bluuebunny/crossref_metadata_2025 huggingface dataset:
Sagittula salina sp. nov., isolated from marine waste
Authors: Satari Leila , Molina-Menor Esther , Vidal-Verdú Àngela , Pascual Javier , Peretó Juli , Porcar Manuel
Published: March 2022

A novel Gram-stain-negative, non-motile, halophilic bacterium designated strain M10.9XT was isolated from the inner sediment of an aluminium can collected from the Mediterranean Sea (València, Spain). Cells of strain M10.9XT were rod-shaped and occasionally formed aggregates. The strain was oxidase-negative and catalase-positive, and showed a slightly psychrophilic, neutrophilic and slightly halophilic metabolism. The phylogenetic analyses revealed that strain M10.9XT was closely related to

Sagittula stellata

E-37T and

Sagittula marina

F028-2T. The genomic G+C content of strain M10.9XT was 65.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization values were 76.6 and 20.9 %, respectively, confirming its adscription to a new species within the genus

Sagittula

. The major cellular fatty acids were C18 : 1
 ω7c/C18 : 1
 ω6c and C16 : 0. The polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid, an unidentified glycolipid, an unidentified phospholipid and an unidentified lipid. According to the resuts of a polyphasic study, strain M10.9XT represents a novel species of the genus

Sagittula

for which the name Sagittula salina sp. nov. (type strain M10.9XT=DSM 112301T=CECT 30307T) is proposed.
Alkaliphilus flagellatus sp. nov., Butyricicoccus intestinisimiae sp. nov., Clostridium mobile sp. nov., Clostridium simiarum sp. nov., Dysosmobacter acutus sp. nov., Paenibacillus brevis sp. nov., Peptoniphilus ovalis sp. nov. and Tissierella simiarum sp. nov., isolated from monkey faeces
Authors: Li Dan-Hua , Abuduaini Rexiding , Du Meng-Xuan , Wang Yu-Jing , Chen Hong-He , Zhou Nan , Zhu Hai-Zhen , Lu Yong , Yu Pei-Jun , Yang Yun-Peng , Jiang Cheng-Ying , Sun Qiang , Liu Chang , Liu Shuang-Jiang
Published: March 2022

Non-human primates harbour diverse microbiomes in their guts. As a part of the China Microbiome Initiatives, we cultivated and characterized the gut microbiome of cynomolgus monkeys (Macaca fascicularis). In this report, we communicate the characterization and taxonomy of eight bacterial strains that were obtained from faecal samples of captive cynomolgus monkeys. The results revealed that they represented eight novel bacterial species. The proposed names of the eight novel species are Alkaliphilus flagellatus (type strain MSJ-5T=CGMCC 1.45007T=KCTC 15974T), Butyricicoccus intestinisimiae MSJd-7T (MSJd-7T=CGMCC 1.45013T=KCTC 25112T), Clostridium mobile (MSJ-11T=CGMCC 1.45009T=KCTC 25065T), Clostridium simiarum (MSJ-4T=CGMCC 1.45006T=KCTC 15975T), Dysosmobacter acutus (MSJ-2T=CGMCC 1.32896T=KCTC 15976T), Paenibacillus brevis MSJ-6T (MSJ-6T=CGMCC 1.45008T=KCTC 15973T), Peptoniphilus ovalis (MSJ-1T=CGMCC 1.31770T=KCTC 15977T) and Tissierella simiarum (MSJ-40T=CGMCC 1.45012T=KCTC 25071T).
Genomic characterization of multidrug-resistant Salmonella serovar Kentucky ST198 isolated in poultry flocks in Spain (2011–2017)
Authors: Samper-Cativiela Clara , Diéguez-Roda Bernabé , Trigo da Roza Filipa , Ugarte-Ruiz María , Elnekave Ehud , Lim Seunghyun , Hernández Marta , Abad David , Collado Soledad , Sáez José Luis , de Frutos Cristina , Agüero Montserrat , Moreno Miguel Ángel , Escudero José Antonio , Álvarez Julio
Published: March 2022

Salmonella

Kentucky is commonly found in poultry and rarely associated with human disease. However, a multidrug-resistant (MDR) S. Kentucky clone [sequence type (ST)198] has been increasingly reported globally in humans and animals. Our aim here was to assess if the recently reported increase of S. Kentucky in poultry in Spain was associated with the ST198 clone and to characterize this MDR clone and its distribution in Spain. Sixty-six isolates retrieved from turkey, laying hen and broiler in 2011–2017 were subjected to whole-genome sequencing to assess their sequence type, genetic relatedness, and presence of antimicrobial resistance genes (ARGs), plasmid replicons and virulence factors. Thirteen strains were further analysed using long-read sequencing technologies to characterize the genetic background associated with ARGs. All isolates belonged to the ST198 clone and were grouped in three clades associated with the presence of a specific point mutation in the gyrA gene, their geographical origin and isolation year. All strains carried between one and 16 ARGs whose presence correlated with the resistance phenotype to between two and eight antimicrobials. The ARGs were located in the

Salmonella

genomic island (SGI-1) and in some cases (bla
SHV-12
, catA1, cmlA1, dfrA and multiple aminoglycoside-resistance genes) in IncHI2/IncI1 plasmids, some of which were consistently detected in different years/farms in certain regions, suggesting they could persist over time. Our results indicate that the MDR S. Kentucky ST198 is present in all investigated poultry hosts in Spain, and that certain strains also carry additional plasmid-mediated ARGs, thus increasing its potential public health significance.
Low hybridization temperatures improve target capture success of invertebrate loci
Authors: Forthman Michael , Gordon Eric R. L. , Kimball Rebecca T.
Published: March 2022

