Publications by authors named "Roman Bauer"

26 Publications

  • Page 1 of 1

Winter is coming: the future of cryopreservation.

BMC Biol 2021 Mar 24;19(1):56. Epub 2021 Mar 24.

Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK.

The preservative effects of low temperature on biological materials have been long recognised, and cryopreservation is now widely used in biomedicine, including in organ transplantation, regenerative medicine and drug discovery. The lack of organs for transplantation constitutes a major medical challenge, stemming largely from the inability to preserve donated organs until a suitable recipient is found. Here, we review the latest cryopreservation methods and applications. We describe the main challenges-scaling up to large volumes and complex tissues, preventing ice formation and mitigating cryoprotectant toxicity-discuss advantages and disadvantages of current methods and outline prospects for the future of the field.
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http://dx.doi.org/10.1186/s12915-021-00976-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7989039PMC
March 2021

Creative Destruction: A Basic Computational Model of Cortical Layer Formation.

Cereb Cortex 2021 Feb 24. Epub 2021 Feb 24.

School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, UK.

One of the most characteristic properties of many vertebrate neural systems is the layered organization of different cell types. This cytoarchitecture exists in the cortex, the retina, the hippocampus, and many other parts of the central nervous system. The developmental mechanisms of neural layer formation have been subject to substantial experimental efforts. Here, we provide a general computational model for cortical layer formation in 3D physical space. We show that this multiscale, agent-based model, comprising two distinct stages of apoptosis, can account for the wide range of neuronal numbers encountered in different cortical areas and species. Our results demonstrate the phenotypic richness of a basic state diagram structure. Importantly, apoptosis allows for changing the thickness of one layer without automatically affecting other layers. Therefore, apoptosis increases the flexibility for evolutionary change in layer architecture. Notably, slightly changed gene regulatory dynamics recapitulate the characteristic properties observed in neurodevelopmental diseases. Overall, we propose a novel computational model using gene-type rules, exhibiting many characteristics of normal and pathological cortical development.
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http://dx.doi.org/10.1093/cercor/bhab003DOI Listing
February 2021

IGFBPs mediate IGF-1's functions in retinal lamination and photoreceptor development during pluripotent stem cell differentiation to retinal organoids.

Stem Cells 2021 Apr 14;39(4):458-466. Epub 2021 Jan 14.

Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.

Development of the retina is regulated by growth factors, such as insulin-like growth factors 1 and 2 (IGF-1/2), which coordinate proliferation, differentiation, and maturation of the neuroepithelial precursors cells. In the circulation, IGF-1/2 are transported by the insulin growth factor binding proteins (IGFBPs) family members. IGFBPs can impact positively and negatively on IGF-1, by making it available or sequestering IGF-1 to or from its receptor. In this study, we investigated the expression of IGFBPs and their role in the generation of human retinal organoids from human pluripotent stem cells, showing a dynamic expression pattern suggestive of different IGFBPs being used in a stage-specific manner to mediate IGF-1 functions. Our data show that IGF-1 addition to culture media facilitated the generation of retinal organoids displaying the typical laminated structure and photoreceptor maturation. The organoids cultured in the absence of IGF-1, lacked the typical laminated structure at the early stages of differentiation and contained significantly less photoreceptors and more retinal ganglion cells at the later stages of differentiation, confirming the positive effects of IGF-1 on retinal lamination and photoreceptor development. The organoids cultured with the IGFBP inhibitor (NBI-31772) and IGF-1 showed lack of retinal lamination at the early stages of differentiation, an increased propensity to generate horizontal cells at mid-stages of differentiation and reduced photoreceptor development at the later stages of differentiation. Together these data suggest that IGFBPs enable IGF-1's role in retinal lamination and photoreceptor development in a stage-specific manner.
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http://dx.doi.org/10.1002/stem.3331DOI Listing
April 2021

Platform to study intracellular polystyrene nanoplastic pollution and clinical outcomes.

Stem Cells 2020 10 2;38(10):1321-1325. Epub 2020 Jul 2.

SPEBO Medical Fertility Hospital, Leskovac, Serbia.

