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  • Effects of aperiodic neural activity on sleep-based emotional memory consolidation across the lifespan
    by Cross, Z. R., Santamaria, A., Coussens, S. W., Kohler, M. J.
    Sleep neurophysiology undergoes significant changes across the lifespan, which coincide with age related differences in memory, particularly for emotional information. However, the mechanisms that underlie these effects remain poorly understood. One potential mechanism is the aperiodic component, which reflects "neural noise", differs across age, and is predictive of perceptual and cognitive processes. In this study, we investigated how intrinsic (i.e., resting state) aperiodic neural activity modulates sleep based emotional memory consolidation across the human lifespan. In a within-subjects, repeated measures […]
  • Regional species coexistence despite local priority effects: the overlooked role of dispersal-community feedback
    by Nell, L. A., Klausmeier, C. A., Fukami, T.
    Many cases of animal-mediated dispersal are non-random, with the animals altering their movement pattern in response to the local species composition of the organisms that the vectoring animals disperse. Yet, this dispersal-community feedback has received little attention in metacommunity ecology. We use a mathematical model to show that dispersal-community feedback can promote regional species coexistence. As a well-characterized system, our model focuses on nectar-inhabiting bacteria and yeast that are dispersed by pollinators and affected by priority effects within flowers once […]
  • How drought and ploidy level shape gene expression and DNA methylation in Phragmites australis
    by Kuprina, K., Haldan, K., Saenko, S., Gulam, M. S., Kreyling, J., Schnittler, M., Bog, M.
    Drought stress significantly affects plant physiology and growth, yet the molecular mechanisms underlying drought responses remain poorly understood. In this study, we investigate how tetraploid and octoploid Phragmites australis (common reed), a key species in wetland ecosystems and paludiculture, respond to drought at the transcriptional and epigenetic levels. Using RNA-seq, we identify changes in gene expression after 20 and 30 days of drought and assess methylation-sensitive amplification polymorphism (MSAP) over 50 days of drought. Transcriptomic analysis reveals that key drought-response […]
  • Development and Clinical Evaluation of a Multiplexed Health Surveillance Panel Using Ultra High-Throughput PRM-MS in an Inflammatory Bowel Disease Cohort.
    by Fu, Q., Remes, P. M., Lee, J., Jacob, C., Li, D., Vegensna, M., Raedschelders, K., Haghani, A., Mengesha, E., Debbas, P., Hoedt, E., Joung, S., Cheng, S., Peterman, S., Fert-Bober, J., Melmed, G. Y., McGovern, D. P. B., Murray, C. I., Van Eyk, J. E.
    Despite advances in clinical proteomics, translating protein biomarker discoveries into clinical use remains challenging due to the technical complexity of the validation process. Targeted MS-based proteomics approaches such as parallel reaction monitoring (PRM) offer sensitive and specific assays for biomarker translation. In this study, we developed a multiplex PRM assay using the Stellar mass spectrometry platform to quantify 57 plasma proteins, including 21 FDA-approved proteins. Loading curves (11-points) were performed at 4 sample throughputs (100, 144, 180, and 300 samples […]
  • Population structure and domestication history of the Javan banteng (Bos javanicus javanicus)
    by Wang, X., Aninta, S. G., Garcia-Erill, G., Li, Z., Khan, A., Liu, X., Bertola, L. D., Dharmayanthi, A. B., Yulianto,, Yonathan,, Rossi, C., Cauble-Sims, R., Rosen, B. D., Hagen, D. E., Heaton, M. P., Smith, T. P. L., Lenstra, J. A., Martins, N. F. G., Sinding, M.-H. S., Agil, M., Purwantara, B., Hvilsom, C., Semiadi, G., Heller, R.
