bluuebunny/crossref_metadata_2025 huggingface dataset:
Artificial Intelligence based breast thermography using radiomic feature extraction versus conventional manual interpretation of breast thermograms in the prediction of breast cancer: a multi-reader study
Authors: Collison Sathiakar
Published: February 2023

Objective

In recent years artificial intelligence-enhanced breast thermography is increasingly being evaluated as an ancillary modality in the evaluation of breast disease. The objective of this study was to evaluate the performance of Thermalytix, a CE-marked system that analyzes thermal images using advanced thermal radiomics against unaided manual interpretation of thermographic images by trained thermologists.

Methods

In this retrospective, multi-reader study, thermal imaging data of 258 women who participated in a previously published clinical trial were used. These images were read manually by 3 trained thermologists independent of each other, using the approved scoring system of the American Association of Thermologists. None of the readers were involved in the collection of the images in the study cases. The images were then evaluated by the Thermalytix system, which is a commercially available software that automatically extracts hotspot, areolar and nipple radiomic parameters with a total of 64 individual radiomic features being analyzed using 3 random forest classifiers configured for 200 decision trees to generate a score predictive of the presence of breast cancer in the region of interest. The manual interpretation and Thermalytix interpretation were compared for sensitivity, specificity, positive predictive value, and negative predictive value and receiver operating characteristic curves were created to estimate prediction accuracy.

Results

Automated Thermalytix had sensitivity and specificity of 95.2% and 66.7% respectively while AUROC of 0.85 (13.7% greater) than manual interpretation. Further, hotspot and vascular scores derived in the automated Thermalytix are the strongest predictors of breast cancer lesions (AUROC: 0.84 and 0.83, respectively).

Conclusions

Overall this suggests that automated AI-based Thermalytix has higher accuracy in the prediction of breast cancer lesions and must be further investigated in the wider women population to validate its use in hospital settings as a screening modality for breast cancer.
Accessible and reliable neurometric testing in humans using a smartphone platform
Authors: Boele H.J. , Jung C. , Sherry S. , Roggeveen L.E.M. , Dijkhuizen S. , Öhman J. , Abraham E. , Uvarov A. , Boele C.P. , Gultig K. , Rasmussen A. , Vinueza-Veloz M.F. , Medina J.F. , Koekkoek S.K.E. , De Zeeuw C.I. , Wang S.S.-H.
Published: February 2023

Tests of human brain circuit function typically require fixed equipment in lab environments. We have developed a smartphone-based platform for neurometric testing. This platform, which uses AI models like computer vision, is optimized for at-home use and produces reproducible, robust results on a battery of tests, including eyeblink conditioning, prepulse inhibition of acoustic startle response, and startle habituation. This approach provides a scalable, universal resource for quantitative assays of central nervous system function.
Household Hardships and Responses to COVID-19 Pandemic-Related Shocks in Eastern Ethiopia
Authors: Muir Jonathan A. , Dheresa Merga , Madewell Zachary J. , Getachew Tamirat , Daraje Gamachis , Mengesha Gezahegn , Whitney Cynthia G. , Assefa Nega , Cunningham Solveig A.
Published: February 2023

Background

COVID-19 resulted in enormous disruption to life around the world. To quell disease spread, governments implemented lockdowns that likely created hardships for households. To improve knowledge of consequences, we examine how the pandemic period was associated with household hardships and assess factors associated with these hardships.

Methods

We conducted a cross-sectional study using quasi-Poisson regression to examine factors associated with household hardships. Data were collected between August and September of 2021 from a random sample of 880 households living within a Health and Demographic Surveillance System (HDSS) located in the Harari Region and the District of Kersa, both in Eastern Ethiopia.

Results

Having a head of household with no education, residing in a rural area, larger household size, lower income and/or wealth, and community responses to COVID-19, including lockdowns and travel restrictions, were independently associated with experiencing household hardships.

Conclusions

Our results identify characteristics of groups at-risk for household hardships during the pandemic; these findings may inform efforts to mitigate the consequences of COVID-19 and future disease outbreaks.
Development and Validation of the Overall Fidelity Enactment Scale for Complex Interventions (OFES-CI)
Authors: Ginsburg Liane , Hoben Matthias , Berta Whitney , Doupe Malcolm , Estabrooks Carole , Norton Peter , Reid Colin , Geerts Ariane , Wagg Adrian
Published: February 2023

