bluuebunny/crossref_metadata_2025 huggingface dataset:
PanPA: generation and alignment of panproteome graphs
Authors: Dabbaghie Fawaz , Srikakulam Sanjay K. , Marschall Tobias , Kalinina Olga V.
Published: January 2023

Motivation

Compared to eukaryotes, prokaryote genomes are more diverse through different mechanisms, including a higher mutation rate and horizontal gene transfer. Therefore, using a linear representative reference can cause a reference bias. Graph-based pangenome methods have been developed to tackle this problem. However, comparisons in DNA space is still challenging due to this high diversity. In contrast, amino acids have higher similarity due to evolutionary constraints, resulting in conserved amino acids that, however, may be encoded by several synonymous codons. Coding regions cover the majority of the genome in prokaryotes. Thus, building panproteomes leverages the high sequence similarity while not losing much of the genome in non-coding regions.

Results

We presentPanPA, a method that takes a set of multiple sequence alignments (MSAs) of proteins or protein clusters, indexes them, and builds a graph for each MSA. In the querying step, it can align DNA or amino acid sequences back to these graphs. We first showcase thatPanPAgenerates correct alignments on a panproteome from 1,350E. coli. To demonstrate that panproteomes allow longer phylogenetic distance comparison, we compare DNA and protein alignments from 1,073S. entericaassemblies againstE. colireference genome, pangenome, and panproteome usingBWA,GraphAligner, andPanPArespectively, wherePanPAwas able to produce around 22% more alignments. We also aligned DNA short-reads WGS sample fromS. entericaagainst theE. colireference withBWAand the panproteome withPanPA, wherePanPAwas able to find alignment for 69% of the reads compared to 5% withBWA

Availability

PanPAis available athttps://github.com/fawaz-dabbaghieh/PanPA

Contact

fawaz@hhu.de,olga.kalinina@helmholtz-hzi.de

Supplementary information

Supplementary data are available atBioinformaticsonline.
Function and Importance of Marine Bacterial Transporters of Plankton Exometabolites
Authors: Schroer William F. , Kepner Hannah E. , Uchimiya Mario , Mejia Catalina , Rodriguez Lidimarie Trujillo , Reisch Christopher R. , Moran Mary Ann
Published: January 2023

Metabolite exchange within marine microbial communities transfers carbon and other major elements through global cycles and forms the basis of microbial interactions. Yet lack of gene annotations and concern about the quality of existing ones remain major impediments to revealing the metabolite-microbial network. We employed an arrayed mutant library of the marine bacteriumRuegeria pomeroyiDSS-3 to experimentally annotate substrates of organic compound transporter systems, using mutant growth and compound drawdown analyses to link transporters to their substrates. Mutant experiments verified substrates for thirteenR. pomeroyitransporters. Four were previously hypothesized based on gene expression data (taurine, glucose/xylose, isethionate, and cadaverine/putrescine/spermidine); five were previously hypothesized based on homology to experimentally annotated transporters in other bacteria (citrate, glycerol,N-acetylglucosamine, fumarate/malate/succinate, and dimethylsulfoniopropionate); and four had no previous annotations (thymidine, carnitine, cysteate, and 3-hydroxybutyrate transporter). These bring the total number of experimentally-verified organic carbon influx transporters to 17 of 126 in theR. pomeroyigenome. In a longitudinal study of a coastal phytoplankton bloom, expression patterns of the experimentally annotated transporters linked them to different stages of the bloom, and also led to the hypothesis that citrate and 3-hydroxybutyrate were among the most highly available bacterial substrates. Improved functional knowledge of these gatekeepers of organic carbon uptake is facilitating better characterization of the surface ocean metabolite network.
Enhanced germination and electrotactic behaviour ofPhytophthora palmivorazoospores in weak electric fields
Authors: Moratto Eleonora , Rothery Stephen , Bozkurt Tolga O. , Sena Giovanni
Published: January 2023

Soil-dwelling microorganisms use a variety of chemical and physical signals to navigate their environment. Plant roots produce endogenous electric fields which result in characteristic current profiles. Such electrical signatures are hypothesised to be used by pathogens and symbionts to track and colonise plant roots.

The oomycete pathogenPhytophthora palmivoragenerates motile zoospores which swim towards the positive pole when exposed to an external electric fieldin vitro.

Here, we provide a quantitative characterization of their electrotactic behaviour in 3D. We found that a weak electric field (0.7 - 1.0 V/cm) is sufficient to induce an accumulation of zoospore at the positive pole, without affecting their encystment rate. We also show that the same external electric field increases the zoospore germination rate and orients the germ tube’s growth. We conclude that several early stages of theP. palmivorainfection cycle are affected by external electric fields.

Taken together, our results are compatible with the hypothesis that pathogens use plant endogenous electric fields for host targeting.
Human-gut phages harbor sporulation genes
Authors: Schwartz DA , Rodríguez-Ramos J , Shaffer M , Flynn R , Daly R , Wrighton KC , Lennon Jay T.
Published: January 2023

Spore-forming bacteria are prevalent in mammalian guts and have implications for host health and nutrition. The production of dormant spores is thought to play an important role in the colonization, persistence, and transmission of these bacteria. Spore formation also modifies interactions among microorganisms such as infection by phages. Recent studies suggest that phages may counter dormancy-mediated defense through the expression of phage-encoded sporulation genes during infection, which can alter the transitions between active and inactive states. By mining genomes and gut-derived metagenomes, we identified sporulation genes that are preferentially encoded by phages that infect spore-forming bacteria. These included genes involved in chromosome partitioning, DNA damage repair, and cell wall-associated functions. In addition, phages contained homologs of sporulation-specific transcription factors, notablyspo0A, the master regulator of sporulation, which could allow phages to control the complex genetic network responsible for spore development. Our findings suggest that phages could influence the formation of bacterial spores with implications for the health of the human gut microbiome, as well as bacterial communities in other environments.

