bluuebunny/crossref_metadata_2025 huggingface dataset:
Bilateral Testicular Mass Presenting as a Rare Manifestation of Extramedullary Plasmacytoma on 18F-FDG PET/CT
Authors: Civan Caner , Apaydin Arikan Evsen , Has Simsek Duygu , Sanli Oner , Kuyumcu Serkan
Published: January 2022

We present the case of a 48-year-old man diagnosed with metastatic Ewing sarcoma who was referred for 18F-FDG PET/CT for treatment response evaluation following chemoradiotherapy. The patient also had complaints of new-onset testicular swelling at the time of imaging. Although the metastatic bone disease showed a complete metabolic response to treatment, 18F-FDG PET/CT demonstrated significantly increased metabolic activity in bilateral testicular mass. Consequently, the patient underwent bilateral orchiectomy, and histopathologic examination revealed bilateral testicular plasmacytoma, a rare manifestation of extramedullary plasmacytoma.
68Ga-DOTATATE Uptake in an Intraosseous Hemangioma, as a Potential Cause of False-Positive PET/CT Finding, Simulating Tumoral Involvement
Authors: Saidi Bahare , Fallahi Babak , Manafi-Farid Reyhaneh , Fard-Esfahani Armaghan , Eftekhari Mohammad
Published: January 2022

We present the case of a 32-year-old man with a history of hypophosphatemia and multiple bone fractures, being evaluated at our center for a potential mesenchymal tumor. 68Ga-DOTATATE PET/CT revealed a highly 68Ga-DOTATATE–avid lesion in the ethmoidal sinus extending to the nasal cavity. Following resection, histologic examination of the specimen confirmed the diagnosis of “intraosseous hemangioma,” a potential cause of false-positive finding of 68Ga-DOTATATE PET/CT imaging in patients being evaluated for occult malignancies, especially at the traumatic/fractured sites.
Increased 68Ga-FAPI Uptake of Symptomatic Intracranial Atherosclerotic Plaque Revealed by PET/MR
Authors: Yang Qiao , Zhang Zongmuyu , Li Mingli , Xu Wei-Hai , Huo Li
Published: January 2022

A 58-year-old man was enrolled in our 68Ga-FAPI PET/MR study for evaluation of stroke etiology. He had left thalamus and cerebellum infarction 6 months ago, and left occipital lobe infarction 2 years ago. 68Ga-FAPI PET/MR showed focal uptake along the low segment of the basilar artery. We hypothesize that the FAPI-avid plaque of basilar artery may account for the embolic events resulting in downstream infarction. Thus FAP-targeted imaging may have a potential for detection of vulnerable plaques.
FTY720 requires vitamin B12-TCN2-CD320 signaling in astrocytes to reduce disease in an animal model of multiple sclerosis
Authors: Jonnalagadda Deepa , Kihara Yasuyuki , Groves Aran , Ray Manisha , Saha Arjun , Lee-Okada Hyeon-Cheol , Furihata Tomomi , Yokomizo Takehiko , Quadros Edward V. , Rivera Richard , Chun Jerold
Published: January 2022

FTY720 (fingolimod) is a sphingosine 1-phosphate (S1P) receptor modulator and sphingosine analogue approved for multiple sclerosis (MS) therapy, which can functionally antagonize the S1P receptor, S1P1. Vitamin B12 (B12) deficiency produces neurological manifestations resembling MS. Here, we report a new mechanism where FTY720 suppresses neuroinflammation by regulating B12 metabolic pathways. Nuclear RNA-seq of c-Fos-activated astrocytes (called ieAstrocytes) from experimental autoimmune encephalomyelitis (EAE) spinal cords identified up-regulation of CD320, a transcobalamin 2 (TCN2)-B12 receptor, by S1P1 inhibition. CD320 was reduced in MS plaques. Deficiency of CD320 or dietary B12 worsened EAE and eliminated FTY720’s efficacy, while concomitantly down-regulating type I interferon signaling. TCN2 functioned as a chaperone for FTY720 and sphingosine, which induced astrocytic CD320 internalization. An accompanying paper identified a requirement for astrocyte sphingosine kinases in FTY720 efficacy and its altered expression in MS brains, molecularly linking MS and B12 deficiency that can be accessed by sphingolipid/fingolimod metabolic pathways.
Heritable and climatic sources of variation in juvenile tree growth in an Austrian common garden experiment of Central European Norway spruce populations
Authors: Morales Laura , Swarts Kelly
Published: January 2022

We leveraged publicly available data on juvenile tree height of 299 Central European Norway spruce populations grown in a common garden experiment across 24 diverse trial locations in Austria and weather data from the trial locations and population provenances to parse the heritable and climatic components of juvenile tree height variation. Principal component analysis of geospatial and weather variables demonstrated high interannual variation among trial environments, largely driven by differences in precipitation, and separation of population provenances based on altitude, temperature, and snowfall. Tree height was highly heritable and modeling the covariance between populations and trial environments based on climatic data led to more stable estimation of heritability and population × environment variance. Climatic similarity among population provenances was highly predictive of population × environment estimates for tree height.
Elevated FAM84B promotes cell proliferation via interacting with NPM1 in esophageal squamous cell carcinoma
Authors: Wang Fang , Cheng Caixia , Wang Xinhui , Chen Fei , Li Hongyi , Zhou Yan , Wang Yanqiang , Hu Xiaoling , Kong Pengzhou , Zhang Ling , Cheng Xiaolong , Cui Yongping
Published: January 2022

