bluuebunny/crossref_metadata_2025 huggingface dataset:
The Presence of a Cost–Volume Relationship in Robotic-assisted Thoracoscopic Lung Resections
Authors: Verma Arjun , Hadaya Joseph , Richardson Shannon , Vadlakonda Amulya , Ramezani Ramin , Revels Sha’Shonda , Benharash Peyman
Published: September 2022

Objective:

To characterize the relationship between institutional robotic-assisted pulmonary lobectomy volume and hospitalization costs.

Background:

The high cost of robotic-assisted thoracoscopic surgery (RATS) is among several drivers of hesitation among nonadopters. Studies examining the impact of institutional experience on costs of RATS lobectomy are lacking.

Methods:

Adults undergoing RATS lobectomy for primary lung cancers were identified from the 2016 to 2018 Nationwide Readmissions Database. A multivariable regression to model hospitalization costs was developed with the inclusion of hospital RATS lobectomy volume as restricted cubic splines. The volume corresponding to the inflection point of the spline was used to categorize hospitals as high- (HVH) or low-volume (LVH). We subsequently examined the association of HVH status with adverse events, length of stay, costs, and 30-day, nonelective readmissions.

Results:

An estimated 14,756 patients underwent RATS lobectomy during the study period, with median cost of $23,000. Upon adjustment for patient and operative characteristics, hospital RATS volume was inversely associated with costs. Although only 17.2% of centers were defined as HVH, 51.7% of patients were managed at these centers. Patients at HVH and LVH had similar age, sex, and distribution of comorbidities. Notably, patients at HVH had decreased risk-adjusted odds of adverse events (adjusted odds ratio: 0.62,P<0.001), as well as significantly reduced length of stay (−0.8 d,P<0.001) and costs (−$3900,P<0.001).

Conclusions:

Increasing hospital RATS lobectomy volume was associated with reduced hospitalization costs. Our findings suggest the presence of streamlined care pathways at high-volume centers, which influence costs of care.
The Presence of Myelinated Nerves and Schwann Cells in White Adipose Tissue: Proximity to Synaptic Vesicle Containing Nerve Terminals and Potential Role in BTBR ob/ob Demyelinating Diabetic Neuropathy
Authors: Willows Jake W. , Gunsch Gilian , Paradie Emma , Blaszkiewicz Magdalena , Tonniges Jeffrey R. , Pino Maria F. , Smith Steven R. , Sparks Lauren M. , Townsend Kristy L.
Published: September 2022

Peripheral neuropathy is a pathophysiological state of nerve degeneration and loss of tissue innervation. The most prominent cause of small fiber neuropathy is diabetes which can be demyelinating in nature, but this has not yet been explored in adipose tissue. Both demyelinating neuropathies and axonopathies implicate Schwann cells (SCs), the peripheral glial required for nerve myelination and regeneration after injury. Here, we perform a comprehensive assessment of SCs and myelination patterns of subcutaneous white adipose tissue (scWAT) nerves, including changes that occur with obesity and other imbalanced energy states in mice and humans. We found that mouse scWAT is densely innervated by both myelinated and unmyelinated sensory and sympathetic nerves. Accordingly, scWAT is home to both myelinating and non-myelinating SCs – the greater proportion of which are myelinating. Furthermore, SCs were found closely associated with synaptic vesicle-containing nerve terminals in scWAT. Obese BTBR ob/ob mice exhibit diabetic peripheral neuropathy in scWAT, and display concordant demyelination specific to small fibers, which was also associated with a decrease in the pan-SC marker Sox10 and compensatory increase in Krox20 gene expression. Together this suggests that adipose SCs may be involved in regulating the plasticity or the neuropathy of adipose tissue nerves.
A third SARS-CoV-2 mRNA vaccine dose in people receiving hemodialysis overcomes B cell defects but elicits a skewed CD4+T cell profile
Authors: Sannier Gérémy , Nicolas Alexandre , Dubé Mathieu , Marchitto Lorie , Nayrac Manon , Tastet Olivier , Tauzin Alexandra , Lima-Barbosa Raphaël , Laporte Mélanie , Cloutier Rose , Flores Alina Sreng , Boutin Marianne , Gong Shang Yu , Benlarbi Mehdi , Ding Shilei , Bourassa Catherine , Gendron-Lepage Gabrielle , Medjahed Halima , Goyette Guillaume , Brassard Nathalie , Ortega-Delgado Gloria-Gabrielle , Niessl Julia , Gokool Laurie , Morrisseau Chantal , Arlotto Pascale , Rios Norka , Tremblay Cécile , Martel-Laferrière Valérie , Prat Alexandre , Bélair Justin , Beaubien-Souligny William , Goupil Rémi , Nadeau-Fredette Annie-Claire , Lamarche Caroline , Finzi Andrés , Suri Rita S. , Kaufmann Daniel E.
Published: September 2022

Cellular immune defects associated with suboptimal responses to SARS-CoV-2 mRNA vaccination in people receiving hemodialysis (HD) are poorly understood. We longitudinally analyzed antibody, B cell, CD4+and CD8+T cell vaccine responses in 27 HD patients and 26 low-risk control individuals (CI). The first two doses elicit weaker B cell and CD8+T cell responses in HD than in CI, while CD4+T cell responses are quantitatively similar. In HD, a third dose robustly boosts B cell responses, leads to convergent CD8+T cell responses and enhances comparatively more Thelper (TH) immunity. Unsupervised clustering of single-cell features reveals phenotypic and functional shifts over time and between cohorts. The third dose attenuates some features of THcells in HD (TNFα/IL-2 skewing), while others (CCR6, CXCR6, PD-1 and HLA-DR overexpression) persist. Therefore, a third vaccine dose is critical to achieve robust multifaceted immunity in hemodialysis patients, although some distinct THcharacteristics endure.
Future COVID19 surges prediction based on SARS-CoV-2 mutations surveillance
Authors: Najar Fares Z. , Linde Evan , Murphy Chelsea , Borin Veniamin A. , Wang Huan , Haider Shozeb , Agarwal Pratul K.
Published: September 2022