SIGNIFICANCE

Phages acquire bacterial genes and use them to alter host metabolism in ways that enhance their fitness. To date, most auxiliary genes replace or modulate enzymes that are used by the host for nutrition or energy production. However, phage fitness is affected by all aspects of host physiology, including decisions that reduce metabolic activity of the cell. Here we focus on endosporulation, a complex and ancient form of dormancy found among the Bacillota that involves hundreds of genes. By coupling homology searches with host classification, we identify 31 phage-encoded homologs of sporulation genes that are mostly limited to phages infecting spore-forming bacteria. Nearly one-third the homologs recovered were regulatory genes suggesting that phages may manipulate host genetic networks by tapping into their control elements. Our findings also suggest a mechanism by which phages can overcome the defensive strategy of dormancy, which may be involved in coevolutionary dynamics of spore-forming bacteria.
Facilitative interaction networks in experimental microbial community dynamics
Authors: Fujita Hiroaki , Ushio Masayuki , Suzuki Kenta , Abe Masato S. , Yamamichi Masato , Okazaki Yusuke , Canarini Alberto , Hayashi Ibuki , Fukushima Keitaro , Fukuda Shinji , Kiers E. Toby , Toju Hirokazu
Published: January 2023

Understanding potential roles of facilitative interactions between species is one of the major challenges in ecology and microbiology. However, we still have limited knowledge of entangled webs of facilitative interactions in ecosystems. By compiling whole-genome shotgun metagenomic data of an experimental microbial community, we tested the hypothesis that architecture of facilitative interaction networks could change through time. A metabolic modeling approach for estimating dependence between microbial genomes (species) allowed us to infer the network structure of potential facilitative interactions at 13 time points through the 110-day monitoring of experimental microbiomes. We then found that positive feedback loops, which were theoretically predicted to promote cascade breakdown of ecological communities, existed within the inferred networks of metabolic interactions prior to the drastic community-compositional shift observed in the microbiome time-series. We further applied “directed-graph” analyses to pinpoint potential keystone species located at the “upper stream” positions of such feedback loops. These analyses on facilitative interactions will help us understand key mechanisms causing catastrophic shifts in microbial community structure.
Secretory and transcriptomic responses of mantle cells to low pH in the Pacific oyster (Crassostrea gigas)
Authors: Zúñiga-Soto Nicolás , Pinto-Borguero Ingrid , Quevedo Claudio , Aguilera Felipe
Published: January 2023

Since the Industrial Revolution, the concentration of atmospheric carbon dioxide (CO2) due to anthropogenic activities has increased at unprecedented rates. One-third of the atmospheric anthropogenic CO2emissions are dissolved in the oceans affecting the chemical equilibrium of seawater, which in turn leads to a decrease in pH and carbonate ion (CO32−) concentration, a phenomenon known as ocean acidification (OA). This chemical disequilibrium can be detrimental to marine organisms (e.g., mollusks) that fabricate mineralized structures based on calcium carbonate (CaCO3). Most studies on the effect of reduced pH in seawater have been conducted on the early developmental stages of shell-building invertebrates, neglecting how adult individuals face OA stress. Here, we evaluate histological, secretory, and transcriptional changes in the mantle of adult oysters (Crassostrea gigas) exposure to ambient (8.0 ± 0.2) and reduced (7.6 ± 0.2) pH during 20 days. Most histological observations did not show differences in terms of mantle cell morphology. However, Alcian Blue/PAS staining revealed significant differences in the number of Alcian Blue positive cells in the mantle edge, suggesting a decrease in the secretory activity in this morphogenetic zone. Transcriptomic analysis revealed 172 differentially expressed genes (DEGs) between mantle tissues from adult oysters kept in normal and reduced pH conditions. Almost 18% of the DEGs encode secreted proteins that are likely to be contributing to shell fabrication and patterning. 17 of 31 DEGs encoding secreted proteins correspond to oyster-specific genes, highlighting the fact that molluscan shell formation is underpinned by a rapidly evolving secretome. The GO analysis of DEGs encoding secreted proteins showed that they are involved in the cellular response to stimulus, response to stress, protein binding, and ion binding, suggesting these biological processes and molecular functions are altered by OA. This study demonstrates that histology and gene expression profiling can advance our understanding of the cellular and molecular mechanisms underlying adult oyster tolerance to low pH conditions.
Widespread Autonomic Physiological Coupling Across the Brain-Body Axis
Authors: Bolt Taylor , Wang Shiyu , Nomi Jason S. , Setton Roni , Gold Benjamin P. , deB.Frederick Blaise , Thomas Yeo B.T. , Jean Chen J. , Picchioni Dante , Spreng R. Nathan , Keilholz Shella D. , Uddin Lucina Q. , Chang Catie
Published: January 2023

