bluuebunny/crossref_metadata_2025 huggingface dataset:
Basal forebrain activation improves working memory in senescent monkeys
Authors: Pennington Kendyl R , Debs Luca , Chung Sophia , Bava Janki , Garin Clément M , Vale Fernando L , Bick Sarah K , Englot Dario J , Terry Alvin V , Constantinidis Christos , Blake David T
Published: March 2024

Brain aging contributes to cognitive decline and risk of dementia. Degeneration of the basal forebrain cholinergic system parallels these changes in aging, Alzheimer’s dementia, Parkinson’s dementia, and Lewy body dementia, and thus is a common element linked to executive function across the lifespan and in disease states. Here, we tested the potential of one-hour daily intermittent basal forebrain stimulation to improve cognition in senescent monkeys, and its mechanisms of action. Stimulation in five animals improved working memory duration in 8-12 weeks across all animals, with peak improvements observed in the first four weeks. In an ensuing three month period without stimulation, improvements were retained. With additional stimulation, performance remained above baseline throughout the 15 months of the study. Studies with a cholinesterase inhibitor produced inconsistent improvements in behavior. One of five animals improved significantly. Manipulating the stimulation pattern demonstrated selectivity for both stimulation and recovery period duration. Brain stimulation led to acute increases in cerebrospinal levels of tissue plasminogen activator, which is an activating element for two brain neurotrophins, Nerve Growth Factor (NGF) and Brain-Derived Growth Factor (BDNF). Stimulation also led to improved glucose utilization in stimulated hemispheres relative to contralateral. Glucose utilization also consistently declines with aging and some dementias. Together, these findings suggest that intermittent stimulation of the nucleus basalis of Meynert improves executive function and reverses some aspects of brain aging.

Highlights

The basal forebrain and its cholinergic projections are the sole source of acetylcholine for the cortical mantle in primates and humans.

Forebrain function tracks cognitive loss throughout the adult lifespan.

One hour per day intermittent stimulation of this region improves executive function behaviors and plausibly reverses some aspects of brain aging, a large risk factor in dementias.

This stimulation exceeds impacts of standard pharmacotherapies, is enduring, recruits brain neurotrophic pathways and improves cortical glucose utilization.
Resistance to PSEN1-selective γ-secretase inhibitors in T-cell acute lymphoblastic leukemia
Authors: Vandersmissen Charlien , Demeyer Sofie , Jacobs Kris , Boogaerts Lien , Fernández Sara Gutiérrez , Segers Heidi , Chávez-Gutiérrez Lucía , Cools Jan
Published: March 2024

PSEN1-selective gamma-secretase inhibitors (GSI), such as MRK-560, are a potential option for the treatment of T-cell acute lymphoblastic leukemia (T-ALL) with NOTCH1 activating mutations, as these show less toxicity compared to broad-spectrum GSIs. However, an important challenge with targeted therapies for cancer treatment is the rapid development of drug resistance. We therefore investigated ifPSEN1mutations could confer resistance to MRK-560 in T-ALL. We performed a CRISPR-mediated mutagenesis screen in a T-ALL cell line to identify mutations leading to MRK-560 resistance and confirmed these findings in additional cell lines. We identified 3 types of resistance mutations. Mutations at the enzyme-drug interface directly disrupt the interaction of MRK-560 with PSEN1. Mutations at the enzyme-substrate interface cause a shift in relative binding affinities towards drug and/or substrate. The third resistance mechanism involves a mutation at the enzyme-substrate interface that hinders the entrance of MRK-560 to the binding pocket. These findings contribute to the understanding of the PSEN1-selectivity of MRK-560 and can help to design other PSEN1-selective GSIs to overcome resistance in cancer therapy.
Particulate Contamination of Human Placenta: Plastic and non-plastic
Authors: Zurub Rewa , Bainbridge Shannon , Rahman Luna , Halappanavar Sabina , Wade Michael G.
Published: March 2024

Recent evidence indicates that the human womb is contaminated with a variety of particulate contaminants. Microplastics (MPs, tiny plastic particles (<5 mm) generated by the breakdown of larger plastic products in the environment) accumulation in human placenta has recently been described. In addition, recent evidence has correlated the number of air pollution particulates in term placentas to the loading of these particles in dust from the gestational parent home. The current study sought to characterize the accumulation of plastic and non-plastic particles (NPP) within the term human placenta. Placenta tissues were collected from healthy, singleton pregnancies following vaginal (n=5) and caesarean section (n=5) deliveries at a tertiary care centre located in an urban Canadian city (Ottawa, ON), with particles detected and characterized by Raman micro-spectroscopy. Both plastic and non-plastic particles were identified in all placentas examined, with an average of 1 ± 1.2 MPs /g and 4 ± 2.9 NPP /g of tissue. Similar tissue concentrations of MPs and NNP were identified in all regions of the placenta (basal plate, chorionic villous, chorionic plate), and did not differ according to mode of delivery. MPs ranged in size (2 - 60 μm), with the most abundant MPs being polyethylene (PE), polypropylene (PP), polystyrene (PS) and polyvinyl chloride (PVC). The most abundantly identified NPP were carbon, graphite, and lead oxide. Collectively, these results demonstrate the accumulation of foreign particles, including MPs, throughout the human placenta. Given the vital functions of the placenta in supporting fetal growth and development, and a potential for MPs to induce toxicity, further investigations into the potential harmful effects of these environmental toxicants on maternal and fetal health is warranted.

