bluuebunny/crossref_metadata_2025 huggingface dataset:
Action-sequence learning, habits and automaticity in obsessive-compulsive disorder
Authors: Banca Paula , Ruiz Maria Herrojo , Gonzalez-Zalba Miguel Fernando , Biria Marjan , Marzuki Aleya A. , Piercy Thomas , Sule Akeem , Fineberg Naomi Anne , Robbins Trevor William
Published: February 2023

Enhanced habit formation, greater automaticity and impaired goal/habit arbitration in obsessive-com-pulsive disorder (OCD) are key hypotheses from the goal/habit imbalance theory of compulsion which have not been directly investigated. This study tests these hypotheses using a combination of newly developed behavioral tasks. First, we trained both OCD patients and healthy controls, using a smartphone app, to perform chunked action sequences. This motor training was conducted daily for one month. Both groups displayed equivalent procedural learning and attainment of habitual perfor-mance (measured with an objective criterion of automaticity), despite greater subjective habitual tendencies in patients with OCD, self-reported via a recently developed questionnaire. Participants were subsequently tested on a re-evaluation task to assess choice between established automatic and novel goal-directed action sequences. This task showed that both groups were sensitive to re-evaluation based on monetary feedback. However, when re-evaluation was based on physical effort, OCD patients showed a pronounced preference for the previously trained habitual sequence, hypothetically due to its intrinsic value. This was particularly evident in patients with higher compulsive symptoms and habitual tendencies, who also engaged significantly more with the motor habit-training app and reported symptom relief at the end of the study. The tendency to attribute higher intrinsic value to familiar actions may be a potential mechanism leading to compulsions and an important addition to the goal/habit imbalance hypothesis in OCD. We also highlight the potential of the app-training as a habit reversal therapeutic tool.
Epidemiology and aetiology of moderate to severe diarrhoea in hospitalised HIV-infected patients ≥5 years old in South Africa, 2018-2021: a case-control analysis
Authors: Johnstone Siobhan L. , Erasmus Linda , Thomas Juno , Groome Michelle J. , du Plessis Nicolette M. , Avenant Theunis , de Villiers Maryke , Page Nicola A.
Published: February 2023

Diarrhoea is a recognised complication of HIV-infection, yet there are limited local aetiological data in this high-risk group. These data are important for informing public health interventions and updating diagnostic and treatment guidelines. This study aimed to determine the pathogenic causes for diarrhoeal admissions in HIV-infected patients compared to hospital controls between July 2018 and November 2021.

Admitted diarrhoeal cases (n=243) and non-diarrhoeal hospital controls (n=101) ≥5 years of age were enrolled at Kalafong, Mapulaneng and Matikwana hospitals. Stool specimens/rectal swabs were collected and pathogen screening performed on multiple platforms. Differences in pathogen detections between cases and controls, stratified by HIV status, were investigated.

The majority (n=164, 67.5%) of diarrhoeal cases with known HIV status were HIV-infected. Pathogens could be detected in 66.3% (n=228) of specimens, with significantly higher detection in cases compared to controls (72.8% versus 50.5%,p<0.001). Amongst HIV-infected participants, prevalence ofCystoisosporaspp. was significantly higher in cases than controls (17.7% versus 0.0%,p=0.028), whileSchistosomawas detected more often in controls than cases (17.4% versus 2.4%,p=0.009). Amongst the HIV-uninfected participants, prevalence ofShigellaspp.,Salmonellaspp. andHelicobacter pyloriwas significantly higher in cases compared to controls (36.7% versus 12.0%,p=0.002; 11.4% versus 0.0%,p=0.012; 10.1% versus 0.0%,p=0.023).

Diarrhoeal aetiology differed by HIV status, withShigellaspp. (36.7%) andSalmonellaspp. (11.4%) having the highest prevalence amongst HIV-uninfected cases andShigellaspp. (18.3%),Cystoisospora(17.7%), andCryptosporidiumspp. (15.9%) having the highest prevalence amongst HIV-infected cases. These differences should be considered for the development of diagnostic and treatment guidelines.
Distribution of Entomopathogenic Nematodes in Some Selected Insect Species in Osogbo Local Government Area of Osun State, Nigeria
Authors: Adeshina Q.O , Rufai A.M , Surakat O.A , Nzeako S.O
Published: February 2023

Entomopathogenic nematodes (EPNs) are leading biological control agents used to combat many insect pests in many regions of the world. This study investigated the distribution of entomopathogenic nematodes in four insect species;Zonocerus variegatus, Mantis religiosa, Butterfly and Moth across dry and rainy seasons in Osogbo Local Government Area of Osun State. Insect samples were collected from different sampling stations (cultivated farmlands, vegetation of grasses, and forested lands) using an entomological sweep net. The insects were dissected in a normal saline medium for the presence of EPN. A further verification was made, 60 soil samples were retrieved randomly from the disturbed agroecosystem (where insects were sampled) and an undisturbed agroecosystem (Osun-Osogbo Groove). The soil samples were screened for EPN presence usingTenebrio molitorlarva (mealworm) as baits, while infected baits are placed on modified white traps to recover EPNs. A total of 876 insects samples comprising;Zonocerus variegatus556 (63.5%),Mantis religiosa36 (4.1%), Butterflies 158 (18.0%) and Moths 126 (14.4%) were collected from the disturbed agroecosystem based on sweep net efficiency and species availability. After screening, only 1 (0.1%) insect specimen (Mantis religiosa) specimen successfully harbour an EPN, identified asMermisspp. Result from statistical analysis indicates that both season and insects age do not have influence on the distribution of EPN (P>0.05). Moreover, the low infectivity of EPN in the sampled insect was presumed to be caused by EPNs’ foraging strategies, flooding and other host of factors. This led to further probing through screening of soil samples. Of all 36 soil samples screened from the disturbed agroecosystem, EPNs had zero prevalence. However, from all the (24) soil samples collected from the undisturbed agroecosystem, EPNs belonging to the genusHeterorhabditiswere recovered and identified using morphological and morphometric characters. The absolute frequency of occurrence of EPN in the disturbed agroecosystem was zero compared to 100% recorded for the undisturbed agroecosystem. This study infers that EPN occurrence, dispersal, and persistence in the ecosystem are found to be adversely affected by intense anthropogenic activities.
Neuroprotective effects of hepatoma-derived growth factor in models of Huntington’s disease
Authors: Voelkl Kerstin , Gutiérrez-Ángel Sara , Keeling Sophie , Koyuncu Seda , Arzberger Thomas , Vilchez David , Klein Rüdiger , Dudanova Irina
Published: February 2023