Target capture approaches are widely used in phylogenomic studies, yet only four experimental comparisons of a critical parameter, hybridization temperature, have been published. These studies provide conflicting conclusions regarding the benefits of lower temperatures during target capture, and none include invertebrates where bait-target divergences may be higher than seen in vertebrate capture studies. Most capture studies use a fixed hybridization temperature of 65°C to maximize the proportion of on-target data, but many invertebrate capture studies report low locus recovery. Lower hybridization temperatures, which might improve locus recovery, are not commonly employed in invertebrate capture studies. We used leaf-footed bugs and relatives (Hemiptera: Coreoidea) to investigate the effect of hybridization temperature on capture success of ultraconserved elements (UCE) targeted by previously published baits derived from divergent hemipteran genomes and other loci targeted by newly designed baits derived from less divergent coreoid transcriptomes. We found touchdown capture approaches with lower hybridization temperatures generally resulted in lower proportions of on-target reads and lower read depth but were associated with more contigs and improved recovery of UCE loci. Low temperatures were also associated with increased numbers of putative paralogs of UCE loci. Hybridization temperatures did not generally affect recovery of newly targeted loci, which we attributed to their lower bait-target divergences (compared to higher divergences between UCE baits and targets) and greater bait tiling density. Thus, optimizingin vitrotarget capture conditions to accommodate low hybridization temperatures can provide a cost-effective, widely applicable solution to improve recovery of protein-coding loci in invertebrates.
Epidemiology of Respiratory Viruses in Acute Respiratory Illnesses in Malaysia: Patterns, Seasonality and Age Distribution
Authors: Low Yoke Lee , Wong Shin Yee , Lee Hor Eric Kim , Muhammed Mohd. Hareeff
Published: March 2022

Objectives

Acute Respiratory Infections (ARIs) are one of the leading causes of childhood morbidity and mortality worldwide. However, there is limited surveillance data on the epidemiological burden of respiratory pathogens in tropical countries like Malaysia. This study aims to estimate the prevalence of respiratory pathogens causing ARIs among children aged <18 years old in Malaysia and their epidemiological characteristics.

Methods

Nasopharyngeal swab specimens received at 12 laboratories located in different states of Malaysia from 2015-2019 were studied. Detection of 18 respiratory pathogens were performed using multiplex PCR.

Results

Data from a total of 23,306 paediatric patients who presented with ARI over a five-year period was studied. Of these, 18538 (79.5%) were tested positive. The most prevalent respiratory pathogens detected in this study were enterovirus/ rhinovirus (6837/ 23000; 29.7%), influenza virus (5176/ 23000; 22.5%) and respiratory syncytial virus (RSV) (3652/ 23000; 15.9%). Throughout the study period, RSV demonstrated the most pronounce seasonality; peak infection occurred during July to September. Whereas the influenza virus was detected year-round in Malaysia. No seasonal variation was noted in other respiratory pathogens. The risk of RSV hospitalisation was found to be significantly higher in children aged less than two years old, whereas hospitalisation rates for the influenza virus peaked at children aged between 3-6 years old.

Conclusions

This study provides insight into the epidemiology and the seasonality of the causative pathogens of ARI among the paediatric population in Malaysia. Knowledge of seasonal respiratory pathogens epidemiological dynamics will facilitate the identification of a target window for vaccination.
Dorsolateral striatum, not motor cortex, is a bottleneck for responding to task-relevant stimuli in a learned whisker detection task in mice
Authors: Zareian Behzad , Lam Angelina , Zagha Edward
Published: March 2022

A learned sensory-motor behavior engages multiple brain regions, including the neocortex and the basal ganglia. How a target stimulus is selected by these regions remains poorly understood. Here, we performed electrophysiological recordings and pharmacological inactivations of motor cortex and dorsolateral striatum to determine the representations within and functions of each region during performance in a selective whisker detection task in male and female mice. From the recording experiments, peak pre-response activity and significant choice probability emerged in the motor cortex before the dorsolateral striatum, suggesting a sensory-to-motor transformation in which the striatum is downstream of motor cortex. We performed pharmacological inactivation studies to determine the necessity of these brain regions for this task. We found that suppressing the dorsolateral striatum, but not motor cortex, severely disrupts responding to task-relevant stimuli, without disrupting the ability to respond. Together these data support the dorsolateral striatum, and not motor cortex, as an essential node in the sensory-to- motor transformation of this whisker detection task.

Significance Statement

We learn to do various sensory-motor behavior in our daily life, such as clicking on a journal article that looks interesting, among other articles. There are parts of our brain that are active when we do these learned behaviors, such as motor cortex and basal ganglia. But what is the order of activation of these regions? Which of them is necessary for responding to task-relevant sensory information? To answer these questions, we trained mice in a whisker-based target selection task and used recording of neural activity and inactivation of subregions within motor cortex and basal ganglia in expert mice. Our findings show dorsolateral striatum, a region within basal ganglia, is a bottleneck for performing task-related sensory-to-motor transformation.
Listeria monocytogenes gene essentiality under laboratory conditions and during macrophage infection
Authors: Fischer Martin , Engelgeh Tim , Rothe Patricia , Fuchs Stephan , Thürmer Andrea , Halbedel Sven
Published: March 2022

