Modelling microelectrode biosensors : free-flow calibration can substantially underestimate tissue concentrations

Microelectrode amperometric biosensors are widely used to measure concentrations of analytes in solution and tissue including acetylcholine, adenosine, glucose and glutamate. A great deal of experimental and modelling effort has been directed at quantifying the response of the biosensors themselves; however, the influence that the macroscopic tissue environment has on biosensor response has not been subjected to the same level of scrutiny. Here we identify an important issue in the way microelectrode biosensors are calibrated that is likely to have led to underestimations of analyte tissue concentrations. Concentration in tissue is typically determined by comparing the biosensor signal to that measured in free-flow calibration conditions. In a free-flow environment the concentration of the analyte at the outer surface of the biosensor can be considered constant. However, in tissue the analyte reaches the biosensor surface by diffusion through the extracellular space. Because the enzymes in the biosensor break down the analyte, a density gradient is set up resulting in a significantly lower concentration of analyte near the biosensor surface. This effect is compounded by the diminished volume fraction (porosity) and reduction in the diffusion coefficient due to obstructions (tortuosity) in tissue. We demonstrate this effect through modelling and experimentally verify our predictions in diffusive environments

Modelling adenosine dynamics in neural tissues

The neuromodulator adenosine is involved in both physiological and pathological activity, such as sleep, epilepsy and stroke. However, the complex processes underlying the release, transport and clearance of adenosine from the extracellular space and their interactions are still poorly quantified. In this thesis I develop the �rst detailed model of the dynamics of adenosine in neural tissue, including intracellular and extracellular metabolism, using parameters taken from an extensive search of the literature. This approach also identifies physiological and metabolic parameters that have yet to be experimentally measured. The model provides estimates of the range of influence of adenosine, the distance where the extracellular concentration is greater than that required for half of the maximum inhibition by the dominant type of adenosine receptors in the cortex, and suggests that under physiological conditions the adenosine signal will be highly localised. The model predicts that adenosine concentration profiles are primarily determined by diffusion and that neuronal transport and metabolism are the dominant clearance mechanisms. The model can be used with either experimental or endogenous sources of adenosine, and I apply it to the bath application of adenosine to a tissue slice, (a method used extensively to study the e�ect of adenosine on synaptic transmission). The model is used to predict the effective dose response curve of bath applied adenosine and to compare the effects of transporter blockers. I then turn to the modelling of biosensors, which are used extensively to measure the concentration of various analytes in tissue, including adenosine. Biosensors are often calibrated in a flow injection system with a known concentration of the analyte. Mathematical and computational models are used to compare the response characteristics of biosensors in this free environment with the tortuous environment in which they are used. An estimated correction factor is obtained together with the sensitivity of this factor to the characteristics of the biosensor. This work provides a framework to move from qualitative studies of changes of adenosine in the brain to quantitative analysis of the spatio-temporal dynamics of adenosine signalling and its in uence on networks of neurons

Using NEURON for Reaction-Diffusion Modeling of Extracellular Dynamics

Development of credible clinically-relevant brain simulations has been slowed due to a focus on electrophysiology in computational neuroscience, neglecting the multiscale whole-tissue modeling approach used for simulation in most other organ systems. We have now begun to extend the NEURON simulation platform in this direction by adding extracellular modeling. The extracellular medium of neural tissue is an active medium of neuromodulators, ions, inflammatory cells, oxygen, NO and other gases, with additional physiological, pharmacological and pathological agents. These extracellular agents influence, and are influenced by, cellular electrophysiology, and cellular chemophysiology—the complex internal cellular milieu of second-messenger signaling and cascades. NEURON's extracellular reaction-diffusion is supported by an intuitive Python-based where/who/what command sequence, derived from that used for intracellular reaction diffusion, to support coarse-grained macroscopic extracellular models. This simulation specification separates the expression of the conceptual model and parameters from the underlying numerical methods. In the volume-averaging approach used, the macroscopic model of tissue is characterized by free volume fraction—the proportion of space in which species are able to diffuse, and tortuosity—the average increase in path length due to obstacles. These tissue characteristics can be defined within particular spatial regions, enabling the modeler to account for regional differences, due either to intrinsic organization, particularly gray vs. white matter, or to pathology such as edema. We illustrate simulation development using spreading depression, a pathological phenomenon thought to play roles in migraine, epilepsy and stroke. Simulation results were verified against analytic results and against the extracellular portion of the simulation run under FiPy. The creation of this NEURON interface provides a pathway for interoperability that can be used to automatically export this class of models into complex intracellular/extracellular simulations and future cross-simulator standardization

