (3D-CMCC-FEM) in a spatially explicit manner at 1 km spatial resolution in a Mediterranean region in southern Italy. Specifically, we developed a methodology to initialize the model that comprehends the use of spatial information derived from the integration of remote sensing (RS) data, the national forest inventory data and regional forest maps to characterize structural features of the main forest species. Gross primary production (GPP) is simulated over the period 2005-2019 and the multiyear predictive capability of the model in simulating GPP is evaluated both aggregated as at species-level by means of independent multiple data sources based on different RS-based products. We show that the model is able to reproduce most of the spatial (∼2800 km2) and temporal (32 years in total) patterns of the observed GPP at both seasonal, annual and interannual time scales, even at the species-level. These new very promising results open the possibility of applying the 3D-CMCC- FEM confidently and robustly to investigate the forests’ behavior under climate and environmental variability over large areas across the highly variable ecological and bio- geographical heterogeneity of the Mediterranean region.

Key Points

We apply a process-based forest model on a regular grid at 1 km spatial resolution in a Mediterranean region.

Initial forest state is estimated using spatially explicit input data derived from remote sensing and national forest inventory data.

The 3D-CMCC-FEM shows comparably estimates in simulating both spatial and temporally the gross primary production, when compared to independent satellite-based products.
ontophylo: Reconstructing the evolutionary dynamics of phenomes using new ontology-informed phylogenetic methods
Authors: Porto Diego S. , Uyeda Josef , Mikó István , Tarasov Sergei
Published: June 2023

1. Reconstructing ancestral states for discrete characters is essential for understanding trait evolution in organisms. However, most existing methods are limited to individual characters and often overlook the hierarchical and interactive nature of traits. Recent advances in phylogenetics now offer the possibility of integrating knowledge from anatomy ontologies to reconstruct multiple discrete character histories. However, practical applications that fully harness the potential of these new approaches are still lacking.

2. This paper introducesontophylo, an R package that extends the PARAMO pipeline to address these limitations.Ontophyloenables the reconstruction of phenotypic entities composed of amalgamated characters, such as entire phenomes or anatomical regions. It offers three new applications: (1) reconstructing evolutionary rates of amalgamated characters using phylogenetic non-homogeneous Poisson process (pNHPP), allowing for rate variation and shifts over time and phylogeny; (2) explicit reconstruction of morphospace dynamics; and (3) direct visualization of evolutionary rates and statistics on vector images of organisms.Ontophyloincorporates ontological knowledge to facilitate these applications.

3. Benchmarking confirms the accuracy of pNHPP in estimating character rates under different evolutionary scenarios, and example applications demonstrate the utility ofontophyloin studying morphological evolution in Hymenoptera using simulated data.

4.Ontophylois easily integrated with other ontologyoriented and general-purpose R packages and offers new opportunities to examine morphological evolution on a phenomic level using new and legacy data.
Deep Learning Glioma Grading with the Tumor Microenvironment Analysis Protocol for A Comprehensive Learning, Discovering, and Quantifying Microenvironmental Features
Authors: Pytlarz M. , Wojnicki K. , Pilanc P. , Kaminska B. , Crimi A.
Published: June 2023

Gliomas are primary brain tumors that arise from neural stem cells or glial precursors. Diagnosis of glioma is based on histological evaluation of pathological cell features and molecular markers. Gliomas are infiltrated by myeloid cells that accumulate preferentially in malignant tumors and their abundance inversely correlates with survival, which is of interest for cancer immunotherapies. To avoid time-consuming and laborious manual examination of the images, a deep learning approach for automatic multiclass classification of tumor grades was proposed. Importantly, as an alternative way of investigating characteristics of brain tumor grades, we implemented a protocol for learning, discovering, and quantifying tumor microenvironment elements on our glioma dataset. Using only single-stained biopsies we derived characteristic differentiating tumor microenvironment phenotypic neighborhoods. A challenge of the study was given by a small sample size of human leukocyte antigen stained on glioma tissue microarrays dataset - 203 images from 5 classes - and imbalanced data distribution. This has been addressed by image augmentation of the underrepresented classes. For this glioma multiclass classification task, a residual neural network architecture has been adapted. On the validation set the average accuracy was 0.72 when the model was trained from scratch, and 0.85 with the pre-trained model. Moreover, the tumor microenvironment analysis suggested a relevant role of the myeloid cells and their accumulation to characterize glioma grades. This promising approach can be used as an additional diagnostic tool to improve assessment during intra-operative examination or sub-typing tissues for treatment selection, despite the challenges caused by the difficult dataset. We present here the distributions and visualizations of extracted tumor inter-dependencies.