Graphical Abstract

Highlights

Both plastic and non-plastic foreign particles were observed in term placentas from Canadian women

Placenta contamination with most of the non-plastic particle types observed has not previously been reported.

Particles were observed in similar frequency in placenta regions corresponding to maternal or fetal circulation suggesting that particles pass unhindered through the placenta.
Circadian Rhythms in Murine Ocular Tissues including Sclera are affected by Neurobasal A Medium Preincubation, Mouse Strain, but not Sex
Authors: Milićević Nemanja , Sandu Cristina , Challet Etienne , Ihalainen Teemu O. , Nymark Soile , Felder-Schmittbuhl Marie-Paule
Published: March 2024

Purpose

Our understanding of ocular clocks has been profoundly advanced by the development of real-time recording of bioluminescence of PER2::LUC knock-in mouse explants. However, the effect of sex, mouse strain and culturing conditions on ocular clocks remains unknown. Here, we studied the role these variables play on PER2::LUC bioluminescence rhythms of ocular tissues: retinas, corneas and posterior eye cups (PEC). We also tested the hypothesis that the sclera contains a circadian oscillator by using scraped PEC as a proxy.

Methods

Retinas, corneas, intact and scraped PECs were obtained from male and female PER2::LUC knock-in mice maintained on either a pigmented C57BL/6J or albino RjOrl:SWISS background. PER2::LUC bioluminescence rhythms in ocular tissues were measured using a Lumicycle®.

Results

We compared PER2::LUC bioluminescence rhythms between ocular tissues and found that all ocular tissues oscillated, including the scraped PEC, which was previously not known to oscillate. The rhythms in scraped PECs had lower amplitudes, longer periods and distinct acrophases compared to other ocular tissues. Ocular tissues of RjOrl:SWISS mice oscillated with higher amplitudes compared to the ones of C57BL/6J, with corneal rhythms being most affected by mouse strain. A 24h preincubation with Neurobasal A medium enhanced rhythms of ocular tissues, whereas sex differences were not detected for these rhythms.

Conclusions

We discovered a novel oscillator in the sclera. PER2::LUC bioluminescence rhythms in murine ocular tissues are enhanced by Neurobasal A medium preincubation, mouse strain but not sex.
CHEMOKINE SIGNALING IN BREAST CANCER: FOCUS ON CC-MOTIF CHEMOKINE LIGANDS
Authors: Kacar Sedat
Published: March 2024

Based on 2020 data from GLOBOCAN, breast cancer holds the highest incidence rate in the majority of countries (159 out of 185 countries) and is the leading cause of mortality in 110 countries Chemokines are 8-10 kDa proteins activating through transmembrane G-coupled receptors (GPCRs) with 24 CC-motif type known human cytokines and 10 respective receptors. Chemokines and chemokines receptors have the potential for new breast cancer therapeutics modalities. In the complex chemokine world, not only one chemokine can bind to multiple receptors but also one receptor can be activated by several chemokine ligands. The fact that immune cells possess the potential to express multiple receptors and also secrete a diverse number of chemokines further intensifies the intricate and challenging to grasp chemokines interaction with receptors and microenvironment. In addition, the implication of chemokines in the malignant activation of tumor cells makes them indispensable contributors to the cancer microenvironment and influences the fate of tumor cells and the overall survival of the patients. Therefore, herein, we aimed in this study at attracting the researchers’ attention to the particular function of all known CC-motif chemokines and to-date findings, their expressional changes in normal, tumor and tumor adjacent tissues, important key effects in breast cancer and more importantly, we analyzed the breast tumor samples’ expression data retrieved from TCGA, Xena UCSC as well as UALCAN database regarding to showing any potential to be a general, subclass-specific or stage-specific marker as well as effects of overall survival of the patients and their correlation with literature findings. Basically, we desire this study to be a sort of reference insights for effects of human CC-motif chemokines in breast cancer or provide ready-to-use source and insights for researchers with the graphs and analyzes from different databases.
An immune signature of postoperative cognitive decline in elderly patients
Authors: Verdonk Franck , Cambriel Amélie , Hedou Julien , Ganio Ed , Bellan Grégoire , Gaudilliere Dyani , Einhaus Jakob , Sabayev Maximilian , Stelzer Ina A. , Feyaerts Dorien , Bonham Adam T. , Ando Kazuo , Choisy Benjamin , Drover David , Heifets Boris , Chretien Fabrice , Aghaeepour Nima , Angst Martin S. , Molliex Serge , Sharshar Tarek , Gaillard Raphael , Gaudilliere Brice
Published: March 2024

Postoperative cognitive decline (POCD) is the predominant complication affecting elderly patients following major surgery, yet its prediction and prevention remain challenging. Understanding biological processes underlying the pathogenesis of POCD is essential for identifying mechanistic biomarkers to advance diagnostics and therapeutics. This longitudinal study involving 26 elderly patients undergoing orthopedic surgery aimed to characterize the impact of peripheral immune cell responses to surgical trauma on POCD. Trajectory analyses of single-cell mass cytometry data highlighted early JAK/STAT signaling exacerbation and diminished MyD88 signaling post-surgery in patients who developed POCD. Further analyses integrating single-cell and plasma proteomic data collected before surgery with clinical variables yielded a sparse predictive model that accurately identified patients who would develop POCD (AUC = 0.80). The resulting POCD immune signature included one plasma protein and ten immune cell features, offering a concise list of biomarker candidates for developing point-of-care prognostic tests to personalize perioperative management of at-risk patients. The code and the data are documented and available athttps://github.com/gregbellan/POCD.

