bluuebunny/crossref_metadata_2025 huggingface dataset:
Patient safety practices in European anaesthesiology
Authors: McCreedy Aimee , Wacker Johannes , Ffrench-O’Carroll Robert , Berthelsen Kasper Gymoese , Kremeňova Tatičová Zuzana , Smith Andrew F.
Published: November 2022

BACKGROUND

Patient safety is a key concern of anaesthesiology practice. However, good practices are often not widely shared between departments and hospitals, whether within or between countries.

OBJECTIVE

We aimed to collect and analyse safety practices and tips from anaesthesiology departments around Europe in order to facilitate successful transfer of safety knowledge.

DESIGN

Review of previously collected safety practices; allocation of numerical scores in order to rank them on 0–5 scales in terms of anticipated impact, and speed, cost, and ease of implementation; free text comment on any possible difficulties or unintended harms which might arise from adopting any of the collected practices.

SETTING

Collaborative remote working of expert group.

PARTICIPANTS

Nineteen experts in patient safety in anaesthesiology from nine European countries.

MAIN OUTCOME MEASURES

Rankings of safety practices for anticipated practice impact, cost, speed, and ease of implementation.

RESULTS

We collected 117 practices. The highest-ranked items for potential beneficial impact were: standardising the layout of drug trolleys (4.82); involving all staff in new safety initiatives in the operating theatre (4.73); ensuring patients’ medical records are available at the time of surgery (4.71); running regular simulation training sessions in departments of anaesthesia (4.67); and creating a difficult airway management trolley (4.65). A major theme to emerge from the qualitative analysis of the experts’ free text comments was the risk that practices aimed at enhancing patient safety might not achieve the effect intended, as introducing new safety activities can cause more mistakes during the implementation phase.

CONCLUSION

Many useful practices to promote patient safety were identified, but as some practices appear to be context-dependent, we recommend that a proper, prospective risk assessment is carried out before they are introduced in a new setting. The full list of items is available online as Supplementary Digital Content, http://links.lww.com/EJA/A785.

TRIAL REGISTRATION

Not applicable.
Combined Therapeutic Penetrating Keratoplasty and Pars Plana Vitrectomy for the Treatment of Infectious Keratitis Endophthalmitis: Mexican Endophthalmitis Study Group Protocol 4
Authors: Velez-Montoya Raul , Rivera-Cortes Mariana A. , Ledesma-Gil Gerardo , Carranza-Casas Mario , Martinez Jaime D. , Levine Harry , Yanuzzi Nicolas A. , Amescua Guillermo , Ahmed Ishrat , Beatson Bradley , Akpek Esen , Arevalo J. Fernando , Fromow-Guerra Jans ,   for the Mexican Endophthalmitis Study Group (Mex-ESG)
Published: November 2022

Purpose:

The purpose of this study was to assess the role of combined surgical treatment of therapeutic penetrating keratoplasty and pars plana vitrectomy in the anatomical and functional outcome of infectious keratitis endophthalmitis.

Methods:

This study reviewed the medical records of 4 participating centers in the United States and Mexico. This study included patients with a clinical diagnosis of infectious keratitis endophthalmitis who had been treated with an early therapeutic penetrating keratoplasty and pars plana vitrectomy as the main treatment for endophthalmitis. From each medical record, the study retrieved demographic data, relevant medical and drug history, baseline clinical manifestation of endophthalmitis, best-corrected visual acuity, and the need for enucleation/evisceration for the control of the infection or any other reason through the follow-up.

Results:

The study included 48 patients (50.15 ± 20.6 years). The mean follow-up time was 13 ± 0.5 months. The mean best-corrected visual acuity at baseline was 2.1 ± 0.25 logarithm of the minimum angle of resolution. At month 12 was 2.09 ± 0.61 logarithm of the minimum angle of resolution (P = 0.9). The overall prevalence of enucleation/evisceration was 8.3% (95% confidence interval: 2.32%–19.98%). The prevalence of a vision of no-light perception was 20.8% (95% confidence interval: 2.32%–19.98%).

Conclusions:

Combined surgery for severe cases of infectious keratitis endophthalmitis eradicates the infection in most cases, while significantly improving the overall outcomes.
Management of acute severe hypertension in youth: from the philosophical to the practical
Authors: Giammattei Victoria C. , Weaver Donald J. , South Andrew M.
Published: November 2022

Purpose of review

Acute severe hypertension remains an uncommon but important source of morbidity and mortality in youth. However, there has been very little progress made in our understanding of how to best manage youth with acute severe hypertension to improve patient outcomes.

Recent findings

Our understanding of what is acute severe hypertension is undergoing a philosophical change. Management of patients with acute severe hypertension is evolving towards more of a risk and outcomes-based approach.