Background. Assessing fidelity in complex interventions is important. Ignoring it increases the risk of discarding potentially effective interventions that failed to work because they were not implemented as intended or, accepting ineffective interventions whose effects were brought about by factors other than the intervention. Unlike simple interventions, fidelity assessment in complex interventions is underexplored and not straightforward. Adapting the evaluative approach used in Objective Structured Clinical Exams (OSCEs), we describe the development and validation of an easy to use, objective approach to fidelity assessment (the Overall Fidelity Enactment Scale for use in complex interventions: OFES-CI). Methods. We developed the OFES-CI and assessed its accuracy using secondary data collected as part of the process evaluation of the SCOPE intervention. Specifically, we compared the OFES-CI ratings obtained from trained study observers during SCOPE intervention workshops to more detailed and comprehensive qualitative fidelity enactment data collected between and during the same workshops (our gold standard). Results. The OFES-CI demonstrates acceptable reliability against our gold standard assessment approach and addresses the practicality problem in fidelity assessment by virtue of its suitable implementation qualities (acceptability, ease of completion, low burden, low training requirements). It can be easily adapted to assess enactment of a variety of complex interventions. Conclusions. Global ratings approaches validated in the context of assessing clinician competence in OSCEs provide a novel, practical and underexplored opportunity to assess fidelity enactment in complex trials. Given important questions that are increasingly being asked regarding evaluation of complex pragmatic interventions, the proposed approach to fidelity assessment, if incorporated into trial evaluation, stands to provide valuable insights not only into why an intervention may succeed or fail but also how we might carry out adaptations of complex interventions when they are needed.
Associations between reported healthcare disruption due to COVID-19 and avoidable hospitalisation: Evidence from seven linked longitudinal studies for England
Authors: Green Mark A. , McKee Martin , Hamilton Olivia , Shaw Richard J. , Macleod John , Boyd Andy ,   The LH&W NCS Collaborative, and Srinivasa Vittal Katikireddi
Published: February 2023

Background

Health services across the UK struggled to cope during the COVID-19 pandemic. Many treatments were postponed or cancelled, although the impact was mitigated by new models of delivery. While the scale of disruption has been studied, much less is known about if this disruption impacted health outcomes. The aim of our paper is to examine whether there is an association between individuals experiencing disrupted access to healthcare during the pandemic and risk of an avoidable hospitalisation.

Methods

We used individual-level data for England from seven longitudinal cohort studies linked to electronic health records from NHS Digital (n = 29 276) within the UK Longitudinal Linkage Collaboration trusted research environment. Avoidable hospitalisations were defined as emergency hospital admissions for ambulatory care sensitive and emergency urgent care sensitive conditions (1stMarch 2020 to 25thAugust 2022). Self-reported measures of whether people had experienced disruption during the pandemic to appointments (e.g., visiting their GP or an outpatient department), procedures (e.g., surgery, cancer treatment) or medications were used as our exposures. Logistic regression models examined associations.

Results

35% of people experienced some form of disrupted access to healthcare. Those whose access was disrupted were at increased risk of any (Odds Ratio (OR) = 1.80, 95% Confidence Intervals (CIs) = 1.34-2.41), acute (OR = 1.68, CIs = 1.13-2.53) and chronic (OR = 1.93, CIs = 1.40-2.64) ambulatory care sensitive hospital admissions. There were positive associations between disrupted access to appointments and procedures to measures of avoidable hospitalisations as well.

Conclusions

Our study presents novel evidence from linked individual-level data showing that people whose access to healthcare was disrupted were more likely to have an avoidable or potentially preventable hospitalisation. Our findings highlight the need to increase healthcare investment to tackle the short- and long-term implications of the pandemic beyond directly dealing with SARS-CoV-2 infections.
A tool to assess risk of bias in studies estimating the prevalence of mental health disorders (RoB-PrevMH)
Authors: Tonia Thomy , Buitrago-Garcia Diana , Peter Natalie , Mesa-Vieira Cristina , Li Tianjing , Furukawa Toshi A. , Cipriani Andrea , Leucht Stefan , Low Nicola , Salanti Georgia
Published: February 2023

Objective

Biases affect how certain we are about the available evidence, however no standard tool for assessing the risk of bias (RoB) in prevalence studies exists. For the purposes of a living systematic review on prevalence of mental health disorders during the COVID-19 pandemic, we developed a RoB tool to evaluate prevalence studies in mental health (RoB-PrevMH) and tested interrater reliability.

Methods

We reviewed existing RoB tools for prevalence studies until September 2020, to develop a tool for prevalence studies in mental health. We tested the reliability of assessments by different users of RoB-PrevMH in 83 studies stemming from two systematic reviews of prevalence studies in mental health. We assessed the interrater agreement by calculating the proportion of agreement and Kappa statistic for each item.

Results

RoB-PrevMH consists of three items that address selection bias and information bias. Introductory and signaling questions guide the application of the tool to the review question. The interrater agreement for the three items was 83%, 90% and 93%. The weighted kappa was 0.63 (95% CI 0.54 to 0.73), 0.71 (95% CI 0.67 to 0.85) and 0.32 (95% CI –0.04 to –0.63), respectively.

Conclusions

We developed a brief, user friendly, and adaptable tool for assessing RoB in studies on prevalence of mental health disorders. Initial results for interrater agreement were fair to substantial. The tool’s validity, reliability, and applicability should be assessed in future projects.
Pharmacokinetics of Cannabidiol: A systematic review and meta-regression analysis
Authors: Moazen-Zadeh Ehsan , Chisholm Alexandra , Bachi Keren , Hurd Yasmin L.
Published: February 2023

Background

In this review, we provide an updated assessment of available evidence on the pharmacokinetics (PK) of cannabidiol (CBD) and explore the impact of different factors on PK outcomes.

Materials and Methods

This systematic review and meta-regression analysis was pre-registered (PROSPERO: CRD42021269857). We systematically searched Medline, Embase, PsychInfo, and Web of Science Core Collection up to November 19, 2022. Trials of CBD in healthy adults were included if they reported at least one of the PK parameters of interest, including Tmax, Cmax, AUC0-t, AUC0-inf, and T1/2, in serum or plasma. Studies of patient populations or CBD co-administration with other medications were excluded. TheNational Heart, Lung, and Blood Institute’s Quality Assessment Tool for Before-After Studies with no Control Groupwas used. Random-effects multivariable meta-regression analysis was conducted.

