bluuebunny/crossref_metadata_2025 huggingface dataset:
The co-occurrence of genetic variants in theTYRandOCA2genes confers susceptibility to albinism
Authors: Green David J. , Michaud Vincent , Lasseaux Eulalie , Plaisant Claudio ,   UK Biobank Eye and Vision Consortium, Fitzgerald Tomas , Birney Ewan , Black Graeme C. , Arveiler Benoît , Sergouniotis Panagiotis I.
Published: January 2023

Although rare genetic conditions are mostly caused by DNA sequence alterations that functionally disrupt individual genes, large-scale studies using genome sequencing have started to unmask additional complexity. Understanding how combinations of variants in different genes shape human phenotypes is expected to provide important insights into the clinical and genetic heterogeneity of rare disorders. We used albinism, an archetypal rare condition associated with hypopigmentation, as an exemplar for the study of genetic interactions. We analysed data from the Genomics England 100,000 Genomes Project alongside a cohort of 1,120 individuals with albinism, and investigated the effect of dual heterozygosity for the combination of two established albinism-related variants:TYR:c.1205G>A (p.Arg402Gln) [rs1126809] andOCA2:c.1327G>A (p.Val443Ile) [rs74653330]. As each of these changes alone is insufficient to cause disease when present in the heterozygous state, we sought evidence of synergistic effects. We found that, when both variants are present, the probability of receiving a diagnosis of albinism is significantly increased (odds ratio 12.8; 95% confidence interval 6.0 – 24.7; p-value 2.1 x 10-8). Further analyses in an independent cohort, the UK Biobank, supported this finding and highlighted that heterozygosity for theTYR:c.1205G>A andOCA2:c.1327G>A variant combination is associated with statistically significant alterations in visual acuity and central retinal thickness (traits that are considered albinism endophenotypes). The approach discussed in this report opens up new avenues for the investigation of oligogenic patterns in apparently Mendelian disorders.
Externally Validated Machine Learning Algorithm Accurately Predicts Medial Tibial Stress Syndrome in Military Trainees; A Multi-Cohort Study
Authors: Shaw Angus , Newman Phillip , Witchalls Jeremy , Hedger Tristan
Published: January 2023

Objectives

Medial Tibial Stress Syndrome (MTSS) is a common musculoskeletal injury, both in sports and the military. There is no reliable treatment and reoccurrence rates are high. Prevention of MTSS is critical to reducing operational burden. Therefore, this study aimed to build a decision-making model to predict the individual risk of MTSS within officer cadets and test the external validity of the model on a separate military population.

Design

Prospective cohort study.

Methods

This study collected a suite of key variables previously established for predicting MTSS. Data was obtained from 107 cadets (34 females and 73 males). A follow-up survey was conducted at 3-months to determine MTSS diagnoses. Six ensemble learning algorithms were deployed and trained 5 times on random stratified samples of 75% of the dataset. The resultant algorithms were tested on the remaining 25% of the dataset and the models were compared for accuracy. The most accurate new algorithm was tested on an unrelated data sample of 123 Australian Navy recruits to establish external validity of the model.

Results

Random Forest modelling was the most accurate in identifying a diagnosis of MTSS; (AUC = 98%). When the model was tested on an external dataset, it performed with an accuracy of 94% (F1= 0.88).

Conclusion

This model is highly accurate in predicting those who will develop MTSS. The model provides important preventive capacity which should be trialled as a risk management intervention.
Origin and adult renewal of the gut lacteal musculature from villus myofibroblasts
Authors: Sanketi Bhargav D. , Mantri Madhav , Huang Liqing , Tavallaei Mohammad A. , Hu Shing , Wang Michael F. Z. , De Vlaminck Iwijn , Kurpios Natasza A.
Published: January 2023

Intestinal smooth muscles are the workhorse of the digestive system. Inside the millions of finger-like intestinal projections called villi, strands of smooth muscle cells contract to propel absorbed dietary fats through the adjacent lymphatic vessel, called the lacteal, sending fats into the blood circulation for energy production. Despite this vital function, how villus smooth muscles form, how they assemble alongside lacteals, and how they repair throughout life remain unknown. Here we combine single-cell RNA sequencing of the mouse intestine with quantitative lineage tracing to reveal the mechanisms of formation and differentiation of villus smooth muscle cells. Within the highly regenerative villus, we uncover a local hierarchy of subepithelial fibroblast progenitors that progress to become mature smooth muscle fibers, via an intermediate contractile myofibroblast-like phenotype. This continuum persists in the adult intestine as the major source of renewal of villus smooth muscle cells during adult life. We further found that the NOTCH3-DLL4 signaling axis governs the assembly of villus smooth muscles alongside their adjacent lacteal, and we show that this is necessary for gut absorptive function. Overall, our data shed light on the genesis of a poorly defined class of intestinal smooth muscle and pave the way for new opportunities to accelerate recovery of digestive function by stimulating muscle repair.
CATD: A reproducible pipeline for selecting cell-type deconvolution methods across tissues
Authors: Pournara Anna Vathrakokoili , Miao Zhichao , Beker Ozgur Yilimaz , Nolte Nadja , Brazma Alvis , Papatheodorou Irene
Published: January 2023