We should be intentional when we consider whether a patient has acute severe hypertension and if they are truly at an increased risk for life-threatening target organ injury. We should consider their specific risk factors to best interpret the risks and benefits of how best to treat a patient with acute severe hypertension, rather than relying on traditional approaches and conventional wisdom. We should always ask ‘why’ when we are pursuing a given management course. Future studies should clearly define the research questions they are investigating to best advance the field to ultimately improve patient outcomes.
Conjugative IncHI2/HI2A plasmids harbouring mcr-9 in colistin-susceptible Escherichia coli isolated from diseased pigs in Japan
Authors: Fukuda Akira , Nakano Hitomi , Suzuki Yasuhiko , Nakajima Chie , Usui Masaru
Published: November 2022

Colistin is a last resort antimicrobial used for the treatment of gram-negative bacterial infections. Plasmid-mediated colistin resistance (mcr) genes are a cause of global concern, and, thus far, mcr-1–10 have been identified. In a previous study, we screened mcr-1–5 in

Escherichia coli

derived from diseased pigs in Japan and reported a high prevalence of mcr-1, -3 and -5. However, the previous report on the prevalence of mcr genes was inaccurate. In the present study, we aimed to clarify the prevalence of all reported variants of mcr in

E. coli

derived from the diseased pigs, which were previously screened for mcr-1–5. Additionally, we also characterized the mcr-9-positive

E. coli

, which was detected in this study. We screened mcr in 120

E. coli

strains from diseased pigs and mcr-positive

E. coli

and an mcr-carrying plasmid were also characterized. One mcr-9-positive colistin-susceptible

E. coli

strain was detected (0.8 %). Plasmid-mediated mcr-9 was transferred to

E. coli

ML4909 as the recipient strain, and it was located on IncHI2/HI2A plasmid p387_L with other antimicrobial resistance genes (ARGs). The region harbouring ARGs including mcr-9, was similar to that on the

Klebsiella pneumoniae

chromosome harbouring mcr-9 isolated in Japan. mcr-3, -5 and -9 were detected (4.2 %) in colistin-susceptible strains. mcr-9 was found to be disseminated via the plasmid IncHI2/HI2A p387_L and transferred and inserted into chromosomes via a transposon. Our results suggest that mcr genes should be monitored regularly, regardless of their susceptibility to colistin.
Clinical isolates of Mycobacterium tuberculosis with different genotypes exhibit distinct host macrophage responses in vitro
Authors: Liang Chen , Li Xiaomeng , Li Qiao , Zhang Xuxia , Ren Weicong , Yao Cong , Pang Yu , Liu Yi , Li Chuanyou , Tang Shenjie
Published: November 2022

Introduction.

Mycobacterium tuberculosis

(M.tb), the causative agent of tuberculosis, can survive as an intracellular parasite after entering macrophages via phagocytosis. M.tb strains are genotypically distinct and engage in diverse pathogen–host interactions, with different host immune responses triggered by different M.tb strains. Importantly, differences in intracellular accumulation and triggering of host macrophage responses during early infection stages are key determinants that shape the final outcomes of host innate immune responses to different M.tb strains.

Hypothesis/Gap Statement. Clinical M.tb strains with different genotypes elicit different host innate immune responses in vitro.

Aim. This work aimed to compare host innate immune responses elicited by genotypically diverse, clinically derived M.tb strains in vitro.

Methodology. RAW264.7 cells were infected with three lineage 2 and lineage 4 clinically derived M.tb strains and strain H37Rv. Strains were evaluated for differences in intracellular growth, induction of macrophage apoptosis, and induction of expression of proinflammatory cytokines and associated pattern recognition receptors.

Results. Highly variable cytokine profiles were observed subsequent to RAW264.7 cell infection with the different strains. The Beijing genotype strain, a modern Beijing strain belonging to lineage 2, induced milder host proinflammatory responses and less apoptosis and exhibited greater intracellular growth as compared to the other strains. Moreover, mRNA expression levels of iNOS in Beijing and MANU2 genotype strains exceeded corresponding levels obtained for the T1 genotype strain. Meanwhile, mRNA expression levels of toll-like receptor (TLR)-encoding genes TLR2 and TLR7 in macrophages infected with the Beijing genotype strain were higher than corresponding levels observed in MANU2 genotype strain-infected macrophages.

Conclusion. The higher intracellular survival rate and lower level of host cell apoptosis associated with macrophage infection with the Beijing genotype strain indicated greater virulence of this strain relative to that of the other strains. Furthermore, in vitro immune responses induced by the Beijing genotype strain were unique in that this strain induced a weaker inflammatory response than was induced by T1 or MANU2 genotype strains. Nevertheless, additional evidence is needed to confirm that Beijing genotype strains possess greater virulence than strains with other genotypes.
Epigenome-wide association study of serum folate in maternal peripheral blood leukocytes
Authors: Fragoso-Bargas N. , Page C.M. , Joubert B.R. , London S.J. , Lee-Ødegård S. , Opsahl J.O. , Sletner L. , Jenum A.K. , Qvigstad E. , Prasad R.B. , Moen G.-H. , Birkeland K.I. , Sommer C.
Published: November 2022

Aim

To perform an epigenome-wide association study (EWAS) of serum folate in maternal blood.

Methods

We performed cross-ancestry (Europeans=302, South Asians=161) and ancestry-specific EWAS in the EPIPREG cohort, followed by methyl quantitative trait loci (mQTL) analysis and association with cardiometabolic phenotypes. We attempted replication using folate intake estimated from a food frequency questionnaire and maternal blood methylation data from MoBa, and in a previous published EWAS of maternal serum folate in cord blood.

Results

cg19888088 (cross-ancestry) inEBF3, cg01952260 (Europeans), and cg07077240 (South Asians) inHERC3were associated with serum folate. cg19888088 and cg01952260 were associated with diastolic blood pressure. cg07077240 was associated with variants inCASC15. The findings were not replicated in the independent samples.