Huntington’s disease (HD) is a movement disorder caused by a mutation in the Huntingtin gene, that leads to severe neurodegeneration and inevitable death of the patients. Molecular mechanisms of HD are still not sufficiently understood, and no cure is currently available. Here, we demonstrate neuroprotective effects of hepatoma-derived growth factor (HDGF) in cellular and mouse models of HD. We show that HDGF expression levels in neuronal cell types inversely correlate with cellular vulnerability to HD. Moreover, lack of endogenous HDGF shortened lifespan and worsened rotarod performance of R6/2 HD model mice. AAV-mediated delivery of HDGF into the brain reduced mutant Huntingtin inclusion body load, but had no significant effect on motor behavior or lifespan. Interestingly, both nuclear and cytoplasmic versions of HDGF were equally efficient in rescuing mutant Huntingtin toxicity in cell culture models of HD. Moreover, extracellular application of a recombinant HDGF protein improved viability of mutant Huntingtin-expressing primary neurons and reduced mutant Huntingtin aggregation in neural progenitor cells differentiated from human patient-derived induced pluripotent stem cells (iPSCs). Our findings provide new insights into the pathomechanisms of HD and suggest neuroprotective potential of HDGF in neurodegeneration.
Luminescence-based screening for extracellular vesicle release modulators reveals a role for PI4KIIIβ in exosome biogenesis upon lysosome inhibition
Authors: Bebelman Maarten P. , Crudden Caitrin , Snieder Bart , Thanou Evangelia , Langedijk Catharina J.M. , Viola Margarida , Eleonora Steven , Baginska Urszula , Cotugno Olaf , Bebelman Jan Paul M. , van Eijndhoven Monique A.J. , Bosch Leontien , Li Ka Wan , Smit Martine J. , van Niel Guillaume , Smit August B. , Verweij Frederik J. , Pegtel D. Michiel
Published: February 2023

Dysregulated extracellular vesicle (EV) release has been implicated in various pathologies, including cancer, neurodegenerative disease and osteoarthritis. Despite clear therapeutic potential, drug screening for EV release modulators has yielded limited success due to the lack of a sensitive and scalable EV read-out system. Here, we employed CRISPR-Cas9 to engineer HEK293 cells expressing HA-NanoLuciferase-(NL)-tagged endogenous CD63. We found that under basal culture conditions, CD63-containing EVs are released via a mechanism that is independent of the exocytic SNARE protein SNAP23, presumably by direct budding from the plasma membrane. Endo-lysosome inhibition by chemical or genetic perturbation of vATPase strongly increased SNAP23 and nSmase2-dependent exosome secretion from intracellular compartments. Proteomic analysis revealed these exosomes are enriched for early- and late endosomal markers, but also for autophagosomal proteins. This suggests that a proportion of these exosomes originate from amphisomes, although chemical inhibition of canonical autophagy did not affect exosome secretion upon lysosome inhibition. Using a broad- spectrum kinase inhibitor screen, we identified and subsequently validated the lipid kinase PI4KIIIβ as a critical mediator of exosome secretion and amphisome-mediated secretory autophagy, upon lysosome inhibition. We conclude that tagging of endogenous CD63 with NanoLuciferase represents a sensitive, scalable reporter strategy that enables identification of (druggable) modulators of EV biogenesis and release under physiological and pathological conditions.
Fractal Structure of Human and Primate Social Networks Optimizes Information Flow
Authors: West B.J. , Culbreth G. , Dunbar R.I.M. , Grigolini P.
Published: February 2023

Primate and human social groups exhibit a fractal structure that has a very limited range of preferred layer sizes, with groups of 5, 15, 50 and (in humans) 150 and 500 predominating. This same fractal distribution is also observed in the distribution of species mean group sizes in primates. Here we demonstrate that this preferential numbering arises because of the critical nature of dynamic self-organization within complex social networks. We calculate the size dependence of the scaling properties of complex social network models and argue that this aggregate behaviour exhibits a form of collective intelligence. Direct calculation establishes that the complexity of social networks as measured by their scaling behaviour is non-monotonic, peaking globally around 150 with a secondary peak at 500 and tertiary peaks centred on 15 and 50, thereby providing a theory-based rationale for the fractal layering of primate and human social groups.
MousePZT: A Simple, Reliable, Low-Cost Device for Vital Sign Monitoring and Respiratory Gating in Mice Under Anesthesia
Authors: Rivera Daniel A. , Buglione Anne E. , Schaffer Chris B.
Published: February 2023