The brain is closely attuned to visceral signals from the body’s internal environment, as evidenced by the numerous associations between neural, hemodynamic, and peripheral physiological signals. We show that these brain-body co-fluctuations can be captured by a single spatiotemporal pattern. Across several independent samples, as well as single-echo and multi-echo fMRI data acquisition sequences, we identify widespread co-fluctuations in the low-frequency range (0.01 - 0.1 Hz) between resting-state global fMRI signals, neural activity, and a host of autonomic signals spanning cardiovascular, pulmonary, exocrine and smooth muscle systems. The same brain-body co-fluctuations observed at rest are elicited by arousal induced by cued deep breathing and intermittent sensory stimuli, as well as spontaneous phasic EEG events during sleep. Further, we show that the spatial structure of global fMRI signals is maintained under experimental suppression of end-tidal carbon dioxide (PETCO2) variations, suggesting that respiratory-driven fluctuations in arterial CO2 accompanying arousal cannot explain the origin of these signals in the brain. These findings establish the global fMRI signal as a significant component of the arousal response governed by the autonomic nervous system.
Immigration and seasonal bottlenecks: High inbreeding despite high genetic diversity in an oscillating population of the biting midge,Culicoides sonorensis(Diptera: Ceratopogonidae)
Authors: Shults Phillip , Zhang Xinmi , Moran Megan , Cohnstaedt Lee W. , Gerry Alec C. , Vargo Edward L. , Eyer Pierre-Andre
Published: January 2023

Most population genetic studies concern spatial genetic differentiation, but far fewer aim at analyzing the temporal genetic changes that occur within populations. Vector species, including mosquitoes and biting midges, are often characterized by oscillating adult population densities, which may affect their dispersal, selection, and genetic diversity over time. Here, we used a population ofCulicoides sonorensisfrom a single site in California to investigate short-term (intra-annual) and long-term (inter-annual) temporal variation in genetic diversity over a three year period. This biting midge species is the primary vector of several viruses affecting both wildlife and livestock, thus a better understanding of the population dynamics of this species can help inform epidemiological studies. We found no significant genetic differentiation between months or years, and no correlation between adult populations and the inbreeding coefficient (FIS). However, we show that repeated periods of low adult abundance during cooler winter months resulted in recurring bottleneck events. Interestingly, we also found a high number of private and rare alleles, which suggests both a large, stable population, as well as a constant influx of migrants from nearby populations. Overall, we showed that the high number of migrants maintains a high level of genetic diversity by introducing new alleles, while this increased diversity is counterbalanced by recurrent bottleneck events potentially purging unfit alleles each year. These results highlight the temporal influences on population structure and genetic diversity inC. sonorensisand provide insight into factors effecting genetic variation that may occur in other vector species with fluctuating populations.
Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic lociin situ
Authors: Tsue Ashley F. , Kania Evan E. , Lei Diana Q. , Fields Rose , McGann Christopher D. , Hershberg Elliot , Deng Xinxian , Kihiu Maryanne , Ong Shao-En , Disteche Christine M. , Kugel Sita , Beliveau Brian J. , Schweppe Devin K. , Shechner David M.
Published: January 2023

Throughout biology, RNA molecules form complex networks of molecular interactions that are central to their function, but remain challenging to investigate. Here, we introduce Oligonucleotide-mediated proximity-interactome MAPping (O-MAP), a straightforward method for elucidating the biomolecules near an RNA of interest, within its native cellular context. O-MAP uses programmable oligonucleotide probes to deliver proximity-biotinylating enzymes to a target RNA, enabling nearby molecules to be enriched by streptavidin pulldown. O-MAP induces exceptionally precise RNA-localizedin situbiotinylation, and unlike alternative methods it enables straightforward optimization of its targeting accuracy. Using the 47S pre-ribosomal RNA and long noncoding RNAXistas models, we develop O-MAP workflows for unbiased discovery of RNA-proximal proteins, transcripts, and genomic loci. This revealed unexpected co-compartmentalization ofXistand other chromatin-regulatory RNAs and enabled systematic characterization of nucleolar-chromatin interactions across multiple cell lines. O-MAP is portable to cultured cells, organoids, and tissues, and to RNAs of various lengths, abundances, and sequence composition. And, O-MAP requires no genetic manipulation and uses exclusively off-the-shelf parts. We therefore anticipate its application to a broad array of RNA phenomena.
The heme-responsive PrrH sRNA regulatesPseudomonas aeruginosapyochelin gene expression
Authors: Hoang Tra-My , Huang Weiliang , Gans Jonathan , Nowak Evan , Barbier Mariette , Wilks Angela , Kane Maureen A. , Oglesby Amanda G.
Published: January 2023

Pseudomonas aeruginosais an opportunistic pathogen that requires iron for growth and virulence, yet this nutrient is sequestered by the innate immune system during infection. When iron is limiting,P. aeruginosaexpresses the PrrF1 and PrrF2 small regulatory RNAs (sRNAs), which post-transcriptionally repress expression of non-essential iron-containing proteins thus sparing this nutrient for more critical processes. The genes for the PrrF1 and PrrF2 sRNAs are arranged in tandem on the chromosome, allowing for the transcription of a longer heme-responsive sRNA, termed PrrH. While the functions of PrrF1 and PrrF2 have been studied extensively, the role of PrrH inP. aeruginosaphysiology and virulence is not well understood. In this study, we performed transcriptomic and proteomic studies to identify the PrrH regulon. In shaking cultures, the pyochelin synthesis proteins were increased in two distinctprrHmutants compared to wild type, while the mRNAs for these proteins were not affected byprrHmutation. We identified complementarity between the PrrH sRNA and sequence upstream of thepchEmRNA, suggesting potential for PrrH to directly regulate expression of genes for pyochelin synthesis. We further showed thatpchEmRNA levels were increased in theprrHmutants when grown in static but not shaking conditions. Moreover, we discovered controlling for the presence of light was critical for examining the impact of PrrH onpchEexpression. As such, our study reports on the first likely target of the PrrH sRNA and highlights key environmental variables that will allow for future characterization of PrrH function.