Increased pollution by plastics has become a serious global environmental problem, but the concerns for human health have been raised after reported presence of microplastics (MPs) and nanoplastics (NPs) in food and beverages. Unfortunately, few studies have investigate the potentially harmful effects of MPs/NPs on early human development and human health. Therefore, we used a new platform to study possible effects of polystyrene NPs (PSNPs) on the transcription profile of preimplantation human embryos and human induced pluripotent stem cells (hiPSCs). Two pluripotency genes, LEFTY1 and LEFTY2, which encode secreted ligands of the transforming growth factor-beta, were downregulated, while CA4 and OCLM, which are related to eye development, were upregulated in both samples. The gene set enrichment analysis showed that the development of atrioventricular heart valves and the dysfunction of cellular components, including extracellular matrix, were significantly affected after exposure of hiPSCs to PSNPs. Finally, using the HiPathia method, which uncovers disease mechanisms and predicts clinical outcomes, we determined the APOC3 circuit, which is responsible for increased risk for ischemic cardiovascular disease. These results clearly demonstrate that better understanding of NPs bioactivities and its implications for human health is of extreme importance. Thus, the presented platform opens further aspects to study interactions between different environmental and intracellular pollutions with the aim to decipher the mechanism and origin of human diseases.
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http://dx.doi.org/10.1002/stem.3244DOI Listing
October 2020

A generative growth model for thalamocortical axonal branching in primary visual cortex.

PLoS Comput Biol 2020 02 13;16(2):e1007315. Epub 2020 Feb 13.

Interdisciplinary Computing and Complex BioSystems Research Group (ICOS), School of Computing Science, Newcastle University, Newcastle upon Tyne, United Kingdom.

Axonal morphology displays large variability and complexity, yet the canonical regularities of the cortex suggest that such wiring is based on the repeated initiation of a small set of genetically encoded rules. Extracting underlying developmental principles can hence shed light on what genetically encoded instructions must be available during cortical development. Within a generative model, we investigate growth rules for axonal branching patterns in cat area 17, originating from the lateral geniculate nucleus of the thalamus. This target area of synaptic connections is characterized by extensive ramifications and a high bouton density, characteristics thought to preserve the spatial resolution of receptive fields and to enable connections for the ocular dominance columns. We compare individual and global statistics, such as a newly introduced length-weighted asymmetry index and the global segment-length distribution, of generated and biological branching patterns as the benchmark for growth rules. We show that the proposed model surpasses the statistical accuracy of the Galton-Watson model, which is the most commonly employed model for biological growth processes. In contrast to the Galton-Watson model, our model can recreate the log-normal segment-length distribution of the experimental dataset and is considerably more accurate in recreating individual axonal morphologies. To provide a biophysical interpretation for statistical quantifications of the axonal branching patterns, the generative model is ported into the physically accurate simulation framework of Cx3D. In this 3D simulation environment we demonstrate how the proposed growth process can be formulated as an interactive process between genetic growth rules and chemical cues in the local environment.
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http://dx.doi.org/10.1371/journal.pcbi.1007315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7018004PMC
February 2020

An in silico hybrid continuum-/agent-based procedure to modelling cancer development: Interrogating the interplay amongst glioma invasion, vascularity and necrosis.

Methods 2021 01 23;185:94-104. Epub 2020 Jan 23.

Department of Mechanical & Manufacturing Engineering, University of Cyprus, Nicosia, Cyprus; Department of Medical Physics & Biomedical Engineering, University College London, London, UK. Electronic address:

This paper develops a three-dimensional in silico hybrid model of cancer, which describes the multi-variate phenotypic behaviour of tumour and host cells. The model encompasses the role of cell migration and adhesion, the influence of the extracellular matrix, the effects of oxygen and nutrient availability, and the signalling triggered by chemical cues and growth factors. The proposed in silico hybrid modelling framework combines successfully the advantages of continuum-based and discrete methods, namely the finite element and agent-based method respectively. The framework is thus used to realistically model cancer mechano-biology in a multiscale fashion while maintaining the resolution power of each method in a computationally cost-effective manner. The model is tailored to simulate glioma progression, and is subsequently used to interrogate the balance between the host cells and small sized gliomas, while the go-or-grow phenotype characteristic in glioblastomas is also investigated. Also, cell-cell and cell-matrix interactions are examined with respect to their effect in (macroscopic) tumour growth, brain tissue perfusion and tumour necrosis. Finally, we use the in silico framework to assess differences between low-grade and high-grade glioma growth, demonstrating significant differences in the distribution of cancer as well as host cells, in accordance with reported experimental findings.
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http://dx.doi.org/10.1016/j.ymeth.2020.01.006DOI Listing
January 2021

Demonstration of a picosecond Bragg switch for hard X-rays in a synchrotron-based pump-probe experiment.

J Synchrotron Radiat 2019 Jul 12;26(Pt 4):1253-1259. Epub 2019 Jun 12.