Cell-type deconvolution methods aim to infer cell composition from bulk transcriptomic data. The proliferation of developed methods, coupled with inconsistent results obtained in many cases, highlights the pressing need for guidance in the selection of appropriate methods. Additionally, the growing accessibility of single-cell RNA sequencing datasets, often accompanied by bulk expression from related samples, enable the benchmark of existing methods. In this study, we conduct a comprehensive assessment of 31 methods, utilising single-cell RNA-sequencing data from diverse human and mouse tissues. Employing various simulation scenarios, we reveal the efficacy of regression-based deconvolution methods, highlighting their sensitivity to reference choices. We investigate the impact of bulk-reference differences, incorporating variables such as sample, study and technology. We provide validation using a gold standard dataset from mononuclear cells and suggest a consensus prediction of proportions when ground truth is not available. We validated the consensus method on data from the stomach and studied its spillover effect. Importantly, we propose the use of the Critical Assessment of Transcriptomic Deconvolution (CATD) pipeline which encompasses functionalities for generating references and pseudo-bulks and running implemented deconvolution methods. CATD streamlines simultaneous deconvolution of numerous bulk samples, providing a practical solution for speeding up the evaluation of newly developed methods.

Availability:https://github.com/Papatheodorou-Group/CATD_snakemake
Phage-specific immune responses impair efficacy of phage therapy targeting VRE in a murine model
Authors: Berkson Julia D. , Allen Garrison B. , Schubert Alyxandria M. , Dunbar Kristin E. , Coryell Michael P. , Sava Rosa L. , Gao Yamei , Wate Claire E. , Hastie Jessica L. , Zimmermann Sally K. , Carlson Paul E.
Published: January 2023

Antimicrobial resistant bacteria are an emerging and prevalent global threat with an urgent need for alternative therapies. Bacteriophage (phage) therapy is a promising approach to address these infections that has gained renewed interest in recent years. Despite this, questions remain regarding the therapeutic use of phages, including the impact that the immune response may have on phage therapy, particularly when this treatment is administered long-term or when reusing a specific phage treatment in a single individual. To investigate this, we developed a mouse model to assess phage treatment using a cocktail of five phages from theMyoviridaeandSiphoviridaefamilies that target vancomycin-resistant enterococcus (VRE) gut colonization. Phage cocktail treatment significantly reduced the intestinal bacterial burden of VRE in mice. We characterized innate and adaptive immune responses elicited against the phage cocktail after one and multiple exposures, respectively. While minimal innate responses were observed after phage administration, two courses of phage therapy induced phage-specific neutralizing antibodies and appeared to accelerate phage clearance from tissues. Interestingly, the myophages in our cocktail induced a more robust neutralizing antibody response than the siphophages. Proteins targeted by phage-specific antibodies were also identified from each phage family of the cocktail. Importantly, we show that this anti-phage immunity reduced the effectiveness of the phage cocktail in our murine model, leading to significantly higher fecal bacterial burden following repeat treatment. Collectively, this study shows the immune system has the potential to impede effectiveness of phage therapy and that the phage-specific immune responses can differ significantly between phages. These findings can help inform decisions about inclusion of specific phages in cocktails for future studies.
Decomposing drivers in avian insectivory: large-scale effects of climate, habitat and bird diversity
Authors: Schillé Laura , Valdés-Correcher Elena , Archaux Frédéric , Bălăcenoiu Flavius , Bjørn Mona Chor , Bogdziewicz Michal , Boivin Thomas , Branco Manuela , Damestoy Thomas , de Groot Maarten , Dobrosavljević Jovan , Duduman Mihai-Leonard , Dulaurent Anne-Maïmiti , Green Samantha , Grünwald Jan , Eötvös Csaba Béla , Faticov Maria , Fernandez-Conradi Pilar , Flury Elisabeth , Funosas David , Galmán Andrea , Gossner Martin M. , Gripenberg Sofia , Grosu Lucian , Hagge Jonas , Hampe Arndt , Harvey Deborah , Houston Rick , Isenmann Rita , Kavčič Andreja , Kozlov Mikhail V. , Lanta Vojtech , Le Tilly Bénédicte , Vaamonde Carlos Lopez , Mallick Soumen , Mäntylä Elina , Mårell Anders , Milanović Slobodan , Molnár Márton , Moreira Xoaquín , Moser Valentin , Mrazova Anna , Musolin Dmitrii L. , Perot Thomas , Piotti Andrea , Popova Anna V. , Prinzing Andreas , Pukinskaya Ludmila , Sallé Aurélien , Sam Katerina , Sedikhin Nickolay V. , Shabarova Tanja , Tack Ayco J. M. , Thomas Rebecca , Thrikkadeeri Karthik , Toma Dragoș , Vaicaityte Grete , van Halder Inge , Varela Zulema , Barbaro Luc , Castagneyrol Bastien
Published: January 2023

Aim

Climate is a major driver of large scale variability in biodiversity, as a likely result of more intense biotic interactions under warmer conditions. This idea fuelled decades of research on plant-herbivore interactions, but much less is known about higher-level trophic interactions. We addressed this research gap by characterizing both bird diversity and avian predation along a climatic gradient at the European scale.

Location

Europe.

Taxon

Insectivorous birds and pedunculate oaks.

Methods

We deployed plasticine caterpillars in 138 oak trees in 47 sites along a 19° latitudinal gradient in Europe to quantify bird insectivory through predation attempts. In addition, we used passive acoustic monitoring to (i) characterize the acoustic diversity of surrounding soundscapes; (ii) approximate bird abundance and activity through passive acoustic recordings and (iii) infer both taxonomic and functional diversity of insectivorous birds from recordings.