Teaser

Modeling immune cell responses and plasma proteomic data predicts postoperative cognitive decline.
Chromatin packing domains persist after RAD21 depletion in 3D
Authors: Li Wing Shun , Carter Lucas M , Almassalha Luay Matthew , Pujadas-Liwag Emily M. , Kuo Tiffany , MacQuarrie Kyle L , Carignano Marcelo , Dravid Vinayak , Kanemaki Masato T. , Szleifer Igal , Backman Vadim
Published: March 2024

Understanding chromatin organization requires integrating measurements of genome connectivity and physical structure. Prior work demonstrates that RAD21 depletion results in the complete loss of topologically associated and loop domains on Hi-C, but the corresponding change in physical structure has not been studied using electron microscopy. Pairing chromatin scanning transmission electron tomography with Hi-C, we study the role of cohesin in regulating the spatially resolved, conformationally defined chromatin packing domains. We find that only 20% of packing domains are lost on electron microscopy upon RAD21 depletion with the effect primarily on small, poorly packed (nascent) domains. Overall, this contrasts with the prevailing understanding of genome regulation, indicating that while cohesin influences domain formation, non-cohesin mediated mechanisms predominantly regulate the 3D genomic physical structure.
Characterization of Composite Agarose-Collagen Hydrogels for Chondrocyte Culture
Authors: Zigan Clarisse , Alston Claudia Benito , Chatterjee Aritra , Solorio Luis , Chan Deva D.
Published: March 2024

To elucidate the mechanisms of cellular mechanotransduction, it is necessary to employ biomaterials that effectively merge biofunctionality with appropriate mechanical characteristics. Agarose and collagen separately are common biopolymers used in cartilage mechanobiology and mechanotransduction studies but lack features that make them ideal for functional engineered cartilage. In this study, agarose (8% w/v and 4% w/v) is blended with collagen type I (4mg/mL) to create composites. We hypothesized that a higher stiffness, composite hydrogel would promote native cartilage-like conditions. To address these questions, acellular and cell-laden studies were completed to assess rheologic and compressive properties, contraction, and structural homogeneity in addition to matrix mechanics, cell proliferation, and glycosaminoglycan production. Over 21 days in culture, cellular 4% agarose – 2mg/mL collagen I hydrogels displayed good structural and bulk mechanical properties, cell proliferation, and continual glycosaminoglycan production, indicating promise towards the development of an effective hydrogel for chondrocyte mechanotransduction and mechanobiology studies.

Graphical Abstract
Chrom-pro: A User-Friendly Toolkit for De-novo Chromosome Assembly and Genomic Analysis
Authors: Song Wei , Ye Tianrui , Liu Shaobo , Shen Dawei , Du Yuhui , Yang Yuening , Lu Yanming , Jin Hulin , Huo Yixin , Piao Weilan , Jin Hua
Published: March 2024

Chromosome-level genome assembly is fundamental to current genomic and post-genomic research, however, the process remains complicated and challenging due to the lack of a standardized automatic workflow. The frequently-used method for high-quality genome assembly generally employs second-generation sequencing (SGS) low error reads, third-generation sequencing (TGS) long reads and Hi-C reads. In this study, we developed a multifunctional toolkit called Chrom-pro that integrated commonly-used algorithms for de novo chromosome-level genome assembly with above three data sets into a user-friendly, automatic workflow. Besides chromosome assembly, Chrom-pro also encompasses multiple functionalities for genome quality assessment, comparative genomic analysis, and structural variant detection, which offers substantial support for downstream research. To evaluate the performance of Chrom-pro software, we tested the software with publicly available sequencing data of mango, pufferfish, and plum, and the excellence was confirmed by achieving a BUSCO completeness score of over 95% as well as high collinearity with the reference genome. Furthermore, we applied Chrom-pro to investigating the impact of different internal algorithm options on the accuracy of chromosome assembly, providing guidance for advancing relevant research in the future. Overall, the development of Chrom-pro will significantly improve the efficiency and quality of chromosome assembly and contributing to the advancement of genomic research.
2.5D Actuating Substrates Enable Decoupling the Mechanical and Biochemical Effects of Muscle Exercise on Motor Neurons
Authors: Bu Angel , Afghah Ferdows , Castro Nicolas , Bawa Maheera , Kohli Sonika , Shah Karina , Rios Brandon , Butty Vincent , Raman Ritu
Published: March 2024

Emergingin vivoevidence suggests that exercise impacts peripheral nerves, but the difficulty of isolating and studying the muscle-specific impact on motor neuronsin vivo, as well as the inability to decouple the biochemical and mechanical impacts of exercise in this setting, motivate investigating this phenomenonin vitro. In this study, we show that tuning the mechanical properties of fibrin hydrogels can generate stable 2.5D motor neuron and contractile skeletal muscle cultures that enable long-term efficient secretome harvesting from exercised tissues. Motor neurons stimulated with muscle-secreted cytokines significantly upregulate neurite outgrowth and migration, with an effect size dependent on exercise intensity. Actuating magnetic microparticles embedded within 2.5D substrates enabled us to dynamically stretch motor neurons and non-invasively mimic the mechanical effects of exercise, revealing that dynamic stretch has an equally significant impact on axonogenesis. RNA sequencing revealed different transcriptomic signatures between groups, with biochemical stimulation having a significantly greater impact on cell signaling related to axon growth and development, neuron projection guidance, and neuron-muscle synapse maturation. Our study thus leverages 2.5D actuating substrates to robustly validate a hypothesized role for muscle exercise in regulating motor neuron growth and maturation through both mechanical and biochemical signaling.
The CCR4/CCL17 axis drives intestinal acute Graft versus Host disease after allogeneic bone marrow transplantation
Authors: Schlaweck Sebastian , Klesse Michelle , Schanz Oliver , Jorch Selina K. , Kristiansen Glen , Toma Marieta , Flores Chrystel , Becker-Gotot Janine , Kurts Christian , Brossart Peter , Wolf Dominik , Heine Annkristin
Published: March 2024

