bluuebunny/crossref_metadata_2025 huggingface dataset:
High School Science Fair: School Location Trends in Student Participation and Experience
Authors: Grinnell Frederick , Dalley Simon , Reisch Joan
Published: February 2023

The findings reported in this paper are based on surveys of U.S. high school students who registered and managed their science and engineering fair (SEF) projects through the online Scienteer website over the three years 2019/20, 2020/21, and 2021/22. Almost 2500 students completed surveys after finishing all their SEF competitions. We added a new question in 2019/20 to our on-going surveys asking the students whether their high school location was urban, suburban, or rural. We learned that overall, 74% of students participating in SEFs indicated that they were from suburban schools. Unexpectedly, very few SEF participants, less than 4%, indicated that they were from rural schools, even though national data show that more than 20% of high school students attend rural schools. Consistent with previous findings, Asian and Hispanic students indicated more successful SEF outcomes than Black and White students. However, whereas Asian students had the highest percentage of SEF participants from suburban vs. urban schools – 81% vs. 18%, Hispanic students had the most balanced representation of participants from suburban vs. urban schools – 55% vs. 39%. Differences in students’ SEF experiences based on gender and ethnicity showed the same patterns regardless of school location. In the few items where we observed statistically significant (probability <.05) differences based on school location, students from suburban schools were marginally favored by only a few percentage points compared to students from urban schools. In conclusion, based on our surveys results most students participating in SEFs come from suburban schools, but students participating in SEFs and coming from urban schools have equivalent SEF experiences, and very few students participating in SEFs come from rural schools.
Masked superstrings as a unified framework for textualk-mer set representations
Authors: Sladký Ondřej , Veselý Pavel , Břinda Karel
Published: February 2023

The popularity ofk-mer-based methods has recently led to the development of compactk-mer-set representations, such as simplitigs/Spectrum-Preserving String Sets (SPSS), matchtigs, and eulertigs. These aim to representk-mer sets via strings that contain individualk-mers as substrings more efficiently than the traditional unitigs. Here, we demonstrate that all such representations can be viewed as superstrings of inputk-mers, and as such can be generalized into a unified framework that we call the masked superstring ofk-mers. We study the complexity of masked superstring computation and prove NP-hardness for bothk-mer superstrings and their masks. We then design local and global greedy heuristics for efficient computation of masked superstrings, implement them in a program called KmerCamel, and evaluate their performance using selected genomes and pan-genomes. Overall, masked superstrings unify the theory and practice of textualk-mer set representations and provide a useful framework for optimizing representations for specific bioinformatics applications.
Universal Design Principle to Enhance Enzymatic Activity using the Substrate Affinity
Authors: Ooka Hideshi , Chiba Yoko , Nakamura Ryuhei
Published: February 2023

Design principles to improve enzymatic activity are essential to promote energy-material conversion using biological systems. For more than a century, the Michaelis-Menten equation has provided a fundamental framework of enzymatic activity. However, there is still no concrete guideline on how the parameters should be optimized to enhance enzymatic activity. Here, we demonstrate that tuning the Michaelis-Menten constant (Km) to the substrate concentration (S) maximizes enzymatic activity. This guideline (Km=S) was obtained by applying the Brønsted (Bell)-Evans-Polanyi (BEP) principle of heterogeneous catalysis to the Michaelis-Menten equation, and is robust even with mechanistic deviations such as reverse reactions and inhibition. Furthermore,KmandSare consistent to within an order of magnitude over an experimental dataset of approximately 1000 wild-type enzymes, suggesting that even natural selection follows this principle. The concept of an optimumKmoffers the first quantitative guideline towards improving enzymatic activity which can be used for highthroughput enzyme screening.
SIGNS OF CENTRAL SENSITIZATION IN PATIENTS WITH MUSCULOSKELETAL DISORDERS AND CHRONIC COMORBIDITIES: A SYSTEMATIC REVIEW AND META-ANALYSES OF OBSERVATIONAL STUDIES
Authors: Sgarbi Mattia , D’Alessandro Davide , Castaldo Matteo , Feller Daniel
Published: February 2023

Objectives

this review aimed to investigate the presence of signs of central sensitization in patients with musculoskeletal disorders and associated chronic comorbidities.

Methods

we conducted a systematic review (prespecified protocol CRD42021228970). Two authors independently searched for primary studies published between 2000 and 2021 in Web of Science and PubMed databases. We searched for studies that investigate the presence of signs of central sensitization in patients with musculoskeletal disorder or migraine and a chronic comorbidity. Two authors independently evaluated the methodological quality of the included studies using the “The Joanna Briggs Institute Critical Appraisal tools”. When studies were judged homogenous enough, we performed a random effect meta–analysis.

Results

we included 14 observational studies. Overall, patients with musculoskeletal disorders or migraine with an associated comorbidity showed more signs of central sensitization compared with healthy subjects.

The quantitative analysis showed that patients with temporomandibular disorders and chronic comorbidities, compared to patients with temporomandibular disorders without comorbidites, have a decreased pressure pain thresholds measured in the masseter area [SMD: -0.52; CI 95%: - 1.02 to -0.03; I2: 67%] and in the trapezius area [SMD: -0.55; CI 95%: -0.96 to -0.14; I2: 0%].

Patients with migraine, chronic low back pain or rheumatoid arthritis and associated fibromyalgia present more signs of central sensitization, measured in different modalities, than subjects without comorbidity.

