Intra-burst firing characteristics as network state parameters

Introduction \ud In our group we are aiming to demonstrate learning and memory capabilities of cultured networks of cortical neurons. A first step is to identify parameters that accurately describe changes in the network due to learning. Usually, such parameters are calculated from the responses to test-stimuli before and after a learning experiment. We propose that parameters should be calculated from the spontaneous activity before and after a learning experiment, as the applying of test-stimuli itself may alter the network. Since bursting is dominant in our cultures, we have investigated its spatio-temporal structure. \ud \ud Methods \ud Networks of cortical neurons were cultured on a MEA. Over a period from 9 to 35 DIV, the spontaneous activity has been measured on a regular basis. Measurements on a single day are always continuous; otherwise cultures are kept in a stove under controlled conditions (37 ˚C, 5% CO2, 100% humidity). Network bursts were detected by analysing the Array-Wide Spiking Rate (AWSR, the sum of activity over all electrodes). Next, we estimated the instantaneous AWSR during a burst by convolving spike-occurrences with a Gaussian function. We investigated the changes in burst profiles over time by aligning them to their peak AWSR. In 4 hour recording sessions, we grouped the burst profiles over 1 hour, resulting in 4 average burst profiles per day. In addition, a sufficient amount of aligned bursts yielded enough data to calculate the contribution of each recording site. \ud \ud Results \ud The burst profiles, calculated over a period of 1 hour, generally show little variation (figure 1). In subsequent hours, the profiles gradually change shape. Over a period of days however, the shape can change dramatically (figure 2). The relatively slow changes over the period of hours indicate an underlying probabilistic structure in the AWSR during bursts. The apparent structure in the burst profiles result from the relationships between individual recording sites, and thus also on the connectivity in the neural network. This is revealed in more detail by showing the contributions of individual sites (figure 3). The spike envelopes have a shape that is too detailed to be described accurately by a small set of parameters. \ud \ud Discussion \ud The burst profiles prove to be stable over a period of one hour, and gradually change their shape over several hours, as has also been suggested in [1]. The day-to-day changes in burst profiles may be the result of these gradual changes, thereby suggesting an intrinsically changing network. However, they can also be the result of putting the cultures back in the stove. The spike envelopes per recording site offer more detailed descriptions of the network state than the burst profiles. This may however be the amount of detail required to reveal the changes made during learning experiments. A subsequent refinement can be made by identifying distinct subgroups of bursts, as has been suggested in [2]

Cultured cortical networks described by conditional firing probabilities

Networks of cortical neurons were grown over multi electrode arrays to enable simultaneous measu-rement of action potentials from 60 electrodes. All possible pairs of electrodes (i,j) were tested for syn-chronized activity. We calculated conditional firing probability (CFPi,j[τ]) as the probability of an action potential at electrode j at t=τ, given that a spike was detected at i at t=0. If a CFPi,j[τ] distribution clearly deviated from flat, electrodes i and j were considered related. A function was fitted to each CFP-curve to obtain parameters for strength and delay. In young cultures the set of identified relationships changed rather quickly. At 16 days in vitro (DIV) 50% of the set changed within one day. Beyond 25 DIV this set stabilized: during a period of a week more than 50% of the set remained intact. Most individual relationships developed rather gradually. Moreover, beyond 25 DIV relational strength appeared quite stable during periods of ≈ 10 hours, with coefficients of variation (100×SD/mean) of ≈ 25% on average. CFP analysis provides a robust method to describe the stable underlying probabilistic structure of highly varying spontaneous activity in cultured cortical networks. It may offer a suitable basis for plasticity studies, in which induced changes should exceed spontaneous fluctuations. CFP analysis is likely to describe the network in sufficient detail to detect subtle changes in individual relationships. Analysis of data continuously recorded for ≈ 6 weeks, showed that highest stability is reached after ≈ 25 DIV, suggesting the 4th and 5th week as a suitable period for plasticity studies.\ud \u

The multi-omic landscape of transcription factor inactivation in cancer

BACKGROUND: Hypermethylation of transcription factor promoters bivalently marked in stem cells is a cancer hallmark. However, the biological significance of this observation for carcinogenesis is unclear given that most of these transcription factors are not expressed in any given normal tissue. METHODS: We analysed the dynamics of gene expression between human embryonic stem cells, fetal and adult normal tissue, as well as six different matching cancer types. In addition, we performed an integrative multi-omic analysis of matched DNA methylation, copy number, mutational and transcriptomic data for these six cancer types. RESULTS: We here demonstrate that bivalently and PRC2 marked transcription factors highly expressed in a normal tissue are more likely to be silenced in the corresponding tumour type compared with non-housekeeping genes that are also highly expressed in the same normal tissue. Integrative multi-omic analysis of matched DNA methylation, copy number, mutational and transcriptomic data for six different matching cancer types reveals that in-cis promoter hypermethylation, and not in-cis genomic loss or genetic mutation, emerges as the predominant mechanism associated with silencing of these transcription factors in cancer. However, we also observe that some silenced bivalently/PRC2 marked transcription factors are more prone to copy number loss than promoter hypermethylation, pointing towards distinct, mutually exclusive inactivation patterns. CONCLUSIONS: These data provide statistical evidence that inactivation of cell fate-specifying transcription factors in cancer is an important step in carcinogenesis and that it occurs predominantly through a mechanism associated with promoter hypermethylation