Neuron Names: A Gene- and Property-Based Name Format, With Special Reference to Cortical Neurons

Precision in neuron names is increasingly needed. We are entering a new era in which classical anatomical criteria are only the beginning toward defining the identity of a neuron as carried in its name. New criteria include patterns of gene expression, membrane properties of channels and receptors, pharmacology of neurotransmitters and neuropeptides, physiological properties of impulse firing, and state-dependent variations in expression of characteristic genes and proteins. These gene and functional properties are increasingly defining neuron types and subtypes. Clarity will therefore be enhanced by conveying as much as possible the genes and properties in the neuron name. Using a tested format of parent-child relations for the region and subregion for naming a neuron, we show how the format can be extended so that these additional properties can become an explicit part of a neuron’s identity and name, or archived in a linked properties database. Based on the mouse, examples are provided for neurons in several brain regions as proof of principle, with extension to the complexities of neuron names in the cerebral cortex. The format has dual advantages, of ensuring order in archiving the hundreds of neuron types across all brain regions, as well as facilitating investigation of a given neuron type or given gene or property in the context of all its properties. In particular, we show how the format is extensible to the variety of neuron types and subtypes being revealed by RNA-seq and optogenetics. As current research reveals increasingly complex properties, the proposed approach can facilitate a consensus that goes beyond traditional neuron types

Pluralitas Agama dalam Keluarga Jawa

Dalam masyarakat Jawa terdapat pemahaman dan pemaknaan sendiri terhadap agama yaitu â€agami ageming ajiâ€. Artinya apa pun agama yang dipeluk sama saja karena semua agama mengajarkan keselamatan. Oleh sebab itu menjadi sebuah fenomena menarik di kalangan masyarakat Jawa karena mereka cenderung lebih toleran dalam menyikapi perbedaaan dan keragaman beragama. Salah satu contoh masyarakat yang menghargai pluralitas agama adalah masyarakat Desa Getas Kaloran Temanggung. Tujuan penelitian ini adalah untuk menjelaskan tentang sejumlah keluarga yang dapat menerima pluralitas agama dan toleransi terhadap pluralitas agama dalam keluarga Jawa. Tulisan ini merupakan hasil penelitian yang menggunakan pendekatan deskriptif kualitatif. Subyek penelitian adalah masyarakat Desa Getas yang memiliki keragaman agama dalam keluarganya. Berdasarkan hasil penelitian dapat disimpulkan bahwa masyarakat Desa Getas dapat menerima pluralitas agama karena menurut mereka agama adalah urusan pribadi seseorang jadi tidak ada pihak yang dapat memaksakan suatu keyakinan kepada individu lain. Pluralitas agama tersebut tidak menimbulkan masalah berarti karena masyarakat memiliki derajat toleransi yang tinggi antar anggota keluarga, yang ditunjukkan melalui saling menghargai dan mengormati dan tidak mencampuri urusan keagamaan orang lain, serta saling membantu antar anggota keluarga untuk memperlancar kegiatan ibadah masing – masing. In Javanese community there is a specific principle on the meaning of religion, namely â€agami ageming ajiâ€. This pilosophy means whatever religion people believe, it doesn’t matter because they all teach salvation. This is an interesting phenomenon among the Javanese community because they tend to be tolerant in dealing with differences and diversity of religion that happen in one household. The objective of this article is to discuss the practices of religious tolerance found in a rural community of Getas, Kaloran, Temanggung Central Java. Techniques of data collection is done by interviews and observation. The study subjects were villagers of Getas, which has a diversity of religion in families. Based on the research results, it can be concluded that the villagers embrace a tradition of religious pluralism because they think religion is one’s personal affairs so that no party can impose a conviction for another individual. The plurality of religion does not cause significant problems because the public has a high degree of tolerance among family members, which is demonstrated through mutual respect and attitude not to interfere in religious affairs of others, and mutual help among family members to facilitate the worship activities of their relatives