Conclusion

Serum folate was associated with methylation at three CpG sites.
Assessment of Attitude and Hesitancy Towards Covid-19 Vaccine among Hepatitis B and C Patients in Pakistan
Authors: Shafiq Farheen , Hassan Mahreen ul , Butt Sadia , Sidique Sadia , Akbar Nazia , Azra  , Rehman Irshad
Published: November 2022

OBJECTIVE

The research aimed to evaluate the attitude and perceptions towards the covid-19 vaccine among Hepatitis B and C patients in Peshawar, Khyber Pakhtunkhwa, Muzaffarabad, Azad Kashmir, Pakistan.

METHODS

A survey-based study was adopted to evaluate the attitude of Hepatitis B and C patients towards immunization against covid-19 in Peshawar (KPK) and Muzaffarabad (AJK) cities of Pakistan. The study continued from January 2020 to February 2021. Participants were also assessed for their perception towards covid-19 vaccination.

RESULTS

A total of 839 (33.6%) individuals participated in the study. About 52 % of Hepatitis B patients were immunized against Covid-19, whereas the number of Hepatitis C patients was recorded at around 48%. About 53.7 % of participants refused to get the vaccine without any reason. About 63.2% of patients showed concern about the insufficient data available on the vaccine safety and efficacy published by the Public Health Department. Individuals with higher education were observed to be more open towards vaccination then those without a formal education. More than half of the participants (61.5 %) were concerned about the interference of the vaccine with their hepatitis treatment whereas 54.7 % patients refused vaccine because of a poor liver condition.

CONCLUSIONS

The data indicated that limited data availability regarding the vaccine efficacy in viral hepatitis patients and negative attitudes of people toward covid-19 vaccination is the main cause of Covid-19 vaccination refusal among hepatitis B and C patients.

DESCRIPTORS

Hepatitis B, Hepatitis C, covid-19, immunization, vaccine refusal, Pakistan.
A Multimodal Atlas of Tumor Metabolism Reveals the Architecture of Gene-Metabolite Co-regulation
Authors: Benedetti Elisa , Liu Eric Minwei , Tang Cerise , Kuo Fengshen , Buyukozkan Mustafa , Park Tricia , Park Jinsung , Correa Fabian , Hakimi A Ari , Intlekofer Andrew , Krumsiek Jan , Reznik Ed
Published: November 2022

Tumor metabolism is controlled by coordinated changes in metabolite abundance and gene expression, but simultaneous quantification of metabolites and transcripts in primary tissue is rare. To overcome this limitation and study gene-metabolite coregulation in cancer, we assembled the Cancer Atlas of Metabolic Profiles (cAMP) of metabolomic and transcriptomic data from 988 tumor/normal specimens spanning 11 cancer types. Meta-analysis of the cAMP revealed two classes of Gene-Metabolite Interactions (GMIs) that transcended cancer types. The first corresponded to a small number of gene-metabolite pairs engaged in direct enzyme-substrate interactions, identifying putative metabolite-pool-size-controlling genes. A second class of GMIs represented a small number of hub metabolites, including quinolinate and NAD+, which correlated to many genes specifically expressed on immune cell populations. These results provide evidence that gene-metabolite coregulation in human tissue arises, in part, from both mechanistic interactions between genes/metabolites, and from metabolic remodeling in specific immune microenvironments.
A microtubule stability switch alters isolated vascular smooth muscle calcium flux in response to matrix rigidity
Authors: Johnson Robert , Wostear Finn , Solanki Reesha , Steward Oliver , Morris Christopher , Bidula Stefan , Warren Derek T
Published: November 2022

During ageing, the extracellular matrix of the aortic wall becomes more rigid. In response, VSMCs generate enhanced contractile forces. Our previous findings demonstrate that VSMC volume is enhanced in response to increased matrix rigidity, but our understanding of mechanisms regulating this process remain incomplete. In this current study, we show that microtubule stability in VSMCs is reduced in response to enhanced matrix rigidity via piezo1-mediated Ca2+influx. Moreover, VSMC volume and Ca2+flux was regulated by microtubule dynamics; microtubule stabilising agents reduced both VSMC volume and Ca2+flux on rigid hydrogels, whereas microtubule destabilising agents increased VSMC volume and Ca2+flux on pliable hydrogels. Finally, we show that disruption of the microtubule deacetylase HDAC6 uncoupled these processes and increased K40 alpha tubulin acetylation, VSMC volume and Ca2+flux on pliable hydrogels, but did not alter VSMC microtubule stability. These findings uncover a microtubule stability switch that controls VSMC volume by regulating Ca2+flux. Together, these data demonstrate that manipulation of microtubule stability can modify VSMC matrix rigidity response.
Miniature spatial transcriptomics for studying parasite-endosymbiont relationships at the micro scale
Authors: Sounart Hailey , Voronin Denis , Masarapu Yuvarani , Chung Matthew , Saarenpää Sami , Ghedin Elodie , Giacomello Stefania
Published: November 2022

