bluuebunny/crossref_metadata_2025 huggingface dataset:
Intracranial aneurysm stiffness assessment using 4D flow MRI
Authors: Koizumi Satoshi , Kin Taichi , Sekine Tetsuro , Kiyofuji Satoshi , Umekawa Motoyuki , Saito Nobuhito
Published: April 2024

Background

Although arterial stiffness is a known biomarker for cardiovascular events and stroke, there is limited information in the literature regarding the stiffness of intracranial aneurysms. This study aimed to assess intracranial aneurysm stiffness using four-dimensional flow magnetic resonance imaging (4D flow MRI).

Methods

A total of 27 aneurysms in 25 patients with internal carotid artery aneurysms were included. Using 4D flow MRI, we measured the arterial pulse waveform during a cardiac cycle at planes proximal and distal to the target aneurysm. The damping of these waveforms through the aneurysm was defined as the aneurysm damping index (ADI) and compared with that of the contralateral side. Additionally, we investigated the clinical factors associated with the ADI.

Results

ADI assessment was successful in all cases. The obtained ADI was 1.18 ± 0.28 (mean ± standard deviation), significantly larger than 1.0 (P=0.0027 [t-test]). The ADI on the aneurysm side was larger than on the contralateral side (1.19 ± 0.30 vs 1.05 ± 0.17, P=0.029 [t-test]). On multivariate analysis, the use of beta-blockers (β=0.46, P=0.015) and smoking history (β=-0.22, P=0.024) showed a significant correlation with ADI.

Conclusions

We proposed a novel method to assess the stiffness of intracranial aneurysms using 4D flow MRI. The quantitative observation of the damping of arterial pulse waves revealed a correlation between ADI and clinical factors, such as the use of antihypertensive drugs and smoking. Further studies should focus on evaluating the aneurysm stiffness and its clinical applications.
Biallelic Variants inCCN2Underlie an Autosomal Recessive Kyphomelic Dysplasia
Authors: Singh Swati , Danda Sumita , Sharma Neetu , Shah Hitesh , Madhuri Vrisha , Altaf Mir Tariq , Padala Nadia Zipporah , Medishetti Raghavender , Ekbote Alka , Bhavani Gandham SriLakshmi , Sevilimedu Aarti , Girisha Katta M
Published: April 2024

Kyphomelic dysplasia is a rare heterogenous group of skeletal dysplasia, characterized by bowing of the limbs, severely affecting femora with distinct facial features. Despite its first description nearly four decades, the precise molecular basis of this condition remained elusive until the recent discovery ofde novovariants in the KIF5B-related kyphomelic dysplasia. We ascertained two unrelated consanguineous families with kyphomelic dysplasia. They had six affected offsprings and we performed a detailed clinical evaluation, skeletal survey, and exome sequencing in three probands. All the probands had short stature, cleft palate, and micro-retrognathia. Radiographs revealed kyphomelic femora, bowing of long bones, radial head dislocations and spondyloepimetaphyseal dysplasia. We noted two novel homozygous variants inCCN2as possible candidates that segregated with the phenotype in the families: a missense variant c.443G>A; p.(Cys148Tyr) in exon 3 and a frameshift variant, c.779_786del; p.(Pro260LeufsTer7) in exon 5.CCN2is crucial for proliferation and differentiation of chondrocytes. Earlier studies have shown thatCcn2-deficient mice exhibit twisted limbs, short and kinked sterna, broad vertebrae, domed cranial vault, shorter mandibles, cleft palate and impaired osteoclastogenesis. We studied the impact ofCCN2knockout in zebrafish models via CRISPR-Cas9 gene editing. F0 knockouts ofccn2ain zebrafish showed altered body curvature, impaired cartilage formation in craniofacial region and either bent or missing tails recapitulating the human phenotype. Our observations in humans and zebrafish combined with previously described skeletal phenotype ofCcn2knock out mice, confirm that biallelic loss of function variants inCCN2result in an autosomal recessive kyphomelic dysplasia.
Apraxic imitation deficits in Alzheimer’s disease are associated with altered dynamic connectivity
Authors: Kuzu Taylan D. , Jaeger Elena , Bonkhoff Anna K. , Wunderle Veronika , Bischof Gérard N. , Giehl Kathrin , Schmieschek Maximilian H. T. , Onur Özgür A. , Jessen Frank , Fink Gereon R. , Drzezga Alexander , Weiss Peter H.
Published: April 2024

Apraxia is a common symptom in individuals with Alzheimer’s disease (AD). However, the neural mechanisms underlying apraxic deficits in AD remain elusive. Therefore, the current study focuses on the association between altered functional connectivity and apraxia in individuals with AD examining the hypothesis that apraxic deficits in AD result from dysfunction in praxis-related networks.

To this aim, we examined the association between changes in static and dynamic functional connectivity (FC) of resting-state networks and apraxia in AD. Resting-state functional MRI data was acquired in 13 patients with tau-and amyloid-positive AD, who underwent an extensive neuropsychological, motor and apraxia assessment, and 13 matched healthy control participants. The static and dynamic functional connectivity of resting state networks revealed by independent component analysis (ICA) were assessed and connectivity measures were correlated with apraxia scores.