Essential versus accessory aspects of cell death: recommendations of the NCCD 2015

Cells exposed to extreme physicochemical or mechanical stimuli die in an uncontrollable manner, as a result of their immediate structural breakdown. Such an unavoidable variant of cellular demise is generally referred to as ‘accidental cell death’ (ACD). In most settings, however, cell death is initiated by a genetically encoded apparatus, correlating with the fact that its course can be altered by pharmacologic or genetic interventions. ‘Regulated cell death’ (RCD) can occur as part of physiologic programs or can be activated once adaptive responses to perturbations of the extracellular or intracellular microenvironment fail. The biochemical phenomena that accompany RCD may be harnessed to classify it into a few subtypes, which often (but not always) exhibit stereotyped morphologic features. Nonetheless, efficiently inhibiting the processes that are commonly thought to cause RCD, such as the activation of executioner caspases in the course of apoptosis, does not exert true cytoprotective effects in the mammalian system, but simply alters the kinetics of cellular demise as it shifts its morphologic and biochemical correlates. Conversely, bona fide cytoprotection can be achieved by inhibiting the transduction of lethal signals in the early phases of the process, when adaptive responses are still operational. Thus, the mechanisms that truly execute RCD may be less understood, less inhibitable and perhaps more homogeneous than previously thought. Here, the Nomenclature Committee on Cell Death formulates a set of recommendations to help scientists and researchers to discriminate between essential and accessory aspects of cell death

Dynamin I phosphorylation by GSK3 controls activity-dependent bulk endocytosis of synaptic vesicles.

Glycogen synthase kinase 3 (GSK3) is a critical enzyme in neuronal physiology; however, it is not yet known whether it has any specific role in presynaptic function. We found that GSK3 phosphorylates a residue on the large GTPase dynamin I (Ser-774) both in vitro and in primary rat neuronal cultures. This was dependent on prior phosphorylation of Ser-778 by cyclin-dependent kinase 5. Using both acute inhibition with pharmacological antagonists and silencing of expression with short hairpin RNA, we found that GSK3 was specifically required for activity-dependent bulk endocytosis (ADBE) but not clathrin-mediated endocytosis. Moreover we found that the specific phosphorylation of Ser-774 on dynamin I by GSK3 was both necessary and sufficient for ADBE. These results demonstrate a presynaptic role for GSK3 and they indicate that a protein kinase signaling cascade prepares synaptic vesicles for retrieval during elevated neuronal activity

Expression profiling identifies genes involved in neoplastic transformation of serous ovarian cancer

Background: The malignant potential of serous ovarian tumors, the most common ovarian tumor subtype, varies from benign to low malignant potential (LMP) tumors to frankly invasive cancers. Given the uncertainty about the relationship between these different forms, we compared their patterns of gene expression. Methods: Expression profiling was carried out on samples of 7 benign, 7 LMP and 28 invasive (moderate and poorly differentiated) serous tumors and four whole normal ovaries using oligonucleotide microarrays representing over 21,000 genes. Results: We identified 311 transcripts that distinguished invasive from benign tumors, and 20 transcripts that were significantly differentially expressed between invasive and LMP tumors at p < 0.01 (with multiple testing correction). Five genes that were differentially expressed between invasive and either benign or normal tissues were validated by real time PCR in an independent panel of 46 serous tumors (4 benign, 7 LMP, 35 invasive). Overexpression of SLPI and WNT7A and down-regulation of C6orf31, PDGFRA and GLTSCR2 were measured in invasive and LMP compared with benign and normal tissues. Over-expression of WNT7A in an ovarian cancer cell line led to increased migration and invasive capacity. Conclusion: These results highlight several genes that may play an important role across the spectrum of serous ovarian tumorigenesis