COVID19 has aptly revealed that airborne viruses such as SARS-CoV-2 with the ability to rapidly mutate, combined with high rates of transmission and fatality can cause a deadly world-wide pandemic in a matter of weeks.1 Apart from vaccines and post-infection treatment options, strategies for preparedness will be vital in responding to the current and future pandemics. Therefore, there is wide interest in approaches that allow predictions of increase in infections (“surges”) before they occur. We describe here real time genomic surveillance particularly based on mutation analysis, of viral proteins as a methodology for a priori determination of surge in number of infection cases. The full results are available for SARS-CoV-2 at http://pandemics.okstate.edu/covid19/, and are updated daily as new virus sequences become available. This approach is generic and will also be applicable to other pathogens.
A neural framework for spontaneous development of orientation selectivity in the primary visual cortex
Authors: Davey Catherine E. , Lloyd Errol K.J. , Kuhlmann Levin , Burkitt Anthony N. , Vidyasagar Trichur R.
Published: September 2022

The mechanism or microcircuitry behind orientation selectivity in primary visual cortex (V1), and the means by which it develops without supervision or visual input, both remain unresolved questions. Work on the developmental question has assumed the prevalent spatial convergence model of orientation selectivity as the target mechanism. Encouraged by growing evidence challenging both the completeness of this model and its developmental viability, we investigated an alternative scheme. Accordingly, we demonstrate computationally how a scheme in which orientation selectivity originates from the orientation biases already in the retina and lateral geniculate nucelus (LGN) can answer both the mechanistic and developmental questions. In this scheme, the divergence of outputs from the retina allows retinal spontaneous activity to create correlations within the LGN. These correlations in turn allow a Hebbian plasticity mechanism to strengthen those LGN inputs to V1 which carry similar orientation biases and thus provide an orientation tuned excitatory input.
Cognition through internal models: Mirror neurons as one manifestation of a broader mechanism
Authors: Aflalo Tyson , Chivukula Srinivas , Zhang Carey , Rosario Emily R. , Pouratian Nader , Andersen Richard A.
Published: September 2022

Cognition relies on transforming sensory inputs into a more generalizable understanding. Mirror neurons are proposed to underlie this process, yet they fail to explain many key features of human thinking and learning. Here we hypothesize that mirror-like responses are one limited view into a more general framework by which internal models of the world are built and used. We recorded populations of single neurons in the human posterior parietal cortex as a participant felt or observed diverse tactile stimuli. We found that mirror-like responses were fragile and embedded within a richer population response that encoded generalizable and compositional features of the stimuli. We speculate that populations of neurons support versatile understanding, not through mirroring, but instead by encoding representational building blocks of cognition.

One-Sentence Summary

Similar neural responses during observed and experienced sensations are mediated by shared compositional building blocks, not mirror neurons.
GOAT: Deep learning-enhanced Generalized Organoid Annotation Tool
Authors: Bremer Jan P. , Baumdick Martin E. , Knorr Marius S. , Wegner Lucy H.M. , Wesche Jasmin , Jordan-Paiz Ana , Jung Johannes M. , Highton Andrew J. , Jäger Julia , Hinrichs Ole , Brias Sebastien , Niersch Jennifer , Müller Luisa , Schreurs Renée R.C.E. , Koyro Tobias , Löbl Sebastian , Mensching Leonore , Konczalla Leonie , Niehrs Annika , Vondran Florian W. R. , Schramm Christoph , Hölzemer Angelique , Oldhafer Karl , Königs Ingo , Kluge Stefan , Perez Daniel , Reinshagen Konrad , Pals Steven T. , Gagliani Nicola , Joosten Sander P. , Topf Maya , Altfeld Marcus , Bunders Madeleine J.
Published: September 2022

Organoids have emerged as a powerful technology to investigate human development, model diseases and for drug discovery. However, analysis tools to rapidly and reproducibly quantify organoid parameters from microscopy images are lacking. We developed a deep-learning based generalized organoid annotation tool (GOAT) using instance segmentation with pixel-level identification of organoids to quantify advanced organoid features. Using a multicentric dataset, including multiple organoid systems (e.g. liver, intestine, tumor, lung), we demonstrate generalization of the tool to annotate a diverse range of organoids generated in different laboratories and high performance in comparison to previously published methods. In sum, GOAT provides fast and unbiased quantification of organoid experiments to accelerate organoid research and facilitates novel high-throughput applications.
A parabrachial-to-amygdala circuit that determines hemispheric lateralization of somatosensory processing
Authors: Allen Heather N. , Chaudhry Sarah , Hong Veronica M. , Lewter Lakeisha A. , Sinha Ghanshyam P. , Carrasquillo Yarimar , Taylor Bradley K. , Kolber Benedict J.
Published: September 2022

Background

The central amygdala (CeA) is a bilateral hub of pain and emotional processing with well-established functional lateralization. We reported that optogenetic manipulation of neural activity in the left and right CeA has opposing effects on bladder pain.