Results

The functional diversity of insectivorous birds increased with warmer climates. Bird predation increased with forest cover and bird acoustic activity but decreased with mean annual temperature and functional richness of insectivorous birds. Contrary to our predictions, climatic clines in bird predation attempts were not directly mediated by changes in insectivorous bird diversity or acoustic activity, but climate and habitat still had independent effects on predation attempts.

Main conclusions

Our study supports the hypothesis of an increase in the diversity of insectivorous birds towards warmer climates, but refutes the idea that an increase in diversity would lead to more predation and advocates for better accounting for activity and abundance of insectivorous birds when studying the large-scale variation in insect-tree interactions.
A decade of hidden phytoplasmas unveiled through citizen science
Authors: Brochu Anne-Sophie , Dionne Antoine , Fall Mamadou Lamine , Pérez-López Edel
Published: January 2023

Climate change is impacting agriculture in many ways, and a contribution from all is required to reduce the imminent loses related to it. Recently, it has been showed that citizen science could be a way to trace the impact of climate change. However, how can citizen science be applied in plant pathology? Here, using as an example a decade of phytoplasma-related diseases reported by growers, agronomists, citizens in general, and confirmed by a government laboratory, we explore a new way of valuing plant pathogens monitoring data deriving from land-users or stakeholders. Through this collaboration we found that in the last decade thirty-four hosts have been affected by phytoplasmas, nine, thirteen and five of these plants were, for the first time, reported phytoplasma hosts in Eastern Canada, in Canada and worldwide, respectively. Another finding of great impact is the first report of a ‘Ca. P. phoenicium’-related strain in Canada, while ‘Ca. P. pruni’ and ‘Ca. P. pyri’ was reported for the first time in Eastern Canada. These findings will have a great impact in the management of phytoplasmas and their insect vectors. Using these insect-vectored bacterial pathogens, we show the needs of new strategies that allow a fast and accurate communication between concerned citizens and those institutions confirming their observations.

Abstract Figure
DESP: Demixing Cell State Profiles from Dynamic Bulk Molecular Measurements
Authors: Youssef Ahmed , Paul Indranil , Crovella Mark , Emili Andrew
Published: January 2023

There is wide interest to determine the dynamic expression of proteins and other molecules that drive phenotypic remodeling in development and pathobiology, but due to technical limitations these systems remain largely unexplored at the foundational resolution of the underlying cell states. Here, we presentDESP, a novel algorithm that leverages independent estimates of cell state proportions, such as from single-cell RNA-sequencing or cell sorting, to resolve the relative contributions of cell states to bulk molecular measurements, most notably quantitative proteomics, recorded in parallel. We appliedDESPto an in-vitro model of the epithelial-to-mesenchymal transition and demonstrated its ability to accurately reconstruct cell state signatures from bulk-level measurements of both the proteome and transcriptome providing insights into transient regulatory mechanisms.DESPprovides a generalizable computational framework for modeling the relationship between bulk and single-cell molecular measurements, enabling the study of proteomes and other molecular profiles at the cell state-level using established bulk-level workflows.
Linking genetic and environmental factors through marker effect networks to understand trait plasticity
Authors: Coletta Rafael Della , Liese Sharon E. , Fernandes Samuel B. , Mikel Mark A. , Bohn Martin O. , Lipka Alexander E. , Hirsch Candice N.
Published: January 2023

Understanding how plants adapt to specific environmental changes and identifying genetic markers associated with phenotypic plasticity can help breeders develop plant varieties adapted to a rapidly changing climate. Here, we propose the use of marker effect networks as a novel method to identify markers associated with environmental adaptability. These marker effect networks are built by adapting commonly used software for building gene co-expression networks with marker effects across growth environments as the input data into the networks. To demonstrate the utility of these networks, we built networks from the marker effects of ∼10,000 non-redundant markers from 400 maize hybrids across nine environments. We demonstrate that networks can be generated using this approach, and that the markers that are co-varying are rarely in linkage disequilibrium, thus representing higher biological relevance. Multiple covarying marker modules associated with different weather factors throughout the growing season were identified within the marker effect networks. Finally, a factorial test of analysis parameters demonstrated marker effect networks are relatively robust to these options, with high overlap in modules associated with the same weather factors across analysis parameters. This novel application of network analysis provides unique insights into phenotypic plasticity, and specific environmental factors that modulate the genome.
Distinct neuroinflammatory signatures exist across genetic and sporadic ALS cohorts
Authors: Rifai Olivia M. , O’Shaughnessy Judi , Dando Owen R. , Munro Alison F. , Sewell Michael D.E. , Abrahams Sharon , Waldron Fergal M. , Sibley Christopher R. , Gregory Jenna M.
Published: January 2023