Results

A total of 112 trial arms from 39 studies were included; 26 trial arms had a “Good” quality, 70 “Fair,” and 16 “Poor.” Eight arms used inhalation CBD, 29 oromucosal, 73 oral, and 2 intravenous. CBD formulations could be categorized to nanotech (n=14), oil-based (n=21), alcohol-based (n=10), water-based (n=12), Sativex (n=17), and Epidiolex (n=22). For single-dose studies, CBD doses ranged between 2-100mg in inhalation, 5-50mg in oromucosal, and 0.42-6000mg in oral administration. Sixty-six trial arms had only male participants or a higher number of males than females. The duration of the PK session was between 4h-164h. A higher CBD dose was associated with higher Cmax, AUC0-t, and AUC0-inf. Compared to oral administration, oromucosal administration was associated with lower Cmax, AUC0-t, and AUC0-inf. Fed status was associated with higher Cmax and AUC0-t when compared to the fasting status. A higher ratio of female participants was associated with lower Tmax in oral administration and higher Cmax.

Conclusion

As expected, CBD dose, route of administration, and diet were major determinants of CBD pharmacokinetics with oral routes providing higher bioavailability and nanotechnology formulations a faster onset. Though CBD appeared to have a faster onset and longer duration in females, more studies are required to delineate the role of biological sex. Factors that influence CBD PK have implications for medication development and appropriate dosing in clinical practice.
RyR1 protein content is reduced in inflammatory and mitochondrial myopathies and induces ER stress
Authors: Vidal Jeremy , Fernandez Eric , Wohlwend Martin , Laurila Pirkka-Pekka , Mejia Andrea Lopez , Ochala Julien , Lopez Mejia Isabel Christina , Lobrinus Johannes Alexandre , Kayser Bengt , Place Nicolas , Zanou Nadège
Published: February 2023

Decreased ryanodine receptor type 1 (RyR1) protein is a hallmark of recessiveRYR1-related myopathies (RyR1-RM), which are caused by recessive mutations in theRYR1gene. It is not clear how the decrease in the RyR1 protein triggers muscular disorders. Furthermore, it is a hot topic whether a decrease in RyR1 protein levels can also occur during non-RYR1-related myopathies. In this study, we first show that reducedRYR1transcripts are associated with various human myopathies, and that RyR1 protein levels are significantly decreased in muscle samples analysed in inflammatory myopathies (IM) and mitochondrial myopathies (MM), both of which are non-RYR1-RM. Secondly, proteomic data show that exclusive depletion of RyR1 proteinin vitrorecapitulates the common altered molecular pathways observed during myopathies. RyR1 protein depletion impairs ER-mitochondria tethering and Ca2+transfer to mitochondria, decreases mitophagy genes and induces an accumulation of dysfunctional mitochondria. This phenomenon is also associated with altered lipid homeostasis with an increase in deleterious sphingolipid species. Finally, decreased RyR1 protein levels lead to an increase in the ER stress markers GRP78-Bip and CHOP in muscle cellin vitro, and in mouse and human muscles. Overall, our results indicate an important role of RyR1 protein depletion and ER stress in the pathogenesis of myopathies.
Relationship between sexting and self-esteem, depression, anxiety, and stress among young people
Authors: Galanis Petros , Katsiroumpa Zoe , Katsiroumpa Aglaia , Tsakalaki Anastasia , Vasilopoulos Stefanos
Published: February 2023

Introduction

The huge spread of the internet and especially of social media has led to new ways of communication, even erotic communication, especially among young people, replacing, in many cases, activities that until now required the face-to-face meeting of individuals.

Aim

To investigate the relationship between sexting and self-esteem, depression, anxiety, and stress among young people. Also, we investigated the impact of demographic characteristics on sexting.

Methods

A cross-sectional study was conducted with 368 young people aged 18-30 years old. We created an anonymous form of the study questionnaire with Google forms and we disseminated it through social media. Thus, we obtained a convenience sample. We used valid scales to measure sexting, self-esteem, depression, anxiety and stress among young people. All scales in our study had very good Cronbach ‘s alpha.

Results

Mean age of the participants was 23.7 years, while 82.3% was females. Mean every day time that participants spent on social media/platforms/applications was 4.7 hours. Participants used more often to communicate with others Instagram (86.8%) and Facebook (62.8%), and then Viber (29.9%), TikTok (9.8%), Snapchat (6%) and WhatsApp (5.1%). Frequency of texting was low among participants, while self-esteem level was average. Moreover, participants had higher levels of stress than depression and anxiety. We found that increased sexting was associated with decreased self-esteem (r=-0.3, p=0.02), increased depression (r=0.4, p=0.001), increased anxiety (r=0.3, p=0.005), and increased stress (r=0.4, p<0.001). Multivariable linear regression analysis identified that increased number of accounts on social media/platforms/applications (coefficient beta=0.07, 95% confidence interval=0.01 to 0.13, p-value=0.023) and increased age (coefficient beta=0.08, 95% confidence interval=0.01 to 0.13, p-value=0.003) was associated with increased sexting.