Family with sequence similarity 84, member B (FAM84B) is a significant copy number amplification gene in the 8q24.21 locus identified by our previous WGS study in esophageal squamous cell carcinoma (ESCC). However, its clinical relevance and potential mechanisms have been elusive. Here, we performed the association analyses between FAM84BAmp and clinicopathological features using our dataset with 507 ESCC samples. The results indicated that, compared with the FAM84Bnon-Amp patients, the FAM84BAmp patients showed a more aggressive and a worse prognosis. Significant correlation was discovered between the expression level of FAM84B and FAM84BAmp in ESCC cohort. Furthermore, we found that the forced expression change of FAM84B can influence ESCC cell proliferation and cell cycle status, which is probably mediated by NPM1. A direct interaction between FAM84B and the C-terminal (189-294aa) of NPM1 was identified, which increased the NPM1 nuclear expression. Over-expression of NPM1 could inhibit the CDKN2A protein expression, which might affect the ESCC cell cycle. Our results indicate FAM84B CNA may be a potential diagnostic and therapeutic biomarker in ESCC, meanwhile, reveal a novel mechanism of FAM84B that it promotes tumorigenesis via interacting with NPM1 and suppressing CDKN2A.
Maternal first trimester metabolic profile in TGA pregnancies - a case-control study
Authors: Huida Johanna , Ojala Tiina , Hautala Johanna , Surcel Heljä-Marja , Priest James R , Helle Emmi
Published: January 2022

Objective

To evaluate the association between maternal first trimester metabolic profile and transposition of the great arteries (TGA) in the offspring.

Design

A matched case-control study using national register data and maternal first trimester blood samples.

Settings

Finland

Patients

A total of 100 mothers with TGA in their offspring and 200 controls matched by the year of birth and sex of the child, and the age and the body mass index (BMI) of the mother.

Interventions

None.

Main outcome measures

To identify the impact of 73 metabolic measure concentrations on the likelihood that a child would be born with TGA.

Results

A higher concentration of four subtypes in extremely large very-low-density lipoprotein (VLDL) particles and one in large VLDL particles were observed in mothers with TGA in their offspring. This finding did not reach statistical significance after multiple testing correction. In the analysis of the subgroups of maternal BMI over 25 and 30 only, the odds ratios (OR) of the metabolic variables were higher compared to the original population. In the group with a BMI over 25 the mean OR was 1.3 (N= 111, total) and in the group with a BMI over 30 the mean OR was 2.1 (N= 42, total).

Conclusions

We found no statistically significant difference between the metabolic profiles of mothers with TGA in their offspring, and their controls. However, the trend in our BMI-matched study potentially indicates that the likelihood of TGA development associates with maternal early-pregnancy metabolic profile, and the association is more pronounced in the subgroups of BMI over 25 and 30. Further studies are needed especially in the higher BMI groups.

What is already known on this topic?

The most important structures of the heart develop during early pregnancy, but studies on the association of maternal metabolomics during the first trimester with CHD development are scarce.

Maternal obesity and diabetes are known risk factors for CHD in the offspring but the precise developmental mechanisms underlying this risk remain unknown.

What this study adds to this topic?

The maternal metabolomic profile in early pregnancy is potentially associated with the likelihood of TGA development in the offspring.

Metabolic markers in obese women may have a stronger association with the development of TGA but this connection requires further studies.
NNeurite: artificial neuronal networks for the unsupervised extraction of axonal and dendritic time-lapse signals
Authors: Chenouard Nicolas , Kouskoff Vladimir , Tsien Richard W. , Gambino Frédéric
Published: January 2022

Fluorescence microscopy of Ca2+ transients in small neurites of the behaving mouse provides an unprecedented view of the micrometer-scale mechanisms supporting neuronal communication and computation, and therefore opens the way to understanding their role in cognition. However, the exploitation of this growing and precious experimental data is impeded by the scarcity of methods dedicated to the analysis of images of neurites activity in vivo. We present NNeurite, a set of mathematical and computational techniques specialized for the analysis of time-lapse microscopy images of neurite activity in small behaving animals. Starting from noisy and unstable microscopy images containing an unknown number of small neurites, NNeurite simultaneously aligns images, denoises signals and extracts the location and the temporal activity of the sources of Ca2+ transients. At the core of NNeurite is a novel artificial neuronal network (NN) which we have specifically designed to solve the non-negative matrix factorization (NMF) problem modeling source separation in fluorescence microscopy images. For the first time, we have embedded non-rigid image alignment in the NMF optimization procedure, hence allowing to stabilize images based on the transient and weak neurite signals. NNeurite processing is free of any human intervention as NN training is unsupervised and the unknown number of Ca2+ sources is automatically obtained by the NN-based computation of a low-dimensional representation of time-lapse images. Importantly, the spatial shapes of the sources of Ca2+ fluorescence are not constrained in NNeurite, which allowed to automatically extract the micrometer-scale details of dendritic and axonal branches, such dendritic spines and synaptic boutons, in the cortex of behaving mice. We provide NNeurite as a free and open-source library to support the efforts of the community in advancing in vivo microscopy of neurite activity.
Uncovering potential interventions for pancreatic cancer patients via mathematical modeling
Authors: Plaugher Daniel , Aguilar Boris , Murrugarra David
Published: January 2022