Several important human infectious diseases are caused by microscale-sized parasitic nematodes like filarial worms. Filarial worms have their own spatial tissue organization and to uncover this tissue structure, we need methods that can spatially resolve these miniature specimens. Most filarial worms evolved a mutualistic association with endosymbiotic bacteriaWolbachia, however, the mechanisms underlying the dependency of filarial worms on the fitness of these bacteria remain unknown. AsWolbachiais essential for the development, reproduction, and survival of filarial worms, we focused on studying a posterior region containing reproductive tissue and developing embryos of adult femaleBrugia malayiworms. To spatially explore howWolbachiainteracts with the worm’s reproductive system, we performed a spatial characterization using Spatial Transcriptomics (ST) across our region of interest. We provide a proof-of-concept for miniature-ST to explore spatial gene expression patterns in small sample types, demonstrating the method’s ability to uncover nuanced tissue region expression patterns, observe the spatial localization of keyB. malayi-Wolbachiapathway genes, and co-localize theB. malayispatial transcriptome inWolbachiatissue regions. We envision our approach to open up new scenarios for the study of infectious diseases caused by micro-scale parasitic worms.
Temporal characteristics of gamma rhythm constrain properties of noise in an inhibition-stabilized network model
Authors: Krishnakumaran R , Ray Supratim
Published: November 2022

Gamma rhythm refers to oscillatory neural activity between 30-80 Hz, often induced in visual cortex by presentation of stimuli such as iso-luminant hues or gratings. Further, the power and peak frequency of gamma depend on the properties of the stimulus such as size and contrast. Gamma also has a typical arch shape, with a narrow trough and a broad peak, which can be replicated by a self-oscillating Wilson-Cowan (WC) model operating in an appropriate regime. However, oscillations in this model are infinitely long, unlike physiological gamma that occurs in short bursts. Further, unlike the model, gamma is faster after stimulus onset and slows down over time. Here, we first characterized gamma burst duration in LFP data recorded from two monkeys while they viewed full screen iso-luminant hues. We then added different types of noise in the inputs to the WC model and tested how that affected duration and temporal dynamics of gamma. While the model failed with the often-used Poisson noise, Ornstein-Uhlenbeck (OU) noise applied to both the excitatory and inhibitory populations in the WC model replicated the duration and slowing of gamma, and also replicated the shape and stimulus dependencies. Therefore, temporal dynamics of gamma oscillations put constraints on the type and properties of underlying neural noise.
Poly ADP-Ribose Signaling is Dysregulated in Huntington Disease
Authors: Maiuri Tamara , Bazan Carlos Barba , Harding Rachel J. , Begeja Nola , Kam Tae-In , Byrne Lauren M. , Rodrigues Filipe B. , Warner Monica M. , Neuman Kaitlyn , Mansoor Muqtasid , Badiee Mohsen , Dasovich Morgan , Wang Keona , Thompson Leslie M , Leung Anthony K. L. , Andres Sara N. , Wild Edward J. , Dawson Ted M. , Dawson Valina L. , Arrowsmith Cheryl H. , Truant Ray
Published: November 2022

Huntington disease (HD) is a genetic neurodegenerative disease caused by CAG expansion in theHuntingtin (HTT)gene, translating to an expanded polyglutamine tract in the huntingtin (HTT) protein. Age at disease onset correlates to CAG repeat length but varies by decades between individuals with identical repeat lengths. Genome-wide association studies link HD modification to DNA repair and mitochondrial health pathways. Clinical studies show elevated DNA damage in HD, even at the premanifest stage. A major DNA repair node influencing neurodegenerative disease is the PARP pathway. Accumulation of poly ADP-ribose (PAR) has been implicated in Alzheimer and Parkinson diseases, as well as cerebellar ataxia. We report that HD mutation carriers have lower cerebrospinal fluid PAR levels than healthy controls, starting at the premanifest stage. Human HD iPSC-derived neurons and patient- derived fibroblasts have diminished PAR response in the context of elevated DNA damage. We have defined a PAR-binding motif in huntingtin, detected huntingtin complexed with PARylated proteins in human cells during stress, and localized huntingtin to mitotic chromosomes upon inhibition of PAR degradation. Direct huntingtin PAR binding was measured by fluorescence polarization and visualized by atomic force microscopy at the single molecule level. While wild type and mutant huntingtin did not differ in their PAR binding ability, purified wild type huntingtin protein increasedin vitroPARP1 activity while mutant huntingtin did not. These results provide insight into an early molecular mechanism of HD, suggesting possible targets for the design of early preventive therapies.

Significance statement

A consensus on dysfunctional DNA repair has emerged in neurodegenerative disease research, with elevated poly ADP-ribose (PAR) signaling more recently implicated. In contrast, we have identified a deficient PAR response in Huntington’s disease (HD) patient spinal fluid samples and cells. This may be explained by the inability of huntingtin protein bearing the HD-causing mutation to stimulate production of PAR the way the wild type protein does. Since drugs that target PAR production and degradation have already been developed, these findings present an exciting avenue for therapeutic intervention for HD.
Fast imaging of millimeter-scale areas with beam deflection transmission electron microscopy
Authors: Zheng Zhihao , Own Christopher S. , Wanner Adrian A. , Koene Randal A. , Hammerschmith Eric W. , Silversmith William M. , Kemnitz Nico , Lu Ran , Tank David W. , Seung H. Sebastian
Published: November 2022