Conclusions

Understanding the relationship between sexting and self-esteem, depression, anxiety, and stress in young people will give policy makers the opportunity to develop appropriate health education programmes to reduce risky sexual behaviors.
HPVsim: An agent-based model of HPV transmission and cervical cancer
Authors: Stuart Robyn M. , Cohen Jamie A. , Kerr Cliff C. , Mathur Prashant ,   National Disease Modeling Consortium of India, Abeysuriya Romesh G. , Zimmermann Marita , Rao Darcy W. , Boudreau Mariah C. , Lee Serin , Yang Luojun , Klein Daniel J.
Published: February 2023

In 2020, the WHO launched its first Global Strategy to Accelerate the Elimination of Cervical Cancer, outlining an ambitious set of targets for countries to achieve over the next decade. At the same time, new tools, technologies, and strategies are in the pipeline that may improve screening performance, expand the reach of prophylactic vaccines, and prevent the acquisition, persistence and progression of oncogenic HPV. Detailed mechanistic modeling can help identify the combinations of current and future strategies to combat cervical cancer. Open-source modeling tools are needed to shift the capacity for such evaluations in-country. Here, we introduce the Human papillomavirus simulator (HPVsim), a new open-source software package for creating flexible agent-based models parameterized with country-specific vital dynamics, structured sexual networks, and co-transmitting HPV genotypes. HPVsim includes a novel methodology for modeling cervical disease progression, designed to be readily adaptable to new forms of screening. The software itself is implemented in Python, has built-in tools for simulating commonly-used interventions, includes a comprehensive set of tests and documentation, and runs quickly (seconds to minutes) on a laptop. Performance is greatly enhanced by HPVsim’s multi-scale modeling functionality. HPVsim is open source under the MIT License and available via both the Python Package Index (via pip install) and GitHub (hpvsim.org).
Co-chaperone BAG3 directly target autophagic degradation via its LC3-interacting regions
Authors: Körschgen Hagen , Baeken Marius , Schmitt Daniel , Nagel Heike , Behl Christian
Published: February 2023

The co-chaperone BAG3 is a hub for a variety of cellular pathways via its multiple domains and its interaction with HSP70 and HSPB8. Under aging and cellular stress conditions in particular, together with molecular chaperones, BAG3 ensures the sequestration of aggregated or aggregation prone ubiquitinated proteins to the autophagic-lysosomal system via ubiquitin receptors. There are emerging indications that BAG3-mediated selective macroautophagy also copes with non-ubiquitinated cargo. Phylogenetically, BAG3 comprises several highly conserved predicted LIRs, LC3-interacting regions, which might directly target BAG3 including its cargo to ATG8 proteins and directly drive their autophagic degradation. Based on pull-down experiments, peptide arrays and proximity ligation assays, our results provide evidence of an interaction of BAG3 with ATG8 proteins. In addition, we could demonstrate that mutations within the LIRs impair co-localization with ATG8 proteins in immunofluorescence. A BAG3 variant mutated in all LIRs results in a substantial decrease of BAG3 levels within purified native autophagic vesicles compared to wild-type BAG3. These results strongly suggest LC3-mediated sequestration of BAG3. Therefore, we conclude that in addition of being a key co-chaperone to HSP70, BAG3 may also act as cargo receptor for client proteins, which would significantly extend the role of BAG3 in selective macroautophagy and protein quality control.

Synopsis

BAG3 ensures sequestration of aggregated ubiquitinated proteins to the autophagic-lysosomal degradation. Based on emerging indications this BAG3-mediated macroautophagy may also cope with non-ubiquitinated clients and comprises conserved predicted LC3 interacting regions, we analyzed the interaction with LC3 proteins. We evidenced an interaction of BAG3 with LC3 proteins by various measures including pull-down experiments, peptide arrays, proximity ligation assays, co-localization and native autophagic vesicles analysis. These results suggest BAG3 may additionally act as cargo receptor for client proteins.

Abstract Figure
Deep Learning-based Identification of Intraocular Pressure-Associated Genes Influencing Trabecular Meshwork Cell and Organelle Morphology
Authors: Greatbatch Connor J , Lu Qinyi , Hung Sandy , Tran Son N , Wing Kristof , Liang Helena , Han Xikun , Zhou Tiger , Siggs Owen M , Mackey David A , Liu Guei-Sheung , Cook Anthony L , Powell Joseph E , Craig Jamie E , MacGregor Stuart , Hewitt Alex W
Published: February 2023

PURPOSE

The exact pathogenesis of primary open-angle glaucoma (POAG) is poorly understood. Genome-wide association studies (GWAS) have recently uncovered many loci associated with variation in intraocular pressure (IOP); a crucial risk factor for POAG. Artificial intelligence (AI) can be used to interrogate the effect of specific genetic knockouts on the morphology of trabecular meshwork cells (TMCs), the regulatory cells of IOP.

METHODS

Sixty-two genes at fifty-five loci associated with IOP variation were knocked out in primary TMC lines. All cells underwent high-throughput microscopy imaging after being stained with a five-channel fluorescent cell staining protocol. A convolutional neural network (CNN) was trained to distinguish between gene knockout and normal control cell images. The area under the receiver operator curve (AUC) metric was used to quantify morphological variation in gene knockouts to identify potential pathological perturbations.