Across all participants, we identified two distinct dynamic FC states using a sliding window approach. Patients with AD exhibited prolonged dwell times in the first state characterized by weaker connectivity and spent overall more time in this state, i.e., showed an increased fraction time in the first state. Apraxic deficits, especially deficits in imitating gestures, correlated significantly with the fraction time of both states as well as with the dwell time of the weakly connected dynamic state.

Data suggest that apraxic imitation deficits in AD are associated with dysfunction of praxis networks characterized by altered dynamic FC.
Systems vaccinology identifies clinical and immunological correlates of SARS-CoV-2 vaccine response in solid-organ transplant recipients
Authors: Gemander Nicolas , Neumann Julika , Veiga Rafael , Etienne Isabelle , Prezzemolo Teresa , Kemlin Delphine , Pannus Pieter , Depickère Stéphanie , Olislagers Véronique , Vu Duc Inès , Waegemans Alexandra , Gerbaux Margaux , Bücken Leoni , Dahma Hafid , Martin Charlotte , Dauby Nicolas , Goossens Maria E , Desombere Isabelle , Roca Carlos P , Willemsen Mathijs , Goriely Stanislas , Le Moine Alain , Marchant Arnaud , Liston Adrian , Humblet-Baron Stephanie
Published: April 2024

Solid organ transplant (SOT) recipients are at enhanced risk of adverse outcomes following infectious challenges due to immunosuppressive treatment and additional comorbidities. Unfortunately, SOT recipients are also poor responders to the key medical intervention to preventing infection: vaccines. Here we performed a systems vaccinology study on a cohort of 59 kidney transplant recipients and 31 lung transplant recipients who received the mRNA Pfizer-BioNTech COVID-19 vaccine. Analyzing the immunological status of the patients prior to vaccination, we were able to identify multiple immunological associates of relatively improved vaccine responses following two or three doses of mRNA-based SARS-CoV-2 vaccine. These immunological associates predicted, with 95.0% and 93.3% accuracy, vaccine response after the second and third dose, respectively. Comparison of the immunological associates with vaccine response in SOT recipients revealed two distinct immune configurations: a non-classical configuration, distinct from the immune state of healthy subjects, associated with responses to two doses of mRNA vaccine and that could be mediated partly by the presence of double negative B cell subsets which are more prominently represented in responsive SOT recipients, and a “normalized” configuration, closer to the immune state of healthy subjects, associated with potent antibody responses to three doses of mRNA vaccine. These results suggest that immunosuppression in SOT recipients can result in distinct immune states associated with different trade-offs in vaccine responsiveness. Immune phenotyping of SOT recipients for immune constellation may be an effective approach for identifying patients most at risk of poor vaccine responses and susceptibility to vaccine-preventable diseases.

One-sentence summary

SOT recipients showed distinct immune states at baseline associated with different profiles of vaccine-associated immune response.
How subject-specific biomechanics influences tendon strains in Achilles tendinopathy patients: A finite element study
Authors: Funaro Alessia , Shim Vickie , Mylle Ine , Vanwanseele Benedicte
Published: April 2024

The treatment of Achilles tendinopathy is challenging, as 40% of patients do not respond to the existing rehabilitation protocols. These rehabilitation protocols do not consider the individual differences in the Achilles tendon (AT) characteristics, which are crucial in creating the optimal strain environment that promotes healing. While previous research suggests an optimal strain for AT regeneration (6% tendon strains), it is still unclear if the current rehabilitation protocols meet this condition. Consequently, this study aimed to investigate the influence of a selection of rehabilitation exercises on strains in patients with Achilles tendinopathy using subject-specific finite element (FE) models of the free AT. Secondly, the study aimed to explain the influence of muscle forces and material properties on the AT strains. The 21 FE models of the AT included the following subject-specific features: geometry estimated from 3D freehand ultrasound images, Elastic modulus estimated from the experimental stress-strain curve, and muscle forces estimated using a combination of 3D motion capture and musculoskeletal modelling. These models were used to determine tendon strain magnitudes and distribution patterns in the mid-portion of the AT. The generalized ranking suggested a progression of exercises to gradually increase the strains in the mid-portion of the AT, starting from the concentric and eccentric exercises and going to more functional exercises, which impose a higher load on the AT: bilateral heel rise (0.031 ± 0.010), bilateral heel drop (0.034 ± 0.009), unilateral heel drop (0.066 ± 0.023), walking (0.069 ± 0.020), unilateral heel drop with flexed knee (0.078 ± 0.023), and bilateral hopping (0.115 ± 0.033). Unilateral heel drop and walking exercises were not significantly different and they both fell within the optimal strain range. However, when examining individual strains, it became evident that there was diversity in exercise rankings among participants, as well as exercises falling within the optimal strain range. Furthermore, the strains were influenced more by the subject-specific muscle forces compared to the material properties. Our study demonstrated the importance of tailored rehabilitation protocols that consider not only individual subject-specific morphological and material characteristics but especially subject-specific muscle forces. These findings make a significant contribution to shape future rehabilitation protocols with a foundation in biomechanics.
Quality of care when using a digital clinical decision support algorithm to manage sick children at primary care health facilities in Tanzania: a cross-sectional cluster randomized controlled trial (DYNAMIC study)
Authors: Tan Rainer , Kavishe Godfrey , Kulinkina Alexandra V , Renggli Sabine , Luwanda Lameck B , Mangu Chacha , Ashery Geofrey , Jorram Margaret , Mtebene Ibrahim Evans , Agrea Peter , Mhagama Humphrey , Keitel Kristina , Le Pogam Marie-Annick , Ntinginya Nyanda , Masanja Honorati , D’Acremont Valérie
Published: April 2024

Digital clinical decision support tools have contributed to improved quality of care at primary care level health facilities. However, data from real-world randomized trials are lacking.