Pancreatic Ductal Adenocarcinoma (PDAC) is widely known for its poor prognosis because it is often diagnosed when the cancer is in a later stage. We built a Boolean model to analyze the microenvironment of pancreatic cancer in order to better understand the interplay between pancreatic cancer, stellate cells, and their signaling cytokines. Specifically, we have used our model to study the impact of inducing four common mutations: KRAS, TP53, SMAD4, and CDKN2A. After implementing the various mutation combinations, we used our stochastic simulator to derive aggressiveness scores based on simulated attractor probabilities and long-term trajectory approximations. These aggression scores were then corroborated with clinical data. Moreover, we found sets of control targets that are effective among common mutations. These control sets contain nodes within both the pancreatic cancer cell and the pancreatic stellate cell, including PIP3, RAF, PIK3 and BAX in pancreatic cancer cell as well as ERK and PIK3 in the pancreatic stellate cell. Many of these nodes were found to be differentially expressed among pancreatic cancer patients in the TCGA database. Furthermore, literature suggests that many of these nodes can be targeted by drugs currently in circulation. The results herein help provide a proof of concept in the path towards personalized medicine through a means of mathematical systems biology. All data and code used for running simulations, statistical analysis, and plotting is available on a GitHub repository at https://github.com/drplaugher/PCC_Mutations.
Predicting patient treatment response and resistance via single-cell transcriptomics of their tumors
Authors: Sinha Sanju , Vegesna Rahulsimham , Dhruba Saugato Rahman , Wu Wei , Kerr D. Lucas , Stroganov Oleg V. , Grishagin Ivan , Aldape Kenneth D. , Blakely Collin M. , Jiang Peng , Thomas Craig J. , Bivona Trever G. , Schäffer Alejandro A. , Ruppin Eytan
Published: January 2022

Tailoring the best treatments to cancer patients is an important open challenge. Here, we build a precision oncology data science and software framework for PERsonalized single-Cell Expression-based Planning for Treatments In Oncology (PERCEPTION). Our approach capitalizes on recently published matched bulk and single-cell transcriptome profiles of large-scale cell-line drug screens to build treatment response models from patients’ single-cell (SC) tumor transcriptomics. First, we show that PERCEPTION successfully predicts the response to monotherapy and combination treatments in screens performed in cancer and patient-tumor-derived primary cells based on SC-expression profiles. Second, it successfully stratifies responders to combination therapy based on the patients’ tumor’s SC-expression in two very recent multiple myeloma and breast cancer clinical trials. Thirdly, it captures the development of clinical resistance to five standard tyrosine kinase inhibitors using tumor SC-expression profiles obtained during treatment in a lung cancer patients’ cohort. Notably, PERCEPTION outperforms state-of-the-art bulk expression-based predictors in all three clinical cohorts. In sum, this study provides a first-of-its-kind conceptual and computational method that is predictive of response to therapy in patients, based on the clonal SC gene expression of their tumors.
Teasing apart the joint effect of demography and natural selection in the birth of a contact zone
Authors: Li Lili , Milesi Pascal , Tiret Mathieu , Chen Jun , Sendrowski Janek , Baison John , Chen Zhiqiang , Zhou Linghua , Karlsson Bo , Berlin Mats , Westin Johan , Garcia-Gil Rosario , Wu Harry , Lascoux Martin
Published: January 2022

Vast population movements induced by recurrent climatic cycles have shaped the genetic structure of plant species. This is especially true in Scandinavia that was repeatedly glaciated. During glacial periods trees were confined to refugia, south and east of the ice sheet, from which they recolonized Scandinavia as the ice melted away. This multi-pronged recolonization led to large contact zones in most species. We leverage large genomic data from 5000 trees to reconstruct the demographic history of Norway spruce (Picea abies) and test for the presence of natural selection during the recolonization process and the establishment of the contact zone. Sweden is today made up of two large genetic clusters, a southern one originating from the Baltics and a Northern one originating from Northern Russia. The contact zone delineating these two clusters closely matches the limit between two major climatic regions. This suggests that natural selection contributed to the establishment and the maintenance of the contact zone. To test this hypothesis we first used Approximate Bayesian Computation; an Isolation-with migration model with genome-wide linked selection fits the data better than a purely neutral one. Secondly, we identified loci characterized by both extreme allele frequency differences between geographic regions and association to the variables defining the climatic zones. These loci, many of which are related to phenology, form clusters present on all linkage groups. Altogether, the current genetic structure reflects the joint effect of climatic cycles, recolonization and selection on the establishment of strong local adaptation and contact zones.