RESULTS

Cells whereRALGPS1had been perturbed demonstrated the greatest morphological variation from normal TMCs (AUC 0.851, SD 0.030), followed byLTBP2(AUC 0.846, SD 0.029) andBCAS3(AUC 0.845, SD 0.020). Of seven multi-gene loci, five had statistically significant differences in AUC (p<0.05) between genes, allowing for pathological gene prioritisation. The mitochondrial channel most frequently showed the greatest degree of morphological variation (33.9% of cell lines).

CONCLUSIONS

We demonstrate a robust method for functionally interrogating genome-wide association signals using high-throughput microscopy and AI. Genetic variations inducing marked morphological variation can be readily identified, allowing for the gene-based dissection of loci associated with complex traits.
Comparison of commercial DNA extraction kits for whole metagenome sequencing of human oral, vaginal, and rectal microbiome samples
Authors: Wright Michelle L. , Podnar Jessica , Longoria Kayla D. , Nguyen Tien C. , Lim Sungju , Garcia Sarina , Wylie Dennis
Published: February 2023

Introduction

Advancements in DNA extraction and sequencing technologies have been fundamental in deciphering the significance of the microbiome related to human health and pathology. Whole metagenome shotgun sequencing (WMS) is gaining popularity in use compared to its predecessor (i.e., amplicon-based approaches). However, like amplicon-based approaches, WMS is subject to bias from DNA extraction methods that can compromise the integrity of sequencing and subsequent findings. The purpose of this study was to evaluate systematic differences among four commercially available DNA extraction kits frequently used for WMS analysis of the microbiome.

Methods

Oral, vaginal, and rectal swabs were collected in replicates of four by a healthcare provider from five participants and randomized to one of four DNA extraction kits. Two extraction blanks and three replicate mock community samples were also extracted using each extraction kit. WMS was completed with NovaSeq 6000 for all samples. Sequencing and microbial communities were analyzed using nonmetric multidimensional scaling and compositional bias analysis.

Results

Extraction kits differentially biased the percentage of reads attributed to microbial taxa across samples and body sites. The PowerSoil Pro kit performed best in approximating expected proportions of mock communities. While HostZERO was biased against gram-negative bacteria, the kit outperformed other kits in extracting fungal DNA. In clinical samples, HostZERO yielded a smaller fraction of reads assigned toHomo sapiensacross sites and had a higher fraction of reads assigned to bacterial taxa compared to other kits. However, HostZERO appears to bias representation of microbial communities and demonstrated the most dispersion by site, particularly for vaginal and rectal samples.

Conclusions

Systematic differences exist among four frequently referenced DNA extraction kits when used for WMS analysis of the human microbiome. Consideration of such differences in study design and data interpretation is imperative to safeguard the integrity of microbiome research and reproducibility of results.
Genome sequence ofOphryocystis elektroscirrha, an apicomplexan parasite of monarch butterflies: cryptic diversity and response to host-sequestered plant chemicals
Authors: Mongue Andrew J. , Martin Simon H. , Manweiler Rachel E. V. , Scullion Helena , Koehn Jordyn L. , de Roode Jacobus C. , Walters James R.
Published: February 2023

Apicomplexa are ancient and diverse organisms which have been poorly characterized by modern genomics. To better understand the evolution and diversity of these single-celled eukaryotes, we sequenced the genome ofOphryocystis elektroscirrha, a parasite of monarch butterflies,Danaus plexippus. The genome is miniscule, totaling only 9 million bases and containing fewer than 3,000 genes. We then compared this new sequence to the two other sequenced invertebrate-infecting apicomplexans,Porospora giganteaandGregarina niphandrodes, which have nearly twice the gene content and found thatO. elektroscirrhashares different orthologs with each sequenced relative, suggesting the true set of universally conserved apicomplexan genes is very small indeed. We investigated sequenced reads from other potential hosts to explore the viability ofin silicoinfection screening. We recovered a similarly sized parasite genome from another butterfly,Danaus chrysippus, that was highly diverged from theO. elektroscirrhareference, possibly representing a distinct species. Using these two new genomes, we investigated potential evolutionary response by parasites to toxic phytochemicals their hosts ingest and sequester. Monarch butterflies are well-known to tolerate toxic cardenolides thanks to changes in the sequence of their Type II ATPase sodium pumps. We show thatOphryocystiscompletely lacks Type II or Type 4 sodium pumps, and related proteins PMCA calcium pumps show extreme sequence divergence compared to other Apicomplexa, demonstrating new avenues of research opened by genome sequencing of non-model Apicomplexa.

Author Summary

There are many relatives ofPlasmodium, the single-celled parasites responsible for malaria, and they infect a wide range of animals, including insects. These parasites have received less attention however, leaving much unknown about them. We sequenced the genome of one such parasite,Ophryocystis elektroscirrha(OE), to compare it to better-studied parasites and shed light on OE’s interaction with its host, the monarch butterfly. We found that OE has a tiny genome with the fewest genes of any sequenced parasite in this group, lacking many genes found in its relatives. Using our new data, we also discovered evidence that infections of other butterfly species that have been attributed to OE may be caused by a previously undiscovered distinct parasite species. And finally, we explored the evolution of a family of genes that may be targeted by medicinal plant compounds in the monarch butterfly’s diet; OE has lost one of these genes and radically changed the sequence of another, setting a direction for future research.
Human Retinal Ganglion Cells Respond to Evolutionarily Conserved Chemotropic Cues for Intra Retinal Guidance and Regeneration
Authors: Subramani Murali , Hook Matthew Van , Rajamoorthy Mohanapriya , Qiu Fang , Ahmad Iqbal
Published: February 2023