Conclusions

we demonstrated that, in general, patients with musculoskeletal disorders and an associated comorbidity showed an increased incidence of signs of central sensitization compared to healthy subjects and patients with musculoskeletal disorders without comorbities.
Increasing representation and diversity in health research: A protocol of the MYHealth Research Training Program for high school students
Authors: Chuisano Samantha A. , Rafferty Jane , Allen Alison , Chang Tammy , Diemer Matthew , Harris Kara , Vaughn Lisa M. , Watkins Daphne C. , DeJonckheere Melissa
Published: February 2023

Background

Despite decades of calls for increased diversity in the health research workforce, disparities exist for many populations, including Black, Indigenous, and People of Color individuals, those from low-income families, and first-generation college students. To increase representation of historically marginalized populations, there is a critical need to develop programs that strengthen their path toward health research careers. High school is a critically important time to catalyze interest and rebuild engagement among youth who may have previously felt excluded from science, technology, engineering, and mathematics (STEM) and health research careers.

Methods

The overall objective of the MYHealth program is to engage high school students in a community-based participatory research program focused on adolescent health. Investigators will work alongside community partners to recruit 9ththrough 12thgraders who self-identify as a member of a group underrepresented in STEM or health research careers (e.g., based on race and ethnicity, socioeconomic status, first generation college student, disability, etc.). MYHealth students are trained to be co-researchers who work alongside academic researchers, which will help them to envision themselves as scientists capable of positively impacting their communities through research. Implemented in three phases, the MYHealth program aims to foster a continuing interest in health research careers by developing: 1) researcher identities, 2) scientific literacy, 3) scientific self-efficacy, and 4) teamwork and leadership self-efficacy. In each phase, students will build knowledge and skills in research, ethics, data collection, data analysis, and dissemination. Students will directly collaborate with and be mentored by a team that includes investigators, community advisors, scientific advisors, and youth peers.

Discussion

Each year, a new cohort of up to 70 high school students will be enrolled in MYHealth. We anticipate the MYHealth program will increase interest and persistence in STEM and health research among groups that have been historically excluded in health research careers.
Cognitive change after subthalamic deep brain stimulation for Parkinson’s disease – a systematic meta-regressive analysis
Authors: Skvarc David R. , Cartmill Tomas , McGillivray Jane A. , Berk Michael , Byrne Linda K.
Published: February 2023

Parkinson’s disease is a progressive neurodegenerative disorder characterised by motor dysfunction and cognitive disruption among other non-motor symptoms. No cure for Parkinson’s disease exists. Deep Brain Stimulation of the Subthalamic Nucleus (DBS STN) has been utilised for control of motor symptoms. However, cognitive deficits are commonly reported after implantation, and few exhaustive analyses exist to quantify and explain them. Our systematic review, meta-analyses, and metaregressions examine within-subjects change across thirteen cognitive domains, from 70 studies and 3000 participants at baseline measurements. Improvement was not observed in any domain, but substantial decline at 12 months was observed for phonemic and categorical fluency, which appeared to stabilise 24 to 36 months. Meta-regression suggests that few study characteristics are predictive of longitudinal outcomes, and we propose that further research into specific surgical or placement effects is necessary to mitigate short-term cognitive change after DBS STN in Parkinson’s disease.
DESIGN AND GENERATION OF A RECOMBINANT GAMMAHERPESVIRUS ENCODING shRNA FROM NATIVE VIRAL tRNA PROMOTER
Authors: Kara Mehmet , Tibbetts Scott
Published: February 2023

Gammaherpesviruses are associated with multiple types of tumour development and understanding the pathogenesis of these viruses has been the subject of many different studies. Throughout the lytic and latent life cycle, these viruses utilize numerous virally encoded miRNAs to regulate the key mechanisms of the infected cell in their favour. Therefore it is important to understand the miRNA and their mRNA target interactions for developing better therapeutics. In this study, the strategy and design of a short hairpin encoding RNA element targeting Blimp1 transcript in the context of viral infection is evaluated. This proof of principle experiment provides a mean to study important miRNA mRNA interactionsin vivo. The very short promoter size of the Murine gammaherpesvirus 68 (MHV68) vtRNA4 and its ability to generate two shRNAs from a ~180 nucleotide sequence is useful if there is a size limit for the shRNA construct.
ClockstaRX: testing molecular clock hypotheses with genomic data
Authors: Duchêne David A. , Duchêne Sebastián , Stiller Josefin , Heller Rasmus , Ho Simon Y. W.
Published: February 2023

Phylogenetic studies of genomic data can provide valuable opportunities for evaluating evolutionary timescales and drivers of rate variation. These analyses require statistical tools based on molecular clocks. We present ClockstaRX, a flexible platform for exploring and testing evolutionary rate signals in phylogenomic data. It implements methods that use information from gene trees in Euclidean space, allowing data transformation, visualization, and hypothesis testing. ClockstaRX implements formal tests of the dimensionality reducibility of the Euclidean space of rates, and for identifying loci and branches that have a large influence on rate variation. Using simulations to evaluate the performance of the methods implemented, we find that inferences about rates can be strongly influenced by the overall amount of rate variation in the data, the shared patterns of among-lineage rate heterogeneity across groups of loci, and missing data. In an analysis of phylogenomic data from birds, we find a higher rate of evolution in introns compared with exons across all lineages. In addition, passerine taxa are highlighted as having unique patterns of genomic evolutionary rates compared with other avian lineages. Drawing on these results, we recommend careful exploratory analyses and filtering before performing phylogenomic analyses using molecular clocks.
TLN468 changes the pattern of tRNA used to read through premature termination codons in CFTR
Authors: Karri Sabrina , Cornu David , Serot Claudia , Biri Lynda , Hatton Aurélie , Pranke Iwona , Sermet-Gaudelus Isabelle , Hinzpeter Alexandre , Bidou Laure , Namy Olivier
Published: February 2023