The role of circulating tumour cells and nucleic acids in blood for the detection of bladder cancer: A systematic review

BACKGROUND: Blood-based biomarkers are a neglected resource in bladder cancer, where the mainstay of focus has been on urinary biomarkers. However, blood-based biomarkers are gaining popularity in other solid cancers, particularly circulating tumour cells (CTCs) and circulating nucleic acids. In this systematic review, we identify and discuss the diagnostic value of CTC, cell-free DNA and RNA based biomarkers in bladder cancer. METHODS: A MEDLINE/Pubmed systematic search was performed using the following keywords: (bladder cancer) AND (blood OR plasma OR serum) AND biomarker AND (DNA OR RNA OR cfDNA OR cell-free DNA OR RNA OR CTC). All studies including blood-based biomarkers based on DNA, RNA and CTCs were reviewed. Of the included studies, studies reporting sensitivity, specificity and/or AUC/ROC values were further described. RESULTS: Systematic searched yielded 47 studies that were eligible, of which 21, 19 and 3 studies reported DNA, RNA and CTC biomarkers respectively. 15 of these studies included sensitivity, specificity and/or AUC/ROC values. Biomarkers sensitivity and specificity ranged widely at 2.4-97.6% and 43.3-100% respectively. Median number of patients recruited in the studies was 56 (IQR 41-90). Only 3 studies included an independent validation cohort. The highest sensitivity and specificity pairing achieved in the validation cohort was 80.0% and 89.1% respectively. CONCLUSIONS: This systematic review provides a comprehensive overview of the blood-based CTC and nucleic acid biomarkers that have been investigated. An overlap in interest of targets between studies suggests that these could be promising biomarkers, but few biomarkers achieve high sensitivity and specificity, and fewer still have been validated independently

Imaging of electric and magnetic fields near plasmonic nanowires

Near-field imaging is a powerful tool to investigate the complex structure of light at the nanoscale. Recent advances in near-field imaging have indicated the possibility for the complete reconstruction of both electric and magnetic components of the evanescent field. Here we study the electro-magnetic field structure of surface plasmon polariton waves propagating along subwavelength gold nanowires by performing phase- and polarization-resolved near-field microscopy in collection mode. By applying the optical reciprocity theorem, we describe the signal collected by the probe as an overlap integral of the nanowire’s evanescent field and the probe’s response function. As a result, we find that the probe’s sensitivity to the magnetic field is approximately equal to its sensitivity to the electric field. Through rigorous modeling of the nanowire mode as well as the aperture probe response function, we obtain a good agreement between experimentally measured signals and a numerical model. Our findings provide a better understanding of aperture-based near-field imaging of the nanoscopic plasmonic and photonic structures and are helpful for the interpretation of future near-field experiments

Imaging of electric and magnetic fields near plasmonic nanowires.

Near-field imaging is a powerful tool to investigate the complex structure of light at the nanoscale. Recent advances in near-field imaging have indicated the possibility for the complete reconstruction of both electric and magnetic components of the evanescent field. Here we study the electro-magnetic field structure of surface plasmon polariton waves propagating along subwavelength gold nanowires by performing phase- and polarization-resolved near-field microscopy in collection mode. By applying the optical reciprocity theorem, we describe the signal collected by the probe as an overlap integral of the nanowire's evanescent field and the probe's response function. As a result, we find that the probe's sensitivity to the magnetic field is approximately equal to its sensitivity to the electric field. Through rigorous modeling of the nanowire mode as well as the aperture probe response function, we obtain a good agreement between experimentally measured signals and a numerical model. Our findings provide a better understanding of aperture-based near-field imaging of the nanoscopic plasmonic and photonic structures and are helpful for the interpretation of future near-field experiments

The benefits of organic farming for biodiversity

Previous studies suggest widespread positive responses of biodiversity to organic farming. Many of these studies, however, have been small-scale. This project tested the generality of habitat and biodiversity differences between matched pairs of organic and non-organic farms containing cereal crops in lowland England on a large-scale across a range of taxa including plants, insects, birds and bats. The extent of both cropped and un-cropped habitats together with their composition and management on a range of scales were also compared. Organic farms was likely to favour higher levels of biodiversity and indeed organic farms tended to support higher numbers of species and overall abundance across most taxa. However, the magnitude of the response differed strikingly; plants showed stronger and more consistent responses than other taxa. Some, but not all, differences in biodiversity between systems appear to be a consequence of differences in habitat quantity