    The domestication of the banteng in Southeast Asia is one of the World's least known livestock domestications, yet a vital component of the agricultural system in Indonesia and surrounding countries. Here we generated the first reference genome of the banteng and used it to analyze a set of 78 resequenced wild and domesticated bantengs, including 19 newly generated whole-genome sequenced samples of which three are historical samples. We found low heterozygosity and significant differentiation, the latter primarily driven by recent […]
  • Lymphatic Malformations with Activating KRAS Mutations Impair Lymphatic Valve Development Through Matrix Metalloproteinases
    by Mastrogiacomo, D. M., Price, A., Fu, Y., Banerjee, R., Knauer, L. A., Li, K., Yang, Y., Davis, G. E., Dellinger, M., Scallan, J. P.
    BACKGROUND: Lymphatic malformations (LMs) are lesions due to inherited or somatic mutations that lead to a defective lymphatic vasculature. Activating KRAS mutations have been identified recently in LM patients with lymphedema, chylous ascites, or life-threatening chylothorax. In a LM mouse model, KRAS mutations are associated with a loss of lymphatic valves, which has been proposed to cause chylothorax via retrograde lymph flow into the pleural space. However, the mechanisms underlying the loss of lymphatic valves are unknown. METHODS: To investigate […]
  • The response of the relationship between carbon components and soil aggregates in vegetable fields to continuous input of different carbon sources
    by Peng, Y. Y., Xilatu, D., Huang, J. L., Peng, Y. Q., PENG, Y., Li, S. X.
    Aims: To address the issue of declining soil organic carbon (SOC) in vegetable fields, this study investigated the effects of continuous input of different carbon sources on soil carbon pool dynamics. Methods: A five-year field plot experiment was conducted to analyze the impact of organic fertilizer, biochar, and their combined application on soil organic carbon components, aggregate stability, and carbon pool characteristics. Results: The continuous application of biochar and organic fertilizer significantly increased the content of soil organic carbon components. […]
  • Lysophosphatidic acid controls autotaxin binding to 1-integrin: impact on disease progression in murine collagen-induced arthritis.
    by Emery, M., Cuero, C. N., Bouazza, L., Internicola, C., Duboeuf, F., Cerecero-Aguirre, P., McCarthy, A. A., Machuca-Gayet, I., Leblanc, R., Peyruchaud, O.
    Autotaxin (ATX) is a lysophospholipase D (lysoPLD) serving as both a lysophosphatidic acid (LPA)-producing enzyme and a LPA docking molecule. ATX binds to the cell surface via interaction with adhesive molecules, including [beta]1-integrin, potentially facilitating LPA access to its specific G protein-coupled receptors. However, the precise protein-protein interaction sequences and their biological implications remain unknown. Here, we identify the interaction domains between ATX and [beta]1-integrin and generate specific blocking antibodies allowing to demonstrate that ATX-[beta]1 binding domain involves a cryptic […]
  • Observational social learning of "know-how" and "know-what" in wild orangutans: evidence from nest-building skill acquisition
    by Permana, A., Permana, J. J., Nellissen, L., Prayogi, E. S., Prasetyo, D., Wich, S. A., van Schaik, C. P., Schuppli, C.
    Immature great apes learn how to build their nests over multiple years, yet how they do so has remained largely unclear. We investigated the detailed role of social learning in the acquisition of nest-building skills in wild Sumatran orangutans (Pongo abelii) using data on nest-building, nest practice, and nest peering behaviour from 44 individuals, collected over 17 years. We found that nest peering (but not being close to a nesting individual without peering) is associated with a significant increase in […]
  • Plasticity induction in the ventromedial prefrontal cortex during REM sleep improves fear extinction memory consolidation
    by Markovic, V., Rizzo, G., Yavari, F., Vicario, C., Nitsche, M.
    Anxiety disorders (ADs) are among the most prevalent mental health conditions, yet first-line treatments often yield only moderate effectiveness. The fear conditioning paradigm is commonly used to investigate fear and extinction learning, revealing deficits in these processes and dysfunctional activity in the ventromedial prefrontal cortex (vmPFC) and amygdala in individuals with ADs. The vmPFC plays a critical role in regulating activity of the amygdala and consolidation of fear extinction memory. Notably, transcranial direct current stimulation (tDCS) has shown promise in […]
  • Hypoxia-induced extracellular matrix changes are conserved in cancer and directly impact radiotherapy benefit
    by Guerrero Quiles, C., Gonzalez Abalos, J., Foussat, A. S., Olympitis, A., Lodhi, T., Smith, V., Reardon, M., Shabbir, R., Lunj, S., Reeves, K., Baker, A., Eyres, M., Marshall, G., Smith, T., Hoskin, P., James, N., Hall, E., Huddart, R., Porta, N., Biolatti, V., Humphries, J. D., Humphries, M., Choudhury, A., West, C.