The Gram-positive bacterium Listeria monocytogenes occurs widespread in the environment and infects humans when ingested along with contaminated food. Such infections are particularly dangerous for risk group patients, for whom they represent a life-threatening disease. To invent novel strategies to control contamination and disease, it is important to identify those cellular processes that maintain pathogen growth in- and outside the host. We here have applied transposon insertion sequencing (Tn-Seq) to L. monocytogenes for the identification of such processes on a genome-wide scale. Our approach classified 394 open reading frames as essential for growth under standard laboratory conditions and identified 42 further genes, which become additionally essential during intracellular growth in macrophages. Most essential genes encode components of the translation machinery, act in chromosome-related processes, cell division and biosynthesis of the cellular envelope. Several cofactor biosynthesis pathways and 29 genes with unknown functions were also essential, opening novel options for the development of anti- listerial drugs. Among the genes specifically required during intracellular growth were known virulence factors, genes compensating intracellular auxotrophies and several cell division genes. Our experiments also highlight the importance of PASTA kinase signalling, glycine metabolism and chromosome segregation for efficient intracellular growth of L. monocytogenes.
Optical control of CRISPR-Cas editing with cyclically caged guide RNAs
Authors: Sun Ying-Jie , Liu Ji , Li Jun-Jin , Zhang Yu , Chen Wen-Da , Cai Wei-Qi , Liu Li , Tang Xin-Jing , Hou Jian , Wang Ming , Cheng Liang
Published: March 2022

The CRISPR/Cas system has been proved as one of the most powerful tools for precise gene editing. However, the approaches for precise control over the genome editing and regulatory events are still desirable. Here, we reported a spatiotemporal and efficient CRISPR/Cas9 and Cpf1-mediated editing with photo-sensitive circular gRNAs. This approach relies on only two or three pre-installed photolabile substituents followed by a simple covalent cyclization, which provides a robust synthesize approach in comparison to heavily modified gRNAs. In established cells stably expressing Cas9, the circular gRNA in coordination with light irradiation could direct a precise cleavage of GFP and VEGFA within a pre-defined cutting region. We have also achieved light-mediated MSTN gene editing in embryos, whereas a new bow-knot-type gRNA showed no background editing in the absence of light irradiation. Together, our work provides a significantly improved method to precisely manipulate where and when genes are edited.
An amphipathic helix in Brl1 is required for membrane fusion during nuclear pore complex biogenesis in S. cerevisiae
Authors: Kralt Annemarie , Wojtynek Matthias , Fischer Jonas S. , Agote-Aran Arantxa , Mancini Roberta , Dultz Elisa , Noor Elad , Uliana Federico , Tatarek-Nossol Marianna , Antonin Wolfram , Onischenko Evgeny , Medalia Ohad , Weis Karsten
Published: March 2022

The nuclear pore complex (NPC) is the central portal for macromolecular exchange between the nucleus and cytoplasm. In all eukaryotes, NPCs assemble into an intact nuclear envelope (NE) during interphase, but the process of NPC biogenesis remains poorly characterized. Furthermore, little is known about how NPC assembly leads to the fusion of the outer and inner NE, and no factors have been identified that could trigger this event. Here we characterize the transmembrane protein Brl1 as an NPC assembly factor required for NE fusion in budding yeast. Brl1 preferentially associates with NPC assembly intermediates and its depletion halts NPC biogenesis, leading to NE herniations that contain inner and outer ring nucleoporins but lack the cytoplasmic export platform. Furthermore, we identify an essential amphipathic helix in the luminal domain of Brl1 that mediates interactions with lipid bilayers. Mutations in this amphipathic helix lead to NPC assembly defects, and cryo-ET analyses reveal multi-layered herniations of the inner nuclear membrane with NPC-like structures at the neck, indicating a failure in NE fusion. Taken together, our results identify a role for Brl1 in NPC assembly and suggest a function of its amphipathic helix in mediating the fusion of the inner and outer nuclear membranes.
Not digested: algal glycans move carbon dioxide into the deep-sea
Authors: Vidal-Melgosa Silvia , Lagator Matija , Sichert Andreas , Priest Taylor , Pätzold Jürgen , Hehemann Jan-Hendrik
Published: March 2022

Marine algae annually synthesize gigatons of glycans from carbon dioxide, exporting it within sinking particles into the deep-sea and underlying sea floor, unless those glycans are digested before by bacteria. Identifying algal glycans in the ocean remains challenging with the molecular resolution of conventional analytic techniques. Whether algal glycans are digested by heterotrophic bacteria during downward transport, before they can transfer carbon dioxide from the ocean surface into the deep-sea or the sea floor, remains unknown. In the Red Sea Shaban Deep, where at 1500 m water depth a brine basin acts as a natural sediment trap, we found its high salt and low oxygen concentration accumulated and preserved exported algal glycans for the past 2500 years. By using monoclonal antibodies specific for glycan structures, we detected fucose-containing sulfated polysaccharide, β-glucan, β-mannan and arabinogalactan glycans, synthesized by diatoms, coccolithophores, dinoflagellates and other algae living in the sunlit ocean. Their presence in deep-sea sediment demonstrates these algal glycans were not digested by bacteria. Instead they moved carbon dioxide from the surface ocean into the deep-sea, where it will be locked away from the atmosphere at least for the next 1000 years. Considering their global synthesis, quantity and stability against degradation during transport through the water column, algal glycans are agents for carbon sequestration.