Importance

In the human host, iron is predominantly in the form of heme, whichPseudomonas aeruginosacan acquire as an iron source during infection. We previously showed that the iron-responsive PrrF sRNAs are critical for mediating iron homeostasis duringP. aeruginosainfection; however the function of the heme-responsive PrrH sRNA remains unclear. In this study, we identified genes for pyochelin siderophore biosynthesis, which mediate uptake of inorganic iron, as a novel target of PrrH regulation. This study therefore highlights a novel relationship between heme availability and siderophore biosynthesis inP. aeruginosa.
VPg impact on Ryegrass mottle virus serine-like 3C protease proteolysis and structure
Authors: Kalnins Gints , Ludviga Rebeka , Kalnciema Ieva , Resevica Gunta , Zeltina Vilija , Bogans Janis , Tars Kaspars , Zeltins Andris , Balke Ina
Published: January 2023

Sobemoviruses encode serine-like 3C proteases (Pro) that participate in the processing and maturation of other virus-encoded proteins. Itscisandtransactivity is mediated by the naturally unfolded virus-genome-linked protein (VPg). NMR studies show a Pro-VPg complex interaction and VPg tertiary structure; however, information regarding structural changes of the Pro-VPg complex during interaction is lacking. Here, we solved a full Pro-VPg 3D structure of ryegrass mottle virus (RGMoV) that demonstrates the structural changes in three different conformations due to VPg interaction with Pro. We identified a unique site of VPg interaction with Pro that was not observed in other sobemoviruses and observed different conformations of the Pro β2 barrel. This is the first report of a full plant Pro crystal structure with its VPg cofactor. We also confirmed the existence of an unusual previously unmapped cleavage site for sobemovirus Pro in the transmembrane domain: E/A. We demonstrated that RGMoV Proin cisactivity is not regulated by VPg and thatin trans, VPg can also mediate Pro in free form. Additionally, we observed Ca2+and Zn2+inhibitory activities on the Pro cleavage activity.

Author summary

The gRNA of sobemoviruses encodes two polyproteins that are processed by a serine protease. We found that in the bacterial expression system, Pro is activein cisandin trans, where onlyin transactivity is mediated by VPg not only in the fusion form with Pro but also in the free form. Here, we present structural changes in the catalytic and substrate-binding sites of Pro caused by VPg, which can explain thein transactivity and structure of sobemovirus VPg C-terminal peptide. In addition, we confirmed a new cleavage site not previously characterized in sobemoviruses. Additionally, Ca2+and Zn2+decreased Pro cleavage activity. This information could provide a better understanding of a serine protease and their proteolytic mechanisms during viral protein maturation.
Electronic data review, client reminders, and expanded clinic hours for improving cervical cancer screening rates after COVID-19 pandemic shutdowns: a multi-component quality improvement program
Authors: Ghosh Sue , Fantes Jackie , Leschly Karin , Mazul Julio , Perkins Rebecca
Published: January 2023

Objective

To improve cervical cancer screening (CCS) rates, the East Boston Neighborhood Health Center (EBNHC) implemented a Quality Improvement (QI) initiative from March to August 2021.

Methods

Staff training was provided. A 21-provider team validated overdue CCS indicated by electronic medical record data. To improve screening, CCS-only sessions were created during regular clinic hours (n=5) and weekends/evenings (n=8). Patients were surveyed on their experience.

Results

6126 charts were reviewed. Of the list of overdue patients, outreach was performed to 1375 patients to schedule the 13 sessions. A total of 459 (33%) of patients completed screening, 622 (45%) could not be reached, and 203 (15%) canceled or missed appointments. The proportion of total active patients who were up to date with CCS increased from 68% in March to 73% in August 2021. Survey results indicated high patient satisfaction, and only 42% of patients would have scheduled CCS without outreach.

Conclusions

The creation of a validated patient chart list and extra clinical sessions devoted entirely to CCS improved up-to-date CCS rates. However, high rates of unsuccessful outreach and cancelations limited sustainability. This information can be used by other community health centers to optimize clinical workflows for CCS.

Funding

All funding was internal from EBNHC Adult Medicine, Family Medicine, and Women’s Health Departments.
A pivotal study on patients’ selection for BRCA1 and BRCA2 mutations by different models in Libyan breast cancer women
Authors: Elmaihub Eanas , Alhudiri Inas , Elzagheid Adam , Elfagi Fakria , Hassen Elham
Published: January 2023

Introduction

The BRCA mutation spectrum of familial breast cancer in Libya remains unknown. Several genetic models developed to predict the probability of BRCA1/2 mutations have not been applied in Libya, where the NCCN criteria are used for highly penetrating breast cancer susceptibility genes. This study aimed to predict BRCA1/2 mutation probability in familial breast cancer and eligibility for genetic testing by using BOADICEA and BRCAPRO models and NCCN criteria.