We conducted a cluster randomized, open-label trial in Tanzania evaluating the use of a digital clinical decision support algorithm (CDSA), enhanced by point-of-care tests, training and mentorship, compared with usual care, among sick children 2 to 59 months old presenting to primary care facilities for an acute illness in Tanzania (ClinicalTrials.govNCT05144763). The primary outcome was the mean proportion of 14 major Integrated Management of Childhood Illness (IMCI) symptoms and signs assessed by clinicians. Secondary outcomes included antibiotic prescription, counselling provided, and the appropriateness of antimalarial and antibiotic prescriptions.

A total of 450 consultations were observed in 9 intervention and 9 control health facilities. The mean proportion of major symptoms and signs assessed in intervention health facilities was 46.4% (range 7.7% to 91.7%) compared to 26.3% (range 0% to 66.7%) in control health facilities, an adjusted difference of 15.1% (95% confidence interval [CI] 4.8% to 25.4%). Only weight, height, and pallor were assessed more often when using the digital CDSA than in controls. Observed antibiotic prescription was 37.3% in intervention facilities, and 76.4% in control facilities (adjusted risk ratio 0.5; 95% CI 0.4 to 0.7; p<0.001). Appropriate antibiotic prescription was 81.9% in intervention facilities and 51.4% in control facilities (adjusted risk ratio 1.5; 95% CI 1.2 to 1.8; p=0.003).

The implementation of a digital CDSA improved only slightly the mean proportion of IMCI symptoms and signs assessed in consultations with sick children, and most symptoms and signs were assessed infrequently. Nonetheless, antibiotics were prescribed less often, and more appropriately Innovative approaches to overcome barriers related to clinicians’ motivation and work environment are needed.
Simulating human-in-the-loop optimization of exoskeleton assistance to compare optimization algorithm performance
Authors: Kutulakos Zoe , Slade Patrick
Published: April 2024

Assistive robotic devices like exoskeletons offer the promise of improving mobility for millions of people. However, developing devices that improve an objective mobility metric is challenging. Human-in-the-loop optimization is a systematic approach for personalizing robotic assistance to maximize a mobility metric that has improved device performance for different metrics and applications. Successfully performing human-in-the-loop optimization requires the experimenter to make many decisions, like selecting the appropriate optimization algorithm, hyperparameters, and convergence criteria. Typically, selecting these experimental settings involves pilot experimentation. We propose an approach that uses a probabilistic surrogate model, mapping assistance parameters to corresponding experimental evaluations of the objective mobility metric, to simulate human-in-the-loop optimization and inform these decisions. In this paper, we form a surrogate model of the metabolic landscape of walking with exoskeleton assistance using an existing experimental dataset. We simulate human-in-the-loop optimization by using a synthetic metabolic landscape model to evaluate the metabolic cost of walking with different assistance parameters, instead of performing an experimental measurement. We perform three simulated scenarios optimizing assistance for an expert subject, a novice subject adapting to the device, and an expert subject with up to 20 assistance parameters. The code and analyses from this work are open-source to promote use by other researchers. Simulation enables direct comparison of optimization settings to inform experimental human-in-the-loop optimization and potentially reduce the resources and time required to develop effective assistive devices.
Blocking MIF secretion enhances CAR T-cell efficacy against neuroblastoma
Authors: Strijker Josephine G. M. , Pascual-Pasto Guillem , Kalmeijer Yannine J. , Kalaitsidou Elisavet , Zhao Chunlong , McIntyre Brendan , Matlaga Stephanie , Visser Lindy L. , Barisa Marta , Himsworth Courtney , Shah Rivani , Muller Henrike , Schild Linda G. , Hains Peter G. , Zhong Qing , Reddel Roger , Robinson Phillip J. , Catena Xavier , Soengas María S. , Margaritis Thanasis , Dekker Frank J. , Anderson John , Molenaar Jan J. , Bosse Kristopher R. , Wu Wei , Wienke Judith
Published: April 2024

While chimeric antigen receptor (CAR) T-cell therapies are showing highly promising first results in neuroblastoma, immunosuppressive tumor microenvironments (TME) limit T cell persistence and durable clinical efficacy. To improve CAR T-cell efficacy further, we applied a multi-omics approach including single-cell RNA sequencing and proteomics, which identified 13 targetable immunosuppressive factors in neuroblastoma. Of these, macrophage migration inhibitory factor (MIF) and midkine (MDK) were validated across multiple published RNA datasets. Moreover, they were secreted in high abundance by neuroblastoma tumoroids. Functional validation experiments revealed MIF as a potent inhibitor of CAR T-cells,in vitroandin vivo.Degradation of MIF by PROTAC technology significantly enhanced CAR T-cell activation targeting GPC2 and B7-H3, providing a potential intervention against MIF. By defining the immunosuppressive effects of neuroblastoma’s TME on CAR T-cell efficacy, particularly the pivotal role of MIF, we provide a therapeutic strategy for improving adoptive cell therapies for this pediatric malignancy.
The pathway to resolve dimeric forms distinguishes plasmids from megaplasmids in Enterobacteriaceae
Authors: Fournes Florian , Campos Manuel , Cury Jean , Schiavon Caroline , Pagès Carine , Touchon Marie , Rocha Eduardo PC , Rousseau Philippe , Cornet François
Published: April 2024