Significance Statement

Understanding how past climatic events, human actions and evolutionary forces contributed to the present distribution of genetic diversity is crucial to predict their reaction to the current climate crisis. Vast distribution shifts induced by past environmental changes, local ecological processes, natural selection and human transfers contributed to the current distribution of Norway spruce across Northern Europe. Genome-wide polymorphisms from thousands of individuals show that Scandinavia was recolonized after the Last Glacial from both south and north. This two-pronged recolonization established a contact zone between two genetic clusters that matches the limit between two major climate zones. The contact zone is shaped and maintained by natural selection on a large number of loci that form blocks of co-adapted loci spread genome-wide.
Influence of data sampling methods on the representation of neural spiking activity in vivo
Authors: van der Heijden Meike E. , Brown Amanda M. , Sillitoe Roy V.
Published: January 2022

In vivo single-unit recordings distinguish the basal spiking properties of neurons in different experimental settings and disease states. Here, we examined over 300 spike trains recorded from Purkinje cells and cerebellar nuclei neurons to test whether data sampling approaches influence the extraction of rich descriptors of firing properties. Our analyses included neurons recorded in awake and anesthetized control mice, as well as disease models of ataxia, dystonia, and tremor. We find that recording duration circumscribes overall representations of firing rate and pattern. Notably, shorter recording durations skew estimates for global firing rate variability towards lower values. We also find that only some populations of neurons in the same mouse are more similar to each other than to neurons recorded in different mice. These data reveal that recording duration and approach are primary considerations when interpreting task-independent single-neuron firing properties. If not accounted for, group differences may be concealed or exaggerated.
Cd59 and inflammation orchestrate Schwann cell development
Authors: Wiltbank Ashtyn T. , Steinson Emma R. , Criswell Stacey J. , Piller Melanie , Kucenas Sarah
Published: January 2022

Efficient neurotransmission is essential for organism survival and is enhanced by myelination. However, the genes that regulate myelin and myelinating glial cell development have not been fully characterized. Data from our lab and others demonstrates thatcd59, which encodes for a small GPI-anchored glycoprotein, is highly expressed in developing zebrafish, rodent, and human oligodendrocytes (OLs) and Schwann cells (SCs), and that patients with CD59 dysfunction develop neurological dysfunction during early childhood. Yet, the function of CD59 in the developing nervous system is currently undefined. In this study, we demonstrate thatcd59is expressed in a subset of developing SCs. Usingcd59mutant zebrafish, we show that developing SCs proliferate excessively, which leads to reduced myelin volume, altered myelin ultrastructure, and perturbed node of Ranvier assembly. Finally, we demonstrate that complement activity is elevated incd59mutants and that inhibiting inflammation restores SC proliferation, myelin volume, and nodes of Ranvier to wildtype levels. Together, this work identifies Cd59 and developmental inflammation as key players in myelinating glial cell development, highlighting the collaboration between glia and the innate immune system to ensure normal neural development.
Two modes of evolution shape bacterial strain diversity in the gut for thousands of generations
Authors: Frazão N. , Konrad A. , Güleresi D. , Lässig M. , Gordo I.
Published: January 2022

How and at what pace bacteria evolve when colonizing healthy hosts remains unclear. Here, by monitoring evolution for more than six thousand generations in the mouse gut, we show that the successful colonization of an invader Escherichia coli depends on the diversity of the existing microbiota and the presence of a closely related strain. Following colonization, two modes of evolution were observed: one in which diversifying selection leads to long-term coexistence of ecotypes and a second in which directional selection propels selective sweeps. These modes can be quantitatively distinguished by the statistics of mutation trajectories. In our experiments, diversifying selection was marked by the emergence of metabolic mutations, and directional selection by acquisition of prophages, which bring their own benefits and costs. In both modes, we observed parallel evolution, with mutation accumulation rates comparable to those typically observed in vitro on similar time scales. Our results show that gut environments can rapidly generate diversifying selection and ecotype formation.
Brain responses in aggression-prone individuals: A systematic review and meta-analysis of functional magnetic resonance imaging (fMRI) studies of anger- and aggression-eliciting tasks
Authors: Nikolic Maja , Pezzoli Patrizia , Jaworska Natalia , Seto Michael C.
Published: January 2022

Background

While reactive aggression (in response to a perceived threat or provocation) is part of humans’ adaptive behavioral repertoire, it can violate social and legal norms. Understanding brain function in individuals with high levels of reactive aggression as they process anger- and aggression-eliciting stimuli is critical for refining interventions. Three neurobiological models of reactive aggression–the limbic hyperactivity, prefrontal hypoactivity, and dysregulated limbic-prefrontal connectivity models–have been proposed. However, these models are based on neuroimaging studies involving mainly healthy individuals, leaving it unclear which model best describes brain function in aggression-prone individuals.

Methods

We conducted a systematic literature search (PubMed and Psycinfo) and Multilevel Kernel Density meta-analysis (MKDA) of nine functional magnetic resonance imaging (fMRI) studies of brain responses to tasks putatively eliciting anger and aggression in aggression-prone individuals alone, and relative to healthy controls.

Results

Aggression-prone individuals exhibited greater activity during reactive aggression relative to baseline in the superior temporal gyrus and in regions comprising the cognitive control and default mode networks (right posterior cingulate cortex, precentral gyrus, precuneus, right inferior frontal gyrus). Compared to healthy controls, aggression-prone individuals exhibited increased activity in limbic regions (left hippocampus, left amygdala, left parahippocampal gyrus) and temporal regions (superior, middle, inferior temporal gyrus), and reduced activity in occipital regions (left occipital cortex, left calcarine cortex).