Methods

BRCA1/2 mutations were retrospectively predicted in 62 unrelated women with familial breast cancer between 2018 and 2021. Logistic regression, ROC analysis, and AUC were used to compare NCCN referral criteria with the BRCAPRO and BOADICEA scores.

Results

Of 62 breast cancer patients, 32 (51.6%) (mean age 43.5±8 years) were predicted by both models as BRCA mutation carriers. BRCAPRO predicted BRCA1 and BRCA2 mutations in 27.4% and 41.9% of the women, respectively. BOADICEA predicted 8% for BRCA1 and 29% for BRCA2. At least one NCCN criterion was met by 50/62 women (80.6%). Three criteria were statistically significant predictors in BRCAPRO and BOADICEA: breast cancer at ≤ 50 years with one or more close blood relatives with breast cancer, breast cancer patient with a close relative of male breast cancer, and triple-negative breast cancer. For the three respective criteria, sensitivity was 0.78, 0.89 and 0.75, specificity was 0.33, 0.39 and 0.22, AUC was 0.72, 0.75 and 0.76, PPV was 78%, 27.5% and 33.3, and NPV was 67%, 97% and 95.5.

Conclusions

BODICEA and BRCAPRO models are suitable for recommending genetic testing for BRCA gene mutations. The NCCN criteria are too broad.
How much disease-risk is due to old age and established risk factors?
Authors: Webster Anthony J.
Published: January 2023

As improved healthcare leads to older populations, individuals will increasingly experience multiple diseases, possibly concurrently (multimorbidity). This article explores whether age and established risk factors are sufficient to explain the incidence rates of multiple, possibly coexisting diseases. By accounting for the limited age-range in UK Biobank data, previous work demonstrated that a Weibull model could accurately describe the incidence of ∼60% of the most common primary hospital diagnoses of diseases. These are used here to predict the age-dependent incidence of diseases with adjustment for established risk factors. A “Poisson binomial” model is combined with these to predict the total number of occurrences of each disease in the UK Biobank cohort that would be expected without pre-existing (prior) disease. For 123 diseases in men and 99 diseases in women, the total observed new cases of each disease (including those from individuals with pre-existing diseases and multimorbidity), were found to be approximately 1.5 times greater than that predicted for individuals without prior disease, and could not be explained by natural statistical variation. The multiple of 1.5 was sufficiently consistent across different diseases to prevent its use for classification of disease types, but there were differences for sub-groups such as smokers with high body mass index, and for some classes of disease (as defined by the International Classification of Diseases version 10). The results suggest that empirical modelling might allow reliable predictions of primary causes of hospital admissions, helping to facilitate the planning of future healthcare needs.
Efficacy and safety of biologic, biosimilars and targeted synthetic DMARDs in moderate-to-severe rheumatoid arthritis with inadequate response to methotrexate: a systematic review and network meta-analysis
Authors: Budtarad Nuttakarn , Prawjaeng Juthamas , Leelahavarong Pattara , Pilasant Songyot , Chanjam Chonticha , Narongroeknawin Pongthorn , Kitumnuaypong Tasanee , Katchamart Wanruchada
Published: January 2023

Objective

To assess the comparative efficacy and safety of approved biologic disease-modifying antirheumatic drugs (bDMARDs), biosimilars, and targeted synthetic disease-modifying antirheumatic drugs (tsDMARDs) for patients with rheumatoid arthritis (RA) who had inadequate responses to methotrexate (MTX).

Results

53 eligible studies were identified and 44 studies were included in a network meta-analysis. Using Surface Under the Cumulative Ranking Curve (SUCRA), tofacitinib (10 mg bid) with MTX [Relative risk (RR) 95% confidence interval (CI) 4.65 (2.98-7.27)] and tofacitinib (10 mg bid) [RR (95%CI)1.96 (1.27-3.03)] were ranked highest among tsDMARDs for increasing remission rate at 24-26 weeks and 48-52 weeks, respectively. For bDMARDs, tocilizumab (8 mg/kg) with MTX was ranked with highest treatment effect for remission at both 24-26 and 48-52 weeks [RR (95%CI) 3.06 (2.27-4.12); RR (95%CI) 2.52 (1.94-3.28)]. For safety, baricitinib (4 mg) and tofacitinib (5 mg bid) with MTX likely showed an increased risk of HZ with statistical significance [for baricitinib, RR (95%CI) 3.52 (1.38-9.02) at 24-26 weeks, and RR (95%CI) 4.20 (1.22-14.48) at 48-52 weeks, and for tofacitinib, RR (95%CI) 5.38 (1.00-28.91) at 48-52 weeks]. No statistically significant safety concerns for serious infection, tuberculosis (TB), cancer, and cardiovascular (CV) events were identified.

Conclusions

For RA patients who failed MTX, bDMARDs, biosimilars, and tsDMARDs monotherapy and combination therapy with MTX provided better treatment outcomes than MTX monotherapy with modest safety concerns within 24-52 weeks. A scarcity of longer-term effects and post-market surveillance necessitates further analyses using long-term patient-level data to improve the medication profile.

Rheumatology key messages

For RA patients who failed MTX and other conventional DMARDs, different types of DMARDs are available.