TESS Hunt for Young and Maturing Exoplanets (THYME). X. A Two-planet System in the 210 Myr MELANGE-5 Association

Young (&lt;500 Myr) planets are critical to studying how planets form and evolve. Among these young planetary systems, multiplanet configurations are particularly useful, as they provide a means to control for variables within a system. Here, we report the discovery and characterization of a young planetary system, TOI-1224. We show that the planet host resides within a young population we denote as MELANGE-5. By employing a range of age-dating methods—isochrone fitting, lithium abundance analysis, gyrochronology, and Gaia excess variability—we estimate the age of MELANGE-5 to be 210 ± 27 Myr. MELANGE-5 is situated in close proximity to previously identified younger (80–110 Myr) associations, Crius 221 and Theia 424/Volans-Carina, motivating further work to map out the group boundaries. In addition to a planet candidate detected by the TESS pipeline and alerted as a TESS object of interest, TOI-1224 b, we identify a second planet, TOI-1224 c, using custom search tools optimized for young stars (Notch and LOCoR). We find that the planets are 2.10 ± 0.09 R⊕ and 2.88 ± 0.10 R⊕ and orbit their host star every 4.18 and 17.95 days, respectively. With their bright (K = 9.1 mag), small (R* = 0.44 R⊙), and cool (Teff = 3326 K) host star, these planets represent excellent candidates for atmospheric characterization with JWST

TESS hunt for young and maturing exoplanets (THYME). X. A two-planet system in the 210 Myr MELANGE-5 association

Funding: P.C.T. was supported by an NSF Graduate Research Fellowship (DGE-1650116), the NC Space Grant Graduate Research Fellowship, the Zonta International Amelia Earhart Fellowship, and the Jack Kent Cooke Foundation Graduate Scholarship. A.W.M. was supported by grants from the NSF CAREER program (AST-2143763) and NASA’s exoplanet research program (XRP 80NSSC21K0393). M.G.B. was supported by an NSF Graduate Research Fellowship (DGE2040435) and the NC Space Grant Graduate Research Fellowship. F.J.P. acknowledges financial support from the grant CEX2021-001131-S funded by MCIN/AEI/ 10.13039/ 501100011033 and through projects PID2019-109522GB-C52 and PID2022-137241NB-C43. This research also received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No. 803193/BEBOP) and from the Science and Technology Facilities Council (STFC; grant No. ST/S00193X/1). The postdoctoral fellowship of K.B. is funded by F.R.S.-FNRS grant T.0109.20 and by the Francqui Foundation. K.A.C. acknowledges support from the TESS mission via subaward s3449 from MIT. M.K. acknowledges support from the MIT Kavli Institute as a Juan Carlos Torres Fellow. This publication benefits from the support of the French Community of Belgium in the context of the FRIA Doctoral Grant awarded to M.T.Young (<500 Myr) planets are critical to studying how planets form and evolve. Among these young planetary systems, multiplanet configurations are particularly useful, as they provide a means to control for variables within a system. Here, we report the discovery and characterization of a young planetary system, TOI-1224. We show that the planet host resides within a young population we denote as MELANGE-5. By employing a range of age-dating methods—isochrone fitting, lithium abundance analysis, gyrochronology, and Gaia excess variability—we estimate the age of MELANGE-5 to be 210 ± 27 Myr. MELANGE-5 is situated in close proximity to previously identified younger (80–110 Myr) associations, Crius 221 and Theia 424/Volans-Carina, motivating further work to map out the group boundaries. In addition to a planet candidate detected by the TESS pipeline and alerted as a TESS object of interest, TOI-1224 b, we identify a second planet, TOI-1224 c, using custom search tools optimized for young stars (Notch and LOCoR). We find that the planets are 2.10 ± 0.09 R⊕ and 2.88 ± 0.10 R⊕ and orbit their host star every 4.18 and 17.95 days, respectively. With their bright (K = 9.1 mag), small (R* = 0.44 R⊙), and cool (Teff = 3326 K) host star, these planets represent excellent candidates for atmospheric characterization with JWST.Peer reviewe