Methods

To determine the influence of calcitonin gene-related peptide (CGRP) signaling from the parabrachial nucleus (PBN) on this diametrically opposed lateralization, we administered CGRP and evaluated the activity of CeA neurons in acute brain slices as well as the behavioral signs of bladder pain in the mouse.

Results

We found that CGRP increased firing in both the right and left CeA neurons. Furthermore, we found that CGRP administration in the right CeA increased behavioral signs of bladder pain and decreased bladder pain-like behavior when administered in the left CeA.

Conclusions

These studies reveal a parabrachial-to-amygdala circuit driven by opposing actions of CGRP that determines hemispheric lateralization of visceral pain.
Using ARCADE (ARChaeplastida Annotation DatabasE) to understand the evolution of genome size in land plants
Authors: Menezes Alison Pelri Albuquerque , Almeida Joao Victor dos Anjos , Del-Bem Luiz-Eduardo , Lobo Francisco Pereira
Published: September 2022

The abundance of plant genomic information caused by the decrease of sequencing costs contrasts with the lack of databases that integrate genome annotation, taxonomy and phenotypes to produce statistically sound, biologically meaningful knowledge. Here we present ARCADE (ARChaeplastida Annotation DatabasE), a database of 171 high-quality archaeplastidian non-redundant proteomes gathered from six primary genomic databases, together with proteome quality metrics and a growing number of associated metadata. As a case study to demonstrate the usefulness of ARCADE, we used it to investigate the expansion and contraction of protein domains associated with the evolution of genome size (hereafter GS). GS varies greatly among land plants and the synthesis of large genomes can be costly to cells. Although GS has been studied extensively for decades, the molecular mechanisms involved in the adaptations of plants to the increase in GS are still poorly understood. We used the annotation and phylogenetic information available in ARCADE, together with estimated GS values available for 83 land plant species, to search for associations between the abundance of protein domain families in these species and GS variation through phylogenetic-aware methods. Additionally, we estimated the GS for the ancestral nodes of the extant land plant species. GS seems to be decreasing along the course of evolution, except for a few branches that might have undergone independent GS increases. We found 7 Pfam correlated with the variation in GS in land plants, mainly related to nucleotide metabolism, DNA repair and genome organization. We found larger genomes to have a greater frequency of the Histone 2A superfamily, responsible for diverse functions, including the nucleosome formation and silencing of transposable elements. These molecular functions we found correlated to GS variation suggests they may be associated with preserving genome stability in larger genomes, and might indicate the evolution of mechanisms to cope with the variation in GS in land plants. ARCADE is available at https://osf.io/2fkvh/.
MultiOMICs landscape of SARS-CoV-2-induced host responses in human lung epithelial cells
Authors: Pinto Sneha M. , Subbannayya Yashwanth , Kim Hera , Hagen Lars , Górna Maria W. , Nieminen Anni I. , Bjørås Magnar , Espevik Terje , Kainov Denis , Kandasamy Richard K.
Published: September 2022

Despite the availability of vaccines and approved therapeutics, the COVID-19 pandemic continues to rise owing to the emergence of newer variants. Several multi-omics studies have made available extensive evidence on host-pathogen interactions and potential therapeutic targets. Nonetheless, an increased understanding of host signaling networks regulated by post-translational modifications and their ensuing effect on the biochemical and cellular dynamics is critical to expanding the current knowledge on the host response to SARS-CoV-2 infections. Here, employing unbiased global transcriptomics, proteomics, acetylomics, phosphoproteomics, and exometabolome analysis of a lung-derived human cell line, we show that SARS-CoV-2 Norway/Trondheim-S15 strain induces time-dependent alterations in the induction of type I IFN response, activation of DNA damage response, dysregulated Hippo signaling, among others. We provide evidence for the interplay of phosphorylation and acetylation dynamics on host proteins and its effect on the altered release of metabolites, especially organic acids and ketone bodies. Together, our findings serve as a resource of potential targets that can aid in designing novel host-directed therapeutic strategies.
DeepRetroMoCo: Deep neural network-based Retrospective Motion Correction Algorithm for Spinal Cord functional MRI
Authors: Mobarak-Abadi Mahdi , Mahmoudi-Aznave Ahmad , Dehghani Hamed , Zarei Mojtaba , Vahdat Shahabeddin , Doyon Julien , Khatibi Ali
Published: September 2022

There are unique challenges in the preprocessing of spinal cord fMRI data, particularly voluntary or involuntary movement artifacts during image acquisition. Despite advances in data processing techniques for movement detection and correction, there are challenges in extrapolating motion correction algorithm developments in the brain cortex to the brainstem and spinal cord. We trained a Deep Learning-based convolutional neural network (CNN) via an unsupervised learning algorithm, called DeepRetroMoCo, to detect and correct motions in axial T2*-weighted spinal cord data. Spinal cord fMRI data from 27 participants were used for training of the network (135 runs for training and 81 runs for testing). We used average temporal signal-to-noise-ratio (tSNR) and Delta Variation Signal (DVARS) of raw and motion-corrected images to compare the outcome of DeepRetroMoco with sct_fmri_moco implemented in the spinal cord toolbox. The average tSNR in the cervical cord was significantly higher when DeepRetroMoco was used for motion correction compared to sct_fmri_moco method. Average DVARS was lower in images corrected by DeepRetroMoco than those corrected by sct_fmri_moco. The average processing time for DeepRetroMoco was also significantly shorter than sct_fmri_moco. Our results suggest that DeepRetroMoCo improves motion correction procedures in fMRI data acquired from the cervical spinal cord.
Behavior shapes retinal motion statistics during natural locomotion
Authors: Muller Karl , Matthis Jonathan S. , Bonnen Kathryn , Cormack Lawrence K. , Huk Alexander C. , Hayhoe Mary
Published: September 2022