Serial section transmission electron microscopy (TEM) has proven to be one of the leading methods for millimeter-scale 3D imaging of brain tissues at nanoscale resolution. It is important to further improve imaging efficiency to acquire larger and more brain volumes. We report here a three fold increase in the speed of TEM by using a beam deflecting mechanism to enable highly efficient acquisition of multiple image tiles (nine) for each motion of the mechanical stage. For millimeter-scale areas, the duty cycle of imaging doubles to more than 30%, yielding a net average imaging rate of 0.3 gigapixels per second. If fully utilized, an array of beam deflection TEMs should be capable of imaging a dataset of cubic millimeter scale in several weeks.
Spatial variation in relative abundances of two butterfly species sharing both host plant and natural enemies
Authors: Colom P. , Traveset A. , Shaw M. R. , Stefanescu C.
Published: November 2022

The decline of insect populations is of great concern because they play an essential part in several services that are key for ecosystem functioning and human well-being. Therefore, full understanding of the processes and factors shaping spatial variation in insects is required for their effective conservation. Here, we study a system comprising two congeneric butterfly species (BrimstoneGonepteryx rhamniand CleopatraG. cleopatra) that share both host plants and natural enemies and analyse whether biotic and/or abiotic factors explain their relative abundances. The two species coexist in continental Spain but not on a nearby archipelago, where only the Cleopatra occurs. The hypotheses tested were based on (H1) dispersal behaviour; (H2) apparent competition mediated via shared parasitoids; and (H3) environmental conditions (overwintering habitat availability, abundance of host plants and temperature). H1 explained differences in Brimstone abundance between climate regions on the mainland since in warmer summers populations increased in cooler areas but decreased in warmer areas. Cleopatra did not show the same pattern but was found to have twice the number of summer adults on one island than on the mainland. It is unlikely that H2 can explain this result because, although richer parasitoid communities were found on the mainland, larval mortality rates were similar. H3 was important in explaining variation in abundances between sites within each climate region even though similar environmental conditions were found on the mainland and on the islands. Our study demonstrates the complexity of any attempt to understand insect population dynamics in space due to the number of factors that are potentially involved. We argue thus that a more comprehensive approach taking into account landscape topography and resource connectivity on a broader scale is required to unravel the factors shaping the relative abundance of insects in island systems.
The role of the thalamus in human reinforcement learning
Authors: Collomb-Clerc Antoine , Gueguen Maëlle C. M. , Lorella Minotti , Philippe Kahane , Vincent Navarro , Fabrice Bartolomei , Romain Carron , Jean Regis , Stephan Chabardès , Palminteri Stefano , Bastin Julien
Published: November 2022

Although the thalamus is supposed to be involved in reinforcement-based decision-making, there is no direct evidence regarding the involvement of this subcortical structure in humans. To fill this gap, we leveraged rare intra-thalamic electrophysiological recordings in patients and found that temporally structured thalamic oscillations encode key learning signals. Our findings also provide neural insight into the computational mechanisms of action inhibition in punishment avoidance learning.
Re-implementation of an algorithm to integrate transcriptome and ChIP-seq data
Authors: Ahmed Mahmoud , Kim Deok Ryong
Published: November 2022

Transcription factor binding to a gene regulatory region induces or represses its expression. Binding and expression target analysis (BETA) integrates the binding and gene expression data to predict this function. First, the regulatory potential of the factor is modeled based on the distance of its binding sites from the transcription start sites in a decay function. Then the differential expression statistics from an experiment where this factor was perturbed represent the binding effect. The rank product of the two values is employed to order in importance. This algorithm was originally implemented in Python. We reimplemented the algorithm in R to take advantage of existing data structures and other tools for downstream analyses. Here, we attempted to replicate the findings in the original BETA paper. We applied the new implementation to the same datasets using default and varying inputs and cutoffs. We successfully replicated the original results. Moreover, we showed that the method was appropriately influenced by varying the input and was robust to choices of cutoffs in statistical testing.
Anin vivomassively parallel platform for deciphering tissue-specific regulatory function
Authors: Brown Ashley R. , Fox Grant A. , Kaplow Irene M. , Lawler Alyssa J. , Phan BaDoi N. , Wirthlin Morgan E. , Ramamurthy Easwaran , May Gemma E. , Chen Ziheng , Su Qiao , McManus C. Joel , Pfenning Andreas R.
Published: November 2022

Genetic studies are rapidly identifying non-protein-coding human disease-associated loci. Understanding the regulatory mechanisms underlying these loci remains a challenge because the causal variants and the tissues in which they act are often unclear. Massively parallel reporter assays (MPRAs) have the potential to link differences in genome sequence, including genetic variants, to tissue-specific regulatory function. Although MPRA and similar technologies have been widely adopted in cell culture, there have been several barriers to widespread use in animals. We overcome these challenges with a new whole-animal MPRA (WhAMPRA), where systemic intravenous AAV effectively transduces the plasmid MPRA library to mouse tissues. Our WhAMPRA approach revealed models of tissue-specific regulation that generally match machine learning model predictions. In addition, we measured the regulatory effects of disrupting MEF2C transcription factor binding sites and impacts of late onset Alzheimer’s disease-associated genetic variations. Overall, our WhAMPRA technology simultaneously determines the transcriptional functions of hundreds of enhancersin vivoacross multiple tissues.
TDCS MODULATES WORKING MEMORY MAINTENANCE PROCESSES IN HEALTHY INDIVIDUALS
Authors: Nikolin Stevan , Martin Donel , Loo Colleen K. , Boonstra Tjeerd W.
Published: November 2022

Background

The effects of tDCS at the prefrontal cortex are often investigated using cognitive paradigms, particularly working memory tasks. However, the neural basis for the neuromodulatory cognitive effects of tDCS, including which subprocesses are affected by stimulation, is not completely understood.