    Our overarching aim was to determine how hypoxia affects the extracellular matrix (ECM). Transcriptomic analysis (21,941 patients; 10 cancer types) identified ECM remodelling as the predominant pathway affected by hypoxia. Multi-omics confirmed that hypoxia impacts ECM organisation and collagen degradation; 53 ECM genes were affected, of which 74% were HIF1/HIF2-regulated. Spatial transcriptomics highlighted different hypoxia remodelling processes in tumour and stroma. Five ECM genes commonly affected in tumour and in vitro constituted a signature. This signature was independently prognostic and […]
  • Development of a Microelectrode Array System for Simultaneous Measurement of Field Potential and Glutamate Release in Brain Slices
    by Hasegawa, A., Matsuda, N., Suzuki, I.
    Disorders of the central nervous system and complex side effects caused by abnormal neurotransmitter release have been widely reported. If neurotransmitter release and field potential (FP) could be simultaneously measured in real time, it would be possible to capture the relationship between changes in neurotransmitter release and alterations in electrical activity. In this study, we developed a novel microelectrode array (MEA) system capable of simultaneously measuring FP and electrochemical (EC) signals. Additionally, we developed an enzyme-modified carbon nanotube (CNT)-MEA capable […]
  • Analysis of β rhythm induction in acute brain slices using field potential imaging with ultra-high-density CMOS-based microelectrode array.
    by Takakhashi, H., Matsuda, N., Suzuki, I.
    Carbachol induced beta rhythms in acute brain slices provide a promising ex vivo platform for evaluating compound effects under arousal-like hippocampal activity. Although microelectrode array (MEA) systems offer a non invasive means of recording network dynamics, conventional MEAs have been limited by low electrode counts and small sensing areas, allowing only fragmented evaluation of neural activity. In this study, we applied field potential imaging (FPI) using an ultra high density (UHD) CMOS MEA comprising 236,880 electrodes to simultaneously and spatially […]
  • UnitRefine: A Community Toolbox for Automated Spike Sorting Curation
    by Jain, A., Greene, R., Halcrow, C., Swann, J., Kleinjohann, A., Spurio, F., Graff, S., Kampa, B., Gall, J., Gruen, S., Buccino, A. P., Hennig, M. H., Musall, S.
    Electrophysiological recordings capture signals from hundreds of neurons simultaneously, but isolating single-unit activity often requires manual curation due to limitations in spike-sorting algorithms. As dataset sizes keep increasing, the time and expertise required for accurate and consistent human curation pose a major challenge for experimental labs. To address this issue, we developed UnitRefine, a classification toolbox that leverages diverse machine-learning algorithms to minimize manual curation efforts. Using acute recordings with Neuropixels probes, we collected a large neural dataset with reproducible […]
  • Dual-site beta transcranial alternating current stimulation during a bimanual coordination task modulates functional connectivity between motor areas
    by Gann, M. A., Paparella, I. A., Zich, C., Grigoras, I., Huertas-Penen, S., Rieger, S. W., Thielscher, A., Sharott, A., Stagg, C. J., Schwab, B. C.