Abstract

Walking through an environment generates retinal motion, which humans rely on to perform a variety of visual tasks. Retinal motion patterns are determined by an interconnected set of factors, including gaze location, gaze stabilization, the structure of the environment, and the walker’s goals. The characteristics of these motion signals have important consequences for neural organization and behavior. However, to date, there are no empirical in situ measurements of how combined eye and body movements interact with real 3D environments to shape the statistics of retinal motion signals. Here, we collect measurements of the eyes, the body, and the 3D environment during locomotion. We describe properties of the resulting retinal motion patterns. We explain how these patterns are shaped by gaze location in the world, as well as by behavior, and how they may provide a template for the way motion sensitivity and receptive field properties vary across the visual field.
An extracellular vesicle targeting ligand that binds to Arc proteins and facilitates Arc transport in vivo
Authors: Lee Peter H. , Anaya Michael , Ladinsky Mark S. , Reitsma Justin M. , Zinn Kai
Published: September 2022

Communication between distant cells can be mediated by extracellular vesicles (EVs) that deliver proteins and RNAs to recipient cells. Little is known about how EVs are targeted to specific cell types. Here we identify the Drosophila cell-surface protein Stranded at second (Sas) as a targeting ligand for EVs. Full-length Sas is present in EV preparations from transfected Drosophila Schneider 2 (S2 cells). Sas is a binding partner for the Ptp10D receptor tyrosine phosphatase, and Sas-bearing EVs preferentially target to cells expressing Ptp10D. We used co-immunoprecipitation and peptide binding to show that the cytoplasmic domain (ICD) of Sas binds to dArc1. dArc1 and mammalian Arc are related to retrotransposon Gag proteins. They form virus-like capsids which encapsulate Arc and other mRNAs and are transported between cells via EVs. The Sas ICD contains a motif required for dArc1 binding that is shared by the mammalian and Drosophila amyloid precursor protein (APP) orthologs, and the Sas and APP ICDs also bind to mammalian Arc. Sas facilitates delivery of dArc1 capsids bearing dArc1 mRNA into distant Ptp10D-expressing recipient cells in vivo.
Fibroblasts generate topographical cues that steer cancer cell migration
Authors: Baschieri Francesco , Illand Abigail , Barbazan Jorge , Zajac Olivier , Henon Clémence , Loew Damarys , Dingli Florent , Vignjevic Danijela Matic , Lévêque-Fort Sandrine , Montagnac Guillaume
Published: September 2022

Fibroblasts play a fundamental role in tumor development. Among other functions, they regulate cancer cells migration through rearranging the extracellular matrix, secreting soluble factors and establishing direct physical contacts with cancer cells. Here, we report that migrating fibroblasts deposit on the substrate a network of tubular structures that serves as guidance cue for cancer cell migration. Such membranous tubular network, hereafter called tracks, is stably anchored to the substrate in a β5 integrin-dependent manner. We found that cancer cells specifically adhere to tracks by using clathrin-coated structures that pinch and engulf tracks. Tracks represent thus a spatial memory of fibroblast migration paths that is read and erased by cancer cells directionally migrating along them. We propose that fibroblast tracks represent a topography-based intercellular communication system capable of steering cancer cells migration.

TEASER

The migration path of fibroblasts is marked by tubules that act as railways to direct following cancer cell migration.
Early life adversity and adult social relationships have independent effects on survival in a wild animal model of aging
Authors: Lange Elizabeth C. , Zeng Shuxi , Campos Fernando A. , Li Fan , Tung Jenny , Archie Elizabeth A. , Alberts Susan C.
Published: September 2022

Does social isolation in adulthood predict survival because socially isolated individuals are already unhealthy due to adversity earlier in life (health selection)? Or do adult social environments directly cause poor health and increased mortality risk (“social causation”)? These alternative hypotheses are difficult to disentangle in humans because prospective data on survival and the environment for both early life and adulthood are rarely available. Using data from the baboon population of Amboseli, Kenya, a model for human behavior and aging, we show that early adversity and adult social isolation contribute independently to reduced adult survival, in support of both health selection and social causation. Further, strong social bonds and high social status can buffer some negative effects of early adversity on survival. These results support a growing change in perspective, away from “either-or” hypotheses and towards a multi-causal perspective that points to multiple opportunities to mitigate the effects of social adversity.

Teaser

Early life environments and adult social bonds have strong, but largely independent effects on survival in wild baboons.
Innovations in double digest restriction-site associated DNA sequencing (ddRAD-Seq) method for more efficient SNP identification
Authors: Magbanua Zenaida V. , Hsu Chuan-Yu , Pechanova Olga , Arick Mark , Grover Corrinne E. , Peterson Daniel G.
Published: September 2022