Nonsense mutations account for 12% of cystic fibrosis (CF) cases. The presence of a premature termination codon (PTC) leads to gene inactivation, which can be countered by the use of drugs stimulating PTC readthrough, restoring production of the full-length protein. We recently identified a new readthrough inducer, TLN468, more efficient than gentamicin.

We measured the readthrough induced by these two drugs with different cystic fibrosis transmembrane conductance regulator (CFTR) PTCs. We then determined the amino acids inserted at the S1196X, G542X, W846X and E1417X PTCs ofCFTRduring readthrough induced by gentamicin or TLN468. TLN468 significantly promoted the incorporation of one specific amino acid, whereas gentamicin did not greatly modify the proportions of the various amino acids incorporated relative to basal conditions. The function of the engineered missense CFTR channels corresponding to these four PTCs was assessed with and without potentiator. For the recoded CFTR, except for E1417Q and G542W, the PTC readthrough induced by TLN468 allowed the expression of CFTR variants that were correctly processed and had significant activity that was enhanced by CFTR modulators. These results suggest that it would be relevant to assess the therapeutic benefit of TLN468 PTC suppression in combination with CFTR modulators in preclinical assays.
Transcriptional Isoforms of NAD+Kinase regulate oxidative stress resistance and melanoma metastasis
Authors: Cascio Graciela , Aguirre Kelsey N. , Church Kellsey P. , Hughes Riley O. , Nease Leona A. , Delclaux Ines , Zerhouni Marwa , Piskounova Elena
Published: February 2023

Metastasizing cancer cells encounter a multitude of stresses throughout the metastatic cascade. Oxidative stress is known to be a major barrier for metastatic colonization, such that metastasizing cancer cells must rewire their metabolic pathways to increase their antioxidant capacity. NADPH is essential for regeneration of cellular antioxidants and several NADPH-regenerating pathways have been shown to play a role in metastasis. We have found that metastatic melanoma cells have increased levels of both NADPH and NADP+suggesting increasedde novobiosynthesis of NADP+.De novobiosynthesis of NADP+occurs through a single enzymatic reaction catalyzed by NAD+kinase (NADK). Here we show that different NADK isoforms are differentially expressed in metastatic melanoma cells, with Isoform 3 being specifically upregulated in metastasis. We find that Isoform 3 is more potent in expanding the NADP(H) pools, increasing oxidative stress resistance and promoting metastatic colonization compared to Isoform 1. We have found that Isoform 3 is transcriptionally upregulated by oxidative stress through the action of NRF2. Together, our work presents a previously uncharacterized role of NADK isoforms in oxidative stress resistance and metastasis and suggests that NADK Isoform 3 is a potential therapeutic target in metastatic disease.
A synthetic signalling network imitating the action of immune cells in response to bacterial metabolism
Authors: Walczak Michal , Mancini Leonardo , Xu Jiayi , Raguseo Federica , Kotar Jurij , Cicuta Pietro , Di Michele Lorenzo
Published: February 2023

State-of-the-art bottom-up synthetic biology allows us to replicate many basic biological functions in artificial cell-like devices. To mimic more complex behaviours, however,artificial cellswould need to perform many of these functions in a synergistic and coordinated fashion, which remains elusive. Here we considered a sophisticated biological response, namely the capture and deactivation of pathogens by neutrophil immune cells, through the process of netosis. We designed a consortium consisting of two synthetic agents – responsive DNA-based particles and antibiotic-loaded lipid vesicles – whose coordinated action mimics the sought immune-like response when triggered by bacterial metabolism. The artificial netosis-like response emerges from a series of interlinked sensing and communication pathways between the live and synthetic agents, and translates into both physical and chemical antimicrobial actions, namely bacteria immobilisation and exposure to antibiotics. Our results demonstrate how advanced life-like responses can be prescribed with a relatively small number of synthetic molecular components, and outlines a new strategy for artificial-cell-based antimicrobial solutions.
A multiomics approach to understanding pathology of Combined D,L-2- Hydroxyglutaric Aciduria and phenylbutyrate as potential treatment
Authors: Phua Yu Leng , D’Annibale Olivia M , Karunanidhi Anuradha , Mohsen Al-Walid , Kirmse Brian , Dobrowolski Steven F , Vockley Jerry
Published: February 2023