Graphical abstract

Highlights

Research highlight 1: We demonstrate that the ResNet-18 architecture with simple data augmentation trained in 10-fold cross-validation performs the multiclass classification relatively well even with a small imbalanced dataset with a high degree of similarities between classes.

Research highlight 2: After supervised subtyping of the tumor, we investigated the usefulness of the protocol for discovery and learning tumor microenvironment elements for the same task. The protocol designed for deriving new biomarkers based on multiplex stained histological samples proved the ability to detect features characteristic of malignant tumors based only on single target stained tissue microarrays. We propose further studies on this topic can help in formulating specific criteria for improvements in diagnosis of gliomas, allowing to avoid the necessity of conducting advanced histopathological analysis or complementing genetic testing of tumor samples.
Three-dimensional anatomy of the early EoceneWhitephippus(Teleostei: Lampriformes) documents parallel conquests of the pelagic environment by multiple teleost lineages
Authors: Davesne Donald , Andrews James V. , Beckett Hermione T. , Giles Sam , Friedman Matt
Published: June 2023

The early Eocene fossil assemblage of the London Clay (Southeastern England) is a key window to the early Paleogene diversification of teleost fishes in the open ocean. Despite their three-dimensional preservation that offers unique insight into skeletal anatomy, the London Clay fossils are still poorly described for the most part. †Whitephippus tamensisis a fossil teleost from this assemblage, known by several well-preserved specimens. Based on a complete description of the known material, including previously hidden structures (braincase, hyoid and branchial arches) revealed through 3D microtomography, we reinterpret †Whitephippusas an early member of the teleost group Lampriformes. More specifically, the anatomy of †Whitephippusindicates that it is likely a member of the so-called ‘pelagic clade’ including modern opahs and oarfishes. This redescription of †Whitephippusprovides the earliest definitive evidence of lampriforms conquering the pelagic environment, alongside numerous other teleost lineages.
Resource competition can explain simplicity in microbial community assembly
Authors: Lee Hyunseok , Bloxham Blox , Gore Jeff
Published: June 2023

Predicting the composition and diversity of communities is a central goal in ecology. While community assembly is considered hard to predict, laboratory microcosms often follow a simple assembly rule based on the outcome of pairwise competitions. This assembly rule predicts that a species that is excluded by another species in pairwise competition cannot survive in a multispecies community with that species. Despite the empirical success of this bottom-up prediction, its mechanistic origin has remained elusive. In this study, we elucidate how this simple pattern in community assembly can emerge from resource competition. Our geometric analysis of a consumer-resource model shows that trio community assembly is always predictable from pairwise outcomes when one species grows faster than another species on every resource. We also identify all possible trio assembly outcomes under three resources and find that only two outcomes violate the assembly rule. Simulations demonstrate that pairwise competitions accurately predict trio assembly with up to 100 resources and the assembly of larger communities containing up to twelve species. We then further demonstrate accurate quantitative prediction of community composition using harmonic mean of pairwise fractions. Finally, we show that cross-feeding between species does not decrease assembly rule prediction accuracy. Our findings highlight that simple community assembly can emerge even in ecosystems with complex underlying dynamics.

Significance

Multispecies microbial communities play an essential role in the health of ecosystems ranging from the ocean to the human gut. A major challenge in microbial ecology is to understand and predict which species can coexist within a community. While a simple empirical rule utilizing only pairwise outcomes successfully predicts multispecies laboratory communities, its mechanistic origin has remained unexplained. Here, we find that the observed simplicity can emerge from competition for resources. Using a generic consumer-resource model, we demonstrate that community assembly of highly complex ecosystems is nevertheless well predicted by pairwise competitions. Our results argue that community assembly can be surprisingly simple despite the potential complexity associated with competition and crossfeeding of many different resources by many different species.
Musashi-2 (MSI2) regulation of DNA damage response in lung cancer
Authors: Bychkov Igor , Deneka Alexander , Topchu Iuliia , Pangeni Rajendra P. , Lengner Christopher , Karanicolas John , Golemis Erica A. , Makhov Petr , Boumber Yanis
Published: June 2023