We present an improved ddRAD-Seq protocol for identifying single nucleotide polymorphisms (SNPs). It utilizes optimally sized restriction enzyme digestion fragments, quick acting ligases that are neutral with the restriction enzyme buffer eliminating buffer exchange steps, and adapters designed to be compatible with Illumina index primers. Library amplification and barcoding are completed in one PCR step, and magnetic beads are used to purify the genomic fragments from the ligation and library generation steps. Our protocol increases the efficiency and decreases the time to complete a ddRAD-Seq experiment. To demonstrate its utility, we compared SNPs from our protocol with those from whole genome resequencing data from Gossypium herbaceum and Gossypium arboreum. Principal component analysis demonstrated that the variability of the combined data was explained by the genotype (PC1) and methodology applied (PC2). Phylogenetic analysis showed that the SNPs from our method clustered with SNPs from the resequencing data of the corresponding genotype. Sequence alignments illustrated that for homozygous loci, more than 90% of the SNPs from the resequencing data were discovered by our method. Our analyses suggest that our ddRAD-Seq method is reliable in identifying SNPs suitable for phylogenetic and association genetic studies while reducing cost and time over known methods.
Extremely sparse models of linkage disequilibrium in ancestrally diverse association studies
Authors: Nowbandegani Pouria Salehi , Wohns Anthony Wilder , Ballard Jenna L. , Lander Eric S. , Bloemendal Alex , Neale Benjamin M. , O’Connor Luke J.
Published: September 2022

Linkage disequilibrium (LD) is the correlation among nearby genetic variants. In genetic association studies, LD is often modeled using massive local correlation matrices, but this approach is slow, especially in ancestrally diverse studies. Here, we introduce LD graphical models (LDGMs), which are an extremely sparse and efficient representation of LD. LDGMs are derived from genome-wide genealogies; statistical relationships among alleles in the LDGM correspond to genealogical relationships among haplotypes. We publish LDGMs and ancestry specific LDGM precision matrices for 18 million common SNPs (MAF>1%) in five ancestry groups, validate their accuracy, and demonstrate order-of-magnitude improvements in runtime for commonly used LD matrix computations. We implement an extremely fast multi-ancestry polygenic prediction method, BLUPx-ldgm, which performs better than a similar method based on the reference LD correlation matrix. LDGMs will enable sophisticated methods that scale to ancestrally genetic association data across millions of variants and individuals.
The native mussel Mytilus chilensis genome reveals adaptative molecular signatures facing the marine environment
Authors: Gallardo-Escárate Cristian , Valenzuela-Muñoz Valentina , Nuñez-Acuña Gustavo , Valenzuela-Miranda Diego , Tapia Fabian , Yévenes Marco , Gajardo Gonzalo , Toro Jorge E. , Oyarzún Pablo A. , Arriagada Gloria , Novoa Beatriz , Figueras Antonio , Roberts Steven , Gerdol Marco
Published: September 2022

The blue mussel Mytilus chilensis is a key socioeconomic species inhabiting the southern coast of Chile. This endemic marine mussel supports a booming aquaculture industry, which entirely relies on artificially collected seeds from natural beds that are translocated to a diverse physical-chemical ocean conditions’ for farming. Furthermore, mussel production is threatened by a broad range of microorganisms, pollution, and environmental stressors that eventually impact its survival and growth. Herein, understanding the genomic basis of the local adaption is pivotal to developing sustainable shellfish aquaculture. We present a high-quality reference genome of M. chilensis, which is the first chromosome-level genome for a Mytilidae member in South America. The assembled genome size was 1.93 Gb, with a contig N50 of 134 Mb. Through Hi-C proximity ligation, 11,868 contigs were clustered, ordered, and assembled into 14 chromosomes in congruence with the karyological evidence. The M. chilensis genome comprises 34,530 genes and 4,795 non-coding RNAs. A total of 57% of the genome contains repetitive sequences with predominancy of LTR-retrotransposons and unknown elements. Comparative genome analysis was conducted among M. chilensis and M. coruscus, revealing genic rearrangements distributed into the whole genome. Notably, Steamer-like elements associated with horizontal transmissible cancer were explored in reference genomes, suggesting putative phylogenetic relationships at the chromosome level in Bivalvia. Genome expression analysis was also conducted, showing putative genomic differences between two ecologically different mussel populations. Collectively, the evidence suggests that local genome adaptation can be analyzed to develop sustainable mussel production. The genome of M. chilensis provides pivotal molecular knowledge for the Mytilus complex evolution and will help to understand how climate change can impact mussel biology.
Respiratory strategy at birth initiates distinct lung injury phenotypes in the preterm lamb lung
Authors: Pereira-Fantini Prue M. , Ferguson Kristin , McCall Karen , Oakley Regina , Perkins Elizabeth , Byars Sean , Williamson Nicholas , Nie Shuai , Tingay David G
Published: September 2022

Bronchopulmonary disease is the chronic manifestation of the acute injury that may accompany ventilation following preterm birth. A lack of clear trial evidence often hampers clinical decision-making during support of the preterm lung at birth. Protein biomarkers have been used to define acute lung injury phenotypes and improve patient selection for specific interventions in adult respiratory distress syndrome. Here we present a mass spectrometry-based approach to profile the protein phenotype associated with three different aeration strategies known to cause different pathophysiological responses when applied at birth to preterm lambs. We were able to identify pathway enrichments specific to both ventilation strategy and lung regions based upon gravity-dependency. Ventilation strategy-specific phenotypes were further delineated by applying partial least square modelling to identify associations between specific proteins and clinical, physiological and morphological outcomes. This work highlights the specificity of lung injury responses to routinely applied birth interventions such as different respiratory support approaches and identified the molecular events associated with each. Furthermore, we demonstrate the capacity to subdivide preterm infants by the direct aetiology and response to lung injury; the first step towards true precision medicine in neonatology.
GRAS-1 is a conserved novel regulator of early meiotic chromosome dynamics inC. elegans
Authors: Martinez-Garcia Marina , Naharro Pedro Robles , Skinner Marnie W. , Baran Kerstin A. , Nadarajan Saravanapriah , Shin Nara , Silva-García Carlos G. , Saito Takamune T. , Beese-Sims Sara , Castaner Ana , Pacheco Sarai , Martinez-Perez Enrique , Jordan Philip W. , Colaiácovo Monica P.
Published: September 2022