At dose- and time point-specific levels, tofacitinib (10 mg bd) showed the highest probability to be the most effective in achieving remission at 24-26 weeks.

An increased risk of herpes zoster was found for baricitinib (4 mg) and tofacitinib (5 mg bid) with MTX.
Chiral Graphene Quantum Dots Enhanced Drug Loading into Exosomes
Authors: Zhang Youwen , Zhu Yini , Kim Gaeun , Wang Ceming , Zhu Runyao , Lu Xin , Chang Hsueh-Chia , Wang Yichun
Published: January 2023

As nanoscale extracellular vesicles secreted by cells, exosomes have enormous potential as safe and effective vehicles to deliver drugs into lesion locations. Despite promising advances with exosome-based drug delivery systems, there are still challenges to drug loading into exosome, which hinder the clinical applications of exosomes. Herein, we report an exogenous drug-agnostic chiral graphene quantum dots (GQDs) exosome-loading platform, based on chirality matching with the exosome lipid bilayer. Both hydrophobic and hydrophilic chemical and biological drugs can be functionalized or adsorbed onto GQDs by π–π stacking and van der Waals interactions. By tuning the ligands and GQD size to optimize its chirality, we demonstrate drug loading efficiency of 66.3% and 64.1% for Doxorubicin and siRNA, which is significantly higher than other reported exosome loading techniques.
Ralstonia solanacearumpandemic lineage strain UW551 overcomes inhibitory xylem chemistry to break tomato bacterial wilt resistance
Authors: Hamilton Corri D. , Zaricor Beatriz , Dye Carolyn Jean , Dresserl Emma , Michaels Renee , Allen Caitilyn
Published: January 2023

Plant pathogenicRalstoniastrains cause bacterial wilt disease by colonizing xylem vessels of many crops, including tomato. Host resistance is the best control for bacterial wilt, but resistance mechanisms of the widely used Hawaii7996 tomato breeding line are unknown. Using growth inex vivoxylem sap as a proxy for host xylem, we found thatRalstoniastrain GMI1000 grows in sap from both healthy plants andRalstonia-infected susceptible plants. However, sap fromRalstonia-infected Hawaii7996 plants inhibitedRalstoniagrowth, suggesting that in response toRalstoniainfection, resistant plants increase inhibitors in their xylem sap. Consistent with this, reciprocal grafting and defense gene expression experiments indicated that Hawaii7996 wilt resistance acts both above- and belowground. Concerningly, Hawaii7996 resistance is broken byRalstoniastrain UW551 of the pandemic lineage that threatens highland tropical agriculture. Unlike otherRalstoniastrains, UW551 grew well in sap fromRalstonia-infected Hawaii7996 plants. Moreover, otherRalstoniastrains could grow in sap from Hawaii7996 plants previously infected by UW551. Thus, UW551 overcomes Hawaii7996 resistance in part by detoxifying inhibitors in xylem sap. Testing a panel of xylem sap compounds identified by metabolomics revealed that no single chemical differentially inhibitsRalstoniastrains that cannot infect Hawaii7996. However, sap fromRalstonia-infected Hawaii7996 contained more phenolic compounds, which are known plant antimicrobial defenses. Culturing UW551 in this sap reduced total phenolic levels, indicating that the resistance-breakingRalstoniastrain degrades these chemical defenses. Together, these results suggest that Hawaii7996 tomato wilt resistance depends at least in part on inducible phenolic compounds in xylem sap.
Developmental changes in individual alpha frequency: Recording EEG data during public engagement events
Authors: Turner Christopher , Baylan Satu , Bracco Martina , Cruz Gabriela , Hanzal Simon , Keime Marine , Kuye Isaac , McNeill Deborah , Ng Zika , van der Plas Mircea , Ruzzoli Manuela , Thut Gregor , Trajkovic Jelena , Veniero Domenica , Wale Sarah P , Whear Sarah , Learmonth Gemma
Published: January 2023

Statistical power in cognitive neuroimaging experiments is often very low. Low sample size can reduce the likelihood of detecting real effects (false negatives) and increase the risk of detecting non-existing effects by chance (false positives). Here we document our experience of leveraging a relatively unexplored method of collecting a large sample size for simple electroencephalography (EEG) studies: by recording EEG in the community during public engagement and outreach events. We collected data from 346 participants (189 females, age range 6-76 years) over 6 days, totalling 29 hours, at local science festivals. Alpha activity (6-15 Hz) was filtered from 30 seconds of signal, recorded from a single electrode placed between the occipital midline (Oz) and inion (Iz) while participants rested with their eyes closed. A total of 289 good quality datasets were obtained. Using this community-based approach, we were able to replicate controlled, lab-based findings: IAF increased during childhood, reaching a peak frequency of 10.28 Hz at 28.1 years old, and slowed again in middle and older age. Total alpha power decreased linearly, but the aperiodic-adjusted alpha power did not change over the lifespan. Aperiodic slopes and intercepts were highest in the youngest participants. There were no associations between these EEG indexes and self-reported fatigue, measured by the Multidimensional Fatigue Inventory. Finally, we present a set of important considerations for researchers who wish to collect EEG data within public engagement and outreach environments.
poolHelper: an R package to help in designing Pool-Seq studies
Authors: Carvalho João , Faria Rui , Butlin Roger K. , Sousa Vítor C.
Published: January 2023