Lung cancer is one of the most common types of cancers worldwide. Non-small cell lung cancer (NSCLC), typically caused byKRASandTP53driver mutations, represents the majority of all new lung cancer diagnoses. Overexpression of the RNA-binding protein (RBP) Musashi-2 (MSI2) has been associated with NSCLC progression. To investigate the role of MSI2 in NSCLC development, we compared the tumorigenesis in mice with lung-specificKras-activating mutation andTrp53deletion, with and withoutMsi2deletion (KP versus KPM2 mice). KPM2 mice showed decreased lung tumorigenesis in comparison with KP mice what supports published data. In addition, using cell lines from KP and KPM2 tumors, and human NSCLC cell lines, we found that MSI2 directly bindsATM/AtmmRNA and regulates its translation. MSI2 depletion impaired DNA damage response (DDR) signaling and sensitized human and murine NSCLC cells to treatment with PARP inhibitorsin vitroandin vivo. Taken together, we conclude that MSI2 supports lung tumorigenesis, in part, by direct positive regulation of ATM protein expression and DDR. This adds the knowledge of MSI2 function in lung cancer development. Targeting MSI2 may be a promising strategy to treat lung cancer.

Significance

This study shows the novel role of Musashi-2 as regulator of ATM expression and DDR in lung cancer.
Polycomb sustains promoters in a deep OFF-state by limiting PIC formation to counteract transcription
Authors: Szczurek Aleksander T. , Dimitrova Emilia , Kelley Jessica R. , Klose Robert J.
Published: June 2023

The Polycomb system plays fundamental roles in regulating gene expression during mammalian development. However, how it controls transcription to enable gene repression has remained enigmatic. Here we employ rapid degron-based depletion coupled with live-cell transcription imaging and single-particle tracking to uncover how the Polycomb system controls transcription in single cells. We discover that the Polycomb system is not a constitutive block to transcription but instead sustains a long-lived deep promoter OFF-state which limits the frequency with which the promoter can enter into a transcribing state. We demonstrate that Polycomb sustains this deep promoter OFF-state by counteracting the binding of factors that enable early transcription pre-initiation complex formation and show that this is necessary for gene repression. Together these important discoveries provide a new rationale for how the Polycomb system controls transcription and suggests a universal mechanism that could enable the Polycomb system to constrain transcription across diverse cellular contexts.
Evaluating Minocycline as a Neuroprotective Agent in an Aged Female Rat MCAO Stroke Model
Authors: Gutierrez Liza , Tutino Vincent M. , Siddiqui Adnan H.
Published: June 2023

The middle cerebral artery occlusion (MCAO) suture model is widely accepted ischemic stroke model. However, researchers routinely use young male rats, ignoring that stroke risk is increased in older, post-menopausal women. To this end, we implemented (120-minute) transient- and permanent-occlusion MCAO models in female retired-breeder rats, examining the endpoint across 1-30 days to identify the optimal time course for the model. We found that in both groups the physical infarct (measured by triphenyltetrazolium chloride -TTC staining), which is present initially, was not detectable 30 days post-MCAO (even if some neurologic symptoms persist). Across shorter time-points (namely 24 hours and 7 days) we found that neurologic scores generally reach a plateau/maximum at ∽7 days, then infarct size gradually decreases over time for rats receiving a permanent MCAO. Across 3 transient occlusion times (60 minutes, 90 minutes, and 120 minutes), the longest gave the most robust result. Overall, the permeant and 120-minute transient MCAO evaluated at 7 days was optimal. Using these two models, we evaluated the neuroprotective qualities of the antibiotic, minocycline. We found that those in the treatment groups experienced a greater improvement in neurologic scores and a larger decrease in infarct size after daily treatment for seven days. This improvement was more prominent in the transiently occluded treatment group than in the permanently occluded group.
CD22L Conjugation to Insulin Attenuates Insulin-Specific B cell Activation
Authors: Apley Kyle D. , Griffith Amber S. , Downes Grant M. , Ross Patrick , Farrell Mark P. , Kendall Peggy , Berkland Cory J.
Published: June 2023

