bluuebunny/crossref_metadata_2025 huggingface dataset:
Indications for Magnetic Resonance Imaging in Patients With Behcet Uveitis
Authors: Borelli Anna , Behr Jordan , Ruggeri Maria , Han Mini , Zhou Yujia , Foster C. Stephen
Published: October 2023

Background:

Behcet disease is a systemic vasculitis, which may involve the eyes and central nervous system. The true prevalence of neurological involvement is not precisely known but may be associated with ocular involvement. This study investigates the association between Behcet uveitis and neuro-Behcet disease.

Methods:

A retrospective single-center analysis was conducted for consecutive patients with Behcet uveitis at the Massachusetts Eye Research and Surgery Institution. Uveitis characteristics, neurological symptoms, fluorescein fundus angiography, and MRI results were recorded.

Results:

Our population included 108 patients with Behcet uveitis, and 26 (24.1%) were found to have neurological involvement associated with Behcet disease. Optic nerve leakage on fundus angiography and neurological symptoms were associated with an increased risk of neurological involvement. Three cases (11.5%) were nonparenchymal, while 23 (88.5%) were parenchymal with lesions in the cortex, subcortical white matter, thalamus, basal ganglia, and brainstem.

Conclusions:

There is a high comorbidity between ocular and neurological involvement in Behcet disease. Careful assessment of neurological symptoms and baseline fluorescein fundus angiography are recommended for patients with Behcet disease. MRI has a high diagnostic yield and should be pursued if there is concern for progressive or pre-existing neurological involvement.
Parasite-mediated manipulation?Toxoplasma gondiiinfection increases risk behaviour towards culling in red deer
Authors: Nava Matteo , Corlatti Luca , Formenti Nicoletta , Trogu Tiziana , Pedrotti Luca , Gugiatti Alessandro , Lanfranchi Paolo , Luzzago Camilla , Ferrari Nicola
Published: October 2023

Parasites can modify host behaviour to increase their chances of survival and transmission.Toxoplasma gondiiis a globally distributed protozoan whose ability to modify host behaviour is well known in taxa such as rats and humans. Less well known are the effects on the behaviour of wild species, with the exception of a few studies on primates and carnivores. Taking advantage of a culling activity conducted in Stelvio National Park (Italy), the serological status ofT. gondiiwas studied in 260 individuals of red deerCervus elaphuswith respect to the risk of being culled. A temporal culling rank index was fitted as a response variable, andT. gondiiserological status as the main explanatory variable in linear models, accounting for covariates such as sex, age, jaw length, bone marrow fat and culling location. The overall seroprevalence ofT. gondiiwas 31.5%, and the selected models suggested that seropositive deer were culled earlier than seronegative ones, but this effect was only evident in females, in individuals with medium–good body condition, and in areas with greater human presence. Our results suggest thatT. gondiimay be involved in risk behaviour in large herbivores, supporting its role as a facilitator of predation risk.
A variable heart rate multi-compartmental coupled model of the cardiovascular and respiratory systems
Authors: Lishak Sam , Grigorian Gevik , George Sandip V. , Ovenden Nicholas C. , Shipley Rebecca J. , Arridge Simon
Published: October 2023

Current mathematical models of the cardiovascular system that are based on systems of ordinary differential equations are limited in their ability to mimic important features of measured patient data, such as variable heart rates (HR). Such limitations present a significant obstacle in the use of such models for clinical decision-making, as it is the variations in vital signs such as HR and systolic and diastolic blood pressure that are monitored and recorded in typical critical care bedside monitoring systems. In this paper, novel extensions to well-established multi-compartmental models of the cardiovascular and respiratory systems are proposed that permit the simulation of variable HR. Furthermore, a correction to current models is also proposed to stabilize the respiratory behaviour and enable realistic simulation of vital signs over the longer time scales required for clinical management. The results of the extended model developed here show better agreement with measured bio-signals, and these extensions provide an important first step towards estimating model parameters from patient data, using methods such as neural ordinary differential equations. The approach presented is generalizable to many other similar multi-compartmental models of the cardiovascular and respiratory systems.
Classification, Observational Practice, and Henry Seebohm’s
The Birds of the Japanese Empire
in Late-Victorian Britain
Authors: Bossoh Nathan
Published: October 2023

In the latter months of 1890 the ornithologist Henry Seebohm (1832–1895) published his transnationally well-received
The birds of the Japanese Empire
. However, although travelling widely to places such as Greece, South Africa and Siberia, Seebohm never visited Japan. Instead, his knowledge of Japanese birds was gathered through second-hand methods including knowledge and network building, specimen acquiring and comparing and the adoption of a novel classification system. These observational methods of Seebohm as an ‘armchair’ practitioner served to enhance his name as an authority on Japanese birds. Despite an increase in scholarship surrounding the emergence of professionalized twentieth-century Japanese imperial ornithology, little attention has been paid to the various Victorian naturalists who were central to its nineteenth-century origins. Therefore, the aim of this paper is to document the importance of one such naturalist by focusing on Seebohm’s active years between 1878 and 1890. Through this analysis I argue that Seebohm’s observational practices, particularly his use of a novel trinomial classification, were central to securing his credibility on Japanese birds despite never visiting Japan, and that consequently his 1890 book became a landmark in the development of ornithology in the Japanese Empire.
Coral larval settlement induction using tissue-associated and exuded coralline algae metabolites and the identification of putative chemical cues
Authors: Quinlan Zachary A. , Bennett Matthew-James , Arts Milou G. I. , Levenstein Mark , Flores Daisy , Tholen Haley M. , Tichy Lucas , Juarez Gabriel , Haas Andreas F. , Chamberland Valérie F. , Latijnhouwers Kelly R. W. , Vermeij Mark J. A. , Johnson Amy Wagoner , Marhaver Kristen L. , Kelly Linda Wegley
Published: October 2023