Retinal ganglion cells (RGCs) connect the retina with the higher centers in the brain for visual perception. Their degeneration leads to irreversible vision loss in glaucoma patients. Since human RGCs (hRGCs) are born during fetal development and connections with the central targets are established before birth, the mechanism underlying their axon growth and guidance remains poorly understood. Here, using RGCs directly generated from human embryonic stem cells, we demonstrate that hRGCs express a battery of guidance receptors. These receptors allow hRGCs to read the spatially arrayed chemotropic cues in the developing rat retina for the centripetal orientation of axons toward the optic disc, suggesting that the mechanism of intra-retinal guidance is conserved in hRGCs. The centripetal orientation of hRGCs axons is not only in response to chemo-repulsion but also involves chemo-attraction, mediated by Netrin-1/DCC interactions. The spatially arrayed chemotropic cues differentially influence hRGCs physiological responses, suggesting that neural activity of hRGCs may facilitate axon growth during inter-retinal guidance. Additionally, we demonstrate that Netrin-1/DCC interactions, besides promoting axon growth, facilitate hRGCs axon regeneration by recruiting the mTOR signaling pathway. The diverse influence of Netrin-1/DCC interactions ranging from axon growth to regeneration may involve recruitment of multiple intracellular signaling pathways as revealed by transcriptome analysis of hRGCs. From the perspective ofex-vivostem cell approach to glaucomatous degeneration, our findings posit thatex-vivogenerated human RGCs are capable of reading the intra-retinal cues for guidance toward the optic disc, the first step toward connecting with the central target to restore vision.
Timing of antibiotic administration determines the spread of plasmid-encoded antibiotic resistance during microbial range expansion
Authors: Ma Yinyin , Ramoneda Josep , Johnson David R.
Published: February 2023

The spread of antibiotic resistance (AR) is a major threat to global health. Plasmid-mediated horizontal gene transfer is the main mechanism by which AR is transferred between cells lying within close spatial proximity to each other. In this study, we address a fundamental question regarding the spread of AR-encoding plasmids: Is there an optimal time to administer antibiotics to minimize plasmid spread within microbial communities? We addressed this question using microbial consortia consisting of twoPseudomonas stutzeristrains, where one is an AR-encoding plasmid donor and the other a potential recipient. We allowed the strains to co-expand across a nutrient-amended surface and administered antibiotics at different points in time. We found that the extents of plasmid transfer and transconjugant proliferation have unimodal relationships with the timing of antibiotic administration, where they reach maxima at intermediate administration times. Using an individual-based model, we found that these unimodal relationships result from an interplay between the probability to acquire plasmids from neighboring cells and the probability of plasmid loss upon cell division. Our study provides novel mechanistic insights into the transfer and proliferation of AR-encoding plasmids within microbial communities and identifies the timing of antibiotic administration as an important determinant of AR spread.
Capsicum chinenseJacq. derived glutaredoxin (CcGRXS12) alters phytohormonal pathways and redox status of the cells to confer resistance against pepper mild mottle virus (PMMoV-I)
Authors: Saravana Kumar R. M. , Ramesh S.V. , Sun Z. , Thankappan Sugitha , Binodh Asish Kanakaraj
Published: February 2023

Glutaredoxins (Grxs) are small, ubiquitous, multi-functional proteins present in different compartments of plant cells. A chloroplast targeted class I GRX (CcGRXS12) gene was isolated fromCapsicum chinenseduring the pepper mild mottle virus (PMMoV) infection. Functional characterization of the gene was performed inN. benthamianatransgenic plants transformed with nativeC. chinense GRX(Nb:GRX),GRX-fused with GFP (Nb:GRX-GFP) andGRXtruncated for the chloroplast targeting sequences but fused with GFP (Nb:Δ2MGRX-GFP). Over-expression ofCcGRXS12inhibits the PMMoV-I accumulation at late stage of infection and is accompanied with the activation of SA- pathway pathogenesis related (PR) transcripts, and suppression of JA/ET- pathway transcripts. Further the reduced accumulation of auxin-induced Glutathione-S-Transferase (pCNT103) inCcGRXS12over expressing lines indicates that the protein could able to protect the plants from the oxidative stress caused by the virus. PMMoV-I infection increases accumulation of pyridine nucleotides (PNs) mainly due to the reduced form of PNs (NAD(P)H) and it was higher inNb:GRX-GFPlines compared to other lines where infection is limited. Apart from biotic stress,CcGRXS12protects the plants from abiotic stress conditions caused by H2O2and herbicide paraquat. CcGRXS12 exhibits GSH-disulphide oxidoreductase activityin vitrohowever devoid of complementary Fe-S cluster assembly mechanism in yeast.
Omicron’s Intrinsic Gene-Gene Interactions Jumped Away from Earlier SARS-CoV-2 Variants and Gene Homologs between Humans and Animals
Authors: Zhang Zhengjun
Published: February 2023