Bacterial genomes contain a plethora of secondary replicons of divergent size. Circular replicons must carry a system for resolving dimeric forms, resulting from recombination between sister copies. These systems use site-specific recombinases. Among these, the XerCD recombinase resolves dimers of chromosomes and certain plasmids using different controls. We have analyzed the dimer resolution functions in enterobacterial secondary replicons and show that, in addition to the main chromosomes, XerCD is preferentially used by small plasmids and by the largest secondary replicons, megaplasmids and secondary chromosomes. Indeed, all replicons longer than 250 kb host an active XerCD recombination site. These sites, in contrast to those of small plasmids, use the same control as chromosomes, coupled to cell division by the FtsK protein. We conclude that a chromosome-like mode of dimer resolution is mandatory for the faithful inheritance of large plasmids and chromids, its acquisition being a prerequisite for the genesis of secondary chromosomes from plasmids.
Temporal Dynamics of Neocortical Development in Organotypic Mouse Cultures: A Comprehensive Analysis
Authors: Bak Aniella , Schmied Katharina , Jakob Morten , Bedogni Francesco , Squire Olivia , Gittel Birgit , Jesinghausen Maik , Schünemann Kerstin , Weber Yvonne , Kampa Björn , van Loo Karen M. J. , Koch Henner
Published: April 2024

Murine organotypic brain slice cultures have been widely used in neuroscientific research and are offering the opportunity to study neuronal function under normal and disease conditions. Despite the brought application, the mechanisms governing the maturation of immature cortical circuitsin vitroare not well understood. In this study, we present a detailed investigation into the development of the neocortexin vitro. Utilizing a holistic approach, we studied organotypic whole-hemisphere brain slice cultures from postnatal mice and tracked the development of the somatosensory area over a five-week period. Our analysis revealed the maturation of passive and active intrinsic properties of pyramidal cells together with their morphology, closely resemblingin vivodevelopment. Detailed Multi-electrode array (MEA) electrophysiological assessments and RNA expression profiling demonstrated stable network properties by two weeks in culture, followed by the transition of spontaneous activity towards more complex patterns including high-frequency oscillations. However, weeks 4 and 5 exhibited increased variability and initial signs of neuronal loss, highlighting the importance of considering developmental stages in experimental design. This comprehensive characterization is vital for understanding the temporal dynamics of the neocortical developmentin vitro, with implications for neuroscientific research methodologies, particularly in the investigation of diseases such as epilepsy and other neurodevelopmental disorders.
Regulation of ROP GTPase cycling between active/inactive states is essential for vegetative organogenesis inMarchantia polymorpha
Authors: Sakai Yuuki , Ueno Aki , Yonetsuka Hiroki , Goh Tatsuaki , Kato Hirotaka , Kondo Yuki , Fukaki Hidehiro , Ishizaki Kimitsune
Published: April 2024

Rho/Rac of plant (ROP) GTPases are a plant-specific subfamily of Rho small GTP-binding proteins that function as molecular switches by being converted to the active state by guanine nucleotide exchange factors (GEFs) and to the inactive state by GTPase-activating proteins (GAPs). The bryophyteMarchantia polymorphacontains single-copy genes encoding ROP (MpROP), two types of GEFs (ROPGEF and SPIKE (SPK)), and two types of GAPs (ROPGAP and ROP enhancer (REN)). MpROP regulates the development of various organs, including the air chambers, rhizoids, and clonal propagule gemmae. While the sole PRONE-type ROPGEF, KARAPPO (MpKAR), plays an essential role in gemma initiation, little is known about thein-plantafunctions of other ROP regulatory factors inM. polymorpha. In this study, we focused on the functions of two types of GAPs: MpROPGAP and MpREN. Loss-of-function Mprengesingle mutants showed pleiotropic defects in thallus growth, air chamber formation, rhizoid tip growth, and gemma development, whereas MpROPGAP mutants showed no detectable abnormalities. Despite the distinctive domain structures of MpROPGAP and MpREN, MpropgapgeMprengedouble mutants showed more severe phenotypes than the Mprengesingle mutants, suggesting redundant functions of MpROPGAP and MpREN in gametophyte organogenesis. Interestingly, overexpression of MpROPGAP, MpREN, anddominant-negativeMpROP(MpROPDN) resulted in similar air chamber defects, as well as loss-of-function of MpRENand MpROPGAPand overexpression ofconstitutively activeMpROP(MpROPCA), suggesting importance of activation/inactivation cycling (or balancing) of MpROP. Furthermore, we proved the contributions of the sole DOCK family GEF, MpSPK, to MpROP-regulated air chamber formation. In summary, our results demonstrate a significant role of the two GAPs in the development of various organs and that the two GEFs are responsible for organogenesis through the control of the MpROP active/inactive cycle in the vegetative growth ofM. polymorpha.
A newly-identified IncY plasmid from multi-drug resistantEscherichia coliisolated from dairy cattle feces in Poland
Authors: Zalewska Magdalena , Błażejewska Aleksandra , Gawor Jan , Adamska Dorota , Goryca Krzysztof , Szeląg Michał , Kalinowski Patryk , Popowska Magdalena
Published: April 2024