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterised by progressive loss of upper and lower motor neurons. ALS is on a pathogenetic disease spectrum with frontotemporal dementia (FTD), with patients sometimes experiencing elements of both conditions (ALS-FTSD). For mutations associated with ALS-FTSD, such as theC9orf72hexanucleotide repeat expansion (HRE), the factors influencing where an individual may lie on this spectrum require further characterisation. Here, using NanoString molecular barcoding with a panel of 770 neuroinflammatory genes, we interrogate inflammatory dysregulation at the level of gene expression. We identified 20 dysregulated neuroinflammatory genes in the motor cortex of deeply clinically phenotyped C9-ALSpost-mortemcases, with enrichment of microglial and inflammatory response gene sets. Our analyses also revealed two distinct ALS-related neuroinflammatory panel signatures (NPS), NPS1 and NPS2, delineated by the direction of expression of proinflammatory, axonal transport and synaptic signalling pathways. Two genes with significant correlations to available clinical metrics were selected for validation:FKBP5andBDNF. FKBP5 and its signalling partner, NF-κB, appeared to have a cell-type-specific staining distribution, with activated (i.e., nuclear) NF-κB immunoreactivity in C9-ALS. Expression ofBDNF, a correlate of disease duration, was confirmed to be higher in individuals with long compared to short disease duration using BaseScope™in situhybridisation. Finally, we compared NPS between C9-ALS cases and those from deeply clinically phenotyped sporadic ALS (sALS) and SOD1-ALS cohorts, with NPS1 and NPS2 appearing across all cohorts. A subset of these signatures was also detected in publicly available RNA-sequencing data from independent C9-ALS and sALS cohorts, underscoring the relevance of these pathways across cohorts. Our findings highlight the importance of tailoring therapeutic approaches based on distinct molecular signatures that exist between and within genetic and sporadic cohorts.
Development and characterization of new patient-derived xenograft (PDX) models of osteosarcoma with distinct metastatic capacities
Authors: Schott Courtney R. , Koehne Amanda L. , Sayles Leanne C. , Young Elizabeth P. , Luck Cuyler , Yu Katharine , Lee Alex G. , Breese Marcus R. , Leung Stanley G. , Xu Hang , Shah Avanthi Tayi , Liu Heng-Yi , Spillinger Aviv , Behroozfard Inge H. , Marini Kieren D. , Dinh Phuong T. , Pons Ventura María V. , Vanderboon Emma N. , Hazard Florette K. , Cho Soo-Jin , Avedian Raffi S. , Mohler David G. , Zimel Melissa , Wustrack Rosanna , Curtis Christina , Sirota Marina , Sweet-Cordero E. Alejandro
Published: January 2023

Models to study metastatic disease in rare cancers are needed to advance preclinical therapeutics and to gain insight into disease biology, especially for highly aggressive cancers with a propensity for metastatic spread. Osteosarcoma is a rare cancer with a complex genomic landscape in which outcomes for patients with metastatic disease are poor. As osteosarcoma genomes are highly heterogeneous, a large panel of models is needed to fully elucidate key aspects of disease biology and to recapitulate clinically-relevant phenotypes. We describe the development and characterization of osteosarcoma patient-derived xenografts (PDXs) and a panel of PDX-derived cell lines. Matched patient samples, PDXs, and PDX-derived cell lines were comprehensively evaluated using whole genome sequencing and RNA sequencing. PDXs and PDX-derived cell lines largely maintained the expression profiles of the patient from which they were derived despite the emergence of whole-genome duplication (WGD) in a subset of cell lines. These cell line models were heterogeneous in their metastatic capacity and their tissue tropism as observed in both intravenous and orthotopic models. As proof-of-concept study, we used one of these models to test the preclinical effectiveness of a CDK inhibitor on the growth of metastatic tumors in an orthotopic amputation model. Single-agent dinaciclib was effective at dramatically reducing the metastatic burden in this model.

Graphical Abstract
Recognition determinants of improved HIV-1 neutralization by a heavy chain matured pediatric antibody
Authors: Kumar Sanjeev , Singh Swarandeep , Chatterjee Arnab , Bajpai Prashant , Sharma Shaifali , Katpara Sanket , Lodha Rakesh , Dutta Somnath , Luthra Kalpana
Published: January 2023

The structural and characteristic features of HIV-1 broadly neutralizing antibodies (bnAbs) from chronically infected pediatric donors are currently unknown. Herein, we characterized a heavy chain matured HIV-1 bnAb 44m, identified from a pediatric elite-neutralizer. Interestingly, in comparison to its wild-type AIIMS-P01 bnAb, 44m exhibited moderately higher level of somatic hypermutations of 15.2%. The 44m neutralized 79% of HIV-1 heterologous viruses (n=58) tested, with a geometric mean IC50titer of 0.36 µg/ml. The cryo-EM structure of 44m Fab in complex with fully-cleaved glycosylated native-like BG505.SOSIP.664.T332N gp140 envelope trimer at 4.4Å resolution revealed that 44m targets the V3-glycan N332-supersite and GDIR motif to neutralize HIV-1 with improved potency and breadth, plausibly attributed by a matured heavy chain as compared to that of wild-type AIIMS-P01. This study further improves our understanding on pediatric HIV-1 bnAbs and structural basis of broad HIV-1 neutralization by 44m may be useful blueprint for vaccine design in future.
Human skeletal muscle methylome after low carbohydrate energy balanced exercise
Authors: Gorski Piotr P. , Turner Daniel C. , Iraki Juma , Morton James P. , Sharples Adam P. , Areta José L.
Published: January 2023