Next-generation sequencing of pooled samples (Pool-seq) is an important tool in population genomics and molecular ecology. In Pool-seq, the relative number of reads with an allele reflects the allele frequencies in the sample. However, unequal individual contributions to the pool and sequencing errors can lead to inaccurate allele frequency estimates. When designing Pool-seq studies, researchers need to decide the pool size (number of individuals) and average depth of coverage (sequencing effort). An efficient sampling design should maximize the accuracy of allele frequency estimates while minimizing the sequencing effort. We introduce an R package,poolHelper, enabling users to simulate Pool-seq data under different combinations of average depth of coverage, pool sizes and number of pools, accounting for unequal individual contribution and sequencing errors, modelled by parameters that users can modify.poolHelpercan be used to assess how different combinations of those parameters influence the error of sample allele frequencies and expected heterozygosity. The mean absolute error is computed by comparing the sample allele frequencies obtained based on individual genotypes with the frequency estimates obtained with Pool-seq. Using simulations under a single population model, we illustrate that increasing the depth of coverage does not necessarily lead to more accurate estimates, reinforcing that finding the best Pool-seq study design is not straightforward. Moreover, we show that simulations can be used to identify different combinations of parameters with similarly low mean absolute errors. ThepoolHelperpackage provides tools for performing simulations with different combinations of parameters before sampling and generating data, allowing users to define sampling schemes that minimize the sequencing effort.
Using RNASeq to investigate the involvement of theOphiocordycepsclock in ant host infection and behavioral manipulation
Authors: Das Biplabendu , Will Ian , Brouns Roos , Brachmann Andreas , de Bekker Charissa
Published: January 2023

Introduction

Parasites can modify host behavior to ensure their own growth and transmission. Multiple species of the fungiOphiocordycepsinfect ants, but in a species-specific manner; one fungal species co-evolved to successfully modify the behavior of one ant species. However, several characteristics of the behavioral modification seem to be similar across differentOphiocordyceps-ant systems, including a preference for the time of the day for manipulating host behavior. In this study, we explored the various mechanisms via which the circadian clock ofOphiocordycepsmight be playing a role in modifying host behavior. We studiedO. camponoti-floridanithat modifies the behavior of its ant hostCamponotus floridanus. To separate the role of the clock in behavior manipulation, from its role in growth and survival, we compared the daily gene expression profile ofO. camponoti-floridanito a generalist, non-manipulating fungal parasite,Beauveria bassiana, which also successfully infects the same ant host.

Results

Majority of the 24h rhythmicO. camponoti-floridanigenes show peak expression before or at the transitions between light and dark. Rhythmic genes inO. camponoti-floridani, for whichB. bassianalacks an ortholog, were overrepresented for enterotoxin genes. Around half of all genes that show 24h rhythms in eitherO. camponoti-floridaniorB. bassianashowed a consistent difference in their temporal pattern of daily expression. At the halfway mark inO. camponoti-floridaniinfections, when diseased ants show a loss of 24h rhythms in daily foraging, several fungal clock genes, includingFrequency, showed differential expression. Network analyses revealed a single gene cluster, containingWhite Collar 1and2, that showed overrepresentation for genes oscillating every 24h in liquid culture as well as genes differentially expressed while growing inside the ant head.

Conclusion

This study identifies several sets of putatively clock-controlled genes and biological processes inO. camponoti-floridanithat likely plays a role in modifying the behavior of its ant host. Differential expression ofO. camponoti-floridaniclock genes or 24h-rhythmic genes during infection is suggestive of either a loss of daily rhythm or a change in the amplitude of rhythmic gene expression. Both possibilities would suggest that a disease-associated change occurs to the functioning of theO. camponoti-floridaniclock, and its output, while the fungi grows inside the ant head.
Functional characterization ofSalmonellaTyphimurium encoded YciF, a domain of unknown function (DUF892) family protein, and its role in protection during bile and oxidative stress
Authors: Singh Madhulika , Penmatsa Aravind , Nandi Dipankar
Published: January 2023

YciF (STM14_2092) is a member of domain of unknown function (DUF892) family. It is an uncharacterized protein, involved in stress responses inSalmonellaTyphimurium. In this study, we investigated the significance of YciF and its DUF892 domain during bile and oxidative stress responses ofS. Typhimurium. Purified wild type YciF forms higher order oligomers, binds to iron and displays ferroxidase activity. Studies on the site-specific mutants revealed that the ferroxidase activity of YciF is dependent on the two metal binding sites present within the DUF892 domain. Transcriptional analysis displayed that the ΔcspE strain, which has compromised expression of YciF, encounters iron toxicity due to dysregulation of iron homeostasis in presence of bile. Utilizing this observation, we demonstrate that the bile mediated iron toxicity in ΔcspE causes lethality, primarily through the generation of reactive oxygen species (ROS). Expression of wild type YciF, but not the three mutants of the DUF892 domain, in ΔcspE alleviate ROS in presence of bile. Our results establish the role of YciF as a ferroxidase that can sequester excess iron in the cellular milieu to counter ROS-associated cell death. In fact, pre-treatment with an iron chelator mitigates the hypersensitivity of ΔcspE to bile.