Comprehensive whole-genome sequencing was performed on two multi-drug resistantEscherichia colistrains isolated from cattle manure from a typical dairy farm in Poland in 2020. The identified strains are resistant to beta-lactams, aminoglycosides, tetracyclines, trimethoprim/sulfamethoxazole, and fluoroquinolones. The complete sequences of the harbored plasmids revealed antibiotic-resistance genes (ARGs) located within many mobile genetic elements (e.g., insertional sequences or transposons), and genes facilitating conjugal transfer or promoting horizontal gene transfer. These plasmids are hitherto undescribed. Similar plasmids have been identified, but not in Poland. The identified plasmids carried resistance genes, including the tetracycline resistance genetet(A), aph family aminoglycoside resistance genesaph(3”)-lbandaph(6)-ld, β-lactam resistance genesblaTEM-1, blaCTX-M-15, sulfonamide resistance genesul2, fluoroquinolone resistance geneqnrS1, and the trimethoprim resistance genedfrA14. The characterized resistance plasmids were categorized into the IncY incompatibility group, indicating a high possibility for dissemination among theEnterobacteriaceae. While similar plasmids (99% identity) have been found in environmental and clinical samples, none have been identified in farm animals. This findings are significant within the One Health framework, as they underline the potential for antimicrobial-resistantE. colifrom livestock and food sources to be transmitted to humans and vice versa. It highlights the need for careful monitoring and strategies to limit the spread of antibiotic resistance in the One Health approach.
Land use effects on soil microbiome composition and traits with consequences for its ecosystem carbon use efficiency
Authors: Cole Lisa , Goodall Tim , Jehmlich Nico , Griffiths Robert I. , Gleixner Gerd , Gubry-Rangin Cecile , Malik Ashish A.
Published: April 2024

The soil microbiome determines the fate of belowground inputs of plant fixed carbon. The shifts in soil properties caused by changes in land use leads to modifications in microbiome structure and function, resulting in either loss or gain of soil organic carbon (SOC). Soil pH is the primary factor regulating microbiome characteristics leading to distinct pathways of microbial carbon cycling, but the underlying mechanisms remain understudied. Here, the taxa-trait relationships behind the variable fate of SOC were investigated across two temperate paired land use intensity contrasts with differing soil pH using metaproteomics, metabarcoding and a13C labelled litter decomposition experiment.13C incorporation into microbial biomass increased with land use intensification in low pH soils but decreased in high pH soils, impacting ecosystem carbon use efficiency (CUE) in opposing directions. Reduction in biosynthesis traits across land use intensity contrasts was due to increased abundance of proteins linked to resource acquisition and stress tolerance. These community-level trait trade-offs were underpinned by land use intensification-induced changes in dominant taxa with distinct traits. These trait changes alter the balance of decomposition and stabilisation of carbon in soil through divergent pH-controlled pathways. In low pH soils, land use intensification alleviates microbial abiotic stress resulting in increased CUE but promotes decomposition and SOC loss. In contrast, in high pH soils, land use intensification increases microbial physiological constraints and decreases CUE, leading to reduced necromass build-up and SOC stabilisation. We demonstrate how microbial CUE can be decoupled from SOC highlighting the need for its careful consideration in predicting or managing SOC storage for soil health and climate change mitigation.
Cockroach social network position does not influence exploration tendency
Authors: Louca Vasilis , Savorelli Smilla , Vuorio Nea , Fisher David N.
Published: April 2024

In group-living organisms, we might expect relationships between social position and exploration, such as if certain patterns of social associations encourage exploration or if certain personality types both link different groups and are more likely to explore their environment. However, directly testing these ideas is challenging as exploration can be hard to track in the field and is a difficult trait to measure in the laboratory. Furthermore, invertebrate exploration is less commonly quantified as their small size makes them hard to track. Here we quantified social networks in multiple groups of the gregarious cockroachBlaptica dubiain the laboratory and related three measures of social network position (representing overall sociability, connectedness in local cliques, and connectedness to the wider network) to measures of exploration either assayed alone or as part of a group. We found none of the social network measures related to either of the measures of exploration, which were themselves not correlated. We also found that sociability and connectedness to the wider network were positively correlated, suggesting a single axis of variation in centrality within a group. We found no effects of mass or sex, but there were differences between the two blocks our experiments were performed in, suggesting some effect of observer variability. Overall, our results suggest that exploration is not linked to social behaviour in this species, that cockroaches differ in the social behaviour along a syndrome integrating sociability and the tendency to move between groups, and that study replication should be encouraged so we can be confident identified trends are robust.
The IncC and IncX1 resistance plasmids present in multi-drug resistantEscherichia colistrains isolated from poultry manure in Poland
Authors: Zalewska Magdalena , Błażejewska Aleksandra , Gawor Jan , Adamska Dorota , Goryca Krzysztof , Szeląg Michał , Kalinowski Patryk , Popowska Magdalena
Published: April 2024