Chromosome movements and licensing of synapsis must be tightly regulated during early meiosis to ensure accurate chromosome segregation and avoid aneuploidy, although how these steps are coordinated is not fully understood. Here we show that GRAS-1, the worm homolog of mammalian GRASP/Tamalin and CYTIP, coordinates early meiotic events with cytoskeletal forces outside the nucleus. GRAS-1 localizes close to the nuclear envelope (NE) in early prophase I and interacts with NE and cytoskeleton proteins. Delayed homologous chromosome pairing, synaptonemal complex (SC) assembly, and DNA double-strand break repair progression are partially rescued by the expression of human CYTIP ingras-1mutants, supporting functional conservation. However,Tamalin, Cytipdouble knockout mice do not exhibit obvious fertility or meiotic defects, suggesting evolutionary differences between mammals.gras-1mutants show accelerated chromosome movement during early prophase I, implicating GRAS-1 in regulating chromosome dynamics. GRAS-1-mediated regulation of chromosome movement is DHC-1-dependent, placing it acting within the LINC-controlled pathway, and depends on GRAS-1 phosphorylation at a C-terminal S/T cluster. We propose that GRAS-1 serves as a scaffold for a multi-protein complex coordinating the early steps of homology search and licensing of SC assembly by regulating the pace of chromosome movement in early prophase I.
Contact Stiffness Provides a Unified Frame of Reference for Understanding the Effects of Extracellular Matrix Mechanics on Cell Behaviors
Authors: Zhao Peng , Zhang Zhaoyi , Zheng Yang , Gao Yina , Cao Jialing , Jiang Mingwei , Jiang Yuxuan , Gao Li , Du Jing , Cao Yanping
Published: September 2022

In interactions between cells and extracellular matrices (ECMs), contact mechanics theory indicates that local ECM deformation depends on both local and non-local forces imposed by cells. In the present study, we investigated the use of a comprehensive variable, contact stiffness (CS), to interpret cell-ECM interactions. CS defines the relationship between the local ECM deformation and the total force from a cell, integrating the effects of individual variables including ECM stiffness, ECM thickness, and cell adhesion area. Through assessments of ECM mechanosensing by human mesenchymal stem cells (hMSCs) under varied CS conditions, we showed that CS scaled well with both yes-associated protein (YAP) activity and the extent of stem cell differentiation. To reveal the cross-scale mechanism underlying mechanosensing, we propose a CS-based motor clutch model, which suggests that various mechanical stimuli affect cells by altering the CS, thus altering the reaction force from the ECM. Using the proposed model, we revealed the contributions of cell architecture evolution to stem cell differentiation and predicted the influence of a non-adjacent ECM layer on cellular mechanosensing. These results demonstrate that the use of CS provides a quantitative predictive framework that allows researchers to address longstanding questions about the effects of ECM mechanics on cell behaviors.
CIDP: A multi-functional platform for designing CRISPR sgRNAs
Authors: Xu Dong , Zhang Jin , Zhao Xianjia , Jiang Heling , Ma Xiongfeng , Pan Weihua
Published: September 2022

Most of sgRNA-design tools can be run under the precondition of the choice of closely-related species. However, it is hard to select an ideal closely-related species, as more and more different species were studied, and this situation was particular seriously in plant studies. Here, we introduced a new software, CRISPR Integrated Design Platform (CIDP), to solve the problem by allowing users to input genomic sequences for designing sgRNAs. The main function of CIDP was to design sgRNAs after building the sgRNA database using the input genomic sequences. Furthermore, in order to minimize the off-target effects, CIDP will search sgRNAs that appear only once across the whole genome on the target sequences. Meanwhile, CIDP set relevant functions to identify shared sgRNAs of a group of genes. Moreover, we also set primer design and sequence extraction functions in CIDP to help users design sgRNAs efficiently.
A time and single-cell resolved model of hematopoiesis
Authors: Kucinski Iwo , Campos Joana , Barile Melania , Severi Francesco , Bohin Natacha , Moreira Pedro N , Allen Lewis , Lawson Hannah , Haltalli Myriam L R , Kinston Sarah J , O’Carroll Dónal , Kranc Kamil R , Göttgens Berthold
Published: September 2022

The paradigmatic tree model of hematopoiesis is increasingly recognized to be limited as it is based on heterogeneous populations and largely inferred from non-homeostatic cell fate assays. Here, we combine persistent labeling with time-series single-cell RNA-Seq to build the first real- time, quantitative model of in vivo tissue dynamics for any mammalian organ. We couple cascading single-cell expression patterns with dynamic changes in differentiation and growth speeds. The resulting explicit linkage between single cell molecular states and cellular behavior reveals widely varying self-renewal and differentiation properties across distinct lineages. Transplanted stem cells show strong acceleration of neutrophil differentiation, illustrating how the new model can quantify the impact of perturbations. Our reconstruction of dynamic behavior from snapshot measurements is akin to how a Kinetoscope allows sequential images to merge into a movie. We posit that this approach is broadly applicable to empower single cell genomics to reveal important tissue scale dynamics information.