Importance

The DUF892 domain has a wide taxonomic distribution encompassing several bacterial pathogens. This domain belongs to the ferritin-like superfamily; however, it has not been biochemically and functionally characterized. This is the first report of characterization of a member of this family. In this study, we demonstrate thatS. Typhimurium YciF is an iron binding protein with ferroxidase activity, which is dependent on the metal binding sites present within the DUF892 domain. It combats iron toxicity and oxidative damage caused due to exposure to bile. The functional characterization of YciF delineates the significance of the DUF892 domain in bacteria. In addition, our studies onS. Typhimurium bile stress response divulged the importance of comprehensive iron homeostasis in bacteria in presence of bactericidal compounds that tend to generate ROS irrespective of their primary targets.
Rectus FemorisMuscle Elasticity and Stiffness Correlates with Maximal Oxygen Consumption in Triathletes
Authors: Gavronski Georg , Reimets Ain , Talts Jaak , Koovit Indrek , Mandel Tõnis , Viir Ragnar , Vasar Eero , Veraksitš Alar
Published: January 2023

VO2max is considered single best indicator of cardiovascular fitness and aerobic endurance. We analyzed retrospectively, are there any relationships between muscle parameters and oxygen consumption in a study where the myoton equipment was used to establish muscle biomechanical properties, such as elasticity, stiffness, and tension (measured as oscillation frequency) in triathletes. Eight muscles were studied in 14 male triathletes over three years. Relaxed and contracted states of muscles were measured. VO2max was recorded in these athletes up to four times during this period. Average values were calculated for each athlete and High (max 71.8–min 62.3 ml/kg/min) and Low (59.1–51.3) oxygen consumption groups were formed. Higher oxygen consumption correlated significantly (r=−0.58; p=0.029) with improved elasticity (represented by smaller decrement values) of therectus femorismuscle in a contracted state. Also, in the High VO2max group, this muscle (in a relaxed state) was significantly more elastic and stiffer at the same time compared to the Low group. An ultrasound registration was also conducted to observe the depth of the device’s impact in the posterior crural muscles. It was confirmed that deep and substantial tissue disturbances were caused by this impact. According to our findings, myotonometry is an adequate method to establish muscle parameters. Elasticity and stiffness of therectus femorismuscle may determine success in triathlon.
Spatial determination and prognostic impact of the fibroblast transcriptome in pancreatic ductal adenocarcinoma
Authors: Croft Wayne , Pearce Hayden , Margielewska-Davies Sandra , Lim Lindsay , Nicol Samantha M. , Zayou Fouzia , Blakeway Daniel , Marcon Francesca , Powell-Brett Sarah , Mahon Brinder , Merard Reena , Zuo Jianmin , Middleton Gary , Roberts Keith , Brown Rachel M. , Moss Paul
Published: January 2023

Pancreatic ductal adenocarcinoma has a poor clinical outcome and responses to immunotherapy are suboptimal. Stromal fibroblasts are a dominant but heterogenous population within the tumor microenvironment and therapeutic targeting of stromal subsets may have therapeutic utility. Here we combined spatial transcriptomics and scRNA-Seq to define the transcriptome of tumor-proximal and tumor-distal cancer-associated fibroblasts (CAFs) and linked this to clinical outcome. Tumor-proximal fibroblasts comprised large populations of myofibroblasts, strongly expressed podoplanin, and were enriched for Wnt ligand signaling. In contrast, inflammatory CAFs were dominant within tumor-distal subsets and expressed complement components and the Wnt-inhibitor SFRP2. Poor clinical outcome was correlated with elevated HIF-1α and podoplanin whilst high level expression of inflammatory and complement genes was predictive of extended survival. These findings demonstrate the extreme transcriptional heterogeneity of CAFs and its determination by apposition to tumor. Selective targeting of tumor-proximal subsets, potentially combined with HIF-1α inhibition and immune stimulation, may offer a multimodal therapeutic approach for this disease.

Graphical Abstract
LACK OF INTERACTIONS BETWEEN PRENATAL IMMUNE ACTIVATION AND Δ9-TETRAHYDROCANNABINOL EXPOSURE DURING ADOLESCENCE IN BEHAVIOURS RELEVANT TO SYMPTOM DIMENSIONS OF SCHIZOPHRENIA IN RATS
Authors: Moreno-Fernández Mario , Ucha Marcos , Reis-de-Paiva Raquel , Marcos Alberto , Ambrosio Emilio , Higuera-Matas Alejandro
Published: January 2023

The causality in the association between cannabis use and the risk of developing schizophrenia has been the subject of intense debate in the last years. The development of animal models recapitulating several aspects of the disease is crucial for shedding light on this issue. Maternal infections are a known risk for schizophrenia. Here, we used the maternal immune activation (MIA) model combined with THC exposure during adolescence to examine several behaviours in rats (working memory in the Y maze, sociability in the three-chamber test, sucrose preference as a measure, prepulse inhibition and formation of incidental associations) that are similar to the different symptom clusters of the disease. To this end, we administered LPS to pregnant dams and when the offspring reached adolescence, we exposed them to a mild dose of THC to examine their behaviour in adulthood. We also studied several parameters in the dams, including locomotor activity in the open field, elevated plus maze performance and their response to LPS, that could predict symptom severity of the offspring, but found no evidence of any predictive value of these variables. In the adult offspring, MIA was associated with impaired working memory and sensorimotor gating, but surprisingly, it increased sociability, social novelty and sucrose preference. THC, on its own, impaired sociability and social memory, but there were no interactions between MIA and THC exposure. These results suggest that, in this model, THC during adolescence does not trigger or aggravate symptoms related to schizophrenia in rats.