Small animal studies in biomedical research often require anesthesia to reduce pain or stress experienced by research animals and to minimize motion artifact for imaging or other measurements. Anesthetized animals should be closely monitored to avoid complications and unintended effects of altered physiology during such procedures. Many currently available monitoring devices can be expensive, invasive, or interfere with experimental design. Here, we present a low-cost device, based on a simple piezoelectric sensor, with a custom circuit and computer software that allows for measurements of both respiratory rate and heart rate in a non-invasive, minimal contact manner. We find the accuracy of the MousePZT device in measuring respiratory and heart rate under anesthesia and with pharmacologically induced changes in heart rate match those of commercial or more invasive systems. We also demonstrate that changes in respiratory rate can precede changes in heart rate associated with alterations in anesthetic depth. Additional circuitry on the device outputs a respiration locked trigger signal for respiratory-gating of imaging or other data acquisition that has high sensitivity and specificity for detecting respiratory cycles. We provide detailed construction documents and all necessary microcontroller and computer software, enabling straightforward adoption of this device.
Complete Workflow for High Throughput Human Single Skeletal Muscle Fiber Proteomics
Authors: Momenzadeh Amanda , Jiang Yuming , Kreimer Simion , Teigen Laura E. , Zepeda Carlos S. , Haghani Ali , Mastali Mitra , Song Yang , Hutton Alexandre , Parker Sarah J , Van Eyk Jennifer E. , Sundberg Christopher W. , Meyer Jesse G.
Published: February 2023

Skeletal muscle is a major regulatory tissue of whole-body metabolism and is composed of a diverse mixture of cell (fiber) types. Aging and several diseases differentially affect the various fiber types, and therefore, investigating the changes in the proteome in a fiber-type specific manner is essential. Recent breakthroughs in isolated single muscle fiber proteomics have started to reveal heterogeneity among fibers. However, existing procedures are slow and laborious requiring two hours of mass spectrometry time per single muscle fiber; 50 fibers would take approximately four days to analyze. Thus, to capture the high variability in fibers both within and between individuals requires advancements in high throughput single muscle fiber proteomics. Here we use a single cell proteomics method to enable quantification of single muscle fiber proteomes in 15 minutes total instrument time. As proof of concept, we present data from 53 isolated skeletal muscle fibers obtained from two healthy individuals analyzed in 13.25 hours. Adapting single cell data analysis techniques to integrate the data, we can reliably separate type 1 and 2A fibers. Sixty-five proteins were statistically different between clusters indicating alteration of proteins involved in fatty acid oxidation, muscle structure and regulation. Our results indicate that this method is significantly faster than prior single fiber methods in both data collection and sample preparation while maintaining sufficient proteome depth. We anticipate this assay will enable future studies of single muscle fibers across hundreds of individuals, which has not been possible previously due to limitations in throughput.
Incomplete transcriptional dosage compensation of vertebrate sex chromosomes is balanced by post-transcriptional compensation
Authors: Lister Nicholas C , Milton Ashley M , Patel Hardip R , Waters Shafagh A , Hanrahan Benjamin J , McIntyre Kim L , Livernois Alexandra M , Wee Lee Kian , Ringel Alessa R. , Mundlos Stefan , Robson Michael I. , Shearwin-Whyatt Linda , Grützner Frank , Marshall Graves Jennifer A. , Ruiz-Herrera Aurora , Waters Paul D
Published: February 2023

Heteromorphic sex chromosomes (XY or ZW) present problems of gene dosage imbalance between the sexes, and with the autosomes. Mammalian X chromosome inactivation was long thought to imply a critical need for dosage compensation in vertebrates. However, the universal importance of sex chromosome dosage compensation was questioned by mRNA abundance measurements that demonstrated sex chromosome transcripts are neither balanced between the sexes or with autosomes in monotreme mammals or birds. Here, we demonstrate unbalanced mRNA levels of X genes in platypus males and females that correlate with differential loading of histone modifications, and confirm that transcripts of Z genes are unbalanced between males and females also in chicken. However, we found that in both species, median male to female protein abundance ratios were 1:1, implying an additional level of post-transcriptional control. We conclude that parity of sex chromosome output is achieved in birds, as well as all mammal groups, by a combination of transcriptional and post-transcriptional control, consistent with an essential role for sex chromosome dosage compensation in vertebrates.
MAP9/MAPH-9 supports axonemal microtubule doublets and modulates motor movement
Authors: Tran Michael V. , Ferguson James W. , Cote Lauren E. , Khuntsariya Daria , Fetter Richard D. , Wang Jennifer T. , Wellard Stephen R. , Sallee Maria D. , Genova Mariya , Eskinazi Sani , Magiera Maria M. , Janke Carsten , Stearns Tim , Lansky Zdenek , Shen Kang , Magescas Jérémy , Feldman Jessica L.
Published: February 2023