Highlights

Cell flux analysis reveals high-resolution kinetics of native bone marrow hematopoiesis

Quantitative model simulates cell behavior in real-time and connects it with gene expression patterns

Distinct lineage-affiliated progenitors have unique self-renewal and differentiation properties

Transplanted HSCs display accelerated stage- and lineage-specific differentiation
AYUKA: A toolkit for fast viral genotyping using whole genome sequencing
Authors: Guerra-Assunção José Afonso , Goldstein Richard , Breuer Judith
Published: September 2022

Technological advances enabled the frequent use of whole genome sequencing in the clinical microbiology laboratory. While generating data is now easier than ever, the computational resources and expertise required for analysis are still a challenge for clinical applications. Since it is not always possible to collect clinical specimens at the peak viral load, sequencing results are also not always amenable for analysis with bioinformatics pipelines that always require high quality data.

Here we present a fast and reliable method, we named AYUKA, for analysis of viral sequencing data that does not require data pre-processing and provides quality control metrics including estimates for sequencing depth and genome coverage, as well as identifying the viral genotypes in a sample and distinguishing mixed infection from recombinants.

This method can be applied to any virus where a classification by genotype is employed and determining it is relevant. We generated a validation dataset composed of cultured and sequenced reference adenoviruses from distinct species, that we compared with the gold standard clinical processing pipeline currently implemented to demonstrate reliability. The validation shows better sensitivity than mapping and perfect specificity in detecting the correct genotypes and in a wide range of adenovirus species. Run time was consistently under one minute per sample on a standard laptop, allowing the analysis of more than 100 samples per hour.

This open-source method is available at https://github.com/afonsoguerra/AYUKA and precomputed databases are available at https://zenodo.org/record/6521576 allowing analysis of raw data straight from the sequencer within minutes on a standard computer, with minimum setup or expertise required to perform the analysis.

The information contained within the AYUKA report can be of use for both the clinical team that collected the sample, but also for guiding the bioinformatics analysis team in the in-depth downstream analyses and genetic epidemiology investigations.
Red light-emitting short Mango-based system enables tracking a mycobacterial small noncoding RNA in infected macrophages
Authors: Bychenko Oksana S. , Khrulev Alexei A. , Svetlova Julia I. , Tsvetkov Vladimir B. , Kamzeeva Polina N. , Skvortsova Yulia V. , Tupertsev Boris S. , Ivanov Igor A. , Aseev Leonid V. , Khodarovich Yuriy M. , Belyaev Evgeny S. , Kozlovskaya Liubov I. , Zatsepin Timofei S. , Azhikina Tatyana L. , Varizhuk Anna M. , Aralov Andrey V.
Published: September 2022

Progress in the studies of RNA metabolism and function relies largely on molecular imaging systems, including those comprising a fluorogenic dye and an aptamer-based fluorescence-activating tag. G4 aptamers of Mango family, typically combined with a duplex/hairpin scaffold, activate fluorescence of a green-emitting dye TO1-biotin and hold great promise for intracellular RNA tracking. Here, we report a new Mango-based imaging platform. Its key advantages are tunability of spectral properties and applicability for visualization of small RNA molecules that require minimal tag size. The former advantage is due to an expanded (green-to-red-emitting) palette of TO1-inspired fluorogenic dyes, and the latter is ensured by the truncated duplex scaffold. To illustrate applicability of the improved platform, we tagged Mycobacterium tuberculosis sncRNA with the shortened aptamer-scaffold tag and visualized it in bacteria and bacteria-infected macrophages using the new red light-emitting Mango-activated dye.
Topical GZ21T inhibits the growth of actinic keratoses in a UVB induced model of skin carcinogenesis
Authors: Bordeaux Zachary A. , Choi Justin , Braun Gabriella , Davis Cole , Marani Melika , Lee Kevin , Samuel Christeen , Adams Jackson , Windom Reed , Pollizzi Anthony , Kambala Anusha , Cornman Hannah , Reddy Sriya V. , Lu Weiying , Oladipo Olusola O. , Alphonse Martin P. , West Cameron E. , Kwatra Shawn G. , Kwatra Madan M.
Published: September 2022

Actinic keratoses (AKs) are premalignant intraepidermal neoplasms that occur as a result of cumulative sun damage. AKs commonly relapse, and up to 16% undergo malignant transformation into cutaneous squamous cell carcinoma (cSCC). There is a need for novel therapies that reduce the quantity and surface area of AKs as well as prevent malignant transformation to cSCCs. We recently showed that GZ17-6.02, an anti-cancer agent composed of curcumin, haramine, and isovanillin, inhibited the growth of H297.T cells. The present study evaluated the efficacy of a novel topical formulation of GZ17-6.02, known as GZ21T, in a murine model of AK generated by exposing SKH1 mice to ultraviolet irradiation. Treatment of mice with topical GZ21T inhibited the growth of AKs by decreasing both lesion count (p=.028) and surface area occupied by tumor (p=.026). GZ21T also suppressed the progression of AKs to cSCC by decreasing the count (p=.047) and surface area (p=.049) of lesions more likely to represent cSCC. RNA sequencing and proteomic analyses revealed that GZ21T suppressed several pathways, including MAPK (p=.026), Pi3K-Akt (p=.028), HIF-1α (p=.030), Wnt (p=.031), insulin (p=.011), and ErbB (p=.006) signaling. GZ21T also upregulated the autophagy-promoting protein AMPK, while suppressing proteins such as PD-L1, glutaminase, pAkt1 S473, and eEF2K.