Acute-Graft-versus-Host disease (aGvHD) is a life-threatening complication after allogeneic stem-cell-transplantation. It is mediated by alloreactive T cells whose trafficking to aGvHD target organs is orchestrated by chemokines.

We here asked whether CCL17 and its corresponding receptor CCR4 are involved in aGvHD development and severity. We applied an experimental mouse model of aGvHD in CCR4/CCL17 knockout mice and analyzed gut biopsies of GvHD patients.

We show that the absence of CCR4 in transplanted T cells induced significantly less severe aGvHD. This was accompanied by reduced expression of Gata3. Mechanistically, only CD4+, but not CD8+CCR4-/-T cells protected from aGvHD. We next identified dendritic cells in the small intestine to produce CCL17, which selectively recruited CD4+T cells. IL-4 production by intestinal CD4+T cells promoted proliferation of CD8+T cells. In line, we detected an upregulation of CCL17 andGata3in human aGvHD samples.

Our results indicate that local CCL17 production in aGvHD target organs recruits T cells, reinforcing local tissue damage and immune cell recruitment. We identified the JAK1/2-inhibitor ruxolitinib to dampen CCL17-expression, thereby reducing GvHD severity.

We here dissect a to date unknown role of the CCL17-CCR4 axis in aGvHD, which might help to develop novel therapeutic strategies.
Examination of the role of mutualism in immune evasion
Authors: Gourmet Lucie , Walker-Samuel Simon , Mallick Parag
Published: March 2024

Though the earliest stages of oncogenesis, post initiation, are not well understood, it is generally appreciated that a successful transition from a collection of dysregulated cells to an aggressive tumor requires complex ecological interactions between cancer cells and their environment. One key component of tumorigenesis is immune evasion. To investigate the interplay amongst the ecological behaviour of mutualism and immune evasion, we used a computational simulation framework. Sensitivity analyses of the growth of a virtual tumor implemented as a 2D-hexagonal lattice model suggests tumor survival depends on the interplay between growth rates, mutualism and immune evasion. In 60% of simulations, cancer clones with low growth rates, but exhibiting mutualism were able to evade the immune system and continue progressing suggesting that tumors with equivalent growth rates and no mutualism are more likely to be eliminated than tumors with mutualism. Tumors with faster growth rates showed a lower dependence upon mutualism for progression. Geostatistical analysis showed decreased spatial heterogeneity over time for polyclonal tumours with a high division rate. Overall, these results suggest that in slow growing tumors, mutualism is critical for early tumorigenesis.
Variety is the spice of life: nongenetic variation in life histories influences population growth and evolvability
Authors: Forsythe Amy B. , Otto Sarah P. , Nelson William A. , Day Troy
Published: March 2024

Individual vital rates are key determinants of lifetime reproductive success, and variability in these rates shapes population dynamics. Previous studies have found that this vital rate hetero-geneity can influence demographic properties including population growth rates, however, the explicit effects of the amount of variation within and the covariance between vital rates that can also vary throughout the lifespan on population growth remains unknown. Here, we explore the analytical consequences of nongenetic heterogeneity on long-term population growth rates and rates of evolution by modifying traditional age-structured population projection matrices to incorporate variation among individual vital rates. The model allows vital rates to be permanent throughout life (“fixed condition”) or to change over the lifespan (“dynamic condition”). We reduce the complexity associated with adding individual heterogeneity to age-structured models through a novel application of matrix collapsing (“phenotypic collapsing”), showing how to collapse in a manner that preserves the asymptotic and transient dynamics of the original matrix. The main conclusion is that nongenetic individual heterogeneity can strongly impact the longterm growth rate and rates of evolution. The magnitude and sign of this impact depends heavily on how the heterogeneity covaries across the lifespan of an organism. Our results emphasize that nongenetic variation cannot simply be viewed as random noise, but rather that it has consistent, predictable effects on fitness and evolvability.
Evolved and plastic gene expression in adaptation to a novel niche
Authors: Steward Rachel A , Ortega Giménez Jesús , Choudhary Shruti , Yi Su , Aken Olivier Van , Runemark Anna
Published: March 2024