The study describes the whole-genome sequencing of two antibiotic-resistant representativeEscherichia colistrains, isolated from poultry manure in 2020. The samples were obtained from a commercial chicken meat production facility in Poland. The antibiotic resistance profile was characterized by co-resistance to β-lactam antibiotics, aminoglycosides, and fluoroquinolones. The three identified resistance plasmids (R-plasmids), pECmdr13.2, pECmdr13.3 and pECmdr14.1, harbored various genes conferring resistance to tetracyclines (tetR[A]) for, aminoglycoside (aph, aacandaadfamilies), β-lactam (blaCMY-2,blaTEM-176), sulfonamide (sul1, sul2), fluoroquinolone (qnrS1), and phenicol (floR). These plasmids, which have not been previously reported in Poland, were found to carry IS26 insertion elements, the intI1-integrase gene, as well as conjugal transfer genes, facilitating horizontal gene transfer. Plasmids pECmdr13.2 and pECmdr14.1 also possessed a mercury resistance gene operon related to transposon Tn1696; this promotes plasmid persistence even without antibiotic selection pressure due to co-selection mechanisms such as co-resistance. The chicken manure-derived plasmids belonged to the IncX1 (narrow host range) and IncC (broad host range) incompatibility groups. Similar plasmids have been identified in various environments, clinical isolates, and farm animals, including cattle, swine, and poultry. This study holds significant importance for the One Health approach, as it highlights the potential for antimicrobial-resistant bacteria from livestock and food sources, particularlyE. coli, to transfer through the food chain to humans and vice versa. This underscores the need for vigilant monitoring of R-plasmids prevalence in the human, animal and natural environments, and to implement strategies to mitigate the spread of antibiotic resistance.
Cameroonian blackflies (Diptera: Simuliidae) harbour a plethora of (RNA) viruses
Authors: De Coninck Lander , Hadermann Amber , Ingletto Ludovica , Colebunders Robert , Njamnshi Kongnyu Gamnsi , Njamnshi Alfred Kongnyu , Mokili John L , Siewe Fodjo Joseph Nelson , Matthijnssens Jelle
Published: April 2024

Strong epidemiological evidence suggests that onchocerciasis may be associated with epilepsy – hence the name onchocerciasis-associated epilepsy (OAE). However, the pathogenesis of OAE still needs to be elucidated, as recent studies failed to detectOnchocerca volvulusin the central nervous system of persons with OAE. Therefore, it was suggested that a potentially neurotropic virus transmitted by blackflies could play a role in triggering OAE. To investigate this hypothesis, adult blackflies were collected in an onchocerciasis-endemic area with a high OAE prevalence in the Ntui Health District, Cameroon. A whole-genome shotgun sequencing approach was used to detect viral sequences in fifty-five pools of ten blackflies. A very high abundance of viral reads was detected across multiple (novel) viral families, including viral families associated with human disease. Although, no genomes closely related to known neurotropic viruses were found in the blackfly virome, the plethora of novel viruses representing novel species, genera and even families, warrant further exploration for their potential to infect vertebrates. These results could serve as a first step for studying the viruses associated with the hematophagous blackfly, which also could be present in their nematode hostO. volvulus. Exploring the diversity of viruses in blackflies should be included in the active surveillance of zoonotic diseases.
Genome mining leads to the identification of a stable and promiscuous Baeyer-Villiger monooxygenase from a thermophilic microorganism
Authors: Bunyat-zada Amir R. , Ducharme Stephan E. , Cleveland Maria E. , Hoffman Esther R. , Howe Graeme W.
Published: April 2024

Baeyer-Villiger monooxygenases are NAD(P)H-dependent flavoproteins that catalyze oxygen insertion reactions which convert ketones to valuable esters and lactones. While these enzymes offer an appealing alternative to traditional Baeyer-Villiger oxidations, these proteins tend to be either too unstable or exhibit too narrow of a substrate scope for implementation as industrial biocatalysts. Here, sequence similarity networks were used to search for novel Baeyer-Villiger monooxygenases that are both stable and substrate promiscuous. Our genome mining efforts led to the identification of an enzyme fromChloroflexotabacterium (strain G233) dubbedssnBVMO that exhibits i) the highest melting temperature recorded to date for a naturally sourced Baeyer-Villiger monooxygenase, ii) a remarkable kinetic stability across a wide range of conditions, and iii) a broad substrate scope that includes linear aliphatic, aromatic, and sterically bulky ketones. Kinetic characterization of this enzyme was undertaken to identify the optimal conditions forssnBVMO catalysis, and a subsequent quantitative assay using propiophenone as a substrate afforded more than 95% conversion. To spur the implementation of this enzyme as an oxidative biocatalyst, several fusion proteins were constructed that linkedssnBVMO to a thermostable phosphite dehydrogenase. These self-sufficient enzymes can recycle NADPH and permit oxidations to be run with sub-stoichiometric quantities of this expensive cofactor. Extensive characterization of these fusion enzymes permitted identification of PTDH-L1-ssnBVMO as the most promising oxidative biocatalyst. Results described herein demonstrate that this new monooxygenase has significant potential as a useful industrial biocatalyst for Baeyer-Villiger oxidations.
MtrAB two-component system is crucial for the intrinsic resistance and virulence ofMycobacterium abscessus
Authors: Zhang Jingran , Ju Yanan , Li Lijie , Hameed Adnan , Yusuf Buhari , Gao Yamin , Fang Cuiting , Tian Xirong , Ding Jie , Ma Wanli , Chen Xinwen , Wang Shuai , Zhang Tianyu
Published: April 2024

Mycobacterium abscessus(Mab) poses serious therapeutic challenges, principally due to its intrinsic resistance to a wide array of antibiotics. The pressing issue of drug resistance has spurred an urgent need to explore novel targets and develop new therapeutic agents against Mab. The MtrAB two-component system, conserved among Actinobacteria, is pivotal for regulating various metabolic processes. Nevertheless, the role of MtrAB in Mab remains elusive.