Pancreatic islet-reactive B lymphocytes promote Type 1 diabetes (T1D) by presenting antigen to islet-destructive T cells. Teplizumab, an anti-CD3 monoclonal, delays T1D onset in patients at risk, but additional therapies are needed to prevent disease entirely. Therefore, bifunctional molecules were designed to selectively inhibit T1D-promoting anti-insulin B cells by conjugating a ligand for the B cell inhibitory receptor CD22 (i.e., CD22L) to insulin, which permit these molecules to concomitantly bind to anti-insulin B cell receptors (BCRs) and CD22. Two prototypes were synthesized: 2:2 insulin-CD22L conjugate on a 4-arm PEG backbone, and 1:1 insulin-CD22L direct conjugate. Transgenic mice (125TgSD) expressing anti-insulin BCRs provided cells for in vitro testing. Cells were cultured with constructs for three days then assessed by flow cytometry. Duplicate wells with anti-CD40 simulated T cell help. Surprisingly, a 2-insulin 4-arm PEG control caused robust proliferation and activation-induced CD86 upregulation. Anti-CD40 further boosted these effects. This was unexpected, as soluble insulin alone has no effect, and may indicate that BCR-crosslinking occurs when antigens are tethered by the PEG backbone. Addition of CD22L via the 2:2 insulin-CD22L conjugate restored B cell properties to that of controls without additional beneficial effect. In contrast, the 1:1 insulin-CD22L direct conjugate significantly reduced anti-insulin B cell proliferation in the presence of anti-CD40. CD22L alone had no effect, and the constructs did not affect WT B cells. Thus, high valency constructs activate anti-insulin B cells, while low-valency antigen-CD22L conjugates co-ligate BCR and CD22, reducing B cell activation in response to simulated T cell help and reducing pathogenic B cell numbers without harming normal cells. Thus, the insulin-CD22L direct conjugate is a promising candidate for preclinical trials to prevent T1D without inducing immunodeficiency
VBCG: 20 validated bacterial core genes for phylogenomic analysis with high fidelity and resolution
Authors: Tian Renmao , Imanian Behzad
Published: June 2023

Background

Phylogenomic analysis has become an inseparable part of studies of bacterial diversity and evolution, and many different bacterial core genes have been collated and used for phylogenomic tree reconstruction. However, these genes have been selected based on their presence and single-copy ratio in all bacterial genomes, leaving out the gene’s ‘phylogenetic fidelity’ unexamined.

Results

From 30,522 complete genomes covering 11,262 species, we examined 148 bacterial core genes that have been previously used for phylogenomic analysis. In addition to the gene presence and single-copy rations, we evaluated the gene’s phylogenetic fidelity by comparing each gene’s phylogeny with its corresponding16S rRNAgene tree. Out of the 148 bacterial genes, 20 validated bacterial core genes (VBCG) were selected as the core gene set with the highest bacterial phylogenetic fidelity. Moreover, the smaller gene set resulted in a higher species presence in the tree than larger gene sets. UsingEscherichiaandSalmonellaas examples of prominent bacterial foodborne pathogens, we demonstrated that the 20 VBCG produced phylogenies with higher fidelity and resolution at species and strain levels while16S rRNAgene tree alone could not.

Conclusion

The 20 validated core gene set improves the fidelity and speed of phylogenomic analysis. Among other uses, this tool improves our ability to explore the evolution, typing and tracking of bacterial strains, such as human pathogens. We have developed a Python pipeline and a desktop graphic app (available on GitHub) for users to perform phylogenomic analysis with high fidelity and resolution.
Emergence of community behaviors in the gut microbiota upon drug treatment
Authors: Garcia-Santamarina Sarela , Kuhn Michael , Devendran Saravanan , Maier Lisa , Driessen Marja , Mateus André , Mastrorilli Eleonora , Brochado Ana Rita , Savitski Mikhail M. , Patil Kiran R. , Zimmermann Michael , Bork Peer , Typas Athanasios
Published: June 2023

Pharmaceuticals can directly inhibit the growth of gut bacteria, but the degree such interactions manifest in complex community settings is an open question. Here we compared the effects of 30 drugs on a 32-species synthetic community with their effects on each community member in isolation. While most individual drug–species interactions remained the same in the community context, communal behaviors emerged in 26% of all tested cases. Cross-protection, during which drug-sensitive species became protected in community, was 6-times more frequent than cross-sensitization, the converse phenomenon. Cross-protection decreased and cross-sensitization increased at higher drug concentrations, suggesting that the resilience of microbial communities can collapse when perturbations get stronger. By metabolically profiling drug-treated communities, we showed that both drug biotransformation and bioaccumulation contribute mechanistically to communal protection. As a proof-of-principle, we molecularly dissected a prominent case: species expressing specific nitroreductases degraded niclosamide, thereby protecting both themselves and sensitive community members.
Comparative chemical genomics inBabesiaspecies identifies the alkaline phosphatase phoD as a novel determinant of resistance
Authors: Keroack Caroline D. , Elsworth Brendan , Tennessen Jacob A. , Paul Aditya S. , Hua Renee , Ramirez-Ramirez Luz , Ye Sida , Moreira Cristina M. , Meyers Marvin J. , Zarringhalam Kourosh , Duraisingh Manoj T.
Published: June 2023