Aims

We investigated the effects of tDCS on working memory task-related spectral activity during and after tDCS to gain better insights into the neurophysiological changes associated with stimulation.

Methods

We reanalysed data from 100 healthy participants grouped by allocation to receive either Sham (0 mA, 0.016 mA, and 0.034 mA) or Active (1 mA or 2 mA) stimulation during a 3-back task. Electroencephalography (EEG) data was used to analyse event-related spectral power in frequency bands associated with working memory performance.

Results

Frontal theta event-related synchronisation (ERS) was significantly reduced post-tDCS in the active group. Participants receiving active tDCS had slower response times following tDCS compared to Sham, suggesting interference with practice effects associated with task repetition. Theta ERS was not significantly correlated with response times or accuracy.

Conclusions

tDCS reduced frontal theta ERS post-stimulation, suggesting a selective disruption to working memory cognitive control and maintenance processes. These findings suggest that tDCS selectively affects specific subprocesses during working memory, which may explain heterogenous behavioural effects.
Spatial scale influences taxon conservation in the eukaryotic virome of a mosquito
Authors: Gil Patricia , Exbrayat Antoni , Loire Etienne , Rakotoarivony Ignace , Charriat Florian , Baldet Thierry , Boisseau Michel , Marie Albane , Frances Benoît , L’Ambert Gregory , Bessat Mohamed , Otify Yehia , Goffredo Maria , Mancini Giuseppe , Busquets-Martí Núria , Birnberg Lotty , Talavera Sandra , Aranda Carlos , Ayari Emna , Mejri Selma , Sghaier Soufien , Bennouna Amal , El Rhaffouli Hicham , Balenghien Thomas , Chlyeh Ghita , Fihri Ouafaa Fassi , Reveillaud Julie , Simonin Yannick , Eloit Marc , Gutierrez Serafin
Published: November 2022

Our knowledge on the diversity of eukaryotic viruses has recently undergone a massive expansion. This diversity could influence host physiology through yet unknown phenomena of potential interest to the fields of health and food production. However, the assembly processes in eukaryotic viromes of terrestrial animals remain elusive. This situation hinders hypothesis-driven tests of virome influence on host physiology. Here, we explore virome assembly at different spatial scales in the eukaryotic virome of the mosquitoCulex pipiens. This mosquito is a vector of human pathogens worldwide. Several new aspects of virome assembly were unveiled through a sampling involving five countries in Africa and Europe and large sample sizes. A group of viruses was conserved inC. pipienspopulations in all countries. This core group represented a relatively large and diverse fraction of the virome. However, core viruses were not shared by all host individuals in a given country, and their infection rates fluctuated between countries and years. Moreover, the distribution of co-infections in individual mosquitoes suggested random co-occurrence of certain core viruses. We also observed differences in the virome depending on geography, with viromes tending to cluster depending on the continent. Thus, our results unveil that taxon conservation in a eukaryotic virome changes with spatial scale. Thus, predictions on virome assembly seem possible at a large geographical scale inC. pipiens.

IMPORTANCE

The study of the eukaryotic virome of mosquitoes is an emerging research field. Beyond its fundamental interest, this field could lead to the development of control tools against the transmission of mosquito-borne human pathogens. However, we yet know little on the assembly patterns in the eukaryotic viromes of mosquitoes, as well as of terrestrial animals in general. This situation hampers the design of hypothesis-driven studies on the influence of the virome on pathogen transmission. Here, we have analyzed virome assembly in the mosquito vectorCulex pipienswithin and between countries in Africa and Europe. Our results show that integrating contrasted spatial scales allows to identify deterministic patterns in virome assembly. Such patterns can guide future studies of virome influence on mosquito physiology.
3D volumetric muscle reconstruction of theAustralopithecus afarensispelvis and limb, with estimations of limb leverage
Authors: Wiseman Ashleigh L. A.
Published: November 2022

To understand how an extinct species may have moved, we first need to reconstruct the missing soft tissues of the skeleton which rarely preserve, with an understanding of segmental volume and the muscular composition within the body. TheAustralopithecus afarensisspecimen AL 288-1 is one of the most complete hominin skeletons. Whilst it is generally accepted that this species walked with an erect limb, the frequency and efficiency of such movement is still debated. Here, 36 muscles of the pelvis and lower limb were reconstructed in the specimen AL 288-1 using 3D polygonal modelling which was guided by imaging scan data and muscle scarring. Reconstructed muscle masses and configurations guided biomechanical modelling of the lower limb in comparison to a modern human. Muscle moment arms were calculated and summed per muscle group. Simulated error margins were computed using Monte Carlo analyses. Results show that the moment arms of both species were comparable, hinting towards similar limb functionality. Moving forward, the polygonal muscle modelling approach has demonstrated promise for reconstructing the soft tissues of hominins and providing information on muscle configuration and space filling. This approach is recommended for future studies aiming to model musculature in extinct taxa.
Genomics of Preaxostyla Flagellates Illuminates the Path Towards the Loss of Mitochondria
Authors: Novák Lukáš V. F. , Treitli Sebastian C. , Pyrih Jan , Hałakuc Paweł , Pipaliya Shweta V. , Vacek Vojtěch , Brzoň Ondřej , Soukal Petr , Eme Laura , Dacks Joel B. , Karnkowska Anna , Eliáš Marek , Hampl Vladimír
Published: November 2022