Combined D, L-2-Hydroxyglutaric Aciduria (D,L-2HGA) is a rare genetic disorder caused by recessive mutations in theSLC25A1gene that encodes the mitochondrial citrate carrier protein (CIC).SLC25A1deficiency leads to a secondary increase in mitochondrial 2-ketoglutarate that, in turn, is reduced to neurotoxic 2-hydroxyglutarate. Clinical symptoms of Combined D,L-2HGA include neonatal encephalopathy, respiratory insufficiency and often with death in infancy. No current therapies exist, although replenishing cytosolic stores by citrate supplementation to replenish cytosolic stores has been proposed. In this study, we demonstrated that patient derived fibroblasts exhibited impaired cellular bioenergetics that were worsened with citrate supplementation. We hypothesized treating patient cells with phenylbutyrate, an FDA approved pharmaceutical drug, would reduce mitochondrial 2-ketoglutarate, leading to improved cellular bioenergetics including oxygen consumption and fatty acid oxidation. Metabolomic and RNA-seq analyses demonstrated a significant decrease in intracellular 2-ketoglutarate, 2-hydroxyglutarate, and in levels of mRNA coding for citrate synthase and isocitrate dehydrogenase. Consistent with the known action of phenylbutyrate, detected levels of phenylacetylglutamine was consistent with the drug acting as 2-ketoglutarate sink in patient cells. Our pre-clinical studies suggest citrate supplementation is unlikely to be an effective treatment of the disorder. However, cellular bioenergetics suggests phenylbutyrate may have interventional utility for this rare disease.
CDK4/6 inhibition enhances SHP2 inhibitor efficacy and is dependent upon restoration of RB function in malignant peripheral nerve sheath tumors
Authors: Wang Jiawan , Calizo Ana , Zhang Lindy , Pino James C. , Lyu Yang , Pollard Kai , Zhang Xiaochun , Larsson Alex T. , Conniff Eric , Llosa Nicolas , Wood David K. , Largaespada David A. , Moody Susan E. , Gosline Sara J. , Hirbe Angela C. , Pratilas Christine A.
Published: February 2023

Malignant peripheral nerve sheath tumors (MPNST) are highly aggressive soft tissue sarcomas with limited treatment options, and novel effective therapeutic strategies are desperately needed. We observe anti-proliferative efficacy of genetic depletion or pharmacological inhibition using the clinically available SHP2 inhibitor (SHP2i) TNO155. Our studies into the signaling response to SHP2i reveal that resistance to TNO155 is partially mediated by reduced RB function, and we therefore test the addition of a CDK4/6 inhibitor (CDK4/6i) to enhance RB activity and improve TNO155 efficacy. In combination, TNO155 attenuates the adaptive response to CDK4/6i, potentiates its anti-proliferative effects, and converges on enhancement of RB activity, with greater suppression of cell cycle and inhibitor-of-apoptosis proteins, leading to deeper and more durable anti-tumor activity inin vitroandin vivopatient-derived models of MPNST, relative to either single agent. Overall, our study provides timely evidence to support the clinical advancement of this combination strategy in patients with MPNST and other tumors driven by loss of NF1.
HIV viral protein R induces loss of DCT1-type renal tubules
Authors: Latt Khun Zaw , Yoshida Teruhiko , Shrivastav Shashi , Abedini Amin , Reece Jeff M. , Sun Zeguo , Lee Hewang , Okamoto Koji , Dagur Pradeep , Heymann Jurgen , Zhao Yongmei , Chung Joon-Yong , Hewitt Stephen , Jose Pedro A. , Lee Kyung , He John Cijiang , Winkler Cheryl A. , Knepper Mark A. , Kino Tomoshige , Rosenberg Avi Z. , Susztak Katalin , Kopp Jeffrey B.
Published: February 2023

Hyponatremia and salt wasting is a common occurance in patients with HIV/AIDS, however, the understanding of its contributing factors is limited. HIV viral protein R (Vpr) contributes to HIV-associated nephropathy. To investigate the effects of Vpr on the expression level of theSlc12a3gene, encoding the Na-Cl cotransporter, which is responsible for sodium reabsorption in distal nephron segments, we performed single-nucleus RNA sequencing of kidney cortices from three wild-type (WT) and three Vpr-transgenic (Vpr Tg) mice. The results showed that the percentage of distal convoluted tubule (DCT) cells was significantly lower in Vpr Tg mice compared with WT mice (P < 0.05), and that in Vpr Tg mice,Slc12a3expression was not different in DCT cell cluster. ThePvalb+DCT1 subcluster had fewer cells in Vpr Tg mice compared with WT (P < 0.01). Immunohistochemistry demonstrated fewerSlc12a3+Pvalb+DCT1 segments in Vpr Tg mice. Differential gene expression analysis comparing Vpr Tg and WT in the DCT cluster showedIer3, an inhibitor of apoptosis, to be the most downregulated gene. These observations demonstrate that the salt-wasting effect of Vpr in Vpr Tg mice is mediated by loss ofSlc12a3+Pvalb+DCT1 segments via apoptosis dysregulation.
SHARE-Topic: Bayesian Interpretable Modelling of Single-Cell Multi-Omic Data
Authors: El Kazwini Nour , Sanguinetti Guido
Published: February 2023