Omicron and its subvariants have become the predominant SARS-CoV-2 variants worldwide. The Omicron’s basic reproduction number (R0) has been close to 20 or higher. However, it is not known what caused such an extremely high R0. This work aims to find an explanation for such high R0 Omicron infection. We found that Omicron’s intrinsic gene-gene interactions jumped away from earlier SARS-CoV-2 variants which can be fully described by a miniature set of genes reported in our earlier work. We found that the gene PTAFR (Platelet Activating Factor Receptor) is highly correlated with Omicron variants, and so is the gene CCNI (Cyclin I), which is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, and frog. The combination of PTAFR and CCNI can lead to a 100% accuracy of differentiating Omicron COVID-19 infection and COVID-19 negative. We hypothesize that Omicron variants were potentially jumped from COVID-19-infected animals back to humans. In addition, there are also several other two-gene interactions that lead to 100% accuracy. Such observations can explain Omicron’s fast-spread reproduction capability as either of those two-gene interactions can lead to COVID-19 infection, i.e., multiplication of R0s leads to a much higher R0. At the genomic level, PTAFR, CCNI, and several other genes identified in this work rise to Omicron druggable targets and antiviral drugs besides the existing antiviral drugs.
Grey matter reshaping of language-related regions depends on tumor lateralization
Authors: Manso-Ortega Lucia , De Frutos-Sagastuy Laura , Gisbert-Muñoz Sandra , Salamon Noriko , Qiao Joe , Walshaw Patricia , Quiñones Ileana , Połczyńska Monika M.
Published: February 2023

A brain tumor in the left hemisphere can decrease language laterality as assessed with fMRI. However, it remains unclear whether or not this decreased language laterality is associated with a structural reshaping of the grey matter, particularly within the language network. Here, we examine if the disruption of language hubs exclusively affects macrostructural properties of contralateral homologues (as suggested by previous research), or whether it affects both hemispheres. This study uses voxel-based morphometry applied to high-resolution MR T1-weighted MPRAGE images from 31 adult patients left-dominant for language. Eighteen patients had brain tumors in the left hemisphere, and 13 had tumors in the right hemisphere. A cohort of 71 healthy individuals matched on age and sex was used as a baseline. We defined 10 ROIs per hemisphere known to subserve language function. Two separate repeated-measures ANOVAs were conducted with the volume per region as the dependent variables. For the patients, tumor lateralization (right versus left) served as a between-subject factor. The current study demonstrated that the presence of a brain tumor generates a global volumetric change affecting left language regions and their contralateral homologues. These changes are mediated by the lateralization of the lesion. Our findings suggest that compensatory functional mechanisms are supported by the rearrangement of the grey matter, although future longitudinal research should determine the temporal course of such changes.
ReplicativeAcinetobacter baumanniistrains interfere with phagosomal maturation by modulating the vacuolar pH
Authors: Distel Jesus S. , Venanzio Gisela Di , Mackel Joseph J. , Rosen David A , Feldman Mario F.
Published: February 2023

Bacterial pneumonia is a common infection of the lower respiratory tract that can afflict patients of all ages. Multidrug-resistant strains ofAcinetobacter baumanniiare increasingly responsible for causing nosocomial pneumonias, thus posing an urgent threat. Alveolar macrophages play a critical role in overcoming respiratory infections caused by this pathogen. Recently, we and others have shown that new clinical isolates ofA. baumannii, but not the common lab strain ATCC 19606 (19606), can persist and replicate in macrophages within spacious vacuoles that we calledAcinetobacterContainingVacuoles (ACV). In this work, we demonstrate that the modernA. baumanniiclinical isolate 398, but not the lab strain 19606, can infect alveolar macrophages and produce ACVsin vivoin a murine pneumonia model. Both strains initially interact with the alveolar macrophage endocytic pathway, as indicated by EEA1 and LAMP1 markers; however, the fate of these strains diverges at a later stage. While 19606 is eliminated in an autophagy pathway, 398 replicates in ACVs and are not degraded. We show that 398 reverts the natural acidification of the phagosome by secreting large amounts of ammonia, a by-product of amino acid catabolism. We propose that this ability to survive within macrophages may be critical for the persistence of clinicalA. baumanniiisolates in the lung during a respiratory infection.
Single-cell mass distributions reveal simple rules for achieving steady-state growth
Authors: Roller Benjamin R.K. , Hellerschmied Cathrine , Wu Yanqi , Miettinen Teemu P. , Manalis Scott R. , Polz Martin F.
Published: February 2023

Optical density is a common method for measuring exponential growth in bacterial batch cultures. However, there is a misconception that such exponential growth is equivalent to steady-state growth, which is a distinct physiological state that improves experimental reproducibility. Determining precisely when steady-state growth occurs is technically challenging and is aided by paired single-cell and population-level measurements. Using microfluidic mass sensors and optical density, we explore when in typical laboratory batch cultures steady-state growth occurs. We show that cell mass increases by an order of magnitude within a few hours of dilution into fresh medium and that steady-state growth is only achieved when cultures are inoculated with high dilutions from overnight stationary phase cultures. At high dilutions,Escherichia coliandVibrio cyclitrophicusgrown in different rich media achieve steady-state growth approximately 4 total biomass doublings after inoculation. We can decompose these dynamics into 3 doublings of average cell mass and 1 doubling of cell number for both species. We also show that batch cultures in rich media depart steady-state growth early in their growth curves at low cell and biomass concentrations. Achieving and maintaining steady-state growth in batch culture is a delicate balancing act, and we provide general guidance for commonly used rich media. Quantifying single-cell mass outside of steady-state growth is an important first step towards understanding how microbes grow in their natural context, where fluctuations pervade at the scale of individual cells.