The notion that mitochondria cannot be lost was shattered with the report of an oxymonadMonocercomonoides exilis, the first eukaryote arguably without any mitochondrion. Yet, questions remain about whether this extends beyond the single species and how this transition took place. The Oxymonadida is a group of gut endobionts taxonomically housed in the Preaxostyla which also contains free-living flagellates of the generaTrimastixandParatrimastix. The latter two taxa harbour conspicuous mitochondrion-related organelles (MROs). Here we report high-quality genome and transcriptome assemblies of two Preaxostyla representatives, the free-livingParatrimastix pyriformisand the oxymonadBlattamonas nauphoetae. We performed thorough comparisons among all available genomic and transcriptomic data of Preaxostyla to further decipher the evolutionary changes towards amitochondriality, endobiosis, and unstacked Golgi. Our results provide insights into the metabolic and endomembrane evolution, but most strikingly the data confirm the complete loss of mitochondria for all three oxymonad species investigated (M. exilis,B. nauphoetae, andStreblomastix strix), suggesting the amitochondriate status is common to a large part if not whole group of Oxymonadida. This observation moves this unique loss to 100 MYA when oxymonad lineage diversified.

Author summary

Mitochondria are nearly ubiquitous components of eukaryotic cells that constitute bodies of animals, fungi, plants, algae, and a broad diversity of single-celled eukaryotes,akaprotists. Many groups of protists have substantially reduced the complexity of their mitochondria because they live in oxygen-poor environments, so they are unable to utilize the most salient feature of mitochondria – their ATP-producing oxidative phosphorylation metabolism. However, for a long time, scientists thought that it is impossible to completely lose a mitochondrion because this organelle provides other essential services to the cell, e.g. synthesis of protein cofactors called iron-sulfur clusters. Detailed investigation of chinchilla symbiont M.exilisdocumented the first case of an organism without mitochondrion, and it also provided a scenario explaining how this unique evolutionary experiment might have happened. In this work, we expand on this discovery by exploring genomes of multiple relatives ofM. exilis. We show that the loss of the mitochondrion is not limited to a single species but possibly extends to its entire group, the oxymonads. We also compare the predicted metabolic capabilities of oxymonads to their closest known mitochondrion-containing relatives and map out various changes that occurred during the transition to amitochondriality.
Autolysosomal exocytosis of lipids protect neurons from ferroptosis
Authors: Ralhan Isha , Chang Jinlan , Moulton Matthew J. , Goodman Lindsey D. , Lee Nathanael Y.J. , Plummer Greg , Pasolli H. Amalia , Matthies Doreen , Bellen Hugo J. , Ioannou Maria S.
Published: November 2022

During oxidative stress neurons release lipids that are internalized by glia. Defects in this coordinated process play an important role in several neurodegenerative diseases. Yet, the mechanisms of lipid release and its consequences on neuronal health are unclear. Here, we demonstrate that lipid-protein particle release by autolysosome exocytosis protects neurons from ferroptosis, a form of cell death driven by lipid peroxidation. We show that during oxidative stress, peroxidated lipids and iron are released from neurons by autolysosomal exocytosis which requires the exocytic machinery; VAMP7 and syntaxin 4. We observe membrane-bound lipid-protein particles by TEM and demonstrate that these particles are released from neurons using cryoEM. Failure to release these lipid-protein particles causes lipid hydroperoxide and iron accumulation and sensitizes neurons to ferroptosis. Our results reveal how neurons protect themselves from peroxidated lipids. Given the number of brain pathologies that involve ferroptosis, defects in this pathway likely play a key role in the pathophysiology of neurodegenerative disease.

Release of lipid-protein particles by autolysosomal exocytosis protects neurons from ferroptosis.
Structure-Function Dynamics of Engineered, Modular Neuronal Networks with Controllable Afferent-Efferent Connectivity
Authors: Winter-Hjelm Nicolai , Tomren Åste Brune , Sikorski Pawel , Sandvig Axel , Sandvig Ioanna
Published: November 2022

Microfluidic devices interfaced with microelectrode arrays have in recent years emerged as powerful platforms for studying and manipulatingin vitroneuronal networks at the micro- and mesoscale. By segregating neuronal populations using microchannels only permissible to axons, neuronal networks can be designed to mimic the highly organized, modular topology of neuronal assemblies in the brain. However, little is known about how the underlying topological features of such engineered neuronal networks contribute to their functional profile. To start addressing this question, a key parameter is control of afferent or efferent connectivity within the network. In this study, we show that a microfluidic device featuring axon guiding channels with geometrical constraints inspired by a Tesla valve effectively promotes unidirectional axonal outgrowth between neuronal nodes, thereby enabling us to control afferent connectivity. Our results moreover indicate that these networks exhibit a more efficient network organization with higher modularity compared to single nodal controls. We verified this by applying designer viral tools to fluorescently label the neurons to visualize the structure of the networks, combined with extracellular electrophysiological recordings using embedded nanoporous microelectrodes to study the functional dynamics of these networks during maturation. We furthermore show that electrical stimulations of the networks induce signals selectively transmitted in a feedforward fashion between the neuronal populations. A key advantage with our microdevice is the ability to longitudinally study and manipulate both the structure and function of neuronal networks with high accuracy. This model system has the potential to provide novel insights into the development, topological organization, and neuroplasticity mechanisms of neuronal assemblies at the micro- and mesoscale in healthy and perturbed conditions.
Micropropagated walnut dependency on phosphate fertilization and arbuscular mycorrhiza for growth, nutrition and quality differ between rootstocks both after acclimatization andpost-acclimatization
Authors: Mortier Emma , Jacquiod Samuel , Jouve Laurent , Martin-Laurent Fabrice , Recorbet Ghislaine , Lamotte Olivier
Published: November 2022