Single-cell sequencing technologies are providing unprecedented insights into the molecular biology of individual cells. More recently, multi-omic technologies have emerged which can simultaneously measure gene expression and the epigenomic state of the same cell, holding the promise to unlock our understanding of the epigenetic mechanisms of gene regulation. However, the sparsity and noisy nature of the data pose fundamental statistical challenges which hinder our ability to extract biological knowledge from these complex data sets. Here we propose SHARE-Topic, a Bayesian generative model of multi-omic single cell data which addresses these challenges from the point of view of topic models. SHARE-Topic identifies common patterns of co-variation between different ‘omic layers, providing interpretable explanations for the complexity of the data. Tested on joint ATAC and expression data, SHARE-Topic was able to provide low dimensional representations that recapitulate known biology, and to define in a principled way associations between genes and distal regulators in individual cells. We illustrate SHARE-Topic in a case study of B-cell lymphoma, studying the usage of alternative promoters in the regulation of the FOXP1 transcription factors.
Effects of combined use of alcohol and delta-9-tetrahydrocannibinol on working memory in Long Evans rats
Authors: Carrica Lauren K. , Choi Chan Young , Walter Francis A. , Noonan Brynn L. , Shi Linyuan , Johnson Clare T. , Bradshaw Heather B. , Liang Nu-Chu , Gulley Joshua M.
Published: February 2023

The increase in social acceptance and legalization of cannabis over the last several years is likely to increase the prevalence of its co-use with alcohol. In spite of this, the potential for effects unique to co-use of these drugs, especially in moderate doses, has been studied relatively infrequently. We addressed this in the current study using a laboratory rat model of voluntary drug intake. Periadolescent male and female Long-Evans rats were allowed to orally self-administer ethanol, Δ9-tetrahydrocannibinol (THC), both drugs, or their vehicle controls from postnatal day (P) 30 to P47. They were subsequently trained and tested on an instrumental behavior task that assesses attention, working memory and behavioral flexibility. Similar to previous work, consumption of THC reduced both ethanol and saccharin intake in both sexes. Blood samples taken 14h following the final self-administration session revealed that females had higher levels of the THC metabolite THC-COOH. There were modest effects of THC on our delayed matching to position (DMTP) task, with females exhibiting reduced performance compared to their control group or male, drug using counterparts. However, there were no significant effects of co-use of ethanol or THC on DMTP performance, and drug effects were also not apparent in the reversal learning phase of the task when non-matching to position was required as the correct response. These findings are consistent with other published studies in rodent models showing that use of these drugs in low to moderate doses does not significantly impact memory or behavioral flexibility following a protracted abstinence period.
A Novel MHC-Independent Mechanism of Tumor Cell Killing by CD8+T Cells
Authors: Lerner Emily , Woroniecka Karolina , D’Anniballe Vincent , Wilkinson Daniel , Lorrey Selena , Waibl-Polania Jessica , Wachsmuth Lucas , Miggelbrink Alexandra , Raj Jude , Mohan Aditya , Cook Sarah , Tomaszewski William , Cui Xiuyu , Khasraw Mustafa , Gunn Michael D. , Fecci Peter E.
Published: February 2023

The accepted paradigm for both cellular and antitumor immunity relies upon tumor cell kill by CD8+T cells recognizing cognate antigens presented in the context of target cell major histocompatibility complex class I (MHC I) molecules. Likewise, a classically described mechanism of tumor immune escape is tumor MHC-I downregulation. Here, we report that CD8+T cells maintain the capacity to kill tumor cells that are entirely devoid of MHC-I expression. This capacity proves to be dependent on interactions between T cell NKG2D and tumor NKG2D ligands (NKG2DL). Necessarily, tumor cell kill in these instances is antigen-independent, although prior T cell antigen-specific activation is required and can be furnished by myeloid cells or even neighboring MHC-replete tumors cells. These mechanisms are activein vivoin mice, as well asin vitroin human tumor systems, and are obviated by NKG2D knockout or blockade. Tumor cell killing following T cell NKG2D engagement is Fas-independent and appears to involve granzyme. These studies potentially obviate the long-advanced notion that downregulation of MHC-I is a viable means of tumor immune escape, and instead identify the NKG2D/NKG2DL axis as a novel therapeutic target for enhancing T cell-dependent anti-tumor immunity against MHC loss variants.
Endothelial cell derived microvesicles modulate cerebrovascular and brain aging via miR-17-5p and serve as potential biomarkers for vascular aging
Authors: Zhang Huiting , Xie Zi , Zhao Yuhui , Chen Yanyu , Xu Xiaobing , Ye Ye , Yang Yuping , Zhong Wangtao , Zhao Bin , Ma Xiaotang
Published: February 2023

Vascular aging, characterized by brain endothelial cells (ECs) senescence and dysfunction, has been known to lead to various age-related cerebrovascular and neurodegenerative diseases. However, its underlying mechanisms remain elusive. ECs derived microvesicles (EMVs) and exosomes (EEXs) carry the characteristics of parent cells and transfer their contents to modulate the functions of recipient cells, holding the potential to evaluate or regulate vascular aging. Here, we found that young or aged ECs released EMVs were more effective than their released EEXs on alleviating or aggravating mice cerebrovascular and brain aging as indicated by SA-β-gal staining, cerebral blood flow, blood brain barrier function, aging related markers and cognitive ability test. We further identified that these EMVs regulated cerebrovascular and brain aging by transferring miR-17-5p and could modulate ECs senescence and functions via miR-17-5p/PI3K/Akt pathway. Plasma EMVs and their contained miR-17-5p (EMV-miR-17-5p) were significantly increased or decreased in the elderly, and were closely correlated with vascular aging. Receiver Operating Characteristic (ROC) analysis showed that the area under the curve was 0.724 for EMVs, 0.77 for EMV-miR-17-5p and 0.815 for their combination for distinguishing vascular aging. Our results revealed the novel roles for EMVs that could more effectively modulate vascular and brain aging than EEXs by regulating ECs functions through miR-17-5p/PI3K/Akt pathway, and also suggested that EMVs and EMV-miR-17-5p represent promising biomarkers and therapeutic targets for vascular aging.
Population dynamics hide phenotypic changes driven by subtle chemical exposures: implications for risk assessments
Authors: del Arco Ana , Becks Lutz , de Vicente Inmaculada
Published: February 2023