Significance statement

Algae and plants use the greenhouse gas carbon dioxide to synthesize polymeric carbohydrates, or glycans, for energy storage, structural support and as protection against invasion by microbes. Glycans provide protection, are carbon sinks and enable carbon sequestration for as long as they are not digested by bacteria or other organisms, which releases the carbon dioxide back in to the atmosphere. In this study, we show that non-digested algal glycans sink into the deep ocean and into marine sediment. Thus, glycans are more than food for animals and prebiotics for bacteria, they are also molecules that remove carbon dioxide from the atmosphere and transfer it to the deep-sea, where it can be stored for 1000 years and longer.
The Metabolomics Workbench File Status Website: A Metadata Repository Promoting FAIR Principles of Metabolomics Data
Authors: Powell Christian D. , Moseley Hunter N.B.
Published: March 2022

Motivation

An updated version of the mwtab Python package for programmatic access to the Metabolomics Workbench (MetabolomicsWB) data repository was released at the beginning of 2021. Along with updating the package to match the changes to MetabolomicsWB’s ‘mwTab’ file format and to enhance the package’s functionality, the package included format validation facilities which were used to detect and catalog file inconsistencies and errors across all publically available datasets in MetabolomicsWB.

Results

The Metabolomics Workbench File Status website was developed to provide continuous validation of MetabolomicsWB data files and a useful interface to find all inconsistencies and errors that are found. This list of detectable issues/errors include format parsing errors, format compliance issues, access problems via MetabolomicsWB’s REST interface, and other small inconsistencies that can hinder reusability. The website uses the mwtab Python package to pull down and validate each available analysis file and then generates an html report. The website is updated on a weekly basis. Moreover, the Python website design utilizes GitHub and GitHub.io, providing an easy to replicate template for implementing other metadata, virtual, and meta-repositories.

Availability

Metabolomics Workbench file status website can be accessed at: https://moseleybioinformaticslab.github.io/mwFileStatusWebsite/. The mwtab Python library is available on GitHub: https://github.com/MoseleyBioinformaticsLab/mwtab, PyPI: https://pypi.org/project/mwtab/, and documentation is available on ReadTheDocs: https://mwtab.readthedocs.io/. Metabolomics Workbench analysis data files used for analysis presented here along with the generated HTML files of the website are available on FigShare: https://doi.org/10.6084/m9.figshare.19221159.

Contact

hunter.moseley@uky.edu

Supplementary information

Supplementary data are available at FigShare online.
Elevated levels of IL-6 in IgA nephropathy patients are induced by an epigenetically driven mechanism modulated by viral and bacterial RNA
Authors: Sallustio Fabio , Picerno Angela , Cimmarusti Maria Teresa , Montenegro Francesca , Curci Claudia , De Palma Giuseppe , Sivo Carmen , Annese Francesca , Fontò Giulia , Stasi Alessandra , Pesce Francesco , Tafuri Silvio , Di Leo Vincenzo , Gesualdo Loreto
Published: March 2022

Immunoglobulin A nephropathy (IgAN) is the most frequent primary glomerulonephritis characterized by the presence of IgA immune complexes in the glomeruli. Recently, a multihit model has been proposed to describe the pathogenesis of IgAN, but it is believed that further predisposing factors are present, including immunological, genetic and environmental factors. Newly, the role of IL-6 in pathogenesis is becoming increasingly important but reason why levels of IL-6 are elevated in IgAN patients is not well understood.

One attainable hypothesis on high levels of IL-6 in IgAN comes out from our recent whole genome DNA methylation screening in IgAN patients, that identified, among others, a hypermethylated region comprising Vault RNA 2-1 (VTRNA2-1), a non-coding RNA.

Here we confirm that VTRNA2-1 is low expressed in IgAN subjects compared to HS and we found that also in transplanted IgAN patients (TP-IgAN), compared to non-IgAN transplanted patients (TP), the VTRNA2-1 transcript was expressed at level very low. We found that in IgAN patients with downregulated VTRNA2-1, PKR is overactivated, coherently with the role of the VTRNA2-1 that binds to PKR and inhibits its phosphorylation. The loss of the VTRNA2-1 natural restrain caused the activation of CREB by PKR, a classical cAMP-inducible CRE-binding factor interacting with a region of the IL-6 promoter and leading to IL-6 production, both in IgAN and in TP-IgAN patients. PKR is normally activated by bacterial and viral RNA and we found that both the RNA poly(I:C), the and the COVID-19 RNA-vaccine stimulation significantly increase the IL-6 levels in PBMCs from HS but had an opposite effect in those from IgAN patients.

In conclusion, the discovery of the upregulated VTRNA2-1/PKR/CREB/IL-6 pathway in IgAN patients may provide novel approach to treat the disease and may be useful for development of precision nephrology and personalized therapy, possibly by checking the VTRNA2-1 methylation level in IgAN patients.
Executable models of immune signaling pathways in HIV-associated atherosclerosis
Authors: Palshikar Mukta G. , Palli Rohith , Tyrell Alicia , Maggirwar Sanjay , Schifitto Giovanni , Singh Meera V. , Thakar Juilee
Published: March 2022