Microtubule doublets (MTDs) are a well conserved compound microtubule structure found primarily in cilia. However, the mechanisms by which MTDs form and are maintainedin vivoremain poorly understood. Here, we characterize microtubule-associated protein 9 (MAP9) as a novel MTD-associated protein. We demonstrate thatC. elegansMAPH-9, a MAP9 homolog, is present during MTD assembly and localizes exclusively to MTDs, a preference that is in part mediated by tubulin polyglutamylation. Loss of MAPH-9 caused ultrastructural MTD defects, dysregulated axonemal motor velocity, and perturbed cilia function. As we found that the mammalian ortholog MAP9 localized to axonemes in cultured mammalian cells and mouse tissues, we propose that MAP9/MAPH-9 plays a conserved role in supporting the structure of axonemal MTDs and regulating ciliary motors.
Similarity in Functional Connectome Architecture Predicts Teenage Grit
Authors: Park Sujin , Park Daeun , Kim M. Justin
Published: February 2023

Grit is a personality trait that encapsulates the tendency to persevere and maintain consistent interest for long-term goals. While prior studies found that grit predicts positive behavioral outcomes, there is a paucity of work providing explanatory evidence from a neurodevelopmental perspective. Based on previous research suggesting the utility of the functional connectome as a developmental measure, we tested the idea that individual differences in grit might be, in part, rooted in brain development in adolescence and emerging adulthood (N= 64, 11-19 years of age). Our analysis showed that grit was associated with connectome stability across conditions and connectome similarity across individuals. Notably, inter-subject representational similarity analysis revealed that teenagers who were grittier shared similar functional connectome architecture with each other, more so than those with lower grit. Our findings suggest that gritty individuals are more likely to follow a specific neurodevelopmental trajectory, which may underpin subsequent beneficial behavioral outcomes.

Statement of Relevance

Maintaining consistent effort and passion for long-term, personally meaningful goals – often referred to as grit – is suggested to be associated with a wide range of positive outcomes such as academic achievement, career success and subjective well-being. Although grit has gained substantial amount of interest not only in the academia but also from the general population, only a handful of studies have examined its neural underpinnings. Here, we examined whether putative developmental measures using whole-brain functional connectivity patterns (i.e., functional connectome) explain individual differences in grit. Using publicly available developmental neuroimaging dataset ranging from early adolescence to emerging adulthood, we found that functional connectome stability within individuals and similarity between individuals uniquely explained self-reported grit. Confirmatory analyses demonstrated the existence of common neural representations shared among gritty teenagers, which were unveiled during movie-watching. These findings highlight that grit may be embedded in the functional connectome architecture during adolescence and emerging adulthood.
Perturbed neurochemical and microstructural organization in a mouse model of prenatal opioid exposure: a multi-modal magnetic resonance study
Authors: Shahid Syed Salman , Grecco Gregory G. , Atwood Brady K. , Wu Yu-Chien
Published: February 2023

Methadone-based treatment for pregnant women with opioid use disorder is quite prevalent in the clinical environment. A number of clinical and animal model-based studies have reported cognitive deficits in infants prenatally exposed to methadone-based opioid treatments. However, the long-term impact of prenatal opioid exposure (POE) on pathophysiological mechanisms that govern neurodevelopmental impairment is not well understood. Using a translationally relevant mouse model of prenatal methadone exposure (PME), the aim of this study is to investigate the role of cerebral biochemistry and its possible association with regional microstructural organization in PME offspring. To understand these effects, 8- week-old male offspring with PME (n=7) and prenatal saline exposure (PSE) (n=7) were scanned in vivo on 9.4 Tesla small animal scanner. Single voxel proton magnetic resonance spectroscopy (1H-MRS) was performed in the right dorsal striatum (RDS) region using a short echo time (TE) Stimulated Echo Acquisition Method (STEAM) sequence. Neurometabolite spectra from the RDS was first corrected for tissue T1 relaxation and then absolute quantification was performed using the unsuppressed water spectra. High-resolution in vivo diffusion MRI (dMRI) for region of interest (ROI) based microstructural quantification was also performed using a multi-shell dMRI sequence. Cerebral microstructure was characterized using diffusion tensor imaging (DTI) and Bingham-neurite orientation dispersion and density imaging (Bingham-NODDI). MRS results in the RDS showed significant decrease in N-acetyl aspartate (NAA), taurine (tau), glutathione (GSH), total creatine (tCr) and glutamate (Glu) concentration levels in PME, compared to PSE group. In the same RDS region, mean orientation dispersion index (ODI) and intracellular volume fraction (VFIC) demonstrated positive associations with tCr in PME group. ODI also exhibited significant positive association with Glu levels in PME offspring. Significant reduction in major neurotransmitter metabolites and energy metabolism along with strong association between the neurometabolites and perturbed regional microstructural complexity suggest a possible impaired neuroadaptation trajectory in PME offspring which could be persistent even into late adolescence and early adulthood.
Effects of orally administered crofelemer on the incidence and severity of neratinib-induced diarrhea in female dogs
Authors: Guy Michael K. , Teixeira Andre , Shirer Allison , Bolognese James , Chaturvedi Pravin
Published: February 2023