Reef-building crustose coralline algae (CCA) are known to facilitate the settlement and metamorphosis of scleractinian coral larvae. In recent decades, CCA coverage has fallen globally and degrading environmental conditions continue to reduce coral survivorship, spurring new restoration interventions to rebuild coral reef health. In this study, naturally produced chemical compounds (metabolites) were collected from two pantropical CCA genera to isolate and classify those that induce coral settlement. In experiments using four ecologically important Caribbean coral species, we demonstrate the applicability of extracted, CCA-derived metabolites to improve larval settlement success in coral breeding and restoration efforts. Tissue-associated CCA metabolites induced settlement of one coral species,Orbicella faveolata, while metabolites exuded by CCA (exometabolites) induced settlement of three species:Acropora palmata,Colpophyllia natansandOrbicella faveolata. In a follow-up experiment, CCA exometabolites fractionated and preserved using two different extraction resins induced the same level of larval settlement as the unfractionated positive control exometabolites. The fractionated CCA exometabolite pools were characterized using liquid chromatography tandem mass spectrometry, yielding 145 distinct molecular subnetworks that were statistically defined as CCA-derived and could be classified into 10 broad chemical classes. Identifying these compounds can reveal their natural prevalence in coral reef habitats and facilitate the development of new applications to enhance larval settlement and the survival of coral juveniles.
Selective enrichment of founding reproductive microbiomes allows extensive vertical transmission in a fungus-farming termite
Authors: Sinotte Veronica M. , Renelies-Hamilton Justinn , Andreu-Sánchez Sergio , Vasseur-Cognet Mireille , Poulsen Michael
Published: October 2023

Mutualistic coevolution can be mediated by vertical transmission of symbionts between host generations. Termites host complex gut bacterial communities with evolutionary histories indicative of mixed-mode transmission. Here, we document that vertical transmission of gut bacterial strains is congruent across parent to offspring colonies in four pedigrees of the fungus-farming termite
Macrotermes natalensis
. We show that 44% of the offspring colony microbiome, including more than 80 bacterial genera and pedigree-specific strains, are consistently inherited. We go on to demonstrate that this is achieved because colony-founding reproductives are selectively enriched with a set of non-random, environmentally sensitive and termite-specific gut microbes from their colonies of origin. These symbionts transfer to offspring colony workers with high fidelity, after which priority effects appear to influence the composition of the establishing microbiome. Termite reproductives thus secure transmission of complex communities of specific, co-evolved microbes that are critical to their offspring colonies. Extensive yet imperfect inheritance implies that the maturing colony benefits from acquiring environmental microbes to complement combinations of termite, fungus and vertically transmitted microbes; a mode of transmission that is emerging as a prevailing strategy for hosts to assemble complex adaptive microbiomes.
Phylogenic characterization and antimicrobial resistance pattern of E.coli strains isolated from patients with urinary tract infection
Authors: Rigvava Sophio , Kusradze Ia , Karumidze Natia , Kharebava Shorena , Tatrishvili Nino , Goderdzishvili Marina
Published: October 2023

Uropathogenic Escherichia coli (UPEC) refers to strains of E.coli bacteria that specifically cause urinary tract infections (UTIs). UPEC is the most common cause of UTIs, accounting for approximately 80-90% of all cases. Treatment for UPEC UTIs typically involves a course of antibiotics, commonly prescribed antibiotics include trimethoprim-sulfamethoxazole, nitrofurantoin, and fluoroquinolones. Within the presented research, we studied 90 E. coli strains isolated during urinary-genital system infections and to determine the pathogroup, we tested each strain for the presence of uropathogenic E. coli (UPEC) specific genes. Of the 90 strains, 81 were identified as UPEC, interestingly, 29 strains had all three genes c3509, c3686 (yrbH) and chuA present, while 22 strains contained only one of the three genes. The majority of isolated UPEC strains belonged to B2-group -54 strains, and strains representing A, B1, F and clade I/II groups were also identified. 12 out of 90 strains could not be grouped. Antibiotic susceptibility testing of isolated bacteria showed that complete resistance to antibiotics was rare, only 2 strains showed resistance to 6 of the antibiotics, but retained sensitivity to nitrofuranthion. The results show that the strains isolated in Georgia in March-May 2022 are not characterized by broad antibiotic resistance, which is most important to those antibiotics that are prescribed for urological infections, only 3-3 of the 90 strains isolated from genitourinary system infections was found to be resistant but none of these strains were resistant to both antibiotics simultaneously.
PhysioFit: a software to quantify cell growth parameters and extracellular fluxes
Authors: Le Grégam Loïc , Guitton Yann , Bellvert Floriant , Heux Stéphanie , Jourdan Fabien , Portais Jean-Charles , Millard Pierre
Published: October 2023