Babesiosisis an emerging zoonosis and widely distributed veterinary infection caused by 100+ species ofBabesiaparasites. The diversity ofBabesiaparasites, coupled with the lack of potent inhibitors necessitates the discovery of novel conserved druggable targets for the generation of broadly effective antibabesials. Here, we describe a comparative chemogenomics (CCG) pipeline for the identification of novel and conserved targets. CCG relies on parallelin vitroevolution of resistance in independent populations of evolutionarily-relatedBabesiaspp. (B. bovisandB. divergens). We identified a potent antibabesial inhibitor from the Malaria Box, MMV019266. We were able to select for resistance to this compound in two species ofBabesia,achieving 10-fold or greater resistance after ten weeks of intermittent selection. After sequencing of multiple independently derived lines in the two species, we identified mutations in a single conserved gene in both species: a membrane-bound metallodependent phosphatase (putatively named PhoD). In both species, the mutations were found in the phoD-like phosphatase domain, proximal to the predicted ligand binding site. Using reverse genetics, we validated that mutations in PhoD confer resistance to MMV019266. We have also demonstrated that PhoD localizes to the endomembrane system and partially with the apicoplast. Finally, conditional knockdown and constitutive overexpression of PhoD alter the sensitivity to MMV019266 in the parasite: overexpression of PhoD results in increased sensitivity to the compound, while knockdown increases resistance, suggesting PhoD is a resistance mechanism. Together, we have generated a robust pipeline for identification of resistance loci, and identified PhoD as a novel determinant of resistance inBabesiaspecies.

Highlights

Use of two species forin vitroevolution identifies a high confidence locus associated with resistance

Resistance mutation in phoD was validated using reverse genetics inB. divergens

Perturbation of phoD using function genetics results in changes in the level of resistance to MMV019266

Epitope tagging reveals localization to the ER/apicoplast, a conserved localization with a similar protein in diatoms

Together, phoD is a novel resistance determinant in multipleBabesia spp.
The impacts of active and self-supervised learning on efficient annotation of single-cell expression data
Authors: Geuenich Michael J. , Gong Dae-won , Campbell Kieran R.
Published: June 2023

A crucial step in the analysis of single-cell data is annotating cells to cell types and states. While a myriad of approaches have been proposed, manual labeling of cells to create training datasets remains tedious and time-consuming. In the field of machine learning, active and self-supervised learning methods have been proposed to improve the performance of a classifier while reducing both annotation time and label budget. However, the benefits of such strategies for single-cell annotation have yet to be evaluated in realistic settings. Here, we perform a comprehensive benchmarking of active and self-supervised labeling strategies across a range of single-cell technologies and cell type annotation algorithms. We quantify the benefits of active learning and self-supervised strategies in the presence of cell type imbalance and variable similarity. We introduce several heuristic procedures tailored to single-cell data — including a marker-aware adaptive reweighting cell selection procedure — that shows competitive performance with existing approaches. In addition, we demonstrate that having prior knowledge of cell type markers improves annotation accuracy. Finally, we summarize our findings into a set of recommendations for those implementing cell type annotation procedures or platforms. An R package implementing the heuristic approaches introduced in this work may be found athttps://github.com/camlab-bioml/leader.
Endocrine pancreas-specificGclcgene deletion causes a severe diabetes phenotype
Authors: Davidson Emily A. , Chen Ying , Singh Surendra , Orlicky David J. , Thompson Brian , Wang Yewei , Charkoftaki Georgia , Furnary Tristan A. , Cardone Rebecca L. , Kibbey Richard G. , Shearn Colin T. , Nebert Daniel W. , Thompson David C. , Vasiliou Vasilis
Published: June 2023

Reduced glutathione (GSH) is an abundant antioxidant that regulates intracellular redox homeostasis by scavenging reactive oxygen species (ROS). Glutamate-cysteine ligase catalytic (GCLC) subunit is the rate-limiting step in GSH biosynthesis. Using thePax6-Credriver mouse line, we deleted expression of theGclcgene in all pancreatic endocrine progenitor cells. Intriguingly,Gclcknockout (KO) mice, following weaning, exhibited an age-related, progressive diabetes phenotype, manifested as strikingly increased blood glucose and decreased plasma insulin levels. This severe diabetes trait is preceded by pathologic changes in islet of weanling mice.GclcKO weanlings showed progressive abnormalities in pancreatic morphology including: islet-specific cellular vacuolization, decreased islet-cell mass, and alterations in islet hormone expression. Islets from newly-weaned mice displayed impaired glucose-stimulated insulin secretion, decreased insulin hormone gene expression, oxidative stress, and increased markers of cellular senescence. Our results suggest that GSH biosynthesis is essential for normal development of the mouse pancreatic islet, and that protection from oxidative stress-induced cellular senescence might prevent abnormal islet-cell damage during embryogenesis.