Novel urinary biomarkers for the detection of bladder cancer: A systematic review

BACKGROUND: Urinary biomarkers for the diagnosis of bladder cancer represents an area of considerable research which has been tested in both patients presenting with haematuria and non-muscle invasive bladder cancer patients requiring surveillance cystoscopy. In this systematic review, we identify and appraise the diagnostic sensitive and specificity of reported novel biomarkers of different 'omic' class and highlight promising biomarkers investigated to date. METHODS: A MEDLINE/Pubmed systematic search was performed between January 2013 and July 2017 using the following keywords: (bladder cancer OR transitional cell carcinoma OR urothelial cell carcinoma) AND (detection OR diagnosis) AND urine AND (biomarker OR assay). All studies had a minimum of 20 patients in both bladder cancer and control arms and reported sensitivity and/or specificity and/or receiver operating characteristics (ROC) curve. QUADAS-2 tool was used to assess risk of bias and applicability of studies. The search protocol was registered in the PROSPERO database (CRD42016049918). RESULTS: Systematic search yielded 115 reports were included for analysis. In single target biomarkers had a sensitivity of 2-94%, specificity of 46-100%, positive predictive value (PPV) of 47-100% and negative predictive value (NPV) of 21-94%. Multi-target biomarkers achieved a sensitivity of 24-100%, specificity of 48-100%, PPV of 42-95% and NPV of 32-100%. 50 studies achieved a sensitivity and specificity of ≥80%. Protein (n = 59) and transcriptomic (n = 21) biomarkers represents the most studied biomarkers. Multi-target biomarker panels had a better diagnostic accuracy compared to single biomarker targets. Urinary cytology with urinary biomarkers improved the diagnostic ability of the biomarker. The sensitivity and specificity of biomarkers were higher for primary diagnosis compared to patients in the surveillance setting. Most studies were case control studies and did not have a predefined threshold to determine a positive test result indicating a possible risk of bias. CONCLUSION: This comprehensive systematic review provides an update on urinary biomarkers of different 'omic' class and highlights promising biomarkers. Few biomarkers achieve a high sensitivity and negative predictive value. Such biomarkers will require external validation in a prospective observational setting before adoption in clinical practice

A functional methylome map of ulcerative colitis

The etiology of inflammatory bowel diseases is only partially explained by the current genetic risk map. It is hypothesized that environmental factors modulate the epigenetic landscape and thus contribute to disease susceptibility, manifestation, and progression. To test this, we analyzed DNA methylation (DNAm), a fundamental mechanism of epigenetic long-term modulation of gene expression. We report a three-layer epigenome-wide association study (EWAS) using intestinal biopsies from 10 monozygotic twin pairs (n = 20 individuals) discordant for manifestation of ulcerative colitis (UC). Genome-wide expression scans were generated using Affymetrix UG 133 Plus 2.0 arrays (layer 1). Genome-wide DNAm scans were carried out using Illumina 27k Infinium Bead Arrays to identify methylation variable positions (MVPs, layer 2), and MeDIP-chip on Nimblegen custom 385k Tiling Arrays to identify differentially methylated regions (DMRs, layer 3). Identified MVPs and DMRs were validated in two independent patient populations by quantitative real-time PCR and bisulfite-pyrosequencing (n = 185). The EWAS identified 61 disease-associated loci harboring differential DNAm in cis of a differentially expressed transcript. All constitute novel candidate risk loci for UC not previously identified by GWAS. Among them are several that have been functionally implicated in inflammatory processes, e.g., complement factor CFI, the serine protease inhibitor SPINK4, and the adhesion molecule THY1 (also known as CD90). Our study design excludes nondisease inflammation as a cause of the identified changes in DNAm. This study represents the first replicated EWAS of UC integrated with transcriptional signatures in the affected tissue and demonstrates the power of EWAS to uncover unexplained disease risk and molecular events of disease manifestation

Pan-cancer deconvolution of cellular composition identifies molecular correlates of antitumour immunity and checkpoint blockade response

The nature and extent of immune cell infiltration into solid tumours are key determinants of therapeutic response. Here, using a novel DNA methylation-based approach to tumour cell fraction deconvolution, we report the integrated analysis of tumour composition and genomics across a wide spectrum of solid cancers. Initially studying head and neck squamous cell carcinoma, we identify two distinct tumour subgroups: ‘immune hot’ and ‘immune cold’, which display differing prognosis, mutation burden, cytokine signalling, cytolytic activity, and oncogenic driver events. We demonstrate the existence of such tumour subgroups pan-cancer, link clonal-neoantigen burden to hot tumours, and show that transcriptional signatures of hot tumours are selectively engaged in immunotherapy responders. We also find that treatment-naive hot tumours are markedly enriched for known immune-resistance genomic alterations and define a catalogue of novel and known mediators of active antitumour immunity, deriving biomarkers and potential targets for precision immunotherapy