Quantification of growth parameters and extracellular uptake and production fluxes is central in systems and synthetic biology. Fluxes can be estimated using various mathematical models by fitting time-course measurements of the concentration of cells and extracellular substrates and products. A single tool is available to non-computational biologists to calculate extracellular fluxes, but it is hardly interoperable and is limited to a single hard-coded growth model. We present our open-source flux calculation software, PhysioFit, which can be used with any growth model and is interoperable by design. PhysioFit includes some of the most common growth models, and advanced users can implement additional models to calculate extracellular fluxes and other growth parameters for metabolic systems or experimental setups that follow alternative kinetics. PhysioFit can be used as a Python library and offers a graphical user interface for intuitive use by end-users and a command-line interface to streamline integration into existing pipelines.

Availability and Implementation

PhysioFit is implemented in Python 3 and was tested on Windows, Unix and MacOS platforms. PhysioFit is also freely available online athttps://workflow4metabolomics.org. The source code, the data and the documentation are freely distributed under GPL3 license athttps://github.com/MetaSys-LISBP/PhysioFit/andhttps://physiofit.readthedocs.io/.
Scaling the fitness effects of mutations with respect to differentially adaptedArabidopsis thalianaaccessions under natural conditions
Authors: Stearns Frank W. , Zhou Juannan , Fenster Charles B.
Published: October 2023

Mutations are the ultimate source of genetic variation for natural selection to act upon. A major question in evolutionary biology is the extent to which new mutations can generate genetic variation under natural conditions to permit adaptive evolution over ecological time scales. Here we collected fitness data for chemically induced (ethylmethane sulfonate, EMS) mutant lines descended from twoArabidopsis thalianaecotypes that show differential adaptation to the local environment of our common garden plot. Using a novel nonparametric Bayesian statistical approach, we found that both ecotypes accumulated substantial proportions of beneficial mutations. The poorly adapted ecotype showed higher variance in the fitness effect of mutations than the well-adapted ecotype. Furthermore, we predict that it takes less than 4000 generations for the fitness space of the two ecotypes to overlap through mutation accumulation, and that a single founder, through mutation accumulation, is able to achieve the species-wide genetic variation in less than 10,000 generations. Our results provide evidence for relatively rapid local adaptation ofArabidopsis thalianain natural conditions through new mutations, as well as the utility of nonparametric Bayesian method for modeling the distribution of fitness effects for field-collected data.
Understanding structural and functional diversity of ATP-PPases using protein domains and functional families in CATH database
Authors: Waman Vaishali P. , Yin Jialin , Sen Neeladri , Firdaus-Raih Mohd , Lam Su Datt , Orengo Christine
Published: October 2023

ATP-Pyrophosphatases (ATP-PPases) are the most primordial lineage of the large and diverse HUP (HIGH-motif proteins,Universal Stress Proteins, ATP-Pyrophosphatase) superfamily. There are four different ATP-PPase substrate-specificity groups, and members of each group show considerable sequence variation across the domains of life despite sharing the same catalytic function. Over the past decade, there has been a >20-fold expansion in the number of ATP-PPase domain structures most recently from advances in protein structure prediction (e.g. Alphafold2). Using the enriched structural information, we have characterised the two most populated ATP-PPase substrate-specificity groups, the NAD-synthases (NAD) and GMP synthases (GMPS). We performed local structural and sequence comparisons between the NADS and GMPS from different domains of life and identified taxonomic-group specific structural functional motifs. As GMPS and NADS are potential drug targets of pathogenic microorganisms includingMycobacterium tuberculosis, structural motifs specific to bacterial GMPS and NADS provide new insights that may aid antibacterial-drug design.
Branching topology of the human embryo transcriptome revealed by entropy sort feature weighting
Authors: Radley Arthur , Smith Austin
Published: October 2023

Single cell transcriptomics (scRNA-seq) transforms our capacity to define cell states and reveal developmental trajectories. Resolution is challenged, however, by high dimensionality and noisy data. Analysis is therefore typically performed after sub-setting to highly variable genes (HVGs). However, existing HVG selection techniques have been found to have poor agreement with one another, and tend to be biased towards highly expressed genes. Entropy sorting provides an alternative mathematical framework for feature subset selection. Here we implement continuous entropy sort feature weighting (cESFW). On synthetic datasets, cESFW outperforms HVG selection in distinguishing cell state specific genes. We apply cESFW to six merged scRNA-seq datasets spanning human early embryo development. Without smoothing or augmenting the raw counts matrices, cESFW generates a high-resolution embedding displaying coherent developmental progression from 8-cell to post-implantation stages, delineating 15 distinct cell states. The embedding highlights sequential lineage decisions during blastocyst development while unsupervised clustering identifies branch point populations. Cells previously claimed to lack a developmental trajectory reside in the first branching region where morula differentiates into Inner Cell Mass (ICM) or Trophectoderm (TE). We quantify the relatedness of pluripotent stem cell cultures to embryo cell types and identify naïve and primed marker genes conserved across culture conditions and the human embryo. Finally, by identifying genes with specifically enriched and dynamic expression during blastocyst formation, we provide markers for staging lineage progression from morula to blastocyst. Together these analyses indicate that cESFW provides the ability to reveal gene expression dynamics in scRNA-seq data that HVG selection can fail to elucidate.
New Interactive Machine Learning Tool for Marine Image Analysis
Authors: Clark H. Poppy , Smith Abraham George , Fletcher Daniel Mckay , Larsson Ann I. , Jaspars Marcel , De Clippele Laurence H.
Published: October 2023