Management guidelines for cancer therapy-related diarrhea (CTD) should be revised because newer targeted therapies have increased CTD burden, with high incidence and/or severity of diarrhea for some agents that inhibit epidermal growth factor receptor and receptor tyrosine kinases. Neratinib, a pan-HER tyrosine kinase inhibitor, approved for breast cancer treatment, causes severe diarrhea in >95% of patients. Crofelemer, a novel intestinal chloride ion channel modulator, is an approved antidiarrheal for patients with HIV receiving antiretroviral therapy. The objective of this study was to evaluate the effectiveness of crofelemer prophylaxis in reducing the incidence and severity of neratinib-induced diarrhea without loperamide in dogs. Female dogs received neratinib orally daily concomitantly with either matching placebo tablets (CTR) or crofelemer 125 mg delayed-release tablet two or four times/day (BID or QID) for 28 consecutive days. At the end of treatment, 37.5%, 75%, and 87.5% of the CTR, BID, and QID dogs were ‘responders’ defined as ≤7 loose/watery stools/week for at least 2 of 4 weeks (p<0.05). The average number of watery stools per week was 9, 6, and 6 in the CTR, BID, and QID groups, respectively (p<0.05). The average number of weeks with no loose/watery stools was 1.3, 2.1, and 2.3 for the CTR, BID, and QID groups, respectively (p<0.05). The weekly mean fecal scores and stool consistency were 5.1, 3.9, and 4.1 for the CTR, BID, and QID groups (p<0.05). In this 28-day preclinical study, crofelemer prophylaxis without loperamide reduced the incidence and severity of neratinib-associated diarrhea in female dogs by 30%.

Ethical Compliance

All procedures performed in studies involving canine participants were in accordance with the ethical standards of the institutional and/or national research committee and applicable Institutional Animal Care and Use Committee (IACUC).
Food availability early in life impacts among and within individual variation in behaviour
Authors: Beyts Cammy , Martin Julien G. A. , Colegrave Nick , Walsh Patrick
Published: February 2023

The availability of food during early life has been proposed as a key proximate mechanism for the development of variation in behaviour among and within individuals.

Individuals can vary amongst each other in their personality, plasticity and predictability and if an individual’s behaviour is correlated across contexts this can lead to behavioural, plasticity and predictability syndromes.

In this study, we used a split brood design to raise African clawed frog tadpoles (Xenopus laevis) on a high or low diet in food availability and measured the distance they swam in a familiar and unfamiliar context eight times during their development.

In a familiar context, we found that there was an increase in among individual variance in plasticity and predictability in the high food treatment. This shows that when resources are not restricted, individuals are not constrained in the expression of their behaviour at certain phenotypic levels.

In an unfamiliar context, we found a different response, with an increase in individual variance in personality in the low but not the high feed tadpoles. As unfamiliar contexts may be riskier, our results highlight that individuals receiving less food may take greater foraging risks in novel contexts.

Across contexts, we found a predictability syndrome in the high but not the low feed tadpoles, highlighting that cross-context behaviours can become decoupled in some developmental conditions but remain intact in others.

Together our findings show that early life conditions contribute to among individual variation in behaviour but that these may only impact the phenotype at specific phenotypic levels and are context specific.

We emphasise that having a fundamental understanding of how early development may promote or constrain individual variation can provide a greater understanding of how individuals and populations may respond to novel conditions brought about by anthropogenic activity.
Yeast extract improves growth in rainbow trout (Oncorhynchus mykiss) fed a fishmeal-free diet and modulates the hepatic and distal intestine transcriptomic profile
Authors: Frohn Laura , Peixoto Diogo , Guyomar Cervin , Teixeira Carla , Terrier Frédéric , Aguirre Pierre , Maman Haddad Sarah , Bobe Julien , Costas Benjamin , Richard Nadège , Pinel Karine , Skiba-Cassy Sandrine
Published: February 2023

Replacing fishmeal with alternative protein sources and improving new ingredients diets with feed additives are major objectives in aquaculture. The aim of this study was to evaluate benefits for rainbow trout (Oncorhynchus mykiss) of supplementing a fishmeal-free diet, composed of processed animal proteins, with yeast extract. Juvenile rainbow trout (initial weight 37 ± 2 g) were fed either with a control diet (19% fishmeal) or with a diet based on terrestrial animal by-products (17%) supplemented or not with 3% of yeast extract. Effects of the diets were evaluated in a 4-week digestibility trial and a 12-week growth experiment. Fish health was investigated by measuring plasma immune markers and performing histological study of the gut. Underlying molecular responses were investigated using unbiased transcriptomic analysis of the liver and distal intestine. Results indicated that supplementing with 3% yeast extract did not influence nutrient digestibility substantially. Nevertheless, fish fed the supplemented fishmeal-free diet grew more than those fed the non-supplemented processed animal protein diet. Plasma and structural parameters indicated no exacerbated immune response or signs of intestinal inflammation in fish fed the fishmeal-free diets. However, plasma total immunoglobulin M levels and intestinal villi were significantly higher in fish fed the diet supplemented with yeast extract. The transcriptomic analysis revealed that the diets influenced immune, inflammatory, pathogen fighting and coagulation gene-related expressions. These results suggest that the dietary inclusion of yeast can enhance a fishmeal-free diet by improving rainbow trout performances and potentially their robustness.
Single-neuron spiking variability in hippocampus dynamically tracks sensory content during memory formation in humans
Authors: Waschke Leonhard , Kamp Fabian , van den Elzen Evi , Krishna Suresh , Lindenberger Ulman , Rutishauser Ueli , Garrett Douglas D.
Published: February 2023

During memory formation, the hippocampus is presumed to represent the “content” of stimuli, but how it does so is unknown. Using computational modelling and human single-neuron recordings, we show that the more precisely hippocampal spiking variability tracks the composite features of each individual stimulus, the better those stimuli are later remembered. We propose that moment-to-moment spiking variability may provide a new window into how the hippocampus constructs memories from the building blocks of our sensory world.
An efficient method for high molecular weight bacterial DNA extraction suitable for shotgun metagenomics from skin swabs
Authors: Serghiou Iliana R. , Baker Dave , Evans Rhiannon , Matthew J. Dalby , Kiu Raymond , Trampari Eleftheria , Phillips Sarah , Watt Rachel , Atkinson Thomas , Murphy Barry , Hall Lindsay J. , Webber Mark A.
Published: February 2023