Conclusions

These findings lend support to the limbic hyperactivity model and further indicate altered temporal and occipital activity in anger- and aggression-eliciting situations that involve face and speech processing.
Machine-learning fromPseudomonas putidaTranscriptomes Reveals Its Transcriptional Regulatory Network
Authors: Lim Hyun Gyu , Rychel Kevin , Sastry Anand V. , Mueller Joshua , Niu Wei , Feist Adam M. , Palsson Bernhard O.
Published: January 2022

Bacterial gene expression is orchestrated by numerous transcription factors (TFs). Elucidating how gene expression is regulated is fundamental to understanding bacterial physiology and engineering it for practical use. In this study, a machine-learning approach was applied to uncover the genome-scale transcriptional regulatory network (TRN) inPseudomonas putida, an important organism for bioproduction. We performed independent component analysis of a compendium of 321 high-quality gene expression profiles, which were previously published or newly generated in this study. We identified 84 groups of independently modulated genes (iModulons) that explain 75.7% of the total variance in the compendium. With these iModulons, we (i) expand our understanding of the regulatory functions of 39 iModulon associated TFs (e.g., HexR, Zur) by systematic comparison with 1,993 previously reported TF-gene interactions; (ii) outline transcriptional changes after the transition from the exponential growth to stationary phases; (iii) capture group of genes required for utilizing diverse carbon sources and increased stationary response with slower growth rates; (iv) unveil multiple evolutionary strategies of transcriptome reallocation to achieve fast growth rates; and (v) define an osmotic stimulon, which includes the Type VI secretion system, as coordination of multiple iModulon activity changes. Taken together, this study provides the first quantitative genome-scale TRN forP. putidaand a basis for a comprehensive understanding of its complex transcriptome changes in a variety of physiological states.
SARS-CoV-2 drives NLRP3 inflammasome activation in human microglia through spike-ACE2 receptor interaction
Authors: Albornoz Eduardo , Amarilla Alberto A , Modhiran Naphak , Parker Sandra , Li Xaria X. , Wijesundara Danushka K. , Zamora Adriana Pliego , McMillan Christopher LD , Liang Benjamin , Peng Nias Y.G. , Sng Julian D.J. , Saima Fatema Tuj , Paramitha Devina , Parry Rhys , Avumegah Michael S. , Isaacs Ariel , Lo Martin , Miranda-Chacon Zaray , Bradshaw Daniella , Salinas-Rebolledo Constanza , Rajapakse Niwanthi W. , Munro Trent , Rojas-Fernandez Alejandro , Young Paul R. , Stacey Katryn J , Khromykh Alexander A. , Chappell Keith J. , Watterson Daniel , Woodruff Trent M.
Published: January 2022

Coronavirus disease-2019 (COVID-19) is primarily a respiratory disease, however, an increasing number of reports indicate that SARS-CoV-2 infection can also cause severe neurological manifestations, including precipitating cases of probable Parkinson’s disease. As microglial NLRP3 inflammasome activation is a major driver of neurodegeneration, here we interrogated whether SARS-CoV-2 can promote microglial NLRP3 inflammasome activation utilising a model of human monocyte-derived microglia. We identified that SARS-CoV-2 isolates can bind and enter microglia, triggering inflammasome activation in the absence of viral replication. Mechanistically, microglial NLRP3 could be both primed and activated with SARS-CoV-2 spike glycoprotein in a NF-κB and ACE2-dependent manner. Notably, virus- and spike protein-mediated inflammasome activation in microglia was significantly enhanced in the presence of α-synuclein fibrils, which was entirely ablated by NLRP3-inhibition. These results support a possible mechanism of microglia activation by SARS-CoV-2, which could explain the increased vulnerability to developing neurological symptoms akin to Parkinson’s disease in certain COVID-19 infected individuals, and a potential therapeutic avenue for intervention.

SIGNIFICANCE STATEMENT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) principally affects the lungs, however there is evidence that the virus can also reach the brain and lead to chronic neurological symptoms. In this study, we examined the interaction SARS-CoV-2 with brain immune cells, by using an ex-vivo model of human monocyte-derived microglia. We identified robust activation of the innate immune sensor complex, NLRP3 inflammasome, in cells exposed to SARS-CoV-2. This was dependent on spike protein-ACE2 receptor interaction and was potentiated in the presence of α-synuclein. We therefore identify a possible mechanism for SARS-CoV-2 and increased vulnerability to developing neurological dysfunction. These findings support a potential therapeutic avenue for treatment of SARS-CoV-2 driven neurological manifestations, through use of NLRP3 inflammasome or ACE2 inhibitors.
Hydrodynamic and Polyelectrolyte Properties of Actin Filaments: Theory and Experiments
Authors: Alva Ernesto , George Annitta , Brancaleon Lorenzo , Marucho Marcelo
Published: January 2022