Atherosclerosis (AS)-associated cardiovascular disease is an important cause of mortality in an aging population of people living with HIV (PLWH). This elevated risk has been attributed to viral infection, anti-retroviral therapy, chronic inflammation, and lifestyle factors. However, rates at which PLWH develop AS vary even after controlling for length of infection, treatment duration, and for lifestyle factors. To investigate the molecular signaling underlying this variation, we sequenced 9368 peripheral blood mononuclear cells (PBMCs) from eight PLWH, four of whom have atherosclerosis (AS+). Additionally, a publicly available dataset of PBMCs from persons before and after HIV infection was used to investigate the effect of acute HIV infection. To characterize dysregulation of pathways rather than just measuring enrichment, we developed the single-cell Boolean Omics Network Invariant Time Analysis (scBONITA) algorithm. scBONITA infers executable dynamic pathway models and performs perturbation analysis to identify high impact genes. These dynamic models are used for pathway analysis and to map sequenced cells to characteristic signaling states (attractor analysis). scBONITA revealed that lipid signaling regulates cell migration into the vascular endothelium in AS+ PLWH. Pathways implicated included AGE-RAGE and PI3K-AKT signaling in CD8+ T cells, and glucagon and cAMP signaling pathways in monocytes. Attractor analysis with scBONITA facilitated pathway-based characterization of cellular states in CD8+ T cells and monocytes. In this manner, we identify critical cell-type specific molecular mechanisms underlying HIV-associated atherosclerosis using a novel computational method.
Whole-genome sequencing of Bacillus thuringiensis strain SY49.1 reveals the detection of novel candidate pesticidal and bioactive compounds isolated from Turkey
Authors: Yılmaz Semih , Idris Abeer Babiker , Ayvaz Abdurrahman , Temizgül Rıdvan , Hassan Mohammed A.
Published: March 2022

Background

Bacillus thuringiensis SY49.1 (Bt SY49.1) strain is a new strain isolated from a soil sample in Adana city which is nestled in the most fertile agricultural area in Turkey. This strain has insecticidal activity against insect pests from different orders. Also, it is characterized by its significant activity against plant fungal infections and as plant growth promotion.

Aims

To report the whole genome sequencing (WGS) and annotation of the Bt SY49.1 strain.

Materials and Methods

The Bt SY49.1 strain was isolated from the soil sample in Adana city by using a sodium acetate enriched medium. Bacterial DNA was extracted then sequenced using Illumina HiSeq technology. After data filtering and quality control, de novo assembly and genomic annotation were applied. Evolutionary and comparative genomic analysis and variant calling were performed using various in silico tools.

Results

The WGS of strain Bt SY49.1 is 6. 32 Mbp long with a GC content of 34.68%. It reveals large numbers of single nucleotide polymorphisms (SNPs) and InDels. The assembled genome contains 6,562 protein-encoding genes. In addition, it encodes various gene inventories for the biosynthesis of bioactive compounds such as insecticidal delta endotoxins, growth stimulatory deaminase and phosphatases, fungicidal thuricin, bacillibactin, petrobactin, fengycin / plipastin, and zwittermycin A.

Conclusion

The strain Bt SY49.1 could have several potential utilities as a source of antibiotics compounds, plant growth promoting metabolites, and biocontrol agents for fungal phytopathogens, and insects. We expect that the draft genome of the Bt SY49.1 strain may provide a model for proper understanding and studying of antimicrobial compound mining, genetic diversity among the B. cereus group, and pathogenicity against insect pests and plant diseases, and growth-promoting activity.
Myoglobin-derived iron causes wound enlargement and impaired regeneration in pressure injuries of muscle
Authors: Nasir N. Jannah M. , Heemskerk Hans , Jenkins Julia , Hamadee N. Hidayah , Bunte Ralph , Tucker-Kellogg Lisa
Published: March 2022

The reasons for poor healing of pressure injuries are poorly understood. Vascular ulcers are worsened by extracellular release of hemoglobin, so we examined the impact of myoglobin (Mb) iron in murine muscle pressure injuries (mPI). Tests used Mb-knockout or treatment with deferoxamine iron chelator (DFO).

Unlike acute injuries from cardiotoxin, mPI regenerated poorly with a lack of viable immune cells, persistence of dead tissue (necro-slough), and abnormal deposition of iron. However, Mb-knockout or DFO-treated mPI displayed a reversal of the pathology: decreased tissue death, decreased iron deposition, decrease in markers of oxidative damage, and higher numbers of intact immune cells. Subsequently, DFO treatment improved myofiber regeneration and morphology.

We conclude that myoglobin iron contributes to tissue death in mPI. Remarkably, a large fraction of muscle death in untreated mPI occurred later than, and was preventable by, DFO treatment, even though treatment started 12 hours after pressure was removed. This demonstrates an opportunity for post-pressure prevention to salvage tissue viability.
Incomplete bunyavirus particles contribute to within-host spread and between-host transmission
Authors: Bermúdez-Méndez Erick , Bronsvoort Kirsten F. , Zwart Mark P. , van de Water Sandra , Cárdenas-Rey Ingrid , Vloet Rianka P. M. , Koenraadt Constantianus J. M. , Pijlman Gorben P. , Kortekaas Jeroen , Schreur Paul J. Wichgers
Published: March 2022

Bunyaviruses lack a specific mechanism to ensure the incorporation of a complete set of genome segments into each virion, explaining the generation of incomplete virus particles lacking one or more genome segments. Such incomplete virus particles, which may represent the majority of particles produced, are generally considered to interfere with virus infection and spread. Using the three-segmented Rift Valley fever virus as a model bunyavirus, we here show that two distinct incomplete virus particle populations that are unable to spread autonomously, are able to efficiently complement each other in both mammalian and insect cells following co-infection. We further show that incomplete virus particles are capable of co-infecting mosquitoes, resulting in the rescue of infectious virus that is able to disseminate to the mosquito salivary glands. Our findings reveal a significant role of incomplete particles in within-host spread and between-host transmission, reminiscent of the life cycle of multipartite viruses.
Colitis-associated intestinal microbiota regulates brain glycine and host behavior in mice
Authors: Morozova Maryana V. , Borisova Mariya A. , Snytnikova Olga A. , Achasova Ksneniya M. , Litvinova Ekaterina A. , Tsentalovich Yuri P. , Kozhevnikova Elena N.
Published: March 2022