Ecological risk assessment of chemicals focuses on the response of different taxa in isolation not taking ecological and evolutionary interplay in communities into account. Its consideration would, however, allow for an improved assessment by testing for implications within and across trophic levels and changes in the phenotypic and genotypic diversity within populations. We present a simple experimental system that can be used to evaluate the ecological and evolutionary responses to chemical exposure at microbial community levels. We exposed a microbial model system of the ciliateTetrahymena thermophila(predator) and the bacteriumPseudomonas fluorescens(prey) to iron released from Magnetic Particles (MP-Fedis), which are Phosphorus (P) adsorbents used in lake restoration. Our results show that while the responses of predator single population size differed across concentrations of MP-Fedisand the responses of prey from communities differed also across concentration of MP-Fedis, the community responses (species ratio) were similar for the different MP-Fedisconcentrations. Looking further at an evolutionary change in the bacterial preys’ defence, we found that MP-Fedisdrove different patterns and dynamics of defence evolution. Overall, our study shows how similar community dynamics mask changes at evolutionary levels what would be overlooked in the design of current risk assessment protocols where evolutionary approaches are not considered.
Automated microarray for single-cell sorting and collection of lymphocytes following HIV reactivation
Authors: Cortés-Llanos Belén , Jain Vaibhav , Volkheimer Alicia , Browne Edward P. , Murdoch David M. , Allbritton Nancy L.
Published: February 2023

A promising strategy to cure HIV infected individuals is to use latency reversing agents (LRAs) to reactivate latent viruses, followed by host clearance of infected reservoir cells. However, reactivation of latent proviruses within infected cells is heterogeneous and often incomplete. This fact limits strategies to cure HIV which may require complete elimination of viable virus from all cellular reservoirs. For this reason, understanding the mechanism(s) of reactivation of HIV within cellular reservoirs is critical to achieve therapeutic success. Methodologies enabling temporal tracking of single cells as they reactivate followed by sorting and molecular analysis of those cells are urgently needed. To this end, microraft arrays were adapted to image T-lymphocytes expressing mCherry under the control of the HIV long terminal repeat (LTR) promoter, in response to the application of various LRAs (prostratin, iBET151, and SAHA). In response to prostratin, iBET151, and SAHA, 30.5 %, 11.2 %, and 12.1 % percentage of cells respectively, reactivated similar to that observed in other experimental systems. The arrays enabled large numbers of single cells (>25,000) to be imaged over time. mCherry fluorescence quantification identified cell subpopulations with differing reactivation kinetics. Significant heterogeneity was observed at the single cell level between different LRAs in terms of time to reactivation, rate of mCherry fluorescence increase upon reactivation, and peak fluorescence attained. In response to prostratin, subpopulations of T lymphocytes with slow and fast reactivation kinetics were identified. Single T-lymphocytes that were either fast or slow reactivators were sorted, and single-cell RNA-sequencing was performed. Different genes associated with inflammation, immune activation, and cellular and viral transcription factors were found. These results advance our conceptual understanding of HIV reactivation dynamics at the single-cell level toward a cure for HIV.
Individual prediction tendencies do not generalise across modalities
Authors: Schubert Juliane , Suess Nina , Weisz Nathan
Published: February 2023

Predictive processing theories, which model the brain as a “prediction machine”, explain a wide range of cognitive functions, including learning, perception and action. Furthermore, it is increasingly accepted that aberrant prediction tendencies play a crucial role in psychiatric disorders. Given this explanatory value for clinical psychiatry, prediction tendencies are often implicitly conceptualised as individual traits or as tendencies that generalise across situations. As this has not yet explicitly been shown, in the current study, we quantify to what extent the individual tendency to anticipate sensory features of high probability generalises across modalities. Using magnetoencephalography (MEG), we recorded brain activity while participants were presented a sequence of four different (either visual or auditory) stimuli, which changed according to predefined transitional probabilities of two entropy levels: ordered vs. random. Our results show that, on a group-level, under conditions of low entropy, stimulus features of high probability are preactivated in the auditory but not in the visual modality. Crucially, the magnitude of the individual tendency to predict sensory events seems not to correlate between the two modalities. Furthermore, reliability statistics indicate poor internal consistency, suggesting that the measures from the different modalities are unlikely to reflect a single, common cognitive process. In sum, our findings suggest that quantification and interpretation of individual prediction tendencies cannot be generalised across modalities.
Identical Tau Filaments in Subacute Sclerosing Panencephalitis and Chronic Traumatic Encephalopathy
Authors: Qi Chao , Hasegawa Masato , Takao Masaki , Sakai Motoko , Sasaki Mayasuki , Mizutani Masashi , Akagi Akio , Iwasaki Yasushi , Miyahara Hiroaki , Yoshida Mari , Scheres Sjors H.W. , Goedert Michel
Published: February 2023