Due to advances in imaging technologies, the rate of marine video and image data collection is drastically increasing. Often these datasets are not analysed to their full potential as extracting information for multiple species, such as their presence and surface area, is incredibly time-consuming. This study demonstrates the potential of a new open-source interactive machine learning tool, RootPainter, to analyse large marine image datasets quickly and accurately. The tool was initially developed to measure plant roots, but here was tested on its ability to measure the presence and surface area of the cold-water coral reef associate sponge species,Mycale lingua, in two types of underwater image data: 18,346 time-lapse images and 1,420 remotely operated vehicle video frames. New corrective annotation metrics integrated with RootPainter, such as dice score and species area error, allow for the objective assessment of when to stop model training and reduce the need for manual model validation. Three highly accurateMycale linguamodels were created using RootPainter, as indicated by their average dice score of 0.94 ± 0.06. Model transfer and optimisation aided in the production of two of these models, increasing analysis efficiency from 6 to 16 times faster than manual annotation in Photoshop, for underwater observatory images. Sponge and surface area measurements were extracted from both datasets allowing future investigation of sponge behaviours and distributions. This study demonstrates that interactive machine learning tools and model sharing have the potential to dramatically increase image analysis speeds, collaborative research, and our collective knowledge on spatiotemporal patterns in biodiversity.
Engineering Regionally-Activated Drugs for Neuroscience
Authors: Huang Zhimin , Mitrofan Andrei , Nouraein Shirin , Horak Clark , Seo Joon Pyung , Harb Manwal , Jin Rongshu , Szablowski Jerzy O.
Published: October 2023

The brain is comprised of multiple regions performing distinct functions. Within each of these regions, there are multiple cell types that can affect brain physiology. Finally, within each cell there are multiple signaling pathways, that, when activated or inhibited, control the cell’s activity, and consequently the brain function. For these reasons, methods that can control the brain with regional, cell-type, and molecular precision have been widely used in neuroscience. However, so far, achieving sustained control over a brain region with that level of specificity relied either on gene delivery or placement of invasive devices. While gene therapy holds great promise, the risks of genomic integration, vector toxicity, vector-directed immune response, high cost, and gene delivery to the brain pose significant challenges. On the other hand, invasive devices enable site-specific delivery of drugs but can also surgically damage the modulated brain region, carrying risks of infection and hemorrhage. Here, we present a new approach that can provide multi-day, noninvasive, site-specific control over specific cell types in the brain without the need to use invasive devices or gene delivery. To achieve this, we introduce a new paradigm called Regionally Activated Interstitial Drugs, orRAID, which delivers a protein-based catalytic centers, or RAID enzymes, to the brain using focused ultrasound blood-brain barrier opening. This catalytic center is designed to attach to the interstitial space in the brain where it remains for days after initial delivery. While the catalytic center is present in the brain, it can locally process an inert BBB permeable prodrug into an active drug, resulting in localized therapy. Our proof-of concept studies demonstrated that the engineered RAID enzymes can retain activity in the brain parenchyma for several days, allowing for noninvasive site-specific induction of neuronal activity that was sufficiently potent to elicit behavioral effects. Overall, the RAID paradigm enabled noninvasive, tunable, temporally-re-solved, site-specific, non-genetic, neuromodulation over multiple days. The RAID paradigm is versatile and can be applied to any enzyme and prodrug pair to control various aspects of central nervous system physiology.
Low exposure to lithium does not induce nephrogenic diabetes insipidus but microcystic dilations of collecting ducts in a long-term rat model
Authors: Tabibzadeh Nahid , Klein Mathieu , Try Mélanie , Poupon Joël , Houillier Pascal , Klein Christophe , Cheval Lydie , Crambert Gilles , Lasaad Samia , Chevillard Lucie , Megarbane Bruno
Published: October 2023

Lithium induces nephrogenic diabetes insipidus (NDI) and microcystic chronic kidney disease (CKD). As clinical studies suggested that NDI is dose-dependent and CKD time-dependent, we investigated the effects of low exposure to lithium in a long-term rat model. Sprague-Dawley rats were randomly fed during six months with normal diet (controls), addition of lithium to diet, or addition of lithium and amiloride to diet, allowing reaching low steady-state plasma lithium concentrations (0.25±0.06 and 0.43±0.16 mmol/L, respectively). Exposure to low plasma lithium concentrations did not induce NDI but microcystic dilations of kidney tubules, identified as collecting ducts (CDs) using immunofluorescent staining. Both hypertrophy, characterized by an increase in the ratio of nuclei per tubular area, and microcystic dilations were observed. Principal cell-to-intercalated cell ratio was higher in dilated than in hypertrophied tubules. There was no correlation between aquaporin-2 mRNA levels and cellular remodelling of CDs. Amiloride/lithium co-administration did not allow significant consistent morphometric and cellular composition changes compared to lithium administration. To conclude, rat low exposure to lithium did not induce overt NDI but microcystic dilations of CDs, which include a marked alteration in cell composition of hypertrophied and dilated CDs, suggesting two distinct underlying pathophysiological mechanisms.
Protein condensate fusion mapping using Hippopede curve
Authors: Sahu Sumon , Ross Jennifer L.
Published: October 2023