GRAPHICAL ABSTRACT
Immunogenicity and Protective Efficacy of a SARS-CoV-2 mRNA Vaccine Encoding Secreted Non-Stabilized Spike Protein in Mice
Authors: Prompetchara Eakachai , Ketloy Chutitorn , Alameh Mohamad-Gabriel , Tarakhet Kittipan , Kaewpang Papatsara , Yostrerat Nongnaphat , Pitakpolrat Patrawadee , Buranapraditkun Supranee , Manopwisedcharoen Suwimon , Thitithanyanont Arunee , Jongkaewwattana Anan , Hunsawong Taweewan , Im-Erbsin Rawiwan , Reed Matthew , Wijagkanalan Wassana , Patarakul Kanitha , Palaga Tanapat , Lam Kieu , Heyes James , Weissman Drew , Ruxrungtham Kiat
Published: September 2022

Establishment of an mRNA vaccine platform in low- and middle-income countries (LMICs) is important to enhance vaccine accessibility and ensure future pandemic preparedness. Here, we describe the preclinical studies of a SARS-CoV-2 mRNA encoding prefusion-unstabilized ectodomain spike protein encapsulated in lipid nanoparticles (LNP) “ChulaCov19”. In BALB/c mice, ChulaCov19 at 0.2, 1, 10, and 30 μg given 2 doses, 21 days apart, elicited robust neutralizing antibody (NAb) and T cells responses in a dose-dependent relationship. The geometric mean titer (GMT) of micro-virus neutralizing (micro-VNT) antibody against wild-type virus was 1,280, 11,762, 54,047, and 62,084, respectively. Higher doses induced better cross-neutralizing antibody against Delta and Omicron variants. This elicited specific immunogenicity was significantly higher than those induced by homologous prime-boost with inactivated (CoronaVac) or viral vector (AZD1222) vaccine. In heterologous prime-boost study, mice primed with either CoronaVac or AZD1222 vaccine and boosted with 5 μg ChulaCov19 generated NAb 7-fold higher against wild-type virus (WT) and was also significantly higher against Omicron (BA.1 and BA.4/5) than homologous CoronaVac or AZD1222 vaccination. AZD1222-prime/mRNA-boost had mean spike-specific IFNγ positive T cells of 3,725 SFC/106 splenocytes, which was significantly higher than all groups except homologous ChulaCov19. Challenge study in human-ACE-2-expressing transgenic mice showed that ChulaCov19 at 1 μg or 10 μg protected mice from COVID-19 symptoms, prevented SARS-CoV-2 viremia, significantly reduced tissue viral load in nasal turbinate, brain, and lung tissues 99.9-100%, and without anamnestic of Ab response which indicated its protective efficacy. ChulaCov19 is therefore a promising mRNA vaccine candidate either as a primary or a boost vaccination and has entered clinical development.
Phosphoproteomics data-driven signalling network inference: does it work?
Authors: Sriraja Lourdes O. , Werhli Adriano , Petsalaki Evangelia
Published: September 2022

The advent in high throughput global phosphoproteome profiling has led to wide phosphosite coverage and therefore the need to predict kinase substrate associations from these datasets. However, for multiple substrates, the regulatory kinase is unknown due to biased and incomplete interactome databases. In this study we compare the performance of six pairwise measures to predict kinase substrate associations using a purely data driven approach on publicly available dynamic time resolved and perturbation phosphoproteome data using mass spectrometry profiling. First, we validated the performance of these measures using as a reference both a literature-based phosphosite-specific protein interaction network and a predicted kinase substrate (KS) interactions set. The overall performance in predicting kinase-substrate associations using pairwise measures across both database-derived and predicted interactomes was poor. To expand into the wider interactome space, the performance of these measures was evaluated against a network compiled from pairs of substrates regulated by the same kinase (substrate-substrate associations). Similar to the kinase substrate predictions, a purely statistical approach to predict substrate-substrate associations was also poor. However, the addition of a sequence similarity filter for substrate-substrate associations led to a boost in performance and to the inference of statistically significant substrate-substrate associations. Our findings imply that the use of a filter to reduce the search space, such as a sequence similarity filter, can be used prior to the application of network inference methods to reduce noise and boost the signal. We also find that the current gold standard for reference sets is not adequate for evaluation as it is limited and context-agnostic. Therefore, there is a need for additional evaluation methods that have increased coverage and take into consideration the context-specific nature of kinase substrate associations.
The Intestinal Microbiome, Dietary Habits, and Physical and Psychological Resilience in Postpartum Women
Authors: Matsunaga Michiko , Takeuchi Mariko , Watanabe Satoshi , Takeda Aya K. , Kikusui Takefumi , Mogi Kazutaka , Nagasawa Miho , Hagihara Keisuke , Myowa Masako
Published: September 2022

The population of postpartum women suffering from mental illness is increasing steadily, particularly under conditions of the COVID-19 pandemic. Identifying factors that contribute to resilience in postpartum women is urgently needed to decrease risks of poor physical and psychological functioning. Studies have linked variations in the intestinal microbiota to depression in clinical samples, but the impacts in postpartum women in a Japanese population are unknown. We conducted two studies to examine the links between intestinal microbiota, physical condition, and psychological state in nonclinical, postpartum Japanese women. Our results show that decreasing Lachnospira and alpha diversity of microbiome is related to high mental health risk (i.e., parenting stress and/or depression). Psychological resilience and physical conditions were associated with relative abundances of genera Blautia, Clostridium, Eggerthella. This study contributes to further understanding of the gut-brain axis mechanisms and supports proposals for interventions to enhance resilience in postpartum women.