The human skin microbiome represents a variety of complex microbial ecosystems that play a key role in host health. Molecular methods to study these communities have been developed but have been largely limited to low-throughput quantification and short amplicon sequencing, providing limited functional information about the communities present. Shotgun metagenomic sequencing has emerged as a preferred method for microbiome studies as it provides more comprehensive information about the species/strains present in a niche and the genes they encode. However, the relatively low bacterial biomass of skin, in comparison to other areas such as the gut microbiome, makes obtaining sufficient DNA for shotgun metagenomic sequencing challenging. Here we describe an optimised high-throughput method for extraction of high molecular weight DNA suitable for shotgun metagenomic sequencing. We validated the performance of the extraction method, and analysis pipeline on skin swabs collected from both adults and babies. The pipeline effectively characterised the bacterial skin microbiota with a cost and throughput suitable for larger longitudinal sets of samples. Application of this method will allow greater insights into community compositions and functional capabilities of the skin microbiome.

Impact Statement

Determining the functional capabilities of microbial communities within different human microbiomes is important to understand their impacts on health. Extraction of sufficient DNA is challenging, especially from low biomass samples, such as skin swabs suitable for shotgun metagenomics, which is needed for taxonomic resolution and functional information. Here we describe an optimised DNA extraction method that produces enough DNA from skin swabs, suitable for shotgun metagenomics, and demonstrate it can be used to effectively characterise the skin microbiota. This method will allow future studies to identify taxonomic and functional changes in the skin microbiota which is needed to develop interventions to improve and maintain skin health.

Data Summary

All sequence data and codes can be accessed at:

NCBI Bio Project ID: PRJNA937622

DOI:https://github.com/quadram-institute-bioscience/coronahit_guppy

DOI:https://github.com/ilianaserghiou/Serghiou-et-al.-2023-Codes
Dissociable roles of human frontal eye fields and early visual cortex in presaccadic attention – evidence from TMS
Authors: Hanning Nina M. , Fernández Antonio , Carrasco Marisa
Published: February 2023

Shortly before each saccadic eye movement, presaccadic attention improves visual sensitivity at the saccade target1–5at the expense of lowered sensitivity at non-target locations6–11. Some behavioral and neural correlates of presaccadic attention and covert attention –which likewise enhances sensitivity, but during fixation12–are similar13. This resemblance has led to the debatable13–18notion that presaccadic and covert attention are functionally equivalent and rely on the same neural circuitry19–21. At a broad scale, oculomotor brain structures (e.g., FEF) are also modulated during covert attention22–24– yet by distinct neuronal subpopulations25–28. Perceptual benefits of presaccadic attention rely on feedback from oculomotor structures to visual cortices29,30(Fig. 1a); micro-stimulation of FEF in non-human primates affects activity in visual cortex31–34and enhances visual sensitivity at the movement field of the stimulated neurons35–37. Similar feedback projections seem to exist in humans: FEF+ activation precedes occipital activation during saccade preparation38,39and FEF TMS modulates activity in visual cortex40–42and enhances perceived contrast in the contralateral hemifield40. We investigated presaccadic feedback in humans by applying TMS to frontal or visual areas during saccade preparation. By simultaneously measuring perceptual performance, we show the causal and differential roles of these brain regions in contralateral presaccadic benefits at the saccade target and costs at non-targets: Whereas rFEF+ stimulation reduced presaccadic costs throughout saccade preparation, V1/V2 stimulation reduced benefits only shortly before saccade onset. These effects provide causal evidence that presaccadic attention modulates perception through cortico-cortical feedback and further dissociate presaccadic and covert attention.
Signatures of co-evolution and co-regulation in the CYP3A and CYP4F genes in humans
Authors: Richard-St-Hilaire Alex , Gamache Isabel , Pelletier Justin , Grenier Jean-Christophe , Poujol Raphael , Hussin Julie G
Published: February 2023

1

Cytochromes P450 (CYP450) are hemoproteins generally involved in the detoxification of the body of xenobiotic molecules. They participate in the metabolism of many drugs and genetic polymorphisms in humans have been found to impact drugs responses and metabolic functions. In this study, we investigate the genetic diversity forCYP450genes. We found that two clusters,CYP3AandCYP4F, are notably differentiated across human populations with evidence for selective pressures acting on both clusters: we found signals of recent positive selection inCYP3AandCYP4Fgenes and signals of balancing selection inCYP4Fgenes. Furthermore, unusual linkage disequilibrium pattern is detected in both clusters, suggesting co-evolution of genes within clusters. Several of these selective signals co-localize with expression quantitative trait loci, which suggest co-regulation and epistasis within these highly important gene families. We also found that SNPs under selection in Africans within theCYP3Acluster are associated toCYP3A5expression levels which are causally associated with reticulocytes count, as established by mendelian randomization. Furthermore, as theCYP3AandCYP4Fsubfamilies are involved in the metabolism of nutrients and drugs, our findings linking natural selection and gene expression in these gene clusters are of importance in understanding population differences in human health.
Discovery and characterization of cross-reactive intrahepatic antibodies in severe alcoholic hepatitis
Authors: Ahmadi Ali Reza , Song Guang , Gao Tianshun , Ma Jing , Han Xiaomei , Hu Mingwen , Cameron Andrew M , Wesson Russell , Philosophe Benjamin , Ottmann Shane , King Elizabeth A , Gurakar Ahmet , Qi Le , Peiffer Brandon , Burdick James , Anders Robert A , Zhou Zhanxiang , Feng Dechun , Lu Hongkun , Chen Chien-Sheng , Qian Jiang , Gao Bin , Zhu Heng , Sun Zhaoli
Published: February 2023