Actin filament’s polyelectrolyte and hydrodynamic properties, their interactions with the biological environment, and external force fields play an essential role in their biological activities in eukaryotic cellular processes. In this article, we introduce a unique approach that combines dynamics and electrophoresis light scattering experiments, an extended semiflexible worm-like chain model, and an asymmetric polymer length distribution theory to characterize the polyelectrolyte and hydrodynamic properties of actin filaments in aqueous electrolyte solutions. A fitting approach was used to optimize the theories and filament models for hydrodynamic conditions. We used the same sample and experimental conditions and considered several g-actin and polymerization buffers to elucidate the impact of their chemical composition, reducing agents, pH values, and ionic strengths on the filament translational diffusion coefficient, electrophoretic mobility, structure factor, asymmetric length distribution, effective filament diameter, electric charge, zeta potential, and semiflexibility. Compared to those values obtained from molecular structure models, our results revealed a lower value of the effective G-actin charge and a more significant value of the effective filament diameter due to the formation of the double layer of the electrolyte surrounding the filaments. Contrary to the data usually reported from electron micrographs, the lower values of our results for the persistence length and average contour filament length agree with the significant difference in the association rates at the filament ends that shift to sub-micro lengths, the maximum of the length distribution.
Benchmarking taxonomic classifiers with Illumina and Nanopore sequence data for clinical metagenomic diagnostic applications
Authors: Govender Kumeren N. , Eyre David W.
Published: January 2022

Culture-independent metagenomic detection of microbial species has the potential to provide rapid and precise real-time diagnostic results. However, it is potentially limited by sequencing and classification errors. We use simulated and real-world data to benchmark rates of species misclassification using 100 reference genomes for each of ten common bloodstream pathogens and six frequent blood culture contaminants (n=1600). Simulating both with and without sequencing error for both the Illumina and Oxford Nanopore platforms, we evaluated commonly used classification tools including Kraken2, Bracken, and Centrifuge, utilising mini (8GB) and standard (30-50GB) databases. Bracken with the standard database performed best, the median percentage of reads across both sequencing platforms identified correctly to the species level was 98.46% (IQR 93.0:99.3) [range 57.1:100]. For Kraken2 with a mini database, a commonly used combination, median species-level identification was 79.3% (IQR 39.1:88.8) [range 11.2:100]. Classification performance varied by species, with E. coli being more challenging to classify correctly (59.4% to 96.4% reads with correct species, varying by tool used). By filtering out shorter Nanopore reads (<3500bp) we found performance similar or superior to Illumina sequencing, despite higher sequencing error rates. Misclassification was more common when the misclassified species had a higher average nucleotide identity to the true species. Our findings highlight taxonomic misclassification of sequencing data occurs and varies by sequencing and analysis workflow. This “bioinformatic contamination” should be accounted for in metagenomic pipelines to ensure accurate results that can support clinical decision making.

Importance

Metagenomics may transform clinical microbiology by enabling more rapid species detection in a potentially unbiased manner and reducing reliance on culture-based approaches. However, it is still limited by ongoing challenges such as sequencing and classification software errors. In this study, we use simulated and real-world data to define the intrinsic rates of species misclassification that occur using Illumina and Oxford Nanopore sequencing platforms with commonly used taxonomic classification tools and databases. We quantify the extent of “bioinformatic contamination” arising from the classification process. This enables us to identify the best performing tools that maximize classification accuracy, and to suggest how taxonomic misclassification can be formally accounted for in clinical diagnostic workflows. Specifically, we specify thresholds for identifying or excluding polymicrobial infections in metagenomic samples, based on rates of misclassification of similar species, which might have clinical implications when treating infection.
Estimation of age-stratified contact rates during the COVID-19 pandemic using a novel inference algorithm
Authors: Pooley Christopher M. , Doeschl-Wilson Andrea B. , Marion Glenn
Published: January 2022

Well parameterised epidemiological models including accurate representation of contacts, are fundamental to controlling epidemics. However, age-stratified contacts are typically estimated from pre-pandemic/peace-time surveys, even though interventions and public response likely alter contacts. Here we fit age-stratified models, including re-estimation of relative contact rates between age-classes, to public data describing the 2020-21 COVID-19 outbreak in England. This data includes age-stratified population size, cases, deaths, hospital admissions, and results from the Coronavirus Infection Survey (almost 9000 observations in all). Fitting stochastic compartmental models to such detailed data is extremely challenging, especially considering the large number of model parameters being estimated (over 150). An efficient new inference algorithm ABC-MBP combining existing Approximate Bayesian Computation (ABC) methodology with model-based proposals (MBP) is applied. Modified contact rates are inferred alongside time-varying reproduction numbers that quantify changes in overall transmission due to pandemic response, and age-stratified proportions of asymptomatic cases, hospitalisation rates and deaths. These inferences are robust to a range of assumptions including the values of parameters that cannot be estimated from available data. ABC-MBP is shown to enable reliable joint analysis of complex epidemiological data yielding consistent parametrisation of dynamic transmission models that can inform data-driven public health policy and interventions.
Indoor Air Quality Intervention in Schools; Effectiveness of a Portable HEPA Filter Deployment in Five Schools Impacted by Roadway and Aircraft Pollution Sources
Authors: Carmona Nancy , Seto Edmund , Gould Timothy , Shirai Jeffry H. , Cummings B.J. , Hayward Lisa , Larson Timothy , Austin Elena
Published: January 2022