We aimed to investigate the human skeletal muscle (SkM) DNA methylome after exercise in low carbohydrate (CHO) energy balance (with high fat) compared with exercise in low-CHO energy deficit (with low fat) conditions. The objective to identify novel epigenetically regulated genes and pathways associated with ‘train-low sleep-low’ paradigms. The sleep-low conditions included 9 males that cycled to deplete muscle glycogen while reaching a set energy expenditure. Post-exercise, low-CHO meals (protein-matched) completely replaced (using high-fat) or only partially replaced (low-fat) the energy expended. The following morning resting baseline biopsies were taken and the participants then undertook 75 minutes of cycling exercise, with skeletal muscle biopsies collected 30 minutes and 3.5 hours post exercise. Discovery of genome-wide DNA methylation was undertaken using Illumina EPIC arrays and targeted gene expression analysis was conducted by RT-qPCR. At baseline participants under energy balance (high fat) demonstrated a predominantly hypermethylated (60%) profile across the genome compared to energy deficit-low fat conditions. However, post exercise performed in energy balance (with high fat) elicited a more prominent hypomethylation signature 30 minutes post-exercise in gene regulatory regions important for transcription (CpG islands within promoter regions) compared with exercise in energy deficit (with low fat) conditions. Such hypomethylation was enriched within pathways related to: IL6-JAK-STAT signalling, metabolic processes, p53 / cell cycle and oxidative / fatty acid metabolism. Hypomethylation within the promoter regions of genes: HDAC2, MECR, IGF2 and c13orf16 were associated with significant increases in gene expression in the post-exercise period in energy balance compared with energy deficit. Furthermore, histone deacetylase, HDAC11 was oppositely regulated at the gene expression level compared with HDAC2, where HDAC11 was hypomethylated yet increased in energy deficit compared with energy balance conditions. Overall, we identify some novel epigenetically regulated genes associated with train-low sleep-low paradigms.
Propionate reinforces epithelial identity and reduces aggressiveness of non-small cell lung carcinoma via chromatin remodelling
Authors: Ramesh Vignesh , Gollavilli Paradesi Naidu , Pinna Luisa , Siddiqui Mohammad Aarif , Jakobsen Simon Toftholm , Boiteux Elisa Le , Olsen Karen Ege , Jensen Ole Nørregaard , Siersbæk Rasmus , Somyajit Kumar , Ceppi Paolo
Published: January 2023

Epithelial to mesenchymal transition (EMT) is a developmental cellular program driving metastasis and chemo-resistance in cancer, but its pharmacological treatment has been so far challenging. Targeting deregulated metabolic processes in cancer is emerging as a realistic therapeutic strategy. Here, we used an EMT-focussed integrative functional genomic approach and identified negative association of the short-chain fatty acids propionate and butanoate with EMT in non-small cell lung cancer (NSCLC) patients. Strikingly, in vitro treatment of lung cancer cell lines with propionate reinforced the epithelial transcriptional program promoting cell adhesion and reverting the aggressive and chemoresistant EMT phenotype. Propionate treatment reduced cells metastatic ability in nude mice and limited lymph nodal spread in a genetic NSCLC mouse model. Further analyses indicated chromatin remodeling via H3K27 acetylation (p300-mediated) as the mechanism shifting the EMT balance towards epithelial state upon propionate. Propionate administration could be tested in the clinic for reducing NSCLC aggressiveness.

Highlights

An EMT-centric investigation of metabolic processes in a comprehensive lung cancer transcriptome profiles identified negative associations between EMT and SCFAs (propionate and butyrate)

Propionate enhances the epithelial features both at the molecular and cellular levels

Pre-treatment of cells with propionate inhibits EMT associated processes including migration and sensitizes the cells to chemotherapeutic drug cisplatin

Oral administration of propionate inhibits EMT-mediated lung colonization ability of NSCLC cells, and lymph node metastasis in a genetic mouse NSCLC model

Molecular mechanistic investigation of propionate revealed chromatin remodelling through p300-mediated histone acetylation in E-cadherin gene regulation along with epithelial features reinforcement
Identifying nonlinear Functional Connectivity with EEG/MEG using Nonlinear Time-Lagged Multidimensional Pattern Connectivity (nTL-MDPC)
Authors: Rahimi Setareh , Jackson Rebecca , Hauk Olaf
Published: January 2023

Investigating task- and stimulus-dependent connectivity is key to understanding how brain regions interact to perform complex cognitive processes. Most existing connectivity analysis methods reduce activity within brain regions to unidimensional measures, resulting in a loss of information. While recent studies have introduced new functional connectivity methods that exploit multidimensional information, i.e., pattern-to-pattern relationships across regions, they have so far mostly been applied to fMRI data and therefore lack temporal information. We recently developed Time-Lagged Multidimensional Pattern Connectivity for EEG/MEG data, which detects linear dependencies between patterns for pairs of brain regions and latencies in event-related experimental designs (Rahimi et al., 2022b). Due to the linearity of this method, it may miss important nonlinear relationships between activity patterns. Thus, we here introduce nonlinear Time-Lagged Multidimensional Pattern Connectivity (nTL-MDPC) as a novel bivariate functional connectivity metric for event-related EEG/MEG applications. nTL-MDPC describes how well patterns in ROIXat time pointtxcan predict patterns of ROIYat time pointtyusing artificial neural networks (ANNs). We evaluated this method on simulated data as well as on an existing EEG/MEG dataset of semantic word processing, and compared it to its linear counterpart (TL-MDPC). We found that nTL-MDPC indeed detected nonlinear relationships more reliably than TL-MDPC in simulations with moderate to high numbers of trials. However, in real brain data the differences were subtle, with identification of some connections over greater time lags but no change in the connections identified. The simulations and EEG/MEG results demonstrate that differences between the two methods are not dramatic, i.e. the linear method can approximate linear and nonlinear dependencies well.