The pathogenesis of antibodies in severe alcoholic hepatitis (SAH) remains unknown. We sought to determine if there was antibody deposition in SAH livers and whether antibodies extracted from SAH livers were cross-reactive against both bacterial antigens and human proteins. We analyzed immunoglobulins (Ig) in explanted livers from SAH patients (n=45) undergoing liver transplantation and tissue from corresponding healthy donors (HD, n=10) and found massive deposition of IgG and IgA isotype antibodies associated with complement fragment C3d and C4d staining in ballooned hepatocytes in SAH livers. Ig extracted from SAH livers, but not patient serum exhibited hepatocyte killing efficacy in an antibody-dependent cell-mediated cytotoxicity (ADCC) assay. Employing human proteome arrays, we profiled the antibodies extracted from explanted SAH, alcoholic cirrhosis (AC), nonalcoholic steatohepatitis (NASH), primary biliary cholangitis (PBC), autoimmune hepatitis (AIH), hepatitis B virus (HBV), hepatitis C virus (HCV) and HD livers and found that antibodies of IgG and IgA isotypes were highly accumulated in SAH and recognized a unique set of human proteins as autoantigens. The use of anE. coliK12 proteome array revealed the presence of unique anti-E. coliantibodies in SAH, AC or PBC livers. Further, both Ig andE. colicaptured Ig from SAH livers recognized common autoantigens enriched in several cellular components including cytosol and cytoplasm (IgG and IgA), nucleus, mitochondrion and focal adhesion (IgG). Except IgM from PBC livers, no common autoantigen was recognized by Ig andE. colicaptured Ig from AC, HBV, HCV, NASH or AIH suggesting no cross-reacting anti-E. coliautoantibodies. The presence of cross-reacting anti-bacterial IgG and IgA autoantibodies in the liver may participate in the pathogenesis of SAH.
Genomic differences and species delimitation: a case for two species in the zoonotic cestodeDipylidium caninum
Authors: Jesudoss Chelladurai Jeba R J , Abraham Aloysius , Quintana Theresa , Smith Vicki , Ritchie Deb
Published: February 2023

Dipylidium caninum(Linnaeus, 1758) is a common zoonotic cestode of dogs and cats worldwide. Previous studies have demonstrated the existence of largely host associated canine and feline genotypes based on infection studies, genetic differences at the nuclear 28S rDNA gene and complete mitochondrial genomes. There have been no comparative studies at a genome-wide scale. Here, we sequenced the genomes of a dog and cat isolate ofDipylidium caninumfrom the United States using the Illumina platform and conducted comparative analyses with the reference draft genome. Complete mitochondrial genomes were used to confirm the genotypes of the isolates.D. caninumcanine and feline genomes generated in this study had mean coverage depths of 45x and 26x and an average identity of 98% and 89% respectively when compared to the reference genome. SNPs were 20 times higher in the feline isolate. Comparison and species delimitation using universally conserved orthologs and protein coding mitochondrial genes revealed that the canine and feline isolates are different species. Data from this study builds a base for future integrative taxonomy. Further genomic studies from geographically diverse populations are necessary to understand implications for taxonomy, epidemiology, veterinary clinical medicine, and anthelmintic resistance.
Pleiotropic contribution ofrbfox1to psychiatric and neurodevelopmental phenotypes in a zebrafish model
Authors: Antón-Galindo Ester , Adel Maja , García-Gonzalez Judit , Leggieri Adele , López-Blanch Laura , Irimia Manuel , Norton William HJ , Brennan Caroline H , Fernàndez-Castillo Noèlia , Cormand Bru
Published: February 2023

RBFOX1is a highly pleiotropic gene that contributes to several psychiatric and neurodevelopmental disorders. Both rare and common variants inRBFOX1have been associated with several psychiatric conditions, but the mechanisms underlying the pleiotropic effects ofRBFOX1are not yet understood. Here we found that, in zebrafish,rbfox1is expressed in spinal cord, mid- and hindbrain during developmental stages. In adults, expression is restricted to specific areas of the brain, including telencephalic and diencephalic regions with an important role in receiving and processing sensory information and in directing behaviour. To investigate the effect ofrbfox1deficiency on behaviour, we usedrbfox1sa15940, arbfox1loss-of-function line. We found thatrbfox1sa15940mutants present hyperactivity, thigmotaxis, decreased freezing behaviour and altered social behaviour. We repeated these behavioural tests in a secondrbfox1loss-of-function line with a different genetic background,rbfox1del19, and found thatrbfox1deficiency affects behaviour similarly in this line, although there were some differences.rbfox1del19mutants present similar thigmotaxis, but stronger alterations in social behaviour and lower levels of hyperactivity thanrbfox1sa15940fish. Taken together, these results suggest thatrbfox1deficiency leads to multiple behavioural changes in zebrafish that might be modulated by environmental, epigenetic and genetic background effects, and that resemble phenotypic alterations present inRbfox1-deficient mice and in patients with different psychiatric conditions. Our study thus highlights the evolutionary conservation ofrbfox1function in behaviour and paves the way to further investigate the mechanisms underlyingrbfox1pleiotropy on the onset of neurodevelopmental and psychiatric disorders.
Phosphorylation motif dictates GPCR C-terminal domain conformation and arrestin interaction
Authors: Guillien Myriam , Mouhand Assia , Sagar Amin , Fournet Aurélie , Allemand Frédéric , Pereira Glaécia A. N. , Thureau Aurélien , Bernadó Pau , Banères Jean-Louis , Sibille Nathalie
Published: February 2023