The English walnut (Juglans regiaL.) is the main species cultivated for the production of edible nuts.In vitromicropropagation of walnut explants, necessary for mass propagation of high-quality walnut rootstocks, needs anex vitroacclimatization phase followed by apost-acclimatization growth in greenhouse when plantlets become photoautotrophic. However, poor survival and slow growth rates are common difficulties encountered in nurseries when establishing micropropagated walnut saplings. As many other fruit and nut bearing trees, walnut exhibits a high dependency on symbiotic soil-borne arbuscular mycorrhizal fungi for better soil nutrient acquisition and development due to a coarse root architecture that notably limits soil inorganic phosphate (Pi) uptake. In the context of rootstock production, we investigated the establishment of seven walnut rootstocks of economic interest (RG2, RG6, R17, RX1, VLACH, VX211, and WIP3) inoculated or not withRhizophagus irregularisunder two contrasting Pi fertilization regimes. We demonstrated that inoculation withR. irregularisdecreases micropropagated walnut rootstock dependency on Pi fertilization both at the acclimatization andpost-acclimatization stages, together with improving quality, sapling biomass production and nutrition of walnut rootstocks. We also showed that these benefits are rootstock-dependent, indicating that walnut mycorrhizal dependency for Pi nutrition varies between cultivars.
Ecological network analysis reveals cancer-dependent chaperone-client interaction structure and robustness in the mitochondria
Authors: Galai Geut , Rotblat Barak , Pilosof Shai
Published: November 2022

Cancer cells alter the expression levels of metabolic enzymes to fuel proliferation. The mitochondrion is a central hub of metabolic reprogramming, where multiple chaperons service hundreds of clients, forming complex chaperone-client interaction networks (CCINs). Studying (i) how network structure varies across cancer types and (ii) the influence of structure on networks’ robustness to chaperon targeting is key to developing cancer-specific drug therapy. We investigate these yet unaddressed questions using theory and methodology from network ecology. We show that CCINs are non-randomly structured across cancer types. Moreover, we identify groups of chaperones that interact with similar clients, providing specialization on clients but also redundancy in the case of chaperone removal on the other. Simulations of network robustness show that this modular structure strongly affects cancer-specific response to chaperon removal. Our results open the door for new hypotheses regarding the ecology and evolution of CCINs and can inform caner-specific drug development strategies.
Developing a temperature-inducible transcriptional rheostat inNeurospora crassa
Authors: Tabilo-Agurto Cyndi , Del Rio-Pinilla Verónica , Eltit-Villarroel Valeria , Goity Alejandra , Muñoz-Guzmán Felipe , Larrondo Luis F.
Published: November 2022

Heat shock protein (hsp) encoding genes, part of the highly conserved Heat Shock Response (HSR), are known to be induced by thermal stress in several organisms. InNeurospora crassa, threehspgenes,hsp30, hsp70, andhsp80, have been characterized; however, the role of definedcis-elements in their response to discrete changes in temperature remains largely unexplored. To fill this gap, while also aiming to obtain a reliable fungal heat-shock inducible system, we analyzed different sections of eachhsppromoter, by assessing the expression of real-time transcriptional reporters. Whereas all three promoters, and their resected versions, were acutely induced by high temperatures, onlyhsp30displayed a broad range of expression and high tunability amply exciding other inducible promoter systems existing in Neurospora, such as Quinic acid- or light-inducible ones. As proof of concept, we employed one of these promoters to control the expression ofclr-2, which encodes for the master regulator of Neurospora cellulolytic capabilities. The resulting strain fails to grow on cellulose at 25°C, whereas it robustly grows if heat shock pulses are delivered daily. Additionally, we designed twohsp30synthetic promoters and characterized these, as well as the native promoters, to a gradient of high temperatures, yielding a wide range of responses to thermal stimuli. Thus, Neurosporahsp30-based promoters represent a new set of modular elements that can be used as a transcriptional rheostat to adjust the expression of a gene of interest or for the implementation of regulated circuitries for synthetic biology and biotechnological strategies.

Importance

Timely and dynamic response to strong temperature rises is paramount for organismal biology. At the same time, inducible promoters are a powerful tool for fungal biotechnological and synthetic biology endeavors. In this work, we analyzed the activity of severalN. crassaheat shock protein (hsp) promoters upon a wide range of temperatures, observing thathsp30exhibits remarkable sensitivity and dynamic range of expression as we chartered the response of this promoter to subtle increases in temperature, while also building synthetic promoters based onhsp30 cis-elements. As proof of concept, we analyzed the ability ofhsp30to provide tight control of a central process such as cellulose degradation. While this study provides an unprecedented description of the regulation of theN. crassa hspgenes it also contributes with a noteworthy addition to the molecular toolset of transcriptional controllers in filamentous fungi.