The Healthy Air, Healthy Schools Study was established in January 2020 to better understand the impact of ultrafine particles (UFP) on indoor air quality in communities surrounding Seattle-Tacoma (Sea-Tac) International Airport. The study team took multipollutant measurements indoor and outdoor air pollution at five participating school locations to infiltration indoors. The schools participating in this project were located within a 7-mile radius of Sea-Tac Airport and within 0.5 miles of an active flight path. Based on experimental measures in an unoccupied classroom, infiltration rates of a) Ultrafine particles of aircraft origin b) Ultrafine particles of traffic origin and c) Wildfire smoke or other outdoor pollutants were characterized before and after the introduction of a classroom based portable HEPA filter intervention. The portable HEPA cleaners were an effective short-term intervention to improve the air quality in classroom environments, reducing the ultrafine particles to approximately 1/10th of that measured outside. Before the HEPA filter deployment, approximately one-half of all outdoor UFPs were measured indoors. This study is unique in focusing on UFP in school settings and demonstrating through multivariate methods that the UFP measured in the classroom space is primarily of outdoor origin. Although existing research suggests that improvements to indoor air quality in homes can significantly improve asthma outcomes, further research is necessary to establish the benefit to student health and academic performance of improved air quality in schools.
A Precision Functional Atlas of Network Probabilities and Individual-Specific Network Topography
Authors: Hermosillo Robert J.M. , Moore Lucille A. , Fezcko Eric , Dworetsky Ally , Pines Adam , Conan Gregory , Mooney Michael A. , Randolph Anita , Adeyemo Babatunde , Earl Eric , Perrone Anders , Carrasco Cristian Morales , Uriarte-Lopez Johnny , Snider Kathy , Doyle Olivia , Cordova Michaela , Nagel Bonnie J. , Feldstein Ewing Sarah W. , Satterthwaite Theodore , Dosenbach Nico , Gratton Caterina , Petersen Steven , Miranda-Domínguez Óscar , Fair Damien A.
Published: January 2022

The brain is organized into a broad set of functional neural networks. These networks and their various characteristics have been described and scrutinized through in vivo resting state functional magnetic resonance imaging (rs-fMRI). While the basic properties of networks are generally similar between healthy individuals, there is vast variability in the precise topography across the population. These individual differences are often lost in population studies due to population averaging which assumes topographical uniformity. We leveraged precision brain mapping methods to establish a new open-source, method-flexible set of precision functional network atlases: the Masonic Institute for the Developing Brain (MIDB) Precision Brain Atlas. Using participants from the Adolescent Brain Cognitive Development (ABCD) study, single subject precision network maps were generated with two supervised network-matching procedures (template matching and non-negative matrix factorization), an overlapping template matching method for identifying integration zones, as well as an unsupervised community detection algorithm (Infomap). From these individualized maps we also generated probabilistic network maps and integration zones for two demographically-matched groups of n∼3000 each. We demonstrate high reproducibility between groups (Pearson’s r >0.999) and between methods (r=0.96), revealing both regions of high invariance and high variability. Compared to using parcellations based on groups averages, the MIDB Precision Brain Atlas allowed us to derive a set of brain regions that are largely invariant in network topography across populations, which provides more reproducible statistical maps of executive function in brain-wide associations. We also explore an example use case for probabilistic maps, highlighting their potential for use in targeted neuromodulation. The MIDB Precision Brain Atlas is expandable to alternative datasets and methods and is provided open-source with an online web interface to encourage the scientific community to experiment with probabilistic atlases and individual-specific topographies to more precisely relate network phenomenon to functional organization of the human brain.
Dynamic control systems that mimic natural regulation of catabolic pathways enable rapid production of lignocellulose-derived bioproducts
Authors: Elmore Joshua R. , Peabody George , Jha Ramesh K. , Dexter Gara N. , Dale Taraka , Guss Adam
Published: January 2022

Expanding the catabolic repertoire of engineered microbial bioproduction hosts enables more complete use of complex feedstocks such as lignocellulosic hydrolysates and deconstructed mixed plastics, but the deleterious effects of existing expression systems limit the maximum carry capacity for heterologous catabolic pathways. Here, we demonstrate use of a conditionally beneficial oxidative xylose catabolic pathway to improve performance of a Pseudomonas putida strain that has been engineered for growth-coupled bioconversion of glucose into the valuable bioproduct cis,cis-muconic acid. In the presence of xylose, the pathway enhances growth rate, and therefore productivity, by >60%, but the metabolic burden of constitutive pathway expression reduces growth rate by >20% in the absence of xylose. To mitigate this growth defect, we develop a xylose biosensor based on the XylR transcription factor from Caulobacter crescentus NA1000 to autonomously regulate pathway expression. We generate a library of engineered xylose-responsive promoters that cover a three order-of-magnitude range of expression levels to tune pathway expression. Using structural modeling to guide mutations, we engineer XylR with two and three orders-of-magnitude reduced sensitivity to xylose and L-arabinose, respectively. A previously developed heterologous xylose isomerase pathway is placed under control of the biosensor, which improves the growth rate with xylose as a carbon source by 10% over the original constitutively expressed pathway. Finally, the oxidative xylose catabolic pathway is placed under control of the biosensor, enabling the bioproduction strain to maintain the increased growth rate in the presence of xylose, without the growth defect incurred from constitutive pathway expression in the absence of xylose. Utilizing biosensors to autonomously regulate conditionally beneficial catabolic pathways is generalizable approach that will be critical for engineering bioproduction hosts bacteria with the wide range of catabolic pathways required for bioconversion of complex feedstocks.
A Protective Inter-Organ Communication Response Against Life-Threatening Malarial Anemia
Authors: Wu Qian , Sacomboio Euclides , de Souza Lara Valente , Martins Rui , Cardoso Sílvia , Ademolue Temitope W. , Paixão Tiago , Lehtimäki Jaakko , Norden Caren , Tharaux Pierre-Louis , Weiss Guenter , Wang Fudi , Ramos Susana , Soares Miguel P.
Published: January 2022