Protein and nucleic acid condensation in cells has been a major focus of biophysical studies in recent years. Such droplets, condensates, or membraneless cellular organelles that form by condensation have been shown to behave like liquid or viscoelastic fluids. In vitro reconstitution of condensates of purified protein and nucleic acid have been used to better understand the phenomena, specifically to quantify the material properties of these condensates. One of the signature properties of a liquid-like condensate is the fusion of two round droplets into a larger droplet. Quantitative imaging and analysis of the fusion process can report the biophysical properties of the condensates, such as surface tension and viscosity in a non-invasive way. Here we take advantage of a model in soft matter physics, hippopede curves, to the condensate fusion problem to estimate these biophysical properties directly and compare the results with existing models in the field. In addition, this method approximates additional parameters such as the surface area and surface curvatures during the fusion process over time.
The transcription factor SpiB regulates Fibroblastic Reticular Cell network and CD8+T cell responses in lymph nodes
Authors: Horsnell Harry L , Cao Wang HJ , Belz Gabrielle T , Mueller Scott N , Alexandre Yannick O
Published: October 2023

Fibroblastic Reticular Cells (FRCs) construct microanatomical niches that support lymph node homeostasis and coordination of immune responses. Transcription factors regulating the functionality of FRCs remain poorly understood. Here we investigate the role of the transcription factor SpiB that is expressed in lymph node FRCs. Conditional ablation of SpiB in FRCs impaired the FRC network in the T cell zone of lymph nodes, leading to reduced numbers of FRCs and altered homeostatic functions including reduced CCL21 and interleukin-7 expression. The size and cellularity of lymph nodes remained intact in the absence of SpiB but the space between the reticular network increased, indicating that although FRCs were reduced in number they stretched to maintain network integrity. Following virus infection, antiviral CD8+T cell responses were impaired, suggesting a role for SpiB expression in FRCs in orchestrating immune responses. Together, our findings reveal a new role for SpiB as a critical regulator of FRC functions and immunity in lymph nodes.
Skeletal muscle BMAL1 is necessary for transcriptional adaptation of local and peripheral tissues in response to endurance exercise training
Authors: Viggars Mark R , Berko Hannah E , Hesketh Stuart J , Wolff Christopher A , Gutierrez-Monreal Miguel A , Martin Ryan A , Jennings Isabel G , Huo Zhiguang , Esser Karyn A
Published: October 2023

Objectives

In this investigation, we addressed the contribution of the core circadian clock factor, BMAL1, in skeletal muscle to both acute transcriptional responses to exercise and transcriptional remodelling in response to exercise training. Additionally, we adopted a systems biology approach to investigate how loss of skeletal muscle BMAL1 altered peripheral tissue homeostasis as well as exercise training adaptations in iWAT, liver, heart, and lung of male mice.

Methods

Combining inducible skeletal muscle specific BMAL1 knockout mice, physiological testing and standardized exercise protocols, we performed a multi-omic analysis (transcriptomics, chromatin accessibility and metabolomics) to explore loss of muscle BMAL1 on muscle and peripheral tissue responses to exercise.

Results

Muscle-specific BMAL1 knockout mice demonstrated a blunted transcriptional response to acute exercise, characterized by the lack of upregulation of well-established exercise responsive transcription factors includingNr4a3andPpargc1a. Six weeks of exercise training in muscle-specific BMAL1 knockout mice induced significantly greater and divergent transcriptomic and metabolomic changes in muscle. Surprisingly, liver, lung, inguinal white adipose and heart showed divergent exercise training transcriptomes with less than 5% of ‘exercise-training’ responsive genes shared for each tissue between genotypes.

Conclusion

Our investigation has uncovered the critical role that BMAL1 plays in skeletal muscle as a key regulator of gene expression programs for both acute exercise and training adaptations. In addition, our work has uncovered the significant impact that altered exercise response in muscle plays in the peripheral tissue adaptation to exercise training. We also note that the transcriptome adaptations to steady state training suggest that without BMAL1, skeletal muscle does not achieve the expected homeostatic program. Our work also demonstrates that if the muscle adaptations diverge to a more maladaptive state this is linked to increased inflammation across many tissues. Understanding the molecular targets and pathways contributing to health vs. maladaptive exercise adaptations will be critical for the next stage of therapeutic design for exercise mimetics.
Dual Ethanolamine Head Groups in Ionizable Lipids Facilitate Phospholipid-free Stable Nanoparticle Formulation for Augmented and Safer mRNA Delivery
Authors: Lu Jing , Jiang Ting , Li Xuechun , Tan Shudan , Zhang Yunsen , Gu Hao , Chen Lin , Guo Junxiang , Yu Rui , Zang Jieying , Ouyang Defang , Yu Hang , Yao Hongwei , Qiu Min , Lin Jinzhong
Published: October 2023

The accelerated advent of mRNA-based therapeutics and vaccines, highlighted by the battle against SARS-CoV-2, underscores the urgency to refine lipid nanoparticles (LNPs) for efficient mRNA delivery. In this work, we introduce a novel series of ionizable lipids characterized by double ethanolamine head groups, significantly amplifying mRNA binding affinity. A succinct three-component formulation is subsequently delineated, obviating the conventional dependency on phospholipids inherent in traditional four-component LNPs. Intriguingly, this formulation enables particle formation under neutral pH conditions, a notable departure from the acidic milieu traditionally required, attributable to the enhanced nonionic interactions predominating in mRNA encapsulation. The resultant particles exhibit exceptional stability, superior mRNA encapsulation efficiency, and maintain robust delivery efficacy. When deployed as a vaccine platform, the formulation elicited pronounced humoral and T-cell immune responses, concurrently exhibiting a favorable toxicity profile with a reduced induction of pro-inflammatory cytokines such as IL-6. Our exploration suggests that by fine-tuning the non-electrostatic interactions between the ionizable lipid and mRNA, the dynamics of particle formation can be considerably divergent from the prevailing paradigms of mRNA-LNP formation, hinting at a broader horizon for lipid optimization within the realm of mRNA delivery systems.
Cortactin interacts with αDystrobrevin-1 and regulates neuromuscular junction morphology
Authors: De Cicco Teresa , Pęziński Marcin , Wójcicka Olga , Rottner Klemens , Prószyński Tomasz J.
Published: October 2023

Background

Neuromuscular junctions allow for transmitting signals from the nervous system to skeletal muscles, triggering their contraction, and their proper organization is essential for breathing and voluntary movements. αDystrobrevin-1 is a cytoplasmic component of the dystrophin-glycoprotein complex and has pivotal functions in regulating the integrity of muscle fibres and neuromuscular junctions. Previous studies identified that αDystrobrevin-1 functions in the organization of the neuromuscular junction and that its phosphorylation in the C-terminus is required in this process.

Methods

We used synthetic peptides corresponding to the phosphorylated tyrosine Y730 at the C-terminal part of αDystrobrevin-1 to precipitate interacting proteins from homogenate of differentiated muscle cells. Isolated proteins were identified by mass spectrometry, and co-immunoprecipitation and bimolecular fluorescence complementation experiments in skeletal muscles were used to validate interactions. We used immunohistochemical analysis and muscle electroporation to study cortactin localization in skeletal muscles. To study the function of cortactin in the neuromuscular system, we used cortactin KO mice. Synaptic morphology was studied using unbiased automatic image analysis, and muscle strength was assessed in grip-strength experiments and an animal’s ability to run on voluntary wheels and a treadmill.

Results

Our proteomic screen identified a number of putative αDystrobrevin-1 interactors recruited to the Y730 site in both its phosphorylated and unphosphorylated state. Amongst various actin regulators, we identified the Arp2/3 complex regulator cortactin. We showed that similarly to αDystrobrevin-1, cortactin is strongly enriched at the neuromuscular postsynaptic machinery and obtained results suggesting that these two proteins interact in cell homogenates and at the neuromuscular junctions. Analysis of synaptic morphology cortactin knockout mice showed abnormalities in the slow-twitching soleus muscle and not in the fast-twitching tibialis. However, muscle strength examination did not reveal apparent deficits in knockout animals.

Conclusions

Our studies identified cortactin as a novel interactor of the dystrophin-glycoprotein complex, pivotal in maintaining muscle and neuromuscular junction integrity. We have shown that cortactin is a novel postsynaptic machinery component that can be essential in organizing the neuromuscular junctions.
Cross-sector collaboration is more effective than single sector actions at mitigating SARS-CoV-2 in white-tailed deer
Authors: Cook Jonathan D. , Rosenblatt Elias , Direnzo Graziella , Campbell Grant Evan H. , Mosher Brittany A. , Arce Fernando , Christensen Sonja , Ghai Ria R. , Runge Michael C.
Published: October 2023

One Health helps achieve optimal health outcomes for people, animals, plants, and their shared environments. We describe a multidisciplinary effort to better understand and mitigate SARS-CoV-2 spread in white-tailed deer across One Health sectors. We first framed the risk problem with three governance sectors that manage captive and wild deer and human public health. The framing included the objectives for each sector, interactions that facilitate human-to-deer and deer-to-deer transmission, and alternatives intended to reduce risk. We then developed a dynamic compartmental model that linked wild and captive deer herds and humans and simulated SARS-CoV-2 dynamics. For baseline conditions, we estimated that median SARS-CoV-2 prevalence in wild and captive herds varied between 0.03 – 0.07, incidence between 0.68 – 1.46, and probability of persistence between 0.64 – 0.97 across 120-day simulations. We then tested single-sector alternatives alone and in combination with other sector actions. We found that single sector alternatives varied in their ability to reduce transmission and that the best performing alternative required collaborative actions among wildlife management, agricultural management, and public health agencies.
Transformation of neural coding for vibrotactile stimuli along the ascending somatosensory pathway
Authors: Lee Kuo-Sheng , Loutit Alastair , de Thomas Wagner Dominica , Sanders Mark , Prsa Mario , Huber Daniel
Published: October 2023