    Background: Communication within brain networks depends on functional connectivity. One promising approach to modulate such connectivity between cortical areas is dual-site transcranial alternating current stimulation (tACS), which non-invasively applies weak alternating currents to two brain areas. Objectives/Hypotheses: In the current study, we aimed to modulate inter-regional functional connectivity with dual-site tACS to bilateral primary motor cortices (M1s) during bimanual coordination and, in turn, alter behaviour. Methods: Using functional magnetic resonance imaging (fMRI), we recorded participants' brain responses during a bimanual […]
  • BRCA1 is a molecular correlate of cell proliferation in human brain development and in Group 3 and 4 medulloblastoma
    by Cheong, I., Sun, X., Lau, L., Kishore, N., Senff-Ribeiro, A., Diaz-Navarro, A., Hajari, H., Mak, E., Ahluwalia, R., Bianchini, L., Singh Sandhu, J., Taylor, M. D., Kutscher, L., Stein, L. D., Pai, S.
    The role of the BRCA1-mediated DNA damage repair pathway in regulating human brain development remains unknown, although it has been studied in mouse development. We report evidence for breast cancer type 1 susceptibility protein (BRCA1) being a molecular correlate of proliferation in human neural progenitor cells and in medulloblastoma (MB), a malignant pediatric hindbrain cancer whose cells resemble undifferentiated neural stem cells. In a computational search for molecules potentially keeping Group 3 (G3) and Group 4 (G4) MB tumour cells […]
  • Primulagenin A is a potent inverse agonist of the nuclear receptor RAR-related orphan receptor gamma (RORγ)
    by Schwarz, P. F., Perhal, A. F., Preglej, T., Breit, L., Schmetterer, K. G., Grienke, U., Janneschütz, J., Chen, Y., Rochel, N., Kirchmair, J., Schützenmeister, N., Rollinger, J. M., Bonelli, M., Dirsch, V. M.
    Throughout history, herbal medicines and natural products have played a crucial role as therapeutics for humans, yet their molecular mechanisms of action often remain elusive. Here, we ask whether primulagenin A (PGA) from the traditionally used herbal substance Primula root, acts via the nuclear receptor ROR{gamma}, a key regulator of pro-inflammatory Th17 cells, which are linked to autoimmune diseases like psoriasis. Luciferase assays revealed a high potency (IC50 ~100 nM) and efficacy (Imax ~ 90%) of PGA as an inverse […]
  • Brain Network Segregation is Associated with Drug Use Severity in Individuals with Opioid Use Disorder
    by Hager, N. M., Wang, X., Ramos-Ralon, A. P., Childress, A. R., Langleben, D. D., Wiers, C. E., Shi, Z.
    Opioid use disorder (OUD) is associated with altered brain network connectivity, particularly in the fronto-parietal (FPN), default mode, and salience (SN) networks. At rest, brain networks that are distinct from each other but are partially connected can optimize neural efficiency and support cognitive performance. Previous research found lower network segregation in people with cognitive impairment, alcohol use disorder, and as people age. Here, we examined brain network segregation (a graph theory-based metric of the network integration/segregation balance) in individuals with […]
  • A guide for Single Particle Tracking: from sample preparation and image acquisition to the analysis of individual trajectories
    by Kobayashi, A., Park, J., Mine-Hattab, J., Fernandez, F. G.
    Live-cell Single-Particle Tracking (SPT) is a powerful super resolution microscopy approach. It allows us to observe live recordings of individual molecules in living cells at high temporal and spatial resolution (100 Hz, 20 nm). Here, we discuss the implementation and application of super-resolution microscopy to quantify the mobility of single molecules in living human cells. We first describe the human cell sample preparation for SPT with an experimental time line overview, then super-resolution microscope setting and procedure to acquire SPT […]
  • BABA: Naturalistic fMRI and MEG recordings during viewing of a reality TV show
    by Li, J., Wang, Q., Wang, Y., Wang, C., Ma, Z., Xu, R., Feng, S., Jiang, X., Meng, Z.
    Recent advances in the cognitive neuroscience of language have embraced naturalistic stimuli such as movies and audiobooks. However, most open-access neuroimaging datasets still focus on single-speaker scenarios, falling short of capturing the complexity of real-life, multi-speaker communication. To address this gap, we present the BABA fMRI and MEG dataset, collected while participants watched a 25-minute excerpt from a Chinese reality TV show featuring 11 speakers, including five fathers and their children. Set in a rural village, the show captures natural […]

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