Arrestin dependent G protein-coupled receptor (GPCR) signaling pathway is regulated by the phosphorylation state of GPCR’s C-terminal domain, but the molecular bases of arrestin:receptor interaction are to be further illuminated. Here we investigated the impact of phosphorylation on the conformational features of the C-terminal region from three Rhodopsin-like GPCRs, the vasopressin V2 Receptor (V2R), the Growth Hormone Secretagogue or ghrelin Receptor type 1a (GHSR) and the β2-Adernergic Receptor (β2AR). Using phosphomimetic variants, we identified pre-formed secondary structure elements, or short linear motif (SLiMs), that undergo specific conformational transitions upon phosphorylation. Of importance, such conformational transition favors arrestin-2 binding. Hence, our results suggest a model in which the cellular signaling specificity of GPCRs is encoded in the phosphorylation-dependent structuration of the C-terminal regions, which will subsequently modulate arrestin conformation and therefore GPCR:arrestin signaling outcomes.
Extensive re-modelling of the cell wall during the development ofStaphylococcus aureusbacteraemia
Authors: Douglas Edward J.A. , Palk Nathanael , Brignoli Tarcisio , Altwiley Dina , Boura Marcia , Laabei Maisem , Recker Mario , Cheung Gordon Y.C. , Liu Ryan , Hsieh Roger C. , Otto Michael , O’Brien Eoin , McLoughlin Rachel M. , Massey Ruth C.
Published: February 2023

Introductory Paragraph / Abstract

The bloodstream represents a hostile environment that bacteria must overcome to cause bacteraemia. To understand how the major human pathogenStaphylococcus aureusmanages this we have utilised a functional genomics approach to identify a number of new loci that affect the ability of the bacteria to survive exposure to serum, the critical first step in the development of bacteraemia. The expression of one of these genes,tcaA,was found to be induced upon exposure to serum, and we show that it is involved in the elaboration of a critical virulence factor, the wall teichoic acids (WTA), within the cell envelope. The activity of the TcaA protein alters the sensitivity of the bacteria to cell wall attacking agents, including antimicrobial peptides, human defence fatty acids, and several antibiotics. This protein also affects the autolytic activity and lysostaphin sensitivity of the bacteria, suggesting that in addition to changing WTA abundance in the cell envelope, it also plays a role in peptidoglycan crosslinking. With TcaA rendering the bacteria more susceptible to serum killing, while simultaneously increasing the abundance of WTA in the cell envelope, it was unclear what effect this protein may have during infection. To explore this, we examined human data and performed murine experimental infections. Collectively, our data suggests that whilst mutations intcaAare selected for during bacteraemia, this protein positively contributes to the virulence ofS. aureusthrough its involvement in altering the cell wall architecture of the bacteria, a process that appears to play a key role in the development of bacteraemia.
mt-LAF3 is a pseudouridine synthase ortholog required for mitochondrial rRNA and mRNA gene expression inTrypanosoma brucei
Authors: McDermott Suzanne M , Pham Vy , Lewis Isaac , Tracy Maxwell , Stuart Kenneth
Published: February 2023

Trypanosoma bruceiand related kinetoplastid parasites possess unique RNA processing pathways, including in their mitochondria, that regulate metabolism and development. Altering RNA composition or conformation through nucleotide modifications is one such pathway, and modifications including pseudouridine regulate RNA fate and function in many organisms. We surveyed pseudouridine synthase (PUS) orthologs in Trypanosomatids, with a particular interest in mitochondrial enzymes due to their potential importance for mitochondrial function and metabolism.T. bruceimt-LAF3 is an ortholog of human and yeast mitochondrial PUS enzymes, and a mitoribosome assembly factor, but structural studies differ in their conclusion as to whether it has PUS catalytic activity. Here, we generatedT. bruceicells that are conditionally null for mt-LAF3 and showed that mt-LAF3 loss is lethal and disrupts mitochondrial membrane potential (ΔΨm). Addition of a mutant gamma-ATP synthase allele to the conditionally null cells permitted ΔΨm maintenance and cell survival, allowing us to assess primary effects on mitochondrial RNAs. As expected, these studies showed that loss of mt-LAF3 dramatically decreases levels of mitochondrial 12S and 9S rRNAs. Notably, we also observed decreases in mitochondrial mRNA levels, including differential effects on edited vs. pre-edited mRNAs, indicating that mt-LAF3 is required for mitochondrial rRNA and mRNA processing, including of edited transcripts. To assess the importance of PUS catalytic activity in mt-LAF3 we mutated a conserved aspartate that is necessary for catalysis in other PUS enzymes and showed it is not essential for cell growth, or maintenance of ΔΨm and mitochondrial RNA levels. Together, these results indicate that mt-LAF3 is required for normal expression of mitochondrial mRNAs in addition to rRNAs, but that PUS catalytic activity is not required for these functions. Instead, our work, combined with previous structural studies, suggests thatT. bruceimt-LAF3 acts as a mitochondrial RNA-stabilizing scaffold.