Gene expression, resulting from complex regulatory interactions, plays an important role in adaptation and speciation. While gene expression historically has been studied in the context of reproductive isolation in speciation research, a role for evolved differences in gene expression in adaptation to novel niches is increasingly appreciated. How gene expression evolves and enables divergent ecological adaptation, and how changes in gene expression relate to genomic architecture and genetic divergence are pressing questions in understanding the processes of adaptation and ecological speciation. Further, how plasticity in gene expression can both contribute to and be affected by the process of ecological adaptation is a crucial component in understanding gene expression evolution. To address these questions, we investigate the role of evolved and plastic gene expression differences in adaptation leveraging an established host plant shift in the peacock flyTephritis conura. Using a cross-fostering design where larvae feed on either natal or alternate host plants, we uncover extensive evolved differences in gene expression between the ecotypes, strikingly in genes associated with processing of host plant chemicals. We find limited evidence for plasticity, with some indications of higher plasticity in the ancestral ecotype where the expression of three gene coexpression modules is altered when larvae are cross-fostered to the derived host plant. Interestingly, we find an enrichment of differentially expressed genes within a large, ecotype-specific inversion in theT. conuragenome. This finding adds to evidence that inversions are important for enabling diversification in the face of gene flow and underscores that effects on gene expression may be key to understanding the role of inversions.
Harnessing Transformers to Generate Protein Sequences Prone to Liquid Liquid Phase Separation
Authors: Wasim Abdul , Pramanik Ushasi , Das Anirban , Latua Pikaso , Rudra Jai S. , Mondal Jagannath
Published: March 2024

Understanding the molecular grammar that governs protein phase separation is essential for advancements in bioinformatics and protein engineering. This study leverages Generative Pre-trained Transformer (GPT)-based Protein Language Models (PLMs) to decode the complex grammar of proteins prone to liquid-liquid phase separation (LLPS). We trained three distinct GPT models on datasets comprising amino acid sequences with varying LLPS propensities: highly predisposed (LLPS+ GPT), moderate (LLPS-GPT), and resistant (PDB* GPT). As training progressed, the LLPS-prone model began to learn embeddings that were distinct from those in LLPS-resistant sequences. These models generated 18,000 protein sequences ranging from 20 to 200 amino acids, which exhibited low similarity to known sequences in the SwissProt database. Statistical analysis revealed subtle but significant differences in amino acid occurrence probabilities between sequences from LLPS-prone and LLPS-resistant models, suggesting distinct molecular grammar underlying their phase separation abilities. Notably, sequences from LLPS+ GPT showed fewer aromatic residues and a higher fraction of charge decoration. Short peptides (20-25 amino acids) generated from LLPS+ GPT underwent computational and wet-lab validation, demonstrating their ability to form phase-separated states in vitro. The generated sequences enriched the existing database and enabled the development of a robust classifier that accurately distinguishes LLPS-prone from non-LLPS sequences. This research marks a significant advancement in using computational models to explore and engineer the vast protein sequence space associated with LLPS-prone proteins.
Crimean-Congo Hemorrhagic Fever Survivors Elicit Protective Non-Neutralizing Antibodies that Target 11 Overlapping Regions on Viral Glycoprotein GP38
Authors: Shin Olivia S. , Monticelli Stephanie R. , Hjorth Christy K. , Hornet Vladlena , Doyle Michael , Abelson Dafna , Kuehne Ana I. , Wang Albert , Bakken Russell R. , Mishra Akaash , Middlecamp Marissa , Champney Elizabeth , Stuart Lauran , Maurer Daniel P. , Li Jiannan , Berrigan Jacob , Barajas Jennifer , Balinandi Stephen , Lutwama Julius J. , Lobel Leslie , Zeitlin Larry , Walker Laura M. , Dye John M. , Chandran Kartik , Herbert Andrew S. , Pauli Noel T. , McLellan Jason S.
Published: March 2024

Crimean-Congo hemorrhagic fever virus can cause lethal disease in humans yet there are no approved medical countermeasures. Viral glycoprotein GP38, unique toNairoviridae, is a target of protective antibodies, but extensive mapping of the human antibody response to GP38 has not been previously performed. Here, we isolated 188 GP38-specific antibodies from human survivors of infection. Competition experiments showed that these antibodies bind across five distinct antigenic sites, encompassing eleven overlapping regions. Additionally, we reveal structures of GP38 bound with nine of these antibodies targeting different antigenic sites. Although GP38-specific antibodies were non-neutralizing, several antibodies were found to have protection equal to or better than murine antibody 13G8 in two highly stringent rodent models of infection. Together, these data expand our understanding regarding this important viral protein and inform the development of broadly effective CCHFV antibody therapeutics.
Nutrient loading from a sustainably certified aquaculture operation dwarfs annual nutrient inputs from a large multi-use watershed, Lake Yojoa, Honduras
Authors: Fadum J.M. , Ross M.V.R. , Tenorio E. A. , Barby C.A. , Hall E.K.
Published: March 2024

Net-pen aquaculture is a popular and increasingly prevalent method for producing large quantities of low-fat protein in freshwater ecosystems across the tropics. While there are numerable social and economic advantages associated with aquaculture, there are also challenges related to the environmental sustainability of aquaculture. Chief among these risks is excessive nutrient loading which can drive rapid eutrophication in aquatic ecosystems. In this study, we compare the estimated annual nutrient loads from the six principal tributaries that contribute to Lake Yojoa to the estimated nutrient load of a large net-pen Tilapia operation located in the central region of the lake. We estimated that the Tilapia farm was responsible for ~ 86% of nitrogen (N) and ~95% of the phosphorus (P) annual contributions to Lake Yojoa. This disproportionate nutrient loading of both N and P suggests that this single aquaculture operation, more so than changes in nutrients inputs from the watershed, was responsible for the previously documented deterioration of the Lake Yojoa ecosystem. This study shows the potential for net-pen aquaculture to have disproportionately negative impacts on freshwater ecosystems, even when operations meet all standards for the current state-of-the-art sustainability certifications. We suggest shifts in metrics that could improve the impact of the certification process so that best practices can reduce the impact of net-pen aquaculture on freshwater ecosystems and arrive at the intended goal of long-term environmental sustainability.
Temporal interference electrical neurostimulation yields fMRI BOLD activation in humans
Authors: Modak Priyamvada , Fine Justin , Colon Brayden , Need Ella , Hulvershorn Leslie , Finn Peter , Brown Joshua W
Published: March 2024