Anemia is a clinical hallmark and independent risk factor of malaria mortality, the disease caused by Plasmodium spp. infection. While malarial anemia arises from parasite-induced hemolysis, whether and how host metabolic adaptation to malaria regulates anemia severity is less understood. Here we demonstrate that reprogramming of organismal iron (Fe) metabolism by the kidneys is a central component of the host metabolic response regulating the pathogenesis of life-threatening malarial anemia. Renal proximal tubule epithelial cells (RPTEC) are the main cell compartment responsible for Fe storage and recycling during Plasmodium infection in mice. Transcriptional reprogramming of RPTEC couples immune resistance to Plasmodium infection to renal Fe export via the induction of the cellular Fe exporter SLC40A1/ferroportin 1. This integrated defense strategy is essential to deliver Fe to erythroblasts and support compensatory erythropoiesis to prevent the development of life-threatening anemia. Failure to mobilize Fe from RPTEC causes acute kidney injury (AKI) and is associated with life-threatening anemia in P. falciparum-infected individuals. These findings reveal an unexpected role of the kidneys in the control of organismal Fe metabolism and anemia severity during malaria.
Novel modification of Luminex assay for characterization of extracellular vesicle populations in biofluids
Authors: Volpert OV , Gershun E , Elgart K , Kalia V , Wu H , Baccarelli AA , Eren E , Kapogiannis D , Verma A , Levin A , Eitan E
Published: January 2022

Most approaches to extracellular vesicle (EV) characterization focus on EV size or density. However, such approaches provide few clues regarding EV origin, molecular composition, and function. New methods to characterize the EV surface proteins may aid our understanding of their origin, physiological roles, and biomarker potential. Recently developed immunoassays for intact EVs based on ELISA, NanoView, SIMOA and MesoScale platforms are highly sensitive, but have limited multiplexing capabilities, whereas MACSPlex FACS enables the detection of multiple EV surface proteins, but requires significant quantities of purified EVs, which limits its adoption. Here, we describe a novel Luminex-based immunoassay, which combines multiplexing capabilities with high sensitivity and, importantly, bypasses the enrichment and purification steps that require larger sample volumes. We demonstrate the method’s specificity for detecting EV surface proteins using multiple EV depletion techniques, EVs of specific cellular origin isolated from culture media, and by co-localization with established EV surface markers. Using this novel approach, we elucidate differences in the tetraspanin profiles of the EVs carrying erythrocyte and neuron markers. Using size exclusion chromatography, we show that plasma EVs of putative neuronal and tissue macrophage origin are eluted in fractions distinct from those derived from erythrocytes, or from their respective cultured cells. In conclusion, our novel multiplexed assay differentiates between EVs from erythrocytes, macrophages, and neurons, and offers a new means for capture, classification, and profiling of EVs from diverse sources.
Single Cell Spatial Analysis Reveals the Topology of Immunomodulatory Purinergic Signaling in Glioblastoma
Authors: Coy Shannon , Wang Shu , Stopka Sylwia A. , Lin Jia-Ren , Rashid Rumana , Yapp Clarence , Ritch Cecily C. , Khadka Prasidda , Regan Michael , Hwang Jaeho , Wen Patrick Y. , Bandopadhayay Pratiti , Ligon Keith L. , Agar Nathalie Y.R. , Sorger Peter K. , Touat Mehdi , Santagata Sandro
Published: January 2022

Glioblastoma develops an immunosuppressive microenvironment that fosters tumorigenesis and resistance to current therapeutic strategies. Here we use multiplexed tissue imaging and single-cell RNA-sequencing to characterize the composition, spatial organization, and clinical significance of extracellular purinergic signaling in glioblastoma. We show that glioblastoma exhibit strong expression of CD39 and CD73 ectoenzymes, correlating with increased adenosine levels. Microglia are the predominant source of CD39, while CD73 is principally expressed by tumor cells, particularly in tumors with amplification of EGFR and astrocyte-like differentiation. Spatially-resolved single-cell analyses demonstrate strong spatial correlation between tumor CD73 and microglial CD39, and that their spatial proximity is associated with poor clinical outcomes. Together, this data reveals that tumor CD73 expression correlates with tumor genotype, lineage differentiation, and functional states, and that core purine regulatory enzymes expressed by neoplastic and tumor-associated myeloid cells interact to promote a distinctive adenosine-rich signaling niche and immunosuppressive microenvironment potentially amenable to therapeutic targeting.