Tailored X-ray Products gGmbH, Berlin, Germany.

A benchmark experiment is reported that demonstrates the shortening of hard X-ray pulses in a synchrotron-based optical pump-X-ray probe measurement. The pulse-shortening device is a photoacoustic Bragg switch that reduces the temporal resolution of an incident X-ray pulse to approximately 7.5 ps. The Bragg switch is employed to monitor propagating sound waves in nanometer thin epitaxial films. From the experimental data, the pulse duration, diffraction efficiency and switching contrast of the device can be inferred. A detailed efficiency analysis shows that the switch can deliver up to 10 photons s in high-repetition-rate synchrotron experiments.
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http://dx.doi.org/10.1107/S1600577519005356DOI Listing
July 2019

Structural connectivity centrality changes mark the path toward Alzheimer's disease.

Alzheimers Dement (Amst) 2019 Dec 18;11:98-107. Epub 2019 Jan 18.

Interdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom.

Introduction: The pathophysiological process of Alzheimer's disease is thought to begin years before clinical decline, with evidence suggesting prion-like spreading processes of neurofibrillary tangles and amyloid plaques.

Methods: Using diffusion magnetic resonance imaging data from the Alzheimer's Disease Neuroimaging Initiative database, we first identified relevant features for dementia diagnosis. We then created dynamic models with the Nathan Kline Institute-Rockland Sample database to estimate the earliest detectable stage associated with dementia in the simulated disease progression.

Results: A classifier based on centrality measures provides informative predictions. Strength and closeness centralities are the most discriminative features, which are associated with the medial temporal lobe and subcortical regions, together with posterior and occipital brain regions. Our model simulations suggest that changes associated with dementia begin to manifest structurally at early stages.

Discussion: Our analyses suggest that diffusion magnetic resonance imaging-based centrality measures can offer a tool for early disease detection before clinical dementia onset.
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http://dx.doi.org/10.1016/j.dadm.2018.12.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6350419PMC
December 2019

An integrated transcriptional analysis of the developing human retina.

Development 2019 01 29;146(2). Epub 2019 Jan 29.

Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK

The scarcity of embryonic/foetal material as a resource for direct study means that there is still limited understanding of human retina development. Here, we present an integrated transcriptome analysis combined with immunohistochemistry in human eye and retinal samples from 4 to 19 post-conception weeks. This analysis reveals three developmental windows with specific gene expression patterns that informed the sequential emergence of retinal cell types and enabled identification of stage-specific cellular and biological processes, and transcriptional regulators. Each stage is characterised by a specific set of alternatively spliced transcripts that code for proteins involved in the formation of the photoreceptor connecting cilium, pre-mRNA splicing and epigenetic modifiers. Importantly, our data show that the transition from foetal to adult retina is characterised by a large increase in the percentage of mutually exclusive exons that code for proteins involved in photoreceptor maintenance. The circular RNA population is also defined and shown to increase during retinal development. Collectively, these data increase our understanding of human retinal development and the pre-mRNA splicing process, and help to identify new candidate disease genes.
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http://dx.doi.org/10.1242/dev.169474DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6361134PMC
January 2019

CRX Expression in Pluripotent Stem Cell-Derived Photoreceptors Marks a Transplantable Subpopulation of Early Cones.

Stem Cells 2019 05 30;37(5):609-622. Epub 2019 Jan 30.

Institute of Genetic Medicine, Newcastle University, Newcastle, United Kingdom.

Death of photoreceptors is a common cause of age-related and inherited retinal dystrophies, and thus their replenishment from renewable stem cell sources is a highly desirable therapeutic goal. Human pluripotent stem cells provide a useful cell source in view of their limitless self-renewal capacity and potential to not only differentiate into cells of the retina but also self-organize into tissue with structure akin to the human retina as part of three-dimensional retinal organoids. Photoreceptor precursors have been isolated from differentiating human pluripotent stem cells through application of cell surface markers or fluorescent reporter approaches and shown to have a similar transcriptome to fetal photoreceptors. In this study, we investigated the transcriptional profile of CRX-expressing photoreceptor precursors derived from human pluripotent stem cells and their engraftment capacity in an animal model of retinitis pigmentosa (Pde6brd1), which is characterized by rapid photoreceptor degeneration. Single cell RNA-Seq analysis revealed the presence of a dominant cell cluster comprising 72% of the cells, which displayed the hallmarks of early cone photoreceptor expression. When transplanted subretinally into the Pde6brd1 mice, the CRX cells settled next to the inner nuclear layer and made connections with the inner neurons of the host retina, and approximately one-third of them expressed the pan cone marker, Arrestin 3, indicating further maturation upon integration into the host retina. Together, our data provide valuable molecular insights into the transcriptional profile of human pluripotent stem cells-derived CRX photoreceptor precursors and indicate their usefulness as a source of transplantable cone photoreceptors. Stem Cells 2019;37:609-622.
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http://dx.doi.org/10.1002/stem.2974DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6519156PMC
May 2019

Laminin γ3 plays an important role in retinal lamination, photoreceptor organisation and ganglion cell differentiation.