Temporal interference electrical neurostimulation (TI) is a relatively new method of non-invasive neurostimulation that may be able to stimulate deep brain regions without stimulating the overlying superficial regions. Despite studies in rodents, almost no studies have investigated its effects on human brain activity along with safety and tolerability profiles. We performed simultaneous TI stimulation and fMRI to investigate the effects of TI on human BOLD signals. Here we show that TI can induce increased BOLD activation in humans, with good safety and tolerability profiles. We also show the limits of spatial precision and explore the nature and causes of additional off target effects. TI may be a promising approach for addressing questions about the causal role of deep brain structures in human cognition and may also afford new clinical treatments.
Investigating the mode of action for wasting produced by tetrachlorodibenzo-p-dioxin (TCDD) in rats using transcriptomics: Evidence for roles of AHR and ARNT in circadian cycling
Authors: Andersen Melvin E. , Barutcu A. Rasim , Black Michael B. , Harrill Joshua A.
Published: March 2024

Single, high doses of TCDD in rats caused wasting, a progressive loss of 30 to 50% body weight and death within several weeks. To identify pathway perturbations at or near doses causing wasting, we examined differentially gene expression (DGE) and pathway enrichment in centrilobular (CL) and periportal (PP) regions of female rat livers following 6 dose levels of TCDD – 0, 3, 22, 100, 300, and 1000 ng/kg/day, 5 days/week for 4 weeks. At the higher doses, rats lost weight, had increased liver/body weight ratios and nearly complete cessation of liver cell proliferation, signs consistent with wasting. DGE curves were left shifted for the CL versus the PP regions. Canonical Phase I and Phase II genes were maximally increased at lower doses and remained elevated at all doses. At lower doses,<22 ng/kg/day in the CL and<100 ng/kg/day, upregulated genes showed transcription factor (TF) enrichment for AHR and ARNT. At the mid- and hi-dose doses, there was a large number of downregulated genes and pathway enrichment for DEGs showed downregulation of many cellular metabolism processes including those for steroids, fatty acid metabolism, pyruvate metabolism and citric acid cycle. There was significant TF enrichment of the hi-dose downregulated genes for RXR, ESR1, LXR, PPARalpha. At the highest dose, there was also pathway enrichment with upregulated genes for extracellular matrix organization, collagen formation, hemostasis and innate immune system. TCDD demonstrates most of its effects through binding the aryl hydrocarbon receptor (AHR) while the downregulation of metabolism genes at higher TCDD doses is known to be independent of AHR binding to DREs. Based on our results with DEG, we provide a hypothesis for wasting in which high doses of TCDD shifts circadian processes away from the resting state leading to greatly reduced synthesis of steroids and complex lipids needed for cell growth and producing gene expression signals consistent with an epithelial-to-mesenchymal transition in hepatocytes.
Rectal Swab DNA Collection Protocol for PCR Genotyping in Rats
Authors: Kaye Audrey E. , Proctor-Bonbright Jacob W. , Yu Jai Y.
Published: March 2024

DNA collection is essential for genotyping laboratory animals. However, common collection methods require tissue amputation, causing discomfort and injury. Rectal swabbing has been proposed as an effective non-invasive alternative, but an evidence-backed protocol for the technique remains unavailable. We evaluate the effect of collection parameters on PCR result quality and present a genotyping protocol that can yield results for a litter of rats within 3-5 hours. We found that samples with 2-8 scrapes produced enough DNA to amplify targets up to ∼1800bp long using PCR. Rectal swabbing produced PCR results with similar quality to ear clip samples, and results were unaffected by residual fecal matter or cell debris. Our protocol enables fast, non-invasive, and repeatable genotyping using commercial PCR reagents.
Transformer-Based Deep Learning Model with Latent Space Regularization for CRISPR-Cas Protein Sequence Classification
Authors: Nammi Bharani , Madugula Sita Sirisha , Pujar Pranav , Arachchige Vindi Mahesha Jayasinghe , Liu Jin , Wang Shouyi
Published: March 2024