Inflammatory bowel diseases (IBD) are chronic and relapsing inflammatory disorders of the gastrointestinal tract with complex etiology and no strategies for complete cure. IBD are often complicated by mental disorders like anxiety and depression, indicating substantial shifts in the gut-brain axis. However, the mechanisms connecting IBD to mental diseases are still under debate. Here we use Muc2 mutant mouse model of chronic colitis to uncouple the effects of the intestinal microbiota on host behavior from chronic inflammation in the gut. Muc2 mutant male mice exhibit high exploratory activity, reduced anxiety-related behaviors, impaired sensorimotor gating, and altered social preference towards males and females. Microbial transfer to wild-type mice via littermate co-housing shows that colitis-associated microbiota rather than inflammation per se defines behavioral features in Muc2 colitis model. Metagenomic profiling and combination of antibiotic treatments revealed that bacterial species Akkermansia muciniphila is associated with the behavioral phenotype in mutants, and that its intestinal abundance correlates with social preference towards males. Metabolomic analysis together with pharmacological inhibition of Gly and NMDA receptors helped us to determine that brain glycine is responsible for the behavioral phenotype in Muc2 mice. Blood and brain metabolic profiles suggest that microbiota-dependent changes in choline metabolism might be involved in regulation of central glycine neurotransmission. Taken together, our data demonstrates that colitis-associated microbiota controls anxiety, sensorimotor gating and social behavior via metabolic regulation of the brain glycinergic system, providing new venues to combat neurological complications of IBD.
Characterizing Low-Frequency Artifacts During Transcranial Temporal Interference Stimulation (tTIS)
Authors: von Conta Jill , Kasten Florian H. , Ćurčić-Blake Branislava , Schellhorn Klaus , Herrmann Christoph S.
Published: March 2022

Transcranial alternating current stimulation (tACS) is a well-established brain stimulation technique to modulate human brain oscillations. However, due to the strong electro-magnetic artifacts induced by the stimulation current, the simultaneous measurement of tACS effects during neurophysiological recordings in humans is challenging. Recently, transcranial temporal interference stimulation (tTIS) has been introduced to stimulate neurons at depth non-invasively. During tTIS, two high-frequency sine waves are applied, that interfere inside the brain, resulting in amplitude modulated waveforms at the target frequency. Given appropriate hardware, we show that neurophysiological data during tTIS may be acquired without stimulation artifacts at low-frequencies. However, data must be inspected carefully for possible low-frequency artifacts. Our results may help to design experimental setups to record brain activity during tTIS, which may foster our understanding of its underlying mechanisms.
Evaluation of the antimicrobial, anti-adhesion, anti-biofilm and cell proliferation assay of a de-novo goji berry extract against periodontal pathogens: a comparative in-vitro study
Authors: Sanghavi Amee Dilip , Chopra Aditi , Shah Ashmeet , Lobo Richard , Shenoy Padmaja A
Published: March 2022

Lycium barbarum, commonly known as goji berry, Chinese berry, or Tibetian berry, is emerging as a popular “superfood” with anti-inflammatory and antioxidant properties. Goji berry is being used for the treatment of various cancers, gastrointestional disorders, stroke, diabetes, Alzheimer’s disease, and glaucoma. However, its use for management of oral inflammatory diseases has not been explored. Therefore, the present study aims to evaluate the antimicrobial, anti-adhesion, and anti-biofilm, and cytotoxic properties of an ethanolic extract of Lycium barbarum (LBE) against oral and periodontal pathogens. The antimicrobial properties of LBE against five microorganisms were tested and compared against Chlorhexidine and doxycycline along with cytotoxicity and cell viability on the gingival fibroblast and modified keratinocyte cell lines. The anti-adhesion and anti-biofilm properties of LBE against Porphyromonas gingivalis, at its minimal bactericidal value, were evaluated. The antimicrobial, anti-adhesion and antibiofilm properties of LBE were found to be comparable to chlorhexidine but less than that of doxycycline. The LBE extract was also compactible to gingival fibroblast tissues and oral keratinocytes at 1 mg/ml. The results proved that goji berry is as effective as chlorhexidine and can be used as a promising natural herb for the management of inflammatory diseases of oral cavity.
PP2A phosphatase regulates cell-type specific cytoskeletal organization to drive dendritic diversification
Authors: Bhattacharjee Shatabdi , Lottes Erin N. , Nanda Sumit , Golshir Andre , Patel Atit A. , Ascoli Giorgio A. , Cox Daniel N.
Published: March 2022

Uncovering molecular mechanisms regulating dendritic diversification is essential to understanding the formation and modulation of functional neural circuitry. Transcription factors play critical roles in promoting dendritic diversity and here, we identify PP2A phosphatase function as a downstream effector of Cut-mediated transcriptional regulation of dendrite development. Mutant analyses of the PP2A catalytic subunit (mts) or the scaffolding subunit (PP2A-29B)reveal cell-type specific regulatory effects with the PP2A complex required to promote dendritic growth and branching inDrosophilaClass IV (CIV) multidendritic (md) neurons, whereas in Class I (CI) md neurons, PP2A functions in restricting dendritic arborization. Cytoskeletal analyses reveal requirements for Mts in regulating microtubule stability/polarity and F-actin organization/dynamics. In CIV neurons,mtsknockdown leads to reductions in dendritic localization of organelles including mitochondria and satellite Golgi outposts, while CI neurons show increased Golgi outpost trafficking along the dendritic arbor. Further,mtsmutant neurons exhibit defects in neuronal polarity/compartmentalization. Finally, genetic interaction analyses suggest β-tubulin subunit 85D is a common PP2A target in CI and CIV neurons, while FoxO is a putative target in CI neurons.
Integrated analysis of Wnt signalling system component gene expression
Authors: Murphy Paula , Armit Chris , Hill Bill , Venkataraman S. , Frankel Patrick , Baldock Richard , Davidson Duncan
Published: March 2022