Cell Death Dis 2018 05 23;9(6):615. Epub 2018 May 23.

Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom.

Laminins are heterotrimeric glycoproteins of the extracellular matrix. Eleven different laminin chains have been identified in vertebrates. They are ubiquitously expressed in the human body, with a distinct tissue distribution. Laminin expression in neural retina and their functional role during human retinogenesis is still unknown. This study investigated the laminin expression in human developing and adult retina, showing laminin α1, α5, β1, β2 and γ1 to be predominantly expressed in Bruch's membrane and the inner limiting membrane. Laminin-332 and laminin γ3 expression were mainly observed in the neural retina during retinal histogenesis. These expression patterns were largely conserved in pluripotent stem cell-derived retinal organoids. Blocking of laminin γ3 function in retinal organoids resulted in the disruption of laminar organisation and synapse formation, the loss of photoreceptor organisation and retinal ganglion cells. Our data demonstrate a unique temporal and spatial expression for laminins and reveal a novel role for laminin γ3 during human retinogenesis.
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http://dx.doi.org/10.1038/s41419-018-0648-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5966411PMC
May 2018

Extracellular matrix component expression in human pluripotent stem cell-derived retinal organoids recapitulates retinogenesis in vivo and reveals an important role for IMPG1 and CD44 in the development of photoreceptors and interphotoreceptor matrix.

Acta Biomater 2018 07 17;74:207-221. Epub 2018 May 17.

Institute of Genetic Medicine, Newcastle University, UK. Electronic address:

The extracellular matrix (ECM) plays an important role in numerous processes including cellular proliferation, differentiation, migration, maturation, adhesion guidance and axonal growth. To date, there has been no detailed analysis of the ECM distribution during retinal ontogenesis in humans and the functional importance of many ECM components is poorly understood. In this study, the expression of key ECM components in adult mouse and monkey retina, developing and adult human retina and retinal organoids derived from human pluripotent stem cells was studied. Our data indicate that basement membrane ECMs (Fibronectin and Collagen IV) were expressed in Bruch's membrane and the inner limiting membrane of the developing human retina, whilst the hyalectins (Versican and Brevican), cluster of differentiation 44 (CD44), photoreceptor-specific ECMs Interphotoreceptor Matrix Proteoglycan 1 (IMPG1) and Interphotoreceptor Matrix Proteoglycan 2 (IMPG2) were detected in the developing interphotoreceptor matrix (IPM). The expression of IMPG1, Versican and Brevican in the developing IPM was conserved between human developing retina and human pluripotent stem cell-derived retinal organoids. Blocking the action of CD44 and IMPG1 in pluripotent stem cell derived retinal organoids affected the development of photoreceptors, their inner/outer segments and connecting cilia and disrupted IPM formation, with IMPG1 having an earlier and more significant impact. Together, our data suggest an important role for IMPG1 and CD44 in the development of photoreceptors and IPM formation during human retinogenesis.

Statement Of Significance: The expression and the role of many extracellular matrix (ECM) components during human retinal development is not fully understood. In this study, expression of key ECM components (Collagen IV, Fibronectin, Brevican, Versican, IMPG1 and IMPG2) was investigated during human retinal ontogenesis. Collagen IV and Fibronectin were expressed in Bruch's membrane; whereas Brevican, Versican, IMPG1 & IMPG2 in the developing interphotoreceptor matrix (IPM). Retinal organoids were successfully generated from pluripotent stem cells. The expression of ECM components was examined in the retinal organoids and found to recapitulate human retinal development in vivo. Using functional blocking experiments, we were able to highlight an important role for IMPG1 and CD44 in the development of photoreceptors and IPM formation.
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http://dx.doi.org/10.1016/j.actbio.2018.05.023DOI Listing
July 2018

Nonlinear growth: an origin of hub organization in complex networks.

R Soc Open Sci 2017 Mar 22;4(3):160691. Epub 2017 Mar 22.

Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; Interdisciplinary Computing and Complex BioSystems Research Group (ICOS), School of Computing Science, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.

Many real-world networks contain highly connected nodes called hubs. Hubs are often crucial for network function and spreading dynamics. However, classical models of how hubs originate during network development unrealistically assume that new nodes attain information about the connectivity (for example the degree) of existing nodes. Here, we introduce hub formation through nonlinear growth where the number of nodes generated at each stage increases over time and new nodes form connections independent of target node features. Our model reproduces variation in number of connections, hub occurrence time, and rich-club organization of networks ranging from protein-protein, neuronal and fibre tract brain networks to airline networks. Moreover, nonlinear growth gives a more generic representation of these networks compared with previous preferential attachment or duplication-divergence models. Overall, hub creation through nonlinear network expansion can serve as a benchmark model for studying the development of many real-world networks.
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http://dx.doi.org/10.1098/rsos.160691DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5383813PMC
March 2017

Developmental self-construction and -configuration of functional neocortical neuronal networks.

PLoS Comput Biol 2014 Dec 4;10(12):e1003994. Epub 2014 Dec 4.

Institute of Neuroinformatics, University/ETH Zürich, Zürich, Switzerland.

The prenatal development of neural circuits must provide sufficient configuration to support at least a set of core postnatal behaviors. Although knowledge of various genetic and cellular aspects of development is accumulating rapidly, there is less systematic understanding of how these various processes play together in order to construct such functional networks. Here we make some steps toward such understanding by demonstrating through detailed simulations how a competitive co-operative ('winner-take-all', WTA) network architecture can arise by development from a single precursor cell. This precursor is granted a simplified gene regulatory network that directs cell mitosis, differentiation, migration, neurite outgrowth and synaptogenesis. Once initial axonal connection patterns are established, their synaptic weights undergo homeostatic unsupervised learning that is shaped by wave-like input patterns. We demonstrate how this autonomous genetically directed developmental sequence can give rise to self-calibrated WTA networks, and compare our simulation results with biological data.
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http://dx.doi.org/10.1371/journal.pcbi.1003994DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256067PMC
December 2014

A computational model incorporating neural stem cell dynamics reproduces glioma incidence across the lifespan in the human population.

PLoS One 2014 19;9(11):e111219. Epub 2014 Nov 19.

Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, Tyne and Wear, United Kingdom.

Glioma is the most common form of primary brain tumor. Demographically, the risk of occurrence increases until old age. Here we present a novel computational model to reproduce the probability of glioma incidence across the lifespan. Previous mathematical models explaining glioma incidence are framed in a rather abstract way, and do not directly relate to empirical findings. To decrease this gap between theory and experimental observations, we incorporate recent data on cellular and molecular factors underlying gliomagenesis. Since evidence implicates the adult neural stem cell as the likely cell-of-origin of glioma, we have incorporated empirically-determined estimates of neural stem cell number, cell division rate, mutation rate and oncogenic potential into our model. We demonstrate that our model yields results which match actual demographic data in the human population. In particular, this model accounts for the observed peak incidence of glioma at approximately 80 years of age, without the need to assert differential susceptibility throughout the population. Overall, our model supports the hypothesis that glioma is caused by randomly-occurring oncogenic mutations within the neural stem cell population. Based on this model, we assess the influence of the (experimentally indicated) decrease in the number of neural stem cells and increase of cell division rate during aging. Our model provides multiple testable predictions, and suggests that different temporal sequences of oncogenic mutations can lead to tumorigenesis. Finally, we conclude that four or five oncogenic mutations are sufficient for the formation of glioma.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0111219PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4237327PMC
July 2015

Simulating cortical development as a self constructing process: a novel multi-scale approach combining molecular and physical aspects.

PLoS Comput Biol 2013 15;9(8):e1003173. Epub 2013 Aug 15.

Institute of Neuroinformatics, University of Zürich/Swiss Federal Institute of Technology Zürich, Switzerland.