Subacute sclerosing panencephalitis (SSPE) occurs in some individuals after measles infection, following a symptom-free period of several years. It resembles chronic traumatic encephalopathy (CTE), which happens after repetitive head impacts or exposure to blast waves, following a symptom-free period. As in CTE, when present, the neurofibrillary changes of SSPE are concentrated in superficial cortical layers. Here we used electron cryo-microscopy of tau filaments from two cases of SSPE to show that the tau folds of SSPE and CTE are identical. Two types of filaments were each made of two identical protofilaments with an extra density in the β-helix region. Like in CTE, the vast majority of tau filaments were Type I, with a minority of Type II filaments. These findings suggest that the CTE tau fold can be caused by different environmental insults, which may be linked by inflammatory changes.
Monitoring plasma nucleosome concentrations to measure disease response and progression in dogs with hematopoietic malignancies
Authors: Wilson-Robles Heather , Warry Emma , Miller Tasha , Jarvis Jill , Matsushita Matthew , Miller Pamela , Herzog Marielle , Turatsinze Jean-Valery , Kelly Theresa K. , Butera S. Thomas , Michel Gaetan
Published: February 2023

Background

Hematopoietic malignancies are extremely common in pet dogs and represent nearly 30% of the malignancies diagnosed in this population each year. Clinicians commonly use existing tools such as physical exam findings, radiographs, ultrasound and baseline blood work to monitor these patients for treatment response and remission. Circulating biomarkers, such as prostate specific antigen or carcinoembryonic antigen, can be useful tools for monitoring treatment response and remission status in human cancer patients. To date, there has a been a lack of useful circulating biomarkers available to veterinary oncology patients.

Methods

Circulating plasma nucleosome concentrations were evaluated at diagnosis, throughout treatment and during remission monitoring for 40 dogs with lymphoma, acute myelogenous leukemia and multiple myeloma. Additionally, C-reactive protein and thymidine kinase-1 levels were recorded.

Results

Plasma nucleosome concentrations were significantly higher at diagnosis and progressive disease than they were when dogs were in remission. All but two dogs had plasma nucleosome concentrations that returned to the low range during treatment. These two dogs had the shortest progression free and overall survival times. Dogs with the highest plasma nucleosome concentrations had a significantly shorter first progression free survival than dogs with lower plasma nucleosome concentrations at diagnosis. Plasma nucleosome concentrations correlated better with disease response and progression than either thymidine kinase or C reactive protein.

Conclusions

Plasma nucleosome concentrations can be a useful tool for treatment monitoring and disease progression in dogs with hematopoietic malignancies.
sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data
Authors: Ng Joseph CF , Garcia Guillem Montamat , Stewart Alexander T , Blair Paul , Dunn-Walters Deborah K , Mauri Claudia , Fraternali Franca
Published: February 2023

Class-switch recombination (CSR) is an integral part of B cell maturation. Steady-state analyses of isotype distribution (e.g. B cell receptor [BCR] repertoire analysis of snapshots during an immune response) do not directly measure CSR dynamics, which is crucial in understanding how B cell maturation is regulated across time. We present sciCSR (pronounced ‘scissor’, single-cell inference of class switch recombination), a computational pipeline which analyses CSR events and dynamics of B cells from single-cell RNA-sequencing (scRNA-seq) experiments. sciCSR re-analyses transcriptomic sequence alignments to differentiate productive heavy-chain immunoglobulin transcripts from germline “sterile” transcripts. From a snapshot of B cell scRNA-seq data, a Markov state model is built by the pipeline to infer the dynamics and direction of CSR. Applying sciCSR on SARS-CoV-2 vaccination time-course scRNA-seq data, we observe that sciCSR predicts, using data from an earlier timepoint in the collected time-course, the isotype distribution of BCR repertoires of subsequent timepoints with high accuracy (cosine similarity ∼ 0.9). sciCSR also recapitulates CSR patterns in mouse models where B cell maturation was perturbed using gene knockouts. sciCSR infers cell state transitions using processes specific to B cells, identifies transitions which are often missed by conventional RNA velocity analyses, and can reveal insights into the regulation of CSR and the dynamics of B cell maturation during an immune response.
Manganese Enhanced Magnetic Resonance Imaging reveals light-induced brain asymmetry in embryo
Authors: Lorenzi Elena , Tambalo Stefano , Vallortigara Giorgio , Bifone Angelo
Published: February 2023

The idea that sensory stimulation to the embryo (in uteroorin ovo) may be crucial for brain development is widespread. Unfortunately, up to now evidence was only indirect because imaging of embryonic brain activityin vivowas not viable. Here we applied for the first time Manganese Enhanced Magnetic Resonance Imaging (MEMRI) to the eggs of domestic chicks. We revealed light-induced brain asymmetry by comparing embryonic brain activityin vivoof eggs that were stimulated by light or maintained in the darkness. Our protocol paves the way to investigation of the effects of a variety of sensory stimulations on brain activity in embryo.

Significance

Sensory stimulation in embryo may be crucial for many aspects of brain and behavioral development (e.g., mother language in humans). However, direct evidence of this is lacking because imaging of embryonic brain activityin vivois not viable. Here we established a new protocol for measuring embryonic brain activityin vivoin domestic chick eggs. We were able to visualize in vivo the effect of light stimulation on the development of structural brain asymmetries of the embryo. The protocol established paves the way for collecting further evidence on the effects of sensory stimulation on embryonic brain activity.
Is environmental enrichment beneficial for laboratory animals? A systematic review of studies in zebrafish
Authors: Gallas-Lopes Matheus , Benvenutti Radharani , Donzelli Nayne I. Z. , Marcon Matheus
Published: February 2023

Environmental enrichment (EE) consists of a series of interventions that are carried out in the home environment to provide greater exposure to sensory stimuli with the objective of mimicking the natural habitat for the animals housed in the laboratory, offering a more complex environment like those found in nature. Some studies have shown the positive effects of EE on zebrafish housed in a laboratory environment. However, this evidence is still very recent and accompanied by contradictory results. Furthermore, there is great variability in the protocols applied, and in the conditions of the tests, tanks, and materials used for creating an EE environment. This substantial variability can bring many uncertainties to the development of future studies and hinder the reproducibility and replicability of research. In this context, the main objective of this study was to carry out a systematic review of the literature aiming to provide an overview of the EE protocols used in zebrafish. We conducted a systematic review following PRISMA recommendations. The literature search was performed in PubMed, Scopus, and Web of Science databases and the studies were selected based on inclusion/exclusion criteria. We performed data extraction and risk of bias analysis of the studies included. A total of 901 articles were identified in the databases and 27 of these studies were included in this review. Among these studies, the effect of EE was evaluated as two different proposals. (1) to improve animal welfare and (2) as an intervention for the prevention of some disorders. Although the zebrafish EE protocols presented a series of experimental differences, the results showed that the benefits of the EE for zebrafish were robust. According to the results described here, the use of EE in the zebrafish home tank provides better welfare and may reduce sources of bias in scientific experiments, such as high-stress levels and fighting events.
Broiler house environment and litter management practices impose selective pressures on antimicrobial resistance genes and virulence factors ofCampylobacter
Authors: Woyda Reed , Oladeinde Adelumola , Endale Dinku , Strickland Timothy , Lawrence Jodie Plumblee , Abdo Zaid
Published: February 2023

Campylobacterinfections are a leading cause of bacterial diarrhea in humans globally. Infections are due to consumption of contaminated food products and are highly associated with chicken meat, with chickens being an important reservoir forCampylobacter. Here, we characterized the genetic diversity ofCampylobacterspecies detected in broiler chicken litter over three consecutive flocks and determined their antimicrobial resistance and virulence factor profiles. Antimicrobial susceptibility testing and whole genome sequencing were performed onCampylobacter jejuni(n = 39) andCampylobacter coli(n = 5) isolates. AllC. jejuniisolates were susceptible to all antibiotics tested whileC. coli(n =4) were resistant to only tetracycline and harbored the tetracycline-resistant ribosomal protection protein (TetO). Virulence factors differed within and across grow houses but were explained by the isolates’ flock cohort, species and multilocus sequence type. Virulence factors involved in the ability to invade and colonize host tissues and evade host defenses were absent from flock cohort 3C. jejuniisolates as compared to flock 1 and 2 isolates. Our results show that virulence factors and antimicrobial resistance genes differed by the isolates’ multilocus sequence type and by the flock cohort they were present in. These data suggest that the house environment and litter management practices performed imposed selective pressures on antimicrobial resistance genes and virulence factors. In particular, the absence of key virulence factors within the final flock cohort 3 isolates suggests litter reuse selected forCampylobacterstrains that are less likely to colonize the chicken host.

Importance

Campylobacteris a leading cause of foodborne illness in the United States due to the consumption of contaminated food products or from mishandling of food products, often associated with chicken meat.Campylobacteris common in the microbiota of avian and mammalian gut; however, the acquisition of antimicrobial resistance genes and virulence factors may result in strains that pose a significant threat to public health. Although there are studies that have investigated the genetic diversity ofCampylobacterstrains isolated from post-harvest chicken samples, there is limited data on the genome characteristics of isolates recovered from pre-harvest broiler production. In this study, we show thatCampylobacter jejuniandCampylobacter colithat differ in their carriage of antimicrobial resistance and virulence factors may differ in their ability to evade host defense mechanisms and colonize the gut of chickens and humans. Furthermore, we found that differences in virulence factor profiles were explained by the species ofCampylobacterand its multilocus sequence type.
Engineering a symbiont as a biosensor for the honey bee gut environment
Authors: Chhun Audam , Moriano-Gutierrez Silvia , Zoppi Florian , Cabirol Amélie , Engel Philipp , Schaerli Yolanda
Published: February 2023

The honey bee is a powerful model system to probe host-gut microbiota interactions, and an important pollinator species for natural ecosystems and for agriculture. While bacterial biosensors can provide critical insight into the complex interplay occurring between a host and its associated microbiota, the lack of methods to non-invasively sample the gut content, and the limited genetic tools to engineer symbionts, have so far hindered their development in honey bees. Here, we built a versatile molecular toolkit to genetically modify symbionts and report for the first time in the honey bee a technique to sample their feces. We reprogrammed the native bee gut bacteriumSnodgrassella alvias a biosensor for IPTG, with engineered cells that stably colonize the gut of honey bees and report in a dose-dependent manner exposure through the expression of a fluorescent protein. We showed that fluorescence readout can be measured in the gut tissues or non-invasively in the feces. These tools and techniques will enable rapid building of engineered bacteria to answer fundamental questions in host-gut microbiota research.