In this study, we uncovered that Mab strains with disruptedmtrA, mtrBor both exhibited heightened susceptibility to a variety of antibiotics with diverse mechanisms of action, in contrast to the wild-type strain. In a murine model, rifabutin, bedaquiline, and amikacin, which were inactive against the wild-type Mab strain, demonstrated efficacy against all themtrA, mtrBandmtrABknockout strains, significantly reducing pulmonary bacterial burdens compared to vehicle controls after ten days of treatment. Notably, the virulence of all themtrA, mtrB, andmtrABknockout strains was highly diminished in the murine model, as evidenced by a substantial decrease in bacterial load in the lungs of mice after 16 days. We observed that all three knockout strains exhibited a significantly reduced growth rate compared to the wild-type strain.

We discovered that cells lackingmtrA, mtrBor both exhibited an elongated cell length and had multiple septa, suggesting that both MtrA and MtrB regulate cell division of Mab. Subsequently, an ethidium bromide accumulation assay disclosed that the absence of eithermtrAormtrBor both significantly increased cell envelope permeability.

In summary, this study suggests thatmtrAandmtrBplay an important role in the intrinsic resistance and virulence of Mab by affecting cell division and altering cell permeability. Consequently, MtrA and MtrB represent promising targets for the discovery of anti-Mab drugs.

HIGHLIGHTS

Knockout ofmtrA, mtrBormtrABleads to increased sensitivity ofM. abscessus in vitroandin vivo.

ThemtrA, mtrBormtrABknockoutM. abscessusstrains exhibit highly reduced virulence.

MtrA and MtrB are potential targets for anti-M. abscessusdrug discovery.

Knockout ofmtrA, mtrBormtrABresults in defective cell division inM. abscessus.
An optical aptamer-based cytokine nanosensor detects macrophage activation by bacterial toxins
Authors: Ryan Amelia K. , Rahman Syeda , Williams Ryan M.
Published: April 2024

Overactive or dysregulated cytokine expression is hallmark of many acute and chronic inflammatory diseases. This is true for acute or chronic infection, neurodegenerative diseases, autoimmune diseases, cardiovascular disease, cancer, and others. Cytokines such as interleukin-6 (IL-6) are known therapeutic targets and biomarkers for such inflammatory diseases. Platforms for cytokine detection are therefore desirable tools for both research and clinical applications. Single-walled carbon nanotubes (SWCNT) are versatile nanomaterials with near-infrared fluorescence that can serve as transducers for optical sensors. When functionalized with an analyte-specific recognition element, SWCNT emission may become sensitive and selective towards the desired target. SWCNT-aptamer sensors are easily assembled, inexpensive, and biocompatible. In this work, we introduced a nanosensor design based on SWCNT and a DNA aptamer specific to IL-6. We first evaluated several SWCNT-aptamer constructs based on this simple direct complexation method, wherein the aptamer both solubilizes the SWCNT and confers sensitivity to IL-6. The sensor limit of detection, 105 ng/mL, lies in the relevant range for pathological IL-6 levels. Upon investigation of sensor kinetics, we found rapid response within seconds of antigen addition which continued over the course of three hours. We found that this sensor construct is stable, and the aptamer is not displaced from the nanotube surface during IL-6 detection. Finally, we investigated the ability of this sensor construct to detect macrophage activation caused by bacterial lipopolysaccharides (LPS) in an in vitro model of disease, finding rapid and sensitive detection of macrophage-expressed IL-6. We are confident further development of this sensor will have novel implications for diagnosis of acute and chronic inflammatory diseases, in addition to contributing to the understanding of the role of cytokines in these diseases.
The RNA landscape of the human commensalSegatella coprireveals a small RNA essential for gut colonization
Authors: El Mouali Youssef , Tawk Caroline , Huang Kun D. , Amend Lena , Lesker Till Robin , Ponath Falk , Vogel Jörg , Strowig Till
Published: April 2024

The bacteriumSegatella copriis a prevalent member of the human gut microbiota associated with both health and disease states, but intrinsic factors that determine its ability to effectively colonize the gut are not understood. By extensive transcriptome mapping ofS. copriand examining human-derived samples, we discover a previously unknown small RNA named hereSegatellaRNA colonization factor (SrcF). We show that SrcF is essential forS. coprigut colonization in a gnotobiotic mouse model. SrcF regulates genes involved in nutrient acquisition, and its own expression is controlled by complex carbohydrates, particularly fructans. Furthermore, SrcF expression is strongly influenced by human microbiome composition and by the breakdown of fructans by cohabitating commensals, suggesting that the breakdown of complex carbohydrates mediates inter-species signaling among commensals beyond its established function in generating energy. Together, this study highlights the contribution of a small RNA as a key regulator in gut colonization.
A tunable and versatile chemogenetic near infrared fluorescent reporter
Authors: Hajji Lina El , Bunel Benjamin , Joliot Octave , Li Chenge , Tebo Alison G. , Rampon Christine , Volovitch Michel , Fischer Evelyne , Pietrancosta Nicolas , Perez Franck , Morin Xavier , Vriz Sophie , Gautier Arnaud
Published: April 2024