Wnt signalling controls patterning and differentiation across many tissues and organs of the developing embryo via temporally and spatially restricted expression of multi-gene families encoding ligands, receptors, pathway modulators and intracellular components. Here we report an integrated analysis of key encoding genes in the 3D space of the mouse embryo across multiple stages of development. We applied a method for 3D/3D image transformation to map all gene expression patterns to a single reference embryo for each stage providing both visual analysis and volumetric mapping allowing computational methods to interrogate the combined expression patterns. We identify novel territories where multiple Wnt and Fzd genes are co-expressed and cross-compare all patterns, including all seven Wnt paralogous gene pairs. The comprehensive analysis allows regions in the embryo where no Wnt or Fzd gene expression is detected, and where single Wnt genes are uniquely expressed, to be revealed. This work provides insight into a level of organisation of the patterns not previously possible, as well as presenting a resource that can be utilised further by the research community for whole system analysis.
Erythritol synthesis in human cells is elevated in response to oxidative stress and regulated by the non-oxidative pentose phosphate pathway
Authors: Ortiz Semira R. , Heinz Alexander , Hiller Karsten , Field Martha S.
Published: March 2022

Erythritol is a predictive biomarker of cardiometabolic diseases and is produced from glucose metabolism through the pentose phosphate pathway (PPP). Little is known regarding the regulation of endogenous erythritol synthesis in humans. In the present study, we investigated the stimuli that promote erythritol synthesis in human cells and characterized potential points of regulation along the PPP. Human A549 lung carcinoma cells were chosen for their known ability to synthesize erythritol. A549 cells were treated with potential substrates for erythritol production, including glucose, fructose, and glycerol. Using siRNA knockdown, we assessed the necessity of enzymes G6PD, TKT, TALDO, and SORD for erythritol synthesis. We also used position-specific 13C-glucose tracers to determine whether the carbons for erythritol synthesis are derived directly from glycolysis or through the oxidative PPP. Finally, we assessed if erythritol synthesis responds to oxidative stress using chemical and genetic models. Intracellular erythritol was directly associated with media glucose concentration. In addition, siRNA knockdown of TKT or SORD inhibited erythritol synthesis, whereas siG6PD did not. Both chemically induced oxidative stress and constitutive activation of the antioxidant response transcription factor NRF2 elevated intracellular erythritol. Our findings indicate that erythritol synthesis is proportional to flux through the PPP and is regulated by non-oxidative PPP enzymes.
Proteomic Profiling of Hypoplastic Lungs Suggests an Underlying Inflammatory Response in the Pathogenesis of Abnormal Lung Development in Congenital Diaphragmatic Hernia
Authors: Wagner Richard , Lieckfeldt Paula , Piyadasa Hadeesha , Markel Moritz , Riedel Jan , Stefanovici Camelia , Peukert Nicole , Patel Daywin , Derraugh Gabrielle , Min Suyin Lum , Gosemann Jan-Hendrik , Deprest Jan , Pascoe Christopher D. , Tse Andrew , Lacher Martin , Mookherjee Neeloffer , Keijzer Richard
Published: March 2022

The pathogenesis of lung hypoplasia in congenital diaphragmatic hernia (CDH), a common birth defect, is poorly understood. The diaphragmatic defect can be repaired surgically, but the abnormal lung development contributes to a high mortality in these patients. To better understand the underlying pathobiology, we used the nitrofen rat model of CDH and characterized the proteome of hypoplastic CDH lungs at the alveolar stage (E21). Amongst the 218 significantly altered proteins between CDH and control lungs were Tenascin C, CREBBP, LYN and STAT3. We showed that Tenascin C was decreased around the distal airway branches in nitrofen and human fetal CDH lungs. In contrast, STAT3 was significantly increased in the airway epithelium of nitrofen lungs at E21. STAT3 inhibition after direct nitrofen exposure to fetal rat lung explants (E14.5) partially reversed the hypoplastic lung phenotype ex vivo by increasing peripheral lung budding. Moreover, we demonstrated that several STAT3 associated cytokines (IL-15, IL-9, IL-2) are increased in fetal tracheal aspirates of CDH survivors compared to non-survivors after fetoscopic tracheal occlusion. Using pathway analysis for significantly altered proteins in our proteomic analysis, we observed an enrichment in inflammatory response associated with Epstein Barr Virus and cytokine signaling in nitrofen CDH lungs. However, we were unable to detect EBV mRNA via in-situ Hybridization in human CDH lungs. With our unbiased proteomics approach, we show for the first time that inflammatory processes are likely underlying the pathogenesis of abnormal lung development in CDH.
Human repair-related Schwann cells adopt functions of antigen-presenting cells in vitro
Authors: Berner Jakob , Weiss Tamara , Sorger Helena , Rifatbegovic Fikret , Kauer Max , Windhager Reinhard , Dohnal Alexander , Ambros Peter F. , Ambros Inge M. , Steinberger Peter , Taschner-Mandl Sabine
Published: March 2022

The plastic potential of Schwann cells (SCs) is increasingly recognized to play a role after nerve injury and in diseases of the peripheral nervous system. In addition, reports on the interaction between SCs and immune cells indicate their involvement in inflammatory processes. However, data about the immunocompetence of human SCs are primarily derived from neuropathies and it is currently unknown whether SCs directly regulate an adaptive immune response after nerve injury.