Current models of embryological development focus on intracellular processes such as gene expression and protein networks, rather than on the complex relationship between subcellular processes and the collective cellular organization these processes support. We have explored this collective behavior in the context of neocortical development, by modeling the expansion of a small number of progenitor cells into a laminated cortex with layer and cell type specific projections. The developmental process is steered by a formal language analogous to genomic instructions, and takes place in a physically realistic three-dimensional environment. A common genome inserted into individual cells control their individual behaviors, and thereby gives rise to collective developmental sequences in a biologically plausible manner. The simulation begins with a single progenitor cell containing the artificial genome. This progenitor then gives rise through a lineage of offspring to distinct populations of neuronal precursors that migrate to form the cortical laminae. The precursors differentiate by extending dendrites and axons, which reproduce the experimentally determined branching patterns of a number of different neuronal cell types observed in the cat visual cortex. This result is the first comprehensive demonstration of the principles of self-construction whereby the cortical architecture develops. In addition, our model makes several testable predictions concerning cell migration and branching mechanisms.
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http://dx.doi.org/10.1371/journal.pcbi.1003173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3744399PMC
February 2014

Developmental origin of patchy axonal connectivity in the neocortex: a computational model.

Cereb Cortex 2014 Feb 6;24(2):487-500. Epub 2012 Nov 6.

Institute of Neuroinformatics, University of Zürich and Swiss Federal Institute of Technology Zürich.

Injections of neural tracers into many mammalian neocortical areas reveal a common patchy motif of clustered axonal projections. We studied in simulation a mathematical model for neuronal development in order to investigate how this patchy connectivity could arise in layer II/III of the neocortex. In our model, individual neurons of this layer expressed the activator-inhibitor components of a Gierer-Meinhardt reaction-diffusion system. The resultant steady-state reaction-diffusion pattern across the neuronal population was approximately hexagonal. Growth cones at the tips of extending axons used the various morphogens secreted by intrapatch neurons as guidance cues to direct their growth and invoke axonal arborization, so yielding a patchy distribution of arborization across the entire layer II/III. We found that adjustment of a single parameter yields the intriguing linear relationship between average patch diameter and interpatch spacing that has been observed experimentally over many cortical areas and species. We conclude that a simple Gierer-Meinhardt system expressed by the neurons of the developing neocortex is sufficient to explain the patterns of clustered connectivity observed experimentally.
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http://dx.doi.org/10.1093/cercor/bhs327DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3888370PMC
February 2014

Role of the polypeptide backbone and post-translational modifications in cross-reactivity of Art v 1, the major mugwort pollen allergen.

Biol Chem 2009 May-Jun;390(5-6):445-51

Christian Doppler Laboratory for Allergy Diagnosis and Therapy, Department of Molecular Biology, University of Salzburg, Hellbrunnerstrasse 34, A-5020 Salzburg, Austria.

Artemisia vulgaris (mugwort) is one of the main causes of late summer pollinosis in Europe, with >95% of patients sensitized to the glycoallergen Art v 1. Despite the importance of this allergen, little is known about its cross-reactive behavior. Here we investigated the occurrence of conserved Art v 1 antigenic determinants in sources known to display clinically relevant cross-reactivity with mugwort pollen. For this purpose, monoclonal antibodies specific for a cysteine-stabilized epitope of the Art v 1 defensin domain and for carbohydrates attached to the proline domain were produced by hybridoma and phage display technologies. Using polyclonal Art v 1-specific rabbit sera and antibodies against both the Art v 1 carbohydrate and polypeptide moieties, we could identify cross-reactive structures in pollen from botanically related Asteraceae weeds (Artemisia absinthium, Helianthus annuus and Ambrosia sp.). Homologous allergens were also recognized by IgE from mugwort-sensitized patients and the reactivity could be decreased by serum pre-incubation with natural and recombinant Art v 1. As no cross-reactive structures could be found in foods associated with mugwort pollinosis, we conclude that Art v 1 is poorly involved in mugwort cross-reactivity to food allergens.
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http://dx.doi.org/10.1515/BC.2009.063DOI Listing
July 2009

A highly potent and cellularly active beta-peptidic inhibitor of the p53/hDM2 interaction.

Chembiochem 2009 Apr;10(6):994-8

The University of Edinburgh, Centre for Translational and Chemical Biology, UK.

New and improved: The incorporation of a 6-chlorotryptophan (6-Cl-Trp) into a beta-peptide (M)-3(14) helix leads to a high-affinity hDM2 inhibitor, as demonstrated by fluorescence fluctuation analysis at single molecule resolution. When conjugated to penetratin, the newly derived hDM2 binder specifically inhibits tumour cell growth in vitro.
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http://dx.doi.org/10.1002/cbic.200800803DOI Listing
April 2009

Terminal adenosyl transferase activity of posttranscriptional regulator HuR revealed by confocal on-bead screening.

J Mol Biol 2009 Feb 14;386(2):435-50. Epub 2008 Dec 14.

Novartis Institutes for BioