bluuebunny/crossref_metadata_2025 huggingface dataset:
A statistical genetics guide to identifying HLA alleles driving complex disease
Authors: Sakaue Saori , Gurajala Saisriram , Curtis Michelle , Luo Yang , Choi Wanson , Ishigaki Kazuyoshi , Kang Joyce B. , Rumker Laurie , Deutsch Aaron J. , Schönherr Sebastian , Forer Lukas , LeFaive Jonathon , Fuchsberger Christian , Han Buhm , Lenz Tobias L. , de Bakker Paul I. W. , Smith Albert V. , Raychaudhuri Soumya
Published: August 2022

The human leukocyte antigen (HLA) locus is associated with more human complex diseases than any other locus. In many diseases it explains more heritability than all other known loci combined. Investigators have now demonstrated the accuracy of in silico HLA imputation methods. These approaches enable rapid and accurate estimation of HLA alleles in the millions of individuals that are already genotyped on microarrays. HLA imputation has been used to define causal variation in autoimmune diseases, such as type I diabetes, and infectious diseases, such as HIV infection control. However, there are few guidelines on performing HLA imputation, association testing, and fine-mapping. Here, we present comprehensive statistical genetics guide to impute HLA alleles from genotype data. We provide detailed protocols, including standard quality control measures for input genotyping data and describe options to impute HLA alleles and amino acids including a web-based Michigan Imputation Server. We updated the HLA imputation reference panel representing global populations (African, East Asian, European and Latino) available at the Michigan Imputation Server (n = 20,349) and achived high imputation accuracy (mean dosage correlation r = 0.981). We finally offer best practice recommendations to conduct association tests in order to define the alleles, amino acids, and haplotypes affecting human traits. This protocol will be broadly applicable to the large-scale genotyping data and contribute to defining the role of HLA in human diseases across global populations.
DBERlibR: Automated Data Analysis for Discipline-Based Education Research
Authors: Song Changsoo , Helikar Resa , Smith Wendy M. , Helikar Tomáš
Published: August 2022

Discipline-Based Education Research (DBER) scientists repeatedly analyze assessment data to ensure question items’ reliability and examine the efficacy of a new educational intervention. Analyzing assessment data comprises multiple steps and statistical techniques that consume much of researchers’ time and are error-prone. While education research continues to grow across many disciplines of science, technology, engineering, and mathematics (STEM), the DBER community lacks tools to streamline education research data analysis. DBERlibR—an R package to streamline and automate DBER data processing and analysis—fills this gap. The package reads user-provided assessment data, cleans them, merges multiple datasets (as necessary), checks assumption(s) for specific statistical techniques (as necessary), applies various statistical tests (e.g., one-way analysis of covariance, one-way repeated-measures analysis of variance), and presents and interprets the results all at once. By providing the most frequently used analytic techniques, this package will contribute to DBER by facilitating the creation and widespread use of evidence-based knowledge and practices. The outputs contain a sample interpretation of the results for users’ convenience. User inputs are minimal; they only need to prepare the data files as instructed and type a function in RStudio to conduct a specific data analysis.
Premorbid performances determine the deleterious effects of nigrostriatal degeneration and pramipexole on behavioural flexibility
Authors: Decourt Mélina , Balado Eric , Francheteau Maureen , Solinas Marcello , Benoît-Marand Marianne , Fernagut Pierre-Olivier
Published: August 2022

Subtle cognitive impairment can occur early in the course of Parkinson’s disease (PD) and may manifest under different forms of executive dysfunction such as impaired cognitive flexibility. The precise contribution of nigrostriatal dopaminergic neurodegeneration to these non-motor features of the disease is poorly known. Whether such cognitive impairment associated with the disease process may also predate and contribute to the development of neuropsychiatric side-effects following dopamine replacement therapy remains largely unknown. To address these issues, we investigated the respective contributions of nigrostriatal degeneration and chronic treatment with the dopamine D3-preferring agonist pramipexole on behavioural flexibility in a rat model of PD. Flexible, intermediate and inflexible rats were identified based on baseline assessment of behavioural flexibility using an operant set-shifting task. Nigrostriatal degeneration was induced by bilateral viral-mediated expression of A53T mutated human α-synuclein in the substantia nigra pars compacta and behavioural flexibility was assessed after induction of nigrostriatal degeneration, and during chronic pramipexole treatment. Nigrostriatal degeneration impaired behavioural flexibility in flexible but not in inflexible rats. Pramipexole induced a decrease of behavioural flexibility that was exacerbated in lesioned rats and in the most flexible individuals. Furthermore, the deficits induced by pramipexole in lesioned rats affected different components of the task between flexible and inflexible individuals. This study demonstrates that nigrostriatal degeneration and pramipexole unequally impair behavioural flexibility, suggesting that the susceptibility to develop non-motor impairments upon treatment initiation could primarily depend on premorbid differences in behavioural flexibility.
Glioblastoma is associated with extensive accelerated brain ageing
Authors: Ainslie Anna P. , Klaver Myrthe , Voshart Daniëlle C. , Gerrits Emma , Eggen Bart J.L. , Bergink Steven , Barazzuol Lara
Published: August 2022

Progressive neurocognitive dysfunction is the leading cause of a reduced quality of life in patients with primary brain tumours. Understanding the mechanisms underlying cognitive impairments that occur in response to a brain tumour and its treatment is essential to improve patients’ quality of life. Here, we show that normal-appearing non-tumour brain regions of patients with glioblastoma display hallmarks of accelerated ageing and share multiple features with Alzheimer’s disease patients. Integrated transcriptomic and tissue analysis shows that normal-appearing brain tissue from glioblastoma patients has a significant overlap with brain tissue from Alzheimer’s disease patients, revealing shared mitochondrial and neuronal dysfunction, and proteostasis deregulation. Overall, the brain of glioblastoma patients undergoes Alzheimer’s disease-like accelerated ageing, providing novel or repurposed therapeutic targets for managing brain cancer-related side effects.
Eyeball translations affect saccadic eye movements beyond brainstem control
Authors: Kirchner Johannes , Watson Tamara , Bauer Jochen , Lappe Markus
Published: August 2022

Vision requires that we rotate our eyes frequently to look at informative structures in the scene. Eye movements are planned by the brain but their execution depends on the mechanical properties of the oculomotor plant, i.e, the arrangement of eyeball position, muscle insertions and pulley locations. Therefore, the biomechanics of rotations is sensitive to eyeball translation because it changes muscle levers. Eyeball translations are little researched as they are difficult to measure with conventional techniques. Here we study the effects of eyeball translation on the coordination of gaze rotation by high-speed MRI recordings of saccadic eye movements during blinks, which are known to produce strong translations. We found that saccades during blinks massively overshoot their targets, and that these overshoots occur in a transient fashion such that the eye is back on target at the time the blink ends. These dynamic overshoots were tightly coupled to the eyeball translation, both in time and in size. Saccades made without blinks were also accompanied by small amounts of transient eyeball retraction, the size of which scaled with saccade amplitude. These findings demonstrate the complex interaction between rotation and translation movements of the eye. The mechanical consequences of eyeball translation on oculomotor control should be considered along with the neural implementation in the brain to understand the generation of eye movements and their disorders.
Task-uninformative visual stimuli improve auditory spatial discrimination: the ambiguous contribution of relative reliability
Authors: Cappelloni Madeline S. , Shivkumar Sabyasachi , Haefner Ralf M. , Maddox Ross K.
Published: August 2022

The brain combines information from multiple sensory modalities to interpret the environment. These processes, collectively known as multisensory integration, have been modeled as Bayesian causal inference, which proposes that perception involves the combination of information from different sensory modalities based on their reliability and their likelihood of stemming from the same causes in the outside world. Bayesian causal inference has explained a variety of multisensory effects in simple tasks but is largely untested in complex sensory scenes where multisensory integration can provide the most benefit. Recently, we presented data challenging the ideal Bayesian model from a new auditory spatial discrimination task in which spatially aligned visual stimuli improve performance despite providing no information about the correct response. Here, we tested the hypothesis that, despite deviating from the ideal observer, the influence of task-uninformative stimuli was still dependent on the reliabilities of auditory and visual cues. We reasoned shorter stimulus durations should lead to less reliable auditory spatial encoding, and hence stronger effects of more reliable visual cues, which are easily localized even at short durations. While our results replicated the effect from our previous study across a wide range of stimulus durations, we did not find a significant increase in effect size with shorter stimuli, leaving our principal question not fully answered.
Perturbations of the T-cell immune repertoire in kidney transplant rejection
Authors: Sigdel Tara K. , Fields Paul A. , Liberto Juliane , Damm Izabella , Kerwin Maggie , Hood Jill , Towfighi Parhom , Sirota Marina , Robins Harlan S. , Sarwal Minnie M. ,   the CMV Systems Immunobiology Group
Published: August 2022

In this cross-sectional and longitudinal analysis of mapping the T-cell repertoire in kidney transplant recipients, we have investigated and validated T-cell clonality, immune repertoire chronology at rejection, and contemporaneous allograft biopsy quantitative tissue injury, to better understand the pathobiology of acute T cell and antibody-mediated kidney transplant rejection. To follow the dynamic evolution of T-cell repertoire changes before and after engraftment and during biopsy-confirmed acute rejection, we sequenced 323 peripheral blood samples from 200 unique kidney transplant recipients, with (n=100) and without (n=100) biopsyconfirmed acute rejection. The results of these studies highlight, for the first time, that patients who develop acute allograft rejection, have lower (p=0.01) T cell fraction even before transplantation, followed by its rise after transplantation and at the time of acute rejection accompanied by high TCR repertoire turnover (p=0.004). Acute rejection episodes occurring after the first 6 months post-transplantation, and those with a component of antibody-mediated rejection, had the highest turnover; p=0.0016) of their TCRs. In conclusion, further prospective validation studies are needed to evaluate the clinical utility of peripheral blood TCR analysis for both pre- and post-transplant immune risk assessment and prediction of different mechanisms of graft rejection.
A small-molecule lycorine derivative reveals Na+/K+-ATPase α3 as an anti-obesity target
Authors: Zhou Yunfu , Zhang Henan , Chen Duozhi , Chen Zhangcheng , Li Yongtao , Tian Chenyang , Zhang Cong , Li Cen , Chang Boran , Zeng Rong , Li Jinsong , Song Xiaomin , Chen Yan , Hao Xiaojiang , Li Lin
Published: August 2022

Obesity poses a global public health challenge and there is a huge unmet medical need for effective and safe anti-obesity therapeutics. Here, we discovered a small-molecule lycorine derivative designated as HLY72 that could potently promote lipolysis and reduce body weight in mice. Further study revealed that Na+/K+-ATPase α3 is the target of HLY72, and the Na+/K+-ATPase inhibitor digitoxin, but not istaroxime which could not go through blood-brain barrier, exhibits similar activities of reducing food intake and promoting lipolysis as HLY72 does in mice. Consistent with these findings, in knockin mice with a digitoxin-binding mutation T807C in Na+/K+-ATPase α3, but not in α1 gene, both digitoxin and HLY72 lose their activities. Furthermore, either chemical inhibition by HLY72 or genetic inhibition by T807C mutation of Na+/K+-ATPase α3 could effectively protect mice from diet-induced obesity. Therefore, we uncovered a previously unknown function of Na+/K+-ATPase α3 in the regulation of lipolysis and energy balance; and revealed a potential treatment and prevention strategy for obesity by targeting Na+/K+-ATPase α3.
High-Resolution 3D Ultra-Short Echo Time MRI with Rosette k-Space Pattern for Brain Iron Content Mapping
Authors: Shen Xin , Özen Ali Caglar , Monsivais Humberto , Sunjar Antonia , Ilbey Serhat , Zheng Wei , Du Yansheng , Chiew Mark , Emir Uzay
Published: August 2022

Background

The iron concentration increases during normal brain development and is identified as a risk factor for many neurodegenerative diseases, it is vital to monitor iron content in the brain non-invasively.

Purpose

This study aimed to quantify in vivo brain iron concentration with a 3D rosette-based ultra-short echo time (UTE) magnetic resonance imaging (MRI) sequence.

Methods

A cylindrical phantom containing nine vials of different iron concentrations (iron (II) chloride) from 0.5 millimoles to 50 millimoles and six healthy subjects were scanned using 3D high-resolution (0.94×0.94×0.94 mm3) rosette UTE sequence at an echo time (TE) of 20 μs.

Results

Iron-related hyperintense signals (i.e., positive contrast) were detected based on the phantom scan, and were used to establish an association between iron concentration and signal intensity. The signal intensities from in vivo scans were then converted to iron concentrations based on the association. The deep brain structures, such as the substantia nigra, putamen, and globus pallidus, were highlighted after the conversion, which indicated potential iron accumulations.

Conclusion

This study suggested that T1-weighted signal intensity could be used for brain iron mapping.
Cerebellar climbing fibers convey behavioral information of multiplex modalities and form functional modules
Authors: Ikezoe Koji , Hidaka Naoki , Manita Satoshi , Murakami Masayoshi , Tsutsumi Shinichiro , Isomura Yoshikazu , Kano Masanobu , Kitamura Kazuo
Published: August 2022

Cerebellar climbing fibers (CFs) convey sensorimotor information and their errors, which are used for motor control and learning. Furthermore, they represent reward-related information. Despite such functional diversity of CF signals, it is still unclear whether each CF conveys the information of single or multiple modalities and how the CFs conveying different information are distributed over the cerebellar cortex. We performed two-photon calcium imaging from cerebellar Purkinje cells (PCs) in mice engaged in a voluntary forelimb lever-pull task and demonstrated that CF responses in 93% of PCs could be explained by the combination of multiple behavioral variables, such as lever movement, licking, and reward delivery. Neighboring PCs exhibited similar CF response properties, formed functional clusters, and shared noise fluctuations of responses. Taken together, individual CFs convey behavioral information on multiplex variables and are spatially organized into the functional modules of the cerebellar cortex.
Climate and land-use shape the spread of zoonotic yellow fever virus
Authors: Hill Sarah C. , Dellicour Simon , Claro Ingra M. , Sequeira Patricia C. , Adelino Talita , Thézé Julien , Wu Chieh-Hsi , Rebello Moreira Filipe Romero , Giovanetti Marta , Li Sabrina L. , de Jesus Jaqueline G. , Colón-González Felipe J. , Chamberlain Heather R. , Pannell Oliver , Tejedor-Garavito Natalia , de Bruycker-Nogueira Fernanda , Fabri Allison A. , Angélica Mares-Guia Maria , Xavier Joilson , Zarebski Alexander E. , Hamlet Arran , Mureb Sallum Maria Anice , da Costa Antonio C. , Manuli Erika R. , Levin Anna S. , Mucci Luís Filipe , Tubaki Rosa Maria , de Menezes Regiane Maria Tironi , de Deus Juliana Telles , Spinola Roberta , Saad Leila , Kallas Esper G. , Wint G.R. William , Peixoto Pedro S. , de Souza Santos Andreza Aruska , Messina Jane P. , Brady Oliver J. , Tatem Andrew J. , Suchard Marc A. , Mendez-Rico Jairo A. , Abreu André , Aguiar Renato Santana , Pybus Oliver G. , Baele Guy , Lemey Philippe , Iani Felipe , Cunha Mariana S. , de Filippis Ana M. Bispo , Sabino Ester C. , Faria Nuno R.
Published: August 2022

Zoonotic viruses that originate in wildlife harm global human health and economic prosperity1. Understanding virus transmission at the human-animal-environment interface is a key component of pandemic risk-reduction2,3. Zoonotic disease emergence is highest in biodiverse, tropical forests undergoing intensive land-use change4,5. Phylodynamic analyses of virus genomes can powerfully test epidemiological hypotheses, but are rarely applied to viruses of animals inhabiting these habitats. Brazil’s densely-populated Atlantic Forest and Cerrado region experienced in 2016–2021 an explosive human outbreak of sylvatic yellow fever, caused by repeated virus spillover from wild neotropical primates6. Here we use yellow fever virus (YFV) genome sequences and epidemiological data from neotropical primates, humans, and mosquito vectors to identify the environmental, demographic, and climatic factors determining zoonotic virus spread. Using portable sequencing approaches we generated 498 YFV genomes, resulting in a well-sampled dataset of zoonotic virus genomes sampled from wild mammals. YFV dispersal velocity was slower at higher elevation, in colder regions, and further away from main roads. Virus lineage dispersal was more frequent through wetter areas, areas with high neotropical primate density and through landscapes covered by mosaic vegetation. Higher temperatures were associated with higher virus effective population sizes, and peaks of transmission in warmer, wetter seasons were associated with higher virus evolutionary rates. Our study demonstrates how zoonotic disease transmission is linked to land-use and climate, underscoring the need for One-Health approaches to reducing the rate of zoonotic spillover.
Multisystem Inflammatory Syndrome in Children Managed in the Outpatient Setting: An EHR-based cohort study from the RECOVER program
Authors: Jhaveri Ravi , Webb Ryan , Razzaghi Hanieh , Schuchard Julia , Mejias Asuncion , Bennett Tellen D. , Jone Pei-Ni , Thacker Deepika , Schulert Grant S. , Rogerson Colin , Cogen Jonathan D. , Bailey L. Charles , Forrest Christopher B. , Lee Grace M. , Rao Suchitra
Published: August 2022

Using electronic health record data combined with primary chart review, we identified 7 children across 8 pediatric medical centers with a diagnosis of Multisystem Inflammatory Syndrome in Children (MIS-C) who were managed as outpatients. These findings should prompt a discussion about modifying the case definition to allow for such a possibility.
Deep Learning Restores Speech Intelligibility in Multi-Talker Interference for Cochlear Implant Users
Authors: Borjigin Agudemu , Kokkinakis Kostas , Bharadwaj Hari M. , Stohl Joshua S.
Published: August 2022

Cochlear implants (CIs) fail to provide the same level of benefit in noisy settings as in quiet. Current noise reduction solutions in hearing aids and CIs only remove predictable, stationary noise, and are ineffective against realistic, non-stationary noise such as multi-talker interference. Recent developments in deep neural network (DNN) models have achieved noteworthy performance in speech enhancement and separation. However, little work has investigated the potential of DNN models in removing multi-talker interference. The research in this regard is even more scarce for CIs. Here, we implemented two DNN models that are well suited for applications in speech audio processing, including (1) recurrent neural network (RNN) and (2) SepFormer. The models were trained with a dataset developed in house (∼30 hours), and then tested with thirteen CI listeners. Both RNN and SepFormer models significantly improved CI listener’s speech intelligibility in noise without compromising the perceived quality of speech. These models not only increased the intelligibility in stationary non-speech noise, but also introduced substantiallymoreimprovements in non-stationaryspeechnoise, where conventional signal processing strategies fall short with little benefits. These results show the promise of using DNN models as a solution for listening challenges in multi-talker noise interference.
Archaic humans have contributed to large-scale variation in modern human T cell receptor genes
Authors: Corcoran Martin , Chernyshev Mark , Mandolesi Marco , Narang Sanjana , Kaduk Mateusz , Sundling Christopher , Färnert Anna , Bernhardsson Carolina , Larena Maximilian , Jakobsson Mattias , Karlsson Hedestam Gunilla B.
Published: August 2022

The human T cell receptor (TCR) genes are critical for mediating immune responses to pathogens, tumors and regulating self-antigen recognition. A detailed analysis and validation of expressed TCR alpha, beta, gamma, and delta genes in 45 donors from 4 human populations: African, East Asian, South Asian, and European, revealed a total of 175 novel TCR variable and junctional alleles. The majority of novel alleles contained coding changes and were present at widely differing frequencies in the populations, a finding confirmed using DNA samples and sequences from the 1000 Genomes Project. Importantly, we identified three Neanderthal-derived, introgressed TCR regions, including a highly divergent novel TRGV4 variant, present in all archaic assemblies, that was frequent in all modern Eurasian population groups. Our results demonstrate significant variation in TCR genes at both individual and population levels, providing a strong incentive for including allelic variation in studies of TCR function in human biology.
Rapid specification of human pluripotent stem cells to functional astrocytes
Authors: Lendemeijer B. , Unkel M. , Mossink B. , Hijazi S. , Sampedro S.G. , Shpak G. , Slump D.E. , van den Hout M.C.G.N. , van IJcken W.F.J. , Bindels E.M.J. , Hoogendijk W.J.G. , Nadif Kasri N. , de Vrij F.M.S. , Kushner S.A.
Published: August 2022

Astrocytes are essential for the formation and maintenance of neural networks through metabolic support, facilitation of synaptic function, and optimization of electrophysiological activity. However, a major technical challenge for investigating astrocyte function and disease-related pathophysiology has been the limited ability to obtain functional human astrocytes. Here we present a novel method to efficiently differentiate human pluripotent stem cell (hPSC)-derived neural progenitors to functional astrocytes in 28 days using a culture medium containing leukemia inhibitory factor (LIF) and bone morphogenetic protein 4 (BMP4). This approach yields highly pure populations of astrocytes expressing canonical astrocyte markers, which we confirmed by immunofluorescence, flow cytometry and RNA sequencing. Human PSC-derived astrocytes efficiently buffer glutamate and robustly support neural network activity. Co-cultures of hPSC-derived astrocytes and neurons on multi-electrode arrays generated robust network activity within 2 days and synchronous network bursts after 6 days. Whole cell patch-clamp recordings revealed an increased frequency of postsynaptic currents in human hPSC-derived neurons co-cultured with hPSC-derived versus primary rodent astrocytes, consistent with a corresponding increase in synapse density. Furthermore, hPSC-derived astrocytes retained their hominid morphology when transplanted into a mouse brain. In conclusion, we present a novel protocol to obtain functional astrocytes from human pluripotent stem cells, providing a platform for investigating human astrocyte function and neuronal-glial interactions.
Deciphering therapeutic efficacy of mycosynthesized silver nanoparticles using entomopathogenic fungi Metarhizium anisopliae against MCF-7 breast cancer cells in vitro
Authors: Nambiar Sujisha S , Mohanty Arman , Patra Arupam , Saini Gurvinder Kaur
Published: August 2022

Green synthesis of silver nanoparticles has gained much interest over few decades in the field of biomedical research due to their ease of synthesis, cost effectiveness, enhanced bioactivity and biocompatibility compared to the chemical synthesis. Recent studies on silver nanoparticles have shown their potential in various fields like antimicrobial, anticancer, larvicidal, catalytic, and wound healing properties. In the present study, entomopathogenic fungi Metarhizium anisopliae was used to synthesize silver nanoparticles. These silver nanoparticles were synthesized and characterized using UV-Vis spectroscopy, FESEM, FETEM and FTIR. Compared to the chemically synthesized silver nanoparticles, the mycosynthesized silver nanoparticles (MaAgNP) showed high yield. The size of mycosynthesized silver nanoparticles was found to be 5-20 nm and was spherical in shape. FTIR results confirmed the possible functional groups that are responsible for the reduction of silver ions. The mycosynthesized silver nanoparticles showed cytotoxicity on human breast cancer cell line (MCF-7) and the calculated IC50 value for MaAgNP was found to be 16.50 μg ml-1 whereas the chemically synthesized silver nanoparticles showed cytotoxicity but with increasing concentration, no further significant reduction in cell viability was observed. The possible reason behind improved cytotoxicity of MaAgNP can be the presence of extracellular secondary metabolites present in the fungal filtrate used to synthesize the nanoparticles. The MaAgNP was also observed to induce cell death through reactive oxygen species (ROS) generation.
Common multi-day rhythms in smartphone behavior
Authors: Ceolini Enea , Ghosh Arko
Published: August 2022

The idea that abnormal human activities follow multi-day rhythms spans ancient beliefs centered on the moon to modern clinical observations in epilepsy and mood disorders. Multi-day rhythms remain obscure in normal human activities. To address multi-day rhythms in healthy human behavior we analyzed over 300 million smartphone touchscreen interactions logging up to 2 years of day-to-day activities (N = 401 subjects). By using non-negative matrix factorization and data-driven clustering of ∼1 million periodograms, we captured a range of multi-day rhythms spanning periods from 7 to 52 days – cutting across age and gender. Despite their common occurrence, any given multi-day rhythm was observed in different parts of the smartphone behavior from one person to the next. There was little support in the data for ubiquitous rhythm drivers like the moon. We propose that multiple multi-day rhythms are a common trait, but their consequences may be uniquely experienced in day-to-day behavior.
Organ-Specific Fuel Rewiring in Acute and Chronic Hypoxia Redistributes Glucose and Fatty Acid Metabolism
Authors: Midha Ayush D. , Zhou Yuyin , Queliconi Bruno B. , Barrios Alec M. , Fong Cyril O. Y. , Blecha Joseph E. , VanBrocklin Henry , Seo Youngho , Jain Isha H.
Published: August 2022

Oxygen deprivation can be detrimental. However, chronic hypoxia is associated with decreased incidence of metabolic syndrome and cardiovascular disease in high-altitude populations. Previously, hypoxic fuel rewiring has primarily been studied in immortalized cells. Here, we describe how systemic hypoxia rewires fuel metabolism to optimize whole-body adaptation. Acclimatization to hypoxia coincided with dramatically lower blood glucose and adiposity. Usingin vivofuel uptake and flux measurements, we found that organs partitioned fuels differently during hypoxia adaption. Acutely, most organs increased glucose uptake and suppressed aerobic glucose oxidation, consistent with previousin vitroinvestigations. In contrast, brown adipose tissue and skeletal muscle became “glucose savers,” suppressing glucose uptake by 3-5-fold. Interestingly, chronic hypoxia produced distinct patterns: the heart relied increasingly on glucose oxidation, and unexpectedly, the brain, kidney, and liver increased fatty acid uptake and oxidation. Hypoxia-induced metabolic plasticity carries therapeutic implications for chronic metabolic diseases and acute hypoxic injuries.
Targeted Deletion of Fgf9 in Tendon Disrupts Mineralization of the Developing Enthesis
Authors: Ganji Elahe , Leek Connor , Duncan William , Patra Debabrata , Ornitz David M. , Killian Megan L.
Published: August 2022

The enthesis is a transitional tissue between tendon and bone that matures postnatally. The development and maturation of the enthesis involve cellular processes likened to an arrested growth plate. In this study, we explored the role of fibroblast growth factor 9 (Fgf9), a known regulator of chondrogenesis and vascularization during bone development, on the structure and function of the postnatal enthesis. First, we confirmed spatial expression of Fgf9 in wildtype tendon and enthesis using in situ hybridization. We then used Cre recombinase driven by the scleraxis promoter (ScxCre) to conditionally inactivate Fgf9 in mouse tendon and enthesis. Characterization of enthesis morphology and mechanical properties in Fgf9ScxCre and wildtype (WT) entheses showed a smaller calcaneal and humeral apophyses, thinner cortical bone at the attachment, increased cellularity, and reduced failure load in mature entheses in Fgf9ScxCre compared to WT littermates. During postnatal development, we found reduced chondrocyte hypertrophy and disrupted type X collagen (Col X) in Fgf9ScxCre entheses. These findings support a model in which tendon-derived Fgf9 regulates the functional development of the enthesis, including its postnatal mineralization.
Progression of vascular function and blood pressure in a mouse model of Kawasaki disease
Authors: DelVechio Mia , Alves Juliano V , Saiyi Alina Z , Singh Shubhnita , Galley Joseph , Awata Wanessa M. C. , Bruder-Nascimento Ariane , Bruder-Nascimento Thiago
Published: August 2022

Background

Kawasaki disease (KD) is a systemic vasculitis of childhood characterized by vascular damage in the acute stage, which can persist into the late stage. Aneurysms, myocardial infarction, and death are long-standing complications associated with KD. The vascular mechanisms in the cardiovascular risk of KD are not fully studied. Herein, we investigated the vascular function and blood pressure regulation in a murine model of KD.

Material and methods

We used the Candida albicans water soluble (CAWS) fraction model. Mice were injected with 4 mg CAWS for five consecutive days and separated into 3 groups. Control (Ctrl): water injected for 5 days; CAWS 7 days (C7): CAWS injected for 5 days plus 2 additional days of wait; CAWS 28 days (C28): CAWS injected for 5 days plus 23 additional days of wait. Blood pressure was analyzed via radiotelemetry. In the end, the heart and arteries were harvested for vasculitis characterization and vascular function in a wire myograph. Rat Aortic Vascular Smooth Muscle cells (RASMC) were used to dissect the molecular mechanisms in vitro.

Main findings

C7 presented elevated inflammatory markers in the coronary area (CA) and abdominal aortae (AA), whereas C28 showed severe vasculitis in CA and AA. No difference was found in blood pressure and heart rate. Vascular dysfunction characterized by higher contractility to norepinephrine (NA) in C7 and C28 was abolished by blocking nitric oxide (NO) production, reactive oxygen species (ROS), and cyclooxygenase (COX)-derived products. RASMC treated with CAWS (10ug/mL) presented an increase in COX2 expression, which was prevented by pre-treating the cells with TAK-242 [Toll like receptor 4 (TLR4) antagonist, 3x10−5M].

Conclusion

Our data indicate that the murine model of KD is associated with vascular dysfunction likely dependent on COX-derived products, oxidant properties, and NO bioavailability. Furthermore, VSMC may present an important role in the genesis of vascular dysfunction and vasculitis via the TLR4 pathway. Finally, the CAWS model seems not to be appropriate to study KD-associated shock. More studies are necessary to understand whether vascular dysfunction and COXs are triggers for vasculitis.
Towards Stewardship of Wild Species and Their Domesticated Counterparts: A Case Study in Northern Wild Rice (Zizania palustrisL.)
Authors: McGilp Lillian , Haas Matthew W. , Shao Mingqin , Millas Reneth , Castell-Miller Claudia , Kern Anthony J. , Shannon Laura M. , Kimball Jennifer A.
Published: August 2022

Northern Wild Rice (NWR;Zizania palustrisL.) is an aquatic, annual grass with significant ecological, cultural, and economic importance to the Great Lakes region of North America. In this study, we assembled and genotyped a diverse collection of 839 NWR individuals using genotyping-by-sequencing (GBS) and obtained 5,955 single-nucleotide polymorphisms (SNPs). Our collection consisted of samples from 12 wild NWR populations collected across Minnesota and Western Wisconsin, some of which were collected over two time points; a representative collection of cultivated NWR varieties and breeding populations; and aZizania aquaticaoutgroup. Using these data, we characterized the genetic diversity, relatedness, and population structure of this broad collection of NWR genotypes. We found that wild populations of NWR clustered primarily by their geographical location, with some clustering patterns likely influenced by historical ecosystem management. Cultivated populations were genetically distinct from wild populations, suggesting limited gene flow between the semi-domesticated crop and its wild counterparts. The first genome-wide scans of putative selection events in cultivated NWR suggest that the crop is undergoing heavy selection pressure for traits conducive to irrigated paddy conditions. Overall, this study presents a large set of SNP markers for use in NWR genetic studies and provides new insights into the gene flow, history, and complexity of wild and cultivated populations of NWR.
Alignment-free microbiome-based classification of fresh produce safety and quality
Authors: Liao Chao , Wang Luxin , Quon Gerald
Published: August 2022

Small samples sizes and loss of up to 50-70% of sequencing data during the data denoising step of preprocessing can limit the statistical power of fresh produce microbiome analyses and prevent detection of important bacterial species associated with produce contamination or quality reduction. Here, we explored an alignment-free analysis strategy using k-mer hashes to identify DNA signatures predictive of produce safety and produce quality, and compared it against the amplicon sequence variant (ASV) strategy that uses a typical denoising step. Random forests (RF)-based classifiers for fresh produce safety and quality using 7-mer hash datasets had significantly higher classification accuracy than those using the ASV datasets. We also demonstrated that the proposed combination of integrating multiple datasets and leveraging an alignment-free 7-mer hash strategy leads to better classification performance for fresh produce safety and quality. Results generated from this study lay the foundation for future studies that wish and need to incorporate and/or compare different microbiome sequencing datasets for the application of machine learning in the area of microbial safety and quality of food.
A molecular switch modulates assembly and host factor binding of the HIV-1 capsid
Authors: Schirra Randall T. , dos Santos Nayara F. B. , Zadrozny Kaneil K. , Kucharska Iga , Ganser-Pornillos Barbie K. , Pornillos Owen
Published: August 2022

Upon entry into a new host cell, the HIV-1 capsid performs multiple essential functions, which include shielding the genome from innate immune sensors1, promoting reverse transcription2 and transporting the core from the entry site at the plasma membrane to the integration site inside the nucleus3,4. The HIV-1 capsid is a fullerene cone made of hexamers and pentamers of the viral CA protein5,6. The two types of capsomers are quasi-equivalent, with the same structural elements mediating distinct inter-subunit contacts. In other studied quasi-equivalent viruses, the capacity of genetically identical subunits to form hexamers and pentamers is conferred by molecular switches. Such a switch has not been previously found in retroviral CA proteins. Here, we report cryoEM structures of the HIV-1 CA pentamer within assembled in vitro capsids at nominal resolutions of 2.4-3.4 Å. Comparison with the hexamer identified an internal loop that adopts distinct conformations, 310 helix in the pentamer and random coil in the hexamer. Designed manipulations of the coil/helix configuration allowed us to control pentamer and hexamer formation in a predictable manner, thus proving its function as a molecular switch. Importantly, the switch controls not only fullerene cone assembly, but also the capsid’s capacity to bind post-entry host factors that are critical for viral replication. Furthermore, the switch forms part of the binding site of the new ultra-potent HIV-1 inhibitor, lenacapavir. These studies reveal that a critical assembly element also controls the post-assembly functions of the capsid, and provide new insights on capsid inhibition and uncoating.
HIV-1 GAG SPECIFICITY FOR PIP2-CONTAINING MEMBRANES MIGHT BE DRIVEN BY MACROMOLECULAR ELECTRIC PROPERTIES RATHER THAN MOLECULAR AFFINITIES
Authors: Socas L. B. P. , Ambroggio E. E.
Published: August 2022

The HIV-1 assembly occurs at the plasma membrane, where the GAG polyprotein plays a crucial role. The GAG-membrane association is directed by the matrix domain (MA), which is myristoylated and has a highly basic region that interacts with the anionic lipids. Several evidence suggests that the presence of phosphatidylinositol-(4,5)-bisphosphate (PIP2) highly influence this binding. In addition, MA also interacts with nucleic acids, which is proposed to be important for the specificity of GAG for PIP2-containing membranes. It is proposed that RNA could have a chaperone function when interacting with the MA domain, preventing GAG from associating with unspecific lipid interfaces. Here, we study the interaction of MA with monolayer and bilayer membrane systems, focused on the specificity for PIP2 and on the possible effects of a GAG N-terminal peptide to impair the binding for either RNA or membrane. We found that RNA decreases the kinetics of the protein association with lipid monolayers but without any effect on the selectivity for PIP2. Interestingly, for bilayer systems, this selectivity increases in presence of both the peptide and RNA, even for highly negative charged compositions, where MA by itself doesn’t discriminate between membranes with or without PIP2. Therefore, we propose that the specificity of MA for PIP2-membranes might be related to the electrostatic properties of both membrane and protein local environments, rather than a simple difference in molecular affinities. This scenario gives a new understanding of the regulation mechanism with a macromolecular view instead of considering molecular interactions within a ligand-receptor model.

Importance

HIV-1 virions are formed at the PM of infected cells through a direct interaction of the viral GAG protein with lipids. This is a finely regulated process governed by the GAG N-terminal matrix domain, MA. Here, we obtained compelling evidence on how this process depends on the local dielectric environments of both, the membrane and MA. Using bio-membrane mimicking systems, we found how MA myristoylation is involved in the interfacial absorption and anchoring of the protein, where the interaction with RNA negatively regulates this process but in a lesser extent when traces of the PIP2 lipid are present. Additionally, an N-terminal GAG-derived peptide competes with MA for the nucleic acid binding and impair the protein-membrane interaction when PIP2 is absent. All these data allowed us to propose a model for MA association with lipid interfaces and how it depends on oligonucleotide binding, lipid composition and competing peptide presence.
Mouse population genetics phenocopies heterogeneity of human Chd8 haploinsufficiency
Authors: Tabbaa Manal , Knoll Allison , Levitt Pat
Published: August 2022

Preclinical models of neurodevelopmental disorders typically use single inbred strains which fail to capture human genetic and symptom heterogeneity that is common clinically. We tested if systematically modeling human genetic diversity in mouse genetic reference panels would recapitulate population and individual differences in responses to a syndromic mutation in the high-confidence autism risk gene, CHD8. Trait disruptions mimicked those seen in human populations, including high penetrance of macrocephaly and disrupted behavior, but with robust strain and sex differences. For every trait, some strains exhibited a range of large effect size disruptions, sometimes in opposite directions, and remarkably others expressed resilience. Thus, systematically introducing genetic diversity into mouse models of neurodevelopmental disorders provides a better framework for discovering individual differences in symptom etiologies and improved treatments.

One-Sentence Summary

Autism trait heterogeneity due to a syndromic gene mutation is recapitulated in mice by incorporating genetic diversity.
Ion Mobility for Unknown Metabolite Identification: Hope or Hype?
Authors: Asef Carter K. , Rainey Markace , Garcia Brianna M. , Gouveia Goncalo J. , Shaver Amanda O. , Leach Franklin E. , Morse Allison M. , Edison Arthur S. , McIntyre Lauren M. , Fernández Facundo M.
Published: August 2022

Ion mobility (IM) spectrometry provides semi-orthogonal data to mass spectrometry (MS), showing promise for identifying unknown metabolites in complex non-targeted metabolomics datasets. While current literature has showcased IM-MS for identifying unknowns under near ideal circumstances, less work has been conducted to evaluate the performance of this approach in metabolomics studies involving highly complex samples with difficult matrices. Here, we present a workflow incorporating de novo molecular formula annotation and MS/MS structure elucidation using SIRIUS 4 with experimental IM collision cross-section (CCS) measurements and machine learning CCS predictions to identify differential unknown metabolites in mutant strains of Caenorhabditis elegans. For many of those ion features this workflow enabled the successful filtering of candidate structures generated by in silico MS/MS predictions, though in some cases annotations were challenged by significant hurdles in instrumentation performance and data analysis. While for 37% of differential features we were able to successfully collect both MS/MS and CCS data, fewer than half of these features benefited from a reduction in the number of possible candidate structures using CCS filtering due to poor matching of the machine learning training sets, limited accuracy of experimental and predicted CCS values, and lack of candidate structures resulting from the MS/MS data. When using a CCS error cutoff of ±3%, an average 28% of candidate structures could be successfully filtered. Herein, we identify and describe the bottlenecks and limitations associated with the identification of unknowns in non-targeted metabolomics using IM-MS to focus and provide insight on areas requiring further improvement.
Targeting neuroinflammation with Abscisic Acid reduces pain sensitivity in females and hyperactivity in males of an ADHD mice model
Authors: Meseguer-Beltrán Maria , Sánchez-Sarasúa Sandra , Landry Marc , Kerekes Nóra , Sánchez-Pérez Ana María
Published: August 2022

Aims

Attention deficit/hyperactivity disorder (ADHD) is a neurodevelopmental syndrome characterized by dopaminergic dysfunction. In this study, we aimed to demonstrate the link between dopaminergic deficit and neuroinflammation underlying ADHD symptoms.

Subjects and Treatment

We used a validated ADHD mice model, that involves perinatal 6-OHDA lesion. Animals were treated with 20mg/L (drinking water) of Abscisic acid (ABA) for one month. We tested behaviour (learning and memory, anxiety, social interactions, and pain) in both females and male mice, in all eight groups (control and lesioned, with/without ABA). Postmortem, we analyzed microglia morphology and Ape1 expression in specific brain areas related to the descending pain inhibitory pathway.

Results

In females, dopaminergic deficit increased pain sensitivity, but not hyperactivity, in contrast to males. This behaviour was associated with inflammatory microglia and lower Ape1 levels in the anterior cingulate cortex (ACC) and posterior insula cortex (IC). ABA treatment reduced inflammation and alleviated pain. In males, ABA reduced hyperactivity, but had no significant effect on inflammation.

Conclusions

This is the first study proving a sex-dependent association between dopamine dysfunction and inflammation in specific brain areas, leading to different behavior outcomes in a mouse model of ADHD. These findings provide new clues for potential treatments.
Quantitative Evaluation of the Cellular Uptake of Nanodiamonds by Monocytes and Macrophages
Authors: Niora Maria , Lerche Mathilde Hauge , Dufva Martin , Berg-Sørensen Kirstine
Published: August 2022

Nanodiamonds (NDs) with NV−defect centers are great probes for bionanotechnology applications, with potential to act as biomarkers for cell differentiation. To explore this concept, uptake of NDs (~120nm) by THP-1 monocytes and monocyte-derived M0-macrophages is studied. The time course analysis of ND uptake by monocytes confirms differing ND-cell interactions and a positive time-dependence. No effect on cell viability, proliferation and differentiation potential into macrophages is observed, while cells saturated with NDs, unload the NDs completely by 25 cell divisions and subsequently take up a second dose effectively. ND uptake variations by THP-1 cells at early exposure-times indicate differing phagocytic capability. The cell fraction that exhibits relatively enhanced ND uptake is associated to a macrophage phenotype which derives from spontaneous monocyte differentiation. In accordance, chemical-differentiation of the THP-1 cells into M0-macrophages triggers increased and homogeneous ND uptake, depleting the fraction of cells that were non-responsive to NDs. These observations verify that ND uptake allows for distinction between the two cell subtypes based on phagocytic capacity. Overall, NDs demonstrate effective cell labeling of monocytes and macrophages, and are promising candidates for tracking biological processes that involve cell differentiation.