Perceiving substrate vibrations is a fundamental component of somatosensation. In mammals, action potentials fired by rapidly adapting mechanosensitive afferents are known to reliably time lock to the cycles of a vibration. This stands in contrast to coding in the higher-order somatosensory cortices, where neurons generally encode vibrations in their firing rates, which are tuned to a preferred vibration frequency. How and where along the ascending neuraxis is the peripheral afferent temporal code of cyclically entrained action potentials transformed into a rate code is currently not clear. To answer this question, we probed the encoding of vibrotactile stimuli with electrophysiological recordings along major stages of the ascending somatosensory pathway in mice. Recordings from individual primary sensory neurons in lightly anesthetized mice revealed that rapidly adapting mechanosensitive afferents innervating Pacinian corpuscles display phase-locked spiking for vibrations up to 2000 Hz. This precise temporal code was reliably preserved through the brainstem dorsal column nuclei. The main transformation step was identified at the level of the thalamus, where we observed a significant loss of phase-locked spike timing information accompanied by a further narrowing of tuning curve widths. Using optogenetic manipulation of thalamic inhibitory circuits, we found that parvalbumin-positive interneurons in thalamic reticular nucleus participate in sharpening frequency selectivity and disrupting the precise spike timing of ascending neural signals encoding vibrotactile stimuli. To test the functional implications of these different neural coding mechanisms, we applied frequency-specific microstimulation within the brainstem, which generated frequency selectivity reminiscent of real vibration responses in the somatosensory cortex, whereas microstimulation within thalamus did not. Finally, we applied microstimulation in the brainstem of behaving mice and demonstrated that frequency-specific stimulation could provide informative and robust signals for learning. Taken together, these findings not only reveal novel features of the computational circuits underlying vibrotactile sensation, but could also guide biomimetic stimulus strategies to activate specific nuclei along the ascending somatosensory pathway for sensory neural prostheses.
Identifying summary statistics for approximate Bayesian computation in a phylogenetic island biogeography model
Authors: Xie Shu , Valente Luis , Etienne Rampal S.
Published: October 2023

Estimation of parameters of evolutionary island biogeography models, such as colonization and diversification rates, is important for a better understanding of island systems. A popular statistical inference framework is likelihood-based estimation of parameters using island species richness and phylogenetic data. Likelihood approaches require that the likelihood can be computed analytically or numerically, but with the increasing complexity of island biogeography models, this is often unfeasible. Simulation-based estimation methods may then be a promising alternative. One such method is approximate Bayesian computation (ABC), which compares summary statistics of the empirical data with the output of model simulations. However, ABC demands the definition of summary statistics that sufficiently describe the data, which is yet to be explored in island biogeography. Here, we propose a set of summary statistics and use it in an ABC framework for the estimation of parameters of an island biogeography model, DAISIE (Dynamic Assembly of Island biota through Speciation, Immigration and Extinction). For this model, likelihood-based inference is possible, which gives us the opportunity to assess the performance of the summary statistics. DAISIE currently only allows maximum likelihood estimation (MLE), so we additionally develop a likelihood-based Bayesian inference framework using Markov Chain Monte Carlo (MCMC) to enable comparison with the ABC results (i.e., making the same assumptions on prior distributions). We simulated phylogenies of island communities subject to colonization, speciation, and extinction using the DAISIE simulation model and compared the estimated parameters using the three inference approaches (MLE, MCMC and ABC). Our results show that the ABC algorithm performs well in estimating colonization and diversification rates, except when the species richness or amount of phylogenetic information from an island are low. We find that compared to island species diversity statistics, summary statistics that make use of phylogenetic and temporal patterns (e.g., the number of species through time) significantly improve ABC inference accuracy, especially in estimating colonization and anagenesis rates, as well as making inference converge considerably faster and perform better under the same number of iterations. Island biogeography is rapidly developing new simulation models that can explain the complexity of island biodiversity, and our study provides a set of informative summary statistics that can be used in island biogeography studies for which likelihood-based inference methods are not an option.
Genome-wide meta-analysis conducted in three large biobanks expands the genetic landscape of lumbar disc herniations
Authors: Salo Ville , Määttä Juhani , Sliz Eeva ,   FinnGen, Reimann Ene , Mägi Reedik ,   Estonian Biobank Research Team, Reis Kadri , Elhanas Abdelrahman G. , Reigo Anu , Palta Priit , Esko Tõnu , Karppinen Jaro , Kettunen Johannes
Published: October 2023

Introductory paragraph

Given that lumbar disc herniation (LDH) is a prevalent spinal condition that causes significant individual suffering and societal costs1, the genetic basis of LDH has received relatively little research. Our aim was to increase understanding of the genetic factors influencing LDH. We performed a genome-wide association analysis (GWAS) of LDH in the FinnGen project and in Estonian and UK biobanks, followed by a genome-wide meta-analysis to combine the results. In the meta-analysis, we identified 41 loci that have not been associated with LDH in prior studies on top of the 23 known risk loci. We detected LDH-associated loci in the vicinity of genes related to inflammation, disc-related structures, and synaptic transmission. Overall, our research contributes to a deeper understanding of the genetic factors behind LDH, potentially paving the way for the development of new therapeutics, prevention methods, and treatments for symptomatic LDH in the future.
Comprehensive Identification of Pathogenic Microbes and Antimicrobial Resistance Genes in Food Products Using Nanopore Sequencing-Based Metagenomics
Authors: Lee Annie Wing-Tung , Ng Iain Chi-Fung , Wong Evelyn Yin-Kwan , Wong Ivan Tak-Fai , Sze Rebecca Po-Po , Chan Kit-Yu , So Tsz-Yan , Zhang Zhipeng , Fung Sharon Ka-Yee , Wong Sally Choi-Ying , Tam Wing-Yin , Lao Hiu-Yin , Lee Lam-Kwong , Leung Jake Siu-Lun , Chan Chloe Toi-Mei , Ng Timothy Ting-Leung , Chow Franklin Wang-Ngai , Leung Polly Hang-Mei , Siu Gilman Kit-Hang
Published: October 2023