Highlights

nTL-MDPC is a bivariate functional connectivity method for event-related EEG/MEG

nTL-MDPC detects linear and nonlinear connectivity at zero and non-zero lags

nTL-MDPC revealed connectivity between ATL hub and semantic control regions

Differences between linear and nonlinear TL-MDPC were small
Confidence is predicted by pre- and post-choice decision signal dynamics
Authors: Grogan John P. , Rys Wouter , Kelly Simon P. , O’Connell Redmond G.
Published: January 2023

It is well established that one’s confidence in a choice can be influenced by new evidence encountered after commitment has been reached, but the processes through which post-choice evidence is sampled remain unclear. To investigate this, we traced the pre- and post-choice dynamics of electrophysiological signatures of evidence accumulation (Centro-parietal Positivity, CPP) and motor preparation (mu/beta band) to determine their sensitivity to participants’ confidence in their perceptual discriminations. Pre-choice CPP amplitudes scaled with confidence both when confidence was reported simultaneously with choice, or when reported 1-second after the initial direction decision. When additional evidence was presented during the post-choice delay period, the CPP continued to evolve after the initial choice, with a more prolonged build-up on trials with lower confidence in the alternative that was finally endorsed, irrespective of whether this entailed a change-of-mind. Further investigation established that this pattern was accompanied by earlier post-choice CPP peak latency, earlier lateralisation of motor preparation signals toward the ultimately chosen response, and faster confidence reports when participants indicated high certainty that they had made a correct or incorrect initial choice. These observations are consistent with confidence-dependent stopping theories according to which post-choice evidence accumulation ceases when a criterion level of confidence in a choice alternative has been reached. Our findings have implications for current models of choice confidence, and predictions they may make about EEG signatures.
Mental search of concepts is supported by egocentric vector representations and restructured grid maps
Authors: Viganò Simone , Bayramova Rena , Doeller Christian F. , Bottini Roberto
Published: January 2023

The human hippocampal-entorhinal system is known to represent both spatial locations and abstract concepts in memory in the form of allocentric cognitive maps. Using fMRI, we show that the human parietal cortex evokes complementary egocentric-like vector representations in conceptual spaces during goal-directed mental search, akin to those observable during physical navigation to determine where a goal is located relative to oneself. Concurrently, grid-like representations, a neural signature of allocentric cognitive maps in entorhinal, prefrontal, and parietal cortices, are restructured as a function of conceptual goal proximity, akin to rodent grid cells firing around reward locations during spatial exploration. These brain mechanisms might support flexible and parallel readout of where target conceptual information is stored in memory, capitalizing on complementary reference frames.
FLInt: Single Shot Safe Harbor Transgene Integration viaFluorescentLandmarkInterference
Authors: Malaiwong Nawaphat , Porta-de-la-Riva Montserrat , Krieg Michael
Published: January 2023

The stable incorporation of transgenes and recombinant DNA material into the host genome is a bottleneck in many bioengineering applications. Due to the low efficiency, identifying the transgenic animals is often a needle in the haystack. Thus, optimal conditions require efficient screening procedures, but also known and safe landing sites that do not interfere with host expression, low input material and strong expression from the new locus. Here, we leverage an existing library of≈300 different loci coding for fluorescent markers that are distributed over all 6 chromosomes inCaenorhabditis elegansas safe harbors for versatile transgene integration sites using CRISPR/Cas9. We demonstrated that a single crRNA was sufficient for cleavage of the target region and integration of the transgene of interest, which can be easily followed by loss of the fluorescent marker. The same loci can also be used for extrachromosomal landing sites and as co-CRISPR markers without affecting body morphology or animal behavior. Thus, our method overcomes the uncertainty of transgene location during random mutagenesis, facilitates easy screening through fluorescence interference and can be used as co-CRISPR markers without further influence in phenotypes.
Elucidating the combined toxicity of aflatoxin B1 and fumonisin B1 on HepG2 cells based on respirometry and transcriptome analyses
Authors: Chen Xiangrong , Abdallah Mohamed F. , Grootaert Charlotte , Van Nieuwerburgh Filip , Rajkovic Andreja
Published: January 2023

Aflatoxin B1 (AFB1) and fumonisin B1 (FB1) are two toxic mycotoxins widely found in food contaminants, and known for their hepatotoxicity in human. However, their combined toxicity still needs to be deeply investigated especially for their harmful effect. Therefore, the current work aimed at investigating the (combined) effect of AFB1 and FB1 on mitochondrial and glycolytic activity of HepG2 cell line, a well-recognizedin vitromodel system to study liver cell function. In our previous work, we studied the impact of a short term exposure to different doses of AFB1, FB1, and their binary mixture (MIX) on the bioenergetic status of HepG2 cells. Seahorse respirometry analysis revealed that the co-exposure, especially at high doses (8 µg/mL for AFB1 and 160 µg/mL for FB1), is more toxic as a result of more inhibition of all parameters of mitochondrial respiration. RNA transcriptome sequencing showed that the p53 signaling pathway, which is a major orchestrator of mitochondrial apoptosis, was differentially expressed. Moreover, the co-exposure has significantly downregulated Cx I, Cx II, Cx III, and Cx IV genes, which represent the onset of the suppressed mitochondrial respiration in HepG2 cells. It was found that FB1 is contributed more to the MIX effects than AFB1.⍰