Importance

Microbiologists have watched clear liquid turn cloudy for over 100 years. While the cloudiness of a culture is proportional to its total biomass, growth rates using such optical density measurements are challenging to interpret when cells change size. Many bacteria adjust their size at different steady-state growth rates, but also when shifting between starvation and growth. Optical density cannot disentangle how mass is distributed among cells of different sizes, and directly measuring how mass is distributed among cells has been a major challenge. Here we use single-cell mass measurements to demonstrate that a population of cells in batch culture achieves a stable mass distribution for only a short period of time. Achieving steady-state growth in rich medium requires low initial biomass concentrations and enough time for the coordination of individual cell and population growth. Steady-state growth is important for reliable cell mass distributions in a culture and we discuss how mass variation outside of steady-state can impact physiology, ecology, and evolution experiments.
Identification of “missing links” in C- and D-ring cleavage of steroids byComamonas testosteroniTA441
Authors: Horinouchi Masae , Hayashi Toshiaki
Published: February 2023

Comamonas testosteroniTA441 degrades steroids aerobically via aromatization and cleavage of the A- and B-ring, followed by D- and C-ring cleavage via b-oxidation. We previously characterized most of the above degradation steps; however, a few intermediate compounds remained unaccounted for. We hypothesized that cleavage of the D-ring at C13-17 required the ScdY hydratase and was followed by cleavage of the C-ring via the ScdL1L2 transferase. The reaction was expected to produce 6-methyl-3,7-dioxo-decane-1,10-dioic acid-Coenzyme A (CoA) ester. To verify this hypothesis, we constructed a plasmid that enabled targeted gene induction in TA441 mutant strains. The major product of ScdL1L2 was found to be 3-hydroxy-6-methyl-7-oxo-decane-1,10-dioic acid-CoA ester; whereas the substrate of ScdY was revealed to be a geminal diol, 17-dihydroxy-9-oxo-1,2,3,4,5,6,10,19-octanorandrost-8(14)-en-7-oic acid-CoA ester. This finding suggests that ScdY catalyzes the addition of a water molecule at C14 of 17-dihydroxy-9-oxo-1,2,3,4,5,6,10,19-octanorandrost-8(14)-en-7-oic acid-CoA ester, leading to D-ring cleavage at C13-17. The C9 ketone of the D-ring cleavage product is then converted to a hydroxyl group, followed by C-ring cleavage to produce 3-hydroxy-6-methyl-7-oxo-decane-1,10-dioic acid-CoA ester. Precise bacterial bile acid degradation pathway will be one of the key to investigate the gut–microbiota–brain axis, which affects human health and disease.

IMPORTANCE

Studies on bacterial steroid degradation were initiated more than 50 years ago primarily to obtain substrates for steroid drugs. The role of steroid-degrading bacteria in relation to human health is attracting growing attention.Comamonas testosteroniTA441 is the leading bacterial model of aerobic steroid degradation and the overall pathway has been outlined previously. However, a few intermediate compounds in C- and D-ring cleavage processes have remained unknown. Here, we identified the missing compounds and can now propose the complete A-, B-, C-, and D-ring cleavage pathway employed by steroid-degrading bacteria. This finding will facilitate the application of such microorganisms for the synthesis of specific steroid derivatives.
Comprehensive summary of steroid metabolism inComamonas testosteroniTA441; entire degradation process of basic four rings and removal of C12 hydroxyl group
Authors: Horinouchi Masae , Hayashi Toshiaki
Published: February 2023

Comamonas testosteroniis one of the representative aerobic steroid-degrading bacterium. We previously revealed the mechanism of steroidal A,B,C,D-ring degradation byC. testosteroniTA441. The corresponding genes are located in two clusters at both ends of a mega-cluster of steroid degradation genes. ORF7 and ORF6 are the only two genes in these clusters, whose function has not been determined. Here, we characterized ORF7 as encoding the dehydrase responsible for converting the C12β hydroxyl group to the C10(12) double bond on the C-ring (SteC), and ORF6 as encoding the hydrogenase responsible for converting the C10(12) double bond to a single bond (SteD). SteA and SteB, encoded just upstream of SteC and SteD, are in charge of oxidizing the C12α hydroxyl group to a ketone group, and of reducing the latter to the C12β hydroxyl group, respectively. Therefore, the C12α hydroxyl group in steroids is removed with SteABCD via the C12 ketone and C12β hydroxyl groups. Given the functional characterization of ORF6 and ORF7, we disclose the entire pathway of steroidal A,B,C,D-ring breakdown byC. testosteroniTA441.

IMPORTANCE

Studies on bacterial steroid degradation were initiated more than 50 years ago, primarily to obtain materials for steroid drugs. Now, their implications for the environment and humans, especially in relation to the infection and the brain-gut-microbiota axis, are attracting increasing attention.Comamonas testosteroniTA441 is the leading model of bacterial aerobic steroid degradation with the ability to break down cholic acid, the main component of bile acids. Bile acids are known for their variety of physiological activities according as their substituent group(s). In this study, we identified and functionally characterized the genes for removal of C12 hydroxyl groups and provide a comprehensive summary of the entire A,B,C,D-ring degradation pathway byC. testosteroniTA441 as the representable bacterial aerobic degradation process of the steroid core structure.