The discovery of the CRISPR-Cas system has significantly advanced genome editing, offering vast applications in medical treatments and life sciences research. Despite their immense potential, the existing CRISPR-Cas proteins still face challenges concerning size, delivery efficiency, and cleavage specificity. Addressing these challenges necessitates a deeper understanding of CRISPR-Cas proteins to enhance the design and discovery of novel Cas proteins for precision gene editing. In this study, we performed extensive deep-learning research on CRISPR-Cas proteins, aiming to develop a classification model capable of distinguishing CAS from non-CAS proteins, as well as discriminating sub-categories of CAS proteins, specifically CAS9 and CAS12. We developed two types of deep learning models: 1) a transformer encoder-based classification model, trained from scratch; and 2) a large protein language model fine-tuned on ProtBert, pre-trained on more than 200 million proteins. To boost learning efficiency for the model trained from scratch, we introduced a novel margin-based loss function to maximize inter-class separability and intra-class compactness in protein sequence embedding latent space of a transformer encoder. The experimental results show that the Fine-Tuned ProtBert-based (FTPB) classification model achieved accuracies of 99.06%, 94.42%, 96.80%, 97.57% for CAS9 vs. Non-CAS, CAS12 vs. Non-CAS, CAS9 vs. CAS12, and multi-class classification of CAS9 vs. CAS12 vs. Non-CAS, respectively. The Latent Space Regularized Max-Margin Transformer (LSRMT) model achieved classification accuracies of 99.81%, 99.81%, 99.06%, 99.27% for the same tasks, respectively. These results demonstrate the effectiveness of the proposed Max-Margin-based latent space regularization in enhancing model robustness and generalization capabilities. Remarkably, the LSRMT model, even when trained on a significantly smaller dataset, outperformed the fine-tuned state-of-the-art large protein model. The high classification accuracies achieved by the LSRMT model demonstrate its proficiency in identifying discriminative features of CAS proteins, marking a significant step towards advancing our understanding of CAS protein structures in future research endeavors.
Thymic dendritic cell-derived IL-27p28 promotes the establishment of functional bias against IFN-γ production in newly generated CD4+T cells through STAT1-related epigenetic mechanisms
Authors: Zhang Jie , Tang Hui , Wu Haoming , Pang Xuewen , Jin Rong , Zhang Yu
Published: March 2024

The newly generated CD4 single-positive (SP) T lymphocytes are featured by enhanced IL-4 but repressed IFN-γ production. The mechanisms underlying this functional bias remain elusive. Previous studies have reported that CD4+T cells from mice harboring DC-specific deletion of IL-27p28 display an increased capacity of IFN-γ production upon TCR stimulation. Here we demonstrated that similarly altered functionality occurred in CD4SP thymocytes, recent thymic emigrants (RTEs), as well as naive T cells from eitherCd11c-p28f/fmice or mice deficient in the α subunit of IL-27 receptor. Therefore, DC-derived IL-27p28-triggered, IL-27Rα-mediated signal is critically involved in the establishment of functional bias against IFN-γ production during their development in the thymus. Epigenetic analyses indicated reduced DNA methylation of theIfnglocus and increased trimethylation of H3K4 at bothIfngandTbx21loci in CD4SP thymocytes fromCd11c-p28f/fmice. Transcriptome profiling demonstrated thatIl27p28ablation resulted in the coordinated up-regulation of STAT1-activated genes. Concurrently, STAT1 was found to be constitutively activated. Moreover, we observed increased accumulation of STAT1 at theIfngandTbx21loci and a strong correlation between STAT1 binding and H3K4me3 modification of these loci. Of note,Il27p28deficiency exacerbated the autoimmune phenotype ofAire-/-mice. Collectively, this study reveals a novel mechanism underlying the functional bias of newly generated CD4+T cells and the potential relevance of such a bias in autoimmunity.

Graphical abstract
Unsupervised generative AI discovers pan-leukocyte dysregulated pathways in single-cell lupus data
Authors: Bolouri Hamid , Cerosaletti Karen , Lacy-Hulbert Adam
Published: March 2024

Comparisons of single-cell RNA-sequencing (scRNA-seq) data from healthy and diseased tissues are widely used to identify cell-type-specific dysregulated genes, pathways, and processes. Accordingly, many sophisticated methods have been developed for this purpose. However, such tools generally require considerable user expertise for optimal performance. Here, we show that unsupervised application of a linearly-decoded Variational Auto Encoder (a generative AI model) to scRNA-seq data recapitulates and extends findings from a seminal recent lupus study and leads to new insights. Thanks to existing software libraries, our approach is straightforward to implement, computationally efficient, methodologically robust, and produces consistent and reproducible results.
Conformational landscape of soluble α-klotho revealed by cryogenic electron microscopy
Authors: Schnicker Nicholas J. , Xu Zhen , Amir Mohammad , Gakhar Lokesh , Huang Chou-Long
Published: March 2024

α-Klotho (KLA) is a type-1 membranous protein that can associate with fibroblast growth factor receptor (FGFR) to form co-receptor for FGF23. The ectodomain of unassociated KLA is shed as soluble KLA (sKLA) to exert FGFR/FGF23-independent pleiotropic functions. The previously determined X-ray crystal structure of the extracellular region of sKLA in complex with FGF23 and FGFR1c suggests that sKLA functions solely as an on-demand coreceptor for FGF23. To understand the FGFR/FGF23-independent pleiotropic functions of sKLA, we investigated biophysical properties and structure of apo-sKLA. Mass photometry revealed that sKLA can form a stable structure with FGFR and/or FGF23 as well as sKLA dimer in solution. Single particle cryogenic electron microscopy (cryo-EM) supported the dimeric structure of sKLA. Cryo-EM further revealed a 3.3Å resolution structure of apo-sKLA that overlays well with its counterpart in the ternary complex with several distinct features. Compared to the ternary complex, the KL2 domain of apo-sKLA is more flexible. 3D variability analysis revealed that apo-sKLA adopts conformations with different KL1-KL2 interdomain bending and rotational angles. The potential multiple forms and shapes of sKLA support its role as FGFR-independent hormone with pleiotropic functions. A comprehensive understanding of the sKLA conformational landscape will provide the foundation for developing klotho-related therapies for diseases.
Integration of pH control into Chi.Bio reactors and demonstration with small-scale enzymatic poly(ethylene terephthalate) hydrolysis
Authors: Denton Mackenzie C.R. , Murphy Natasha P. , Norton-Baker Brenna , Lua Mauro , Steel Harrison , Beckham Gregg T.
Published: March 2024