Environmental Implication

Aflatoxin B1 (AFB1) and fumonisin B1 (FB1) are two main mycotoxins that frequently (co-)contaminate maize and maize-based ingredients in several parts of the world. Both toxins are well-known for their hepatotoxicity in humans as the liver is their main target organ. However, the combined toxicity of AFB1 and FB1 still needs to be deeply investigated especially for their effect on cellular respiration. In this study, we proved that a binary mixture of AFB1 and FB1 is more toxic on mitochondrial respiration, and disrupted the p53 signaling pathway to induce apoptosis, which promised a novel insight of hazardous materials-induced hepatic damage.
Characterization of 3D organotypic epithelial tissues reveals tonsil-specific differences in tonic interferon signaling
Authors: Jackson Robert , Rajadhyaksha Esha V , Loeffler Reid S , Flores Caitlyn E , Van Doorslaer Koenraad
Published: January 2023

Three-dimensional (3D) culturing techniques can recapitulate the stratified nature of multicellular epithelial tissues. Organotypic 3D epithelial tissue culture methods have several applications, including the study of tissue development and function, drug discovery and toxicity testing, host-pathogen interactions, and the development of tissue-engineered constructs for use in regenerative medicine. We grew 3D organotypic epithelial tissues from foreskin, cervix, and tonsil-derived primary cells and characterized the transcriptome of thesein vitrotissue equivalents. Using the same 3D culturing method, all three tissues yielded stratified squamous epithelium, validated histologically using basal and superficial epithelial cell markers. The goal of this study was to use RNA-seq to compare gene expression patterns in these three types of epithelial tissues to gain a better understanding of the molecular mechanisms underlying their function and identify potential therapeutic targets for various diseases. Functional profiling by over-representation and gene set enrichment analysis revealed tissue-specific differences:i.e., cutaneous homeostasis and lipid metabolism in foreskin, extracellular matrix remodeling in cervix, and baseline innate immune differences in tonsil. Specifically, tonsillar epithelia may play an active role in shaping the immune microenvironment of the tonsil balancing inflammation and immune responses in the face of constant exposure to microbial insults. Overall, these data serve as a resource, with gene sets made available for the research community to explore, and as a foundation for understanding the epithelial heterogeneity and how it may impact theirin vitrouse. An online resource is available to investigate these data (https://viz.datascience.arizona.edu/3DEpiEx/).
Hospital and urban wastewaters shape the structure and active resistome of environmental biofilms
Authors: Buelow Elena , Dauga Catherine , Carrion Claire , Mathé-Hubert Hugo , Achaibou Sophia , Gaschet Margaux , Jové Thomas , Chesneau Olivier , Kennedy Sean P. , Ploy Marie-Cecile , Da Re Sandra , Dagot Christophe
Published: January 2023

Background

Demonstration of the transfer, dynamics, and regulation of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in a complex environmental matrix is yet experimentally challenging, with many essential open questions such as how and where transfer and dissemination of ARGs happens in nature. The extent and conditions of MGEs transfer that carry ARGs is still largely unexplored in natural environments and microbial communities. Biofilms are structures that include high density multi-species bacterial communities embedded in self-produced extracellular polymeric substances (EPS) constituting a matrix that facilitates gene transfer and where bacteria exhibit high tolerance to stress and to antibiotics. In this study we implemented a sampling and analysis approach that allows phenotypic and genomic analyses ofin situand reconstitutedin vitrohospital and urban wastewater (WW) biofilms. To assess the potential of hospital and urban WW biofilms to efficiently disseminate ARGs in the WW system, we explored the EPS within the biofilm matrix and assessed the expression of the resistome (ARGs) and mobilome (MGEs) by metatranscriptomics.

Results

We first showed that a) the composition of EPS differs depending on their growth environment (in situandin vitro) and their sampling origin (hospital vs urban WW) and that b) a low amount of ciprofloxacin impacted the composition of the EPS. Next, the metatranscriptomic approach showed that a) expression of ARGs and MGEs increase upon adding a low amount of ciprofloxacin for biofilms from hospital WW but not for those from urban WW and b) that expression of specific plasmids that carry individual or multiple ARGs varies depending on the WW origins of the biofilms. When the same plasmids were expressed in both, urban and hospital WW biofilms, they carried and expressed different ARGs.

Conclusion

We show that hospital and urban wastewaters shape the structure and active resistome of environmental biofilms, and we confirmed that hospital WW is an important hot spot for the dissemination and selection of AMR. The different responses to antibiotic pressure in hospitalvsurban biofilms, coupled with differences in biofilm structure helps delineate distinct characteristics of hospital and urban WW biofilms highlighting the relationships between the resistome and its expression in environmental biofilms and their surrounding ecosystems.
Comprehensive longitudinal study of home-cage activity, including climbing, reveals new complex phenotypic profile in the N171-82Q HD mouse model with implications for refined preclinical studies
Authors: Bains Rasneer S. , Forrest Hamish , Sillito Rowland R. , Armstrong J. Douglas , Stewart Michelle , Nolan Patrick M. , Wells Sara E.
Published: January 2023

Monitoring the activity of mice within their home cage is proving to be a powerful tool for revealing subtle and early-onset phenotypes in mouse models. Video tracking, in particular, lends itself to automated machine-learning technologies that have the potential to improve the manual annotations carried out by humans. This type of recording and analysis is particularly powerful in objective phenotyping, monitoring behaviors with no experimenter intervention. In this study, we focus on non-evoked voluntary behaviors, which do not require any contact with the animal or exposure to specialist equipment. We show that the monitoring of climbing on the wire cage lid of a standard individually ventilated cage (IVC) yields reproducible data reflecting complex phenotypes of individual mouse inbred strains and of a widely used mouse model of neurodegeneration. In addition, performing such measurements in the home-cage environment, over several 24-hour periods, allows for the collection of comprehensive behavioral and activity data, which reveals prolific sexual dimorphism and biphasic changes in locomotor activity. Here we present data from home-cage analysis, which reveals the complexity of unprovoked behavior in both wild-type and mutant mice. This has the potential to greatly enhance the characterization of mouse strains, detect early and subtle signs of disease and increase reproducibility in preclinical studies.
Mycobacterium tuberculosisresides in lysosome-poor monocyte-derived lung cells during chronic infection
Authors: Zheng Weihao , Chang I-Chang , Limberis Jason , Budzik Jonathan M. , Zha B. Shoshana , Howard Zach , Chen Lucas , Ernst Joel D.
Published: January 2023