Here, we performed a comprehensive analysis of the immunomodulatory capacities of human repair-related SCs (hrSCs), which recapitulate SC response to nerve injury in vitro. We used our previously established protocol for the culture of primary hrSCs from human peripheral nerves and analyzed the transcriptome, secretome, and cell surface proteins for signatures and markers relevant in innate and adaptive immunity, performed phagocytosis assays, and monitored T-cell subset activation in co-cultures with autologous human T-cells.

Our findings show that hrSCs are highly phagocytic, which is in line with high MHCII expression. In addition, hrSCs express co-regulatory molecules, such as CD40, CD80, B7H3, CD58, CD86, HVEM, release a plethora of chemoattractants, matrix remodelling proteins and pro- as well as anti-inflammatory cytokines, and upregulate the T-cell inhibiting PD-L1 molecule upon pro-inflammatory stimulation with IFNγ. Furthermore, hrSC contact reduced the number and activation status of allogenic CD4+ and CD8+ T-cells.

This study demonstrates that hrSCs possess features and functions typical for professional antigen presenting cells in vitro, and suggest a new role of these cells as negative regulators of T-cell immunity during nerve regeneration.

Main points

Human repair-related Schwann cells (hrSC) function as professional antigen presenting cells.

HrSCs up-regulate PD-L1 upon pro-inflammatory IFNγ stimulation.

HrSCs hamper CD4+ and CD8+ T-cell activation.

Graphical abstract
A comparison of six DNA extraction protocols for 16S, ITS, and shotgun metagenomic sequencing of microbial communities
Authors: Shaffer Justin P. , Carpenter Carolina S. , Martino Cameron , Salido Rodolfo A. , Minich Jeremiah J. , Bryant MacKenzie , Sanders Karenina , Schwartz Tara , Humphrey Gregory , Swafford Austin D. , Knight Rob
Published: March 2022

Microbial communities contain a broad phylogenetic diversity of organisms, however the majority of methods center on describing bacteria and archaea. Fungi are important symbionts in many ecosystems, and are potentially important members of the human microbiome, beyond those that can cause disease. To expand our analysis of microbial communities to include fungal ITS data, we compared five candidate DNA extraction kits against our standardized protocol for describing bacteria and archaea using 16S rRNA gene amplicon- and shotgun metagenomics sequencing. We present results considering a diverse panel of host-associated and environmental sample types, and comparing the cost, processing time, well-to-well contamination, DNA yield, limit of detection, and microbial community composition among protocols. Across all criteria, we found the MagMAX Microbiome kit to perform best. The PowerSoil Pro kit performed comparably, but with increased cost per sample and overall processing time. The Zymo MagBead, NucleoMag Food, and Norgen Stool kits were included.

Accession numbers

Raw sequence data were deposited at the European Nucleotide Archive (accession#: ERP124610) and raw and processed data are available at Qiita (Study ID: 12201). All processing and analysis code is available on GitHub (github.com/justinshaffer/Extraction_kit_testing).

Methods summary

To allow for downstream applications involving fungi in addition to bacteria and archaea, we compared five DNA extraction kits with our previously established, standardized protocol for extracting DNA for microbial community analysis. Across ten diverse sample types, we found one extraction kit to perform comparably or better than our standardized protocol. Our conclusion is based on per-sample comparisons of DNA yield, the number of quality-filtered sequences generated, the limit of detection of microbial cells, microbial community alpha-diversity, beta-diversity, and taxonomic composition, and extent of well-to-well contamination.
The MIF SNP rs755622 is a germline determinant of tumor immune activation in Glioblastoma
Authors: Alban Tyler J. , Grabowski Matthew M. , Otvos Balint , Bayik Defne , Zalavadia Ajay , Makarov Vlad , Troike Katie , McGraw Mary , Rabljenovic Anja , Lauko Adam , Neumann Chase , Roversi Gustavo , Waite Kristin A. , Cioffi Gino , Patil Nirav , Tran Thuy T. , McCortney Kathleen , Steffens Alicia , Diaz C. Marcela , Brown J. Mark , Egan Kathleen M. , Horbinski Craig M. , Barnholtz-Sloan Jill S. , Vogelbaum Michael A. , Bucala Richard , Chan Timothy A. , Ahluwalia Manmeet S. , Lathia Justin D.
Published: March 2022

While immunotherapies have shown durable responses for multiple tumors, their efficacy remains limited in some advanced cancers, including glioblastoma. This may be due to differences in the immune landscape, as the glioblastoma microenvironment strongly favors immunosuppressive myeloid cells, which are linked to an elevation in immune-suppressive cytokines, including macrophage migration inhibitory factor (MIF). We now find that a single-nucleotide polymorphism (SNP) rs755622 in the MIF promoter associates with increased leukocyte infiltration in glioblastoma. Furthermore, we identified lactotransferrin expression as being associated with the rs755622 SNP, which could also be used as a biomarker for immune infiltrated tumors. These findings provide the first example in glioblastoma of a germline SNP that underlies differences in the immune microenvironment and identifies high lactotransferrin as a potential factor promoting immune activation.