Foodborne pathogens, particularly antimicrobial-resistant (AMR) bacteria, remain a significant threat to global health. Conventional culture-based approaches for detecting infectious agents are limited in scope and time-consuming. Metagenomic sequencing of food products offers a rapid and comprehensive approach to detect pathogenic microbes, including AMR bacteria. In this study, we used nanopore-based metagenomic sequencing to detect pathogenic microbes and antimicrobial resistance genes (ARGs) in 260 food products, including raw meat, sashimi, and ready-to-eat (RTE) vegetables. We identifiedClostridium botulinumandStaphylococcus aureusas the predominant foodborne pathogens in the food samples, particularly prevalent in fresh, peeled, and minced foods. Importantly, RTE-vegetables, which harboredAcinetobacter baumanniiandToxoplasma gondiias the dominant foodborne pathogens, displayed the highest abundance of carbapenem resistance genes among the different food types. ExclusiveblaCTX-Mgene-carrying plasmids were found in both RTE-vegetables and sashimi. Additionally, we assessed the impact of host DNA and sequencing depth on microbial profiling and ARG detection, highlighting the preference for nanopore sequencing over Illumina for ARG detection. A lower sequencing depth of around 25,000 is adequate for effectively profiling bacteria in food samples, whereas a higher sequencing depth of approximately 700,000 is required to detect ARGs. Our workflow provides insights into the development of food safety monitoring tools and can assess the potential risk to human health from foodborne pathogens and ARGs. This approach has the potential to revolutionize the screening of food products and enable more efficient and accurate detection of foodborne pathogens and ARGs, thereby reducing the risks of foodborne illness and improving public health.
ZHX2 alleviates vascular remodeling and smooth muscle cell proliferation by transcriptional regulation of GADD45G
Authors: Fan Siyuan , Yang Liuye , Wu Xuelian , Wu Yichen , Wang Pengchao , Qiao Baoru , Li Yue , Huang Kai , Zheng Zhe
Published: October 2023

Objective

This study explores the role of ZHX2 in vascular remodeling, specifically focusing on its effects on VSMC proliferation, migration, and neointima formation following vascular injury. Methods and Results: Data from both human atherosclerotic samples and a mouse carotid injury model indicated a decrease in ZHX2 levels.In vivo, ZHX2 overexpression reduced neointima formation in mice subjected to carotid artery ligation.In vitro, ZHX2 inhibited the proliferation and migration of primary VSMCs. Conversely, specific knockout of ZHX2 in SMCsin vivoor knockdown of ZHX2 in primary VSMCs had opposite effects. RNA- seq analysis revealed that ZHX2 overexpression significantly affected the expression of cell cycle-related genes. Using Chromatin Immunoprecipitation Sequencing (ChIP-seq) and luciferase reporter assays, we demonstrated that ZHX2 plays a crucial role in the transcriptional regulation of GADD45G, identifying GADD45G as the downstream target responsible for ZHX2-mediated effects. Conclusions: ZHX2 emerges as a key player in pathological vascular remodeling, suppressing VSMC proliferation and migration through its regulatory impact on GADD45G transcription and cell cycle-related gene expression.
The guide RNA sequence dictates the slicing kinetics and conformational dynamics of the Argonaute silencing complex
Authors: Wang Peter Y. , Bartel David P.
Published: October 2023

The RNA-induced silencing complex (RISC), which powers RNA interference (RNAi), consists of a guide RNA and an Argonaute protein that slices target RNAs complementary to the guide. We find that for different guide-RNA sequences, slicing rates of perfectly complementary, bound targets can be surprisingly different (>250-fold range), and that faster slicing confers better knockdown in cells. Nucleotide sequence identities at guide-RNA positions 7, 10, and 17 underlie much of this variation in slicing rates. Analysis of one of these determinants implicates a structural distortion at guide nucleotides 6–7 in promoting slicing. Moreover, slicing directed by different guide sequences has an unanticipated, 600-fold range in 3′-mismatch tolerance, attributable to guides with weak (AU-rich) central pairing requiring extensive 3′ complementarity (pairing beyond position 16) to more fully populate the slicing-competent conformation. Together, our analyses identify sequence determinants of RISC activity and provide biochemical and conformational rationale for their action.

HIGHLIGHTS

Sequence of guide RNA can alter slicing rate of fully paired substrate by 250-fold

Sequences that cause more rapid slicing direct more efficient RNAi in cells

Strong central pairing imparts tolerance for mismatches to the guide 3′ region

This tolerance is attributable to more fully populating the slicing conformation