Mycobacterium tuberculosis(Mtb) infects cells in multiple lung myeloid cell subsets and causes chronic infection despite innate and adaptive immune responses. However, the mechanisms allowing Mtb to evade elimination are not fully understood. Here, using new methods, we determined that after T cell responses have developed, CD11clomonocyte-derived lung cells termed MNC1 (mononuclear cell subset 1), harbor more live Mtb compared to alveolar macrophages (AM), neutrophils, and less permissive CD11chiMNC2. Bulk RNA sequencing of sorted cells revealed that the lysosome biogenesis pathway is underexpressed in MNC1. Functional assays confirmed that Mtb-permissive MNC1 have less lysosome content, acidification, and proteolytic activity than AM, and less nuclear TFEB, a master regulator of lysosome biogenesis. Mtb infection does not drive lysosome deficiency in MNC1 in vivo. Instead, Mtb recruits MNC1 and MNC2 to the lungs for its spread from AM to these cell subsets as a virulence mechanism that requires the Mtb ESX-1 secretion system. The c-Abl tyrosine kinase inhibitor nilotinib activates TFEB and enhances lysosome function of primary macrophages in vitro and MNC1 and MNC2 in vivo, improving control of Mtb infection. Our results indicate that Mtb exploits lysosome-poor monocyte-derived cells for in vivo persistence, suggesting a potential target for host-directed tuberculosis therapy.

One Sentence Summary

Virulent Mtb recruits and exploits intrinsically lysosome-deficient lung mononuclear cell subsets to resist elimination during chronic infection.
Structural insights into regulation of TRPM7 divalent cation uptake by the small GTPase ARL15
Authors: Mahbub Luba , Kozlov Guennadi , Zong Pengyu , Tetteh Sandra , Nethramangalath Thushara , Knorn Caroline , Jiang Jianning , Shahsavan Ashkan , Lee Emma , Yue Lixia , Runnels Loren W. , Gehring Kalle
Published: January 2023

Cystathionine-β-synthase (CBS)-pair domain divalent metal cation transport mediators (CNNMs) are an evolutionarily conserved family of magnesium transporters. They promote efflux of Mg2+ions on their own or uptake of divalent cations when coupled to the transient receptor potential ion channel subfamily M member 7 (TRPM7). Recently, ADP-ribosylation factor-like GTPase 15 (ARL15) has been identified as CNNM binding partner and an inhibitor of divalent cation influx by TRPM7. Here, we characterize ARL15 as a GTP-binding protein and demonstrate that it binds the CNNM CBS-pair domain with low micromolar affinity. The crystal structure of the complex between ARL15 GTPase domain and CNNM2 CBS-pair domain reveals the molecular determinants of the interaction and allowed the identification of mutations in ARL15 and CNNM2 mutations that abrogate binding. Loss of CNNM binding prevented ARL15 suppression of TRPM7 channel activity in support of previous reports that the proteins function as a ternary complex. Binding experiments with phosphatase of regenerating liver 2 (PRL2 or PTP4A2) revealed that ARL15 and PRLs compete for binding CNNM, suggesting antagonistic regulation of divalent cation transport by the two proteins.
Alanine replacements in the structured C-terminal domain of the prion protein reveal conformationally variable regions as major determinants for prion propagation
Authors: Bhamra Savroop K. , Arora Parineeta , Hosszu Laszlo L. P. , Bieschke Jan , Clarke Anthony R. , Collinge John , Jat Parmjit S.
Published: January 2023

Mutational analysis of the cellular prion protein (PrPC) has revealed various regions of the protein that modulate prion propagation. However, most approaches involve deletions, insertions, or replacements in the presence of the wild-type cellular protein, which may mask the true phenotype. Here, site-directed alanine mutagenesis of PrPCwas conducted to identify sites particularly a ‘surface patch’ of the protein pertinent to prion propagation in the absence of the wild-type prion protein. Mutations were targeted to the helical, sheet and loop regions of PrPC, or a combination thereof and the mutated proteins expressed in PK1 cells in which endogenous PrPChad been silenced. PK1 cells are a clone of mouse neuroblastoma cells that are highly susceptible to Rocky Mountain Laboratory mouse prions. Using the scrapie cell assay, a highly sensitive cell culture-based bioassay for quantifying infectious titres of mouse prions, we found that all mutations within the structured 121-230 domain, irrespective of secondary structure, severely reduced prion propagation. The reduction was most pronounced for mutations within conformationally variable regions of the protein (G123A.L124A.G125A and V188A.T191A.T192A) and those neighbouring or within helix 1 (S134A.R135A.M153A and H139A.G141A.D146A). While mutations G123A and G125A would likely disrupt the structure of the prion fibril, the other mutations are unlikely to cause disruption. Our data therefore suggests that conformationally variable regions within the structured domain of PrPCare the major determinants of prion propagation efficacy.