Near-infrared (NIR) fluorescent reporters provide additional colors for highly multiplexed imaging of cells and organisms, and enable imaging with less toxic light and higher contrast and depth. Here, we present the engineering of nirFAST, a small tunable chemogenetic NIR fluorescent reporter that is brighter than top-performing NIR fluorescent proteins in cultured mammalian cells. nirFAST is a small genetically encoded protein of 14 kDa that binds and stabilizes the fluorescent state of synthetic, highly cell-permeant, fluorogenic chromophores (so-called fluorogens) that are otherwise dark when free. Engineered to emit NIR light, nirFAST can also emit far-red or red lights through change of chromophore. nirFAST allows the imaging of proteins in live cultured mammalian cells, chicken embryo tissues and zebrafish larvae. Its near infrared fluorescence provides an additional color for high spectral multiplexing. We showed that nirFAST is well-suited for stimulated emission depletion (STED) nanoscopy, allowing the efficient imaging of proteins with subdiffraction resolution in live cells. nirFAST enabled the design of a chemogenetic green-NIR fluorescent ubiquitination-based cell cycle indicator (FUCCI) for the monitoring of the different phases of the cell cycle. Finally, bisection of nirFAST allowed the design of a fluorogenic chemically induced dimerization technology with NIR fluorescence readout, enabling the control and visualization of protein proximity.
Adolescent Seizure Impacts Oligodendrocyte Development, Neuronal-Glial Circuit Formation, and Myelination
Authors: Foutch Kylie , Tilton Iris , Cooney Aundrea , Brock Robert , Gupta Raghav , Bender Cole , Franzia Chloe , Garcia Mary Francis , Deneen Jeni , Baldemor Megan , Reyes Christopher Arellano , Moura Daniela , Noguchi Hirofumi , Cocas Laura
Published: April 2024

Myelin sheaths, formed by oligodendrocyte cells in the CNS, are vital for rapid conduction of electrical signals down neuronal axons. Oligodendrocyte progenitors differentiate and myelinate axons during development and following demyelinating injury. However, the mechanisms that drive the timing and specificity of developmental myelination are not well understood. It is known that oligodendrocyte progenitors receive synapses from neurons, providing a potential mechanism for neuronal-glial communication. We have previously shown that changing neuronal activity affects the proliferation of oligodendrocyte cells and neuron to OPC connections. We hypothesized that OPC proliferation and differentiation would be affected by pathological neuronal activity during adolescent development, when developmental myelination is occurring, and that this would also impact neuron to OPC connectivity and myelination. We used kainic acid to induce a seizure, then analyzed changes in the rate of OPC proliferation and differentiation five days later in the cerebral cortex, corpus callosum, and hippocampus. We found that OPC proliferation increased, the overall numbers of OPCs increased, and the number of mature oligodendrocytes decreased. We measured changes in the myelination to determine whether seizure activity directly affected myelination rate in adolescent development, and found decreased myelin in the cerebral cortex, corpus callosum, and hippocampus. We used viral monosynaptic circuit tracing to determine whether connections between neurons and OPCs were affected by seizure activity, and found a decrease in neuron to OPC connections in seizure mice compared to controls. Finally, we measured changes in the presence of kir4.1 potassium channels in OPCs, an important regulator of OPC membrane potential as well as an ion channel important for myelination, and found that there was a decrease in the number of potassium channels on OPCs after adolescent seizure. These findings provide insight into the response of the adolescent brain to seizure activity, as well as how seizures affect neuronal glial connections, OPC development and myelin formation, with the goal of understanding how these mechanisms may be important for treatment of demyelination after seizure and in epilepsy.
Integrating HiTOP and RDoC Frameworks Part I: Genetic Architecture of Externalizing and Internalizing Psychopathology
Authors: Davis Christal N. , Khan Yousef , Toikumo Sylvanus , Jinwala Zeal , Boomsma Dorret I. , Levey Daniel F. , Gelernter Joel , Kember Rachel L. , Kranzler Henry R.
Published: April 2024

Background

There is considerable comorbidity between externalizing (EXT) and internalizing (INT) psychopathology. Understanding the shared genetic underpinnings of these spectra is crucial for advancing knowledge of their biological bases and informing empirical models like the Research Domain Criteria (RDoC) and Hierarchical Taxonomy of Psychopathology (HiTOP).

Methods

We applied genomic structural equation modeling to summary statistics from 16 EXT and INT traits in European-ancestry individuals (n = 16,400 to 1,074,629). Traits included clinical (e.g., major depressive disorder, alcohol use disorder) and subclinical measures (e.g., risk tolerance, irritability). We tested five confirmatory factor models to identify the best fitting and most parsimonious genetic architecture and then conducted multivariate genome-wide association studies (GWAS) of the resulting latent factors.

Results

A two-factor correlated model, representing EXT and INT spectra, provided the best fit to the data. There was a moderate genetic correlation between EXT and INT (r = 0.37, SE = 0.02), with bivariate causal mixture models showing extensive overlap in causal variants across the two spectra (94.64%, SE = 3.27). Multivariate GWAS identified 409 lead genetic variants for EXT, 85 for INT, and 256 for the shared traits.

Conclusions

The shared genetic liabilities for EXT and INT identified here help to characterize the genetic architecture underlying these frequently comorbid forms of psychopathology. The findings provide a framework for future research aimed at understanding the shared and distinct biological mechanisms underlying psychopathology, which will help to refine psychiatric classification systems and potentially inform treatment approaches.