Small-scale bioreactors that are affordable and accessible would be of major benefit to the research community. In previous work, an open-source, automated bioreactor system was designed to operate up to the 30 mL scale with online optical monitoring, stirring, and temperature control, and this system, dubbed Chi.Bio, is now commercially available at a cost that is typically 1-2 orders of magnitude less than commercial bioreactors. In this work, we further expand the capabilities of the Chi.Bio system by enabling continuous pH monitoring and control through hardware and software modifications. For hardware modifications, we sourced low-cost, commercial pH circuits and made straightforward modifications to the Chi.Bio head plate to enable continuous pH monitoring. For software integration, we introduced closed-loop feedback control of the pH measured inside the Chi.Bio reactors and integrated a pH-control module into the existing Chi.Bio user interface. We demonstrated the utility of pH control through the small-scale depolymerization of the synthetic polyester, poly(ethylene terephthalate) (PET), using a benchmark cutinase enzyme, and compared this to 250 mL bioreactor hydrolysis reactions. The results in terms of PET conversion and rate, measured both by base addition and product release profiles, are statistically equivalent, with the Chi.Bio system allowing for a 20-fold reduction of purified enzyme required relative to the 250 mL bioreactor setup. Through inexpensive modifications, the ability to conduct pH control in Chi.Bio reactors widens the potential slate of biochemical reactions and biological cultivations for study in this system, and may also be adapted for use in other bioreactor platforms.
Vegetative stage and soil horizon determine direction and magnitude of rhizosphere priming effects in contrasting treeline soils
Authors: Michel Jennifer , Fontaine Sébastien , Revaillot Sandrine , Piccon-Cochard Catherine , Whitaker Jeanette
Published: March 2024

Treelines in high latitudes and high altitudes are considered sentinels of global change. This manifests in accelerated encroachment of trees and shrubs and enhanced plant productivity, with currently unknown implications for the carbon balance of these biomes. Given the large soil organic carbon stocks in many treeline soils, we here wondered whether introducing highly productive plants would accelerate carbon cycling through rhizosphere priming effects and if certain soils would be more vulnerable to carbon loss from positive priming than others.

To test this, organic and mineral soils were sampled above and below treelines in the Swedish sub-arctic and the Peruvian Andes. A greenhouse experiment was then performed to quantify plant-induced changes in soil mineralisation rates (rhizosphere priming effect) and new C formation using natural abundance labelling and the C4-species Cynodon dactylon. Several environmental, plant, soil and microbial parameter were monitored during the experiment to complement the observations on soil C cycling.

Priming was predominantly positive at the beginning of the experiment, then systematically decreased in all soils during the plant growth season to be mostly negative at the end of the experiment at plant senescence. Independent of direction of priming, the magnitude of priming was always greater in organic than in corresponding mineral soils, which was best explained by the higher C contents of these soils. Integrated over the entire study period, the overall impact of priming (positive and negative) on the soil C balance was mostly negligible. Though, net soil C loss was observed in organic soils from the sub-arctic tundra in Sweden.

Most notably, positive and negative priming effects were not mutually exclusive, rather omnipresent across ecosystems, depending on sampling time. The direction of priming seems to be fluctuating with plant productivity, rhizosphere carbon inputs and nutrient uptake. This highlights the need for integrative long-term studies if we aim to understand priming effects at ecosystem scale and greenhouse and laboratory studies must be validated in situ to enable reliable ecological upscaling.
Causal Brain Network Evaluates Surgical Outcomes in Patients with Drug-Resistant Epilepsy
Authors: Wang Yalin , Liu Minghui , Lin Wentao , Zheng Weihao , Wang Tiancheng , Liu Yaqing , Peng Hong , Chen Wei , Hu Bin
Published: March 2024

Network neuroscience has greatly facilitated epilepsy studies; meanwhile, drug-resistant epilepsy (DRE) is increasingly recognized as a brain network disorder. Unfortunately, surgical success rates in patients with DRE are still very limited, varying 30% ∼ 70%. At present, there is almost no systematic exploration of intracranial electrophysiological brain network closely related to surgical outcomes, and it is not clear which brain network methodologies can effectively promote DRE precision medicine. In this retrospective comparative study, we included multicenter datasets, containing electrocorticogram (ECoG) data from 17 DRE patients with 55 seizures. Ictal ECoG within clinically-annotated epileptogenic zone (EZ) and non-epileptogenic zone (NEZ) were separately computed using six different algorithms to construct causal brain networks. All the brain network results were divided into two groups, successful and failed surgery. Statistical results based on the Mann-Whitney-U-test show that: causal connectivity of α-frequency band (8 ∼ 13 Hz) in EZ calculated by convergent cross mapping (CCM) gains the most significant differences between the surgical success and failure groups, with aPvalue of 7.85e-08 and Cohen’s d effect size of 0.77. CCM-defined EZ brain network can also distinguish the successful and failed surgeries considering clinical covariates (clinical centers, DRE types) withP< 0. 001. Based on the brain network features, machine learning models are established to predict the surgical outcomes. Among them, SVM classifier with Gaussian kernel function and Bayesian Optimization demonstrates the highest average accuracy of 84.48% through 5-fold cross validation, further indicating that the CCM-defined EZ brain network is a reliable biomarker for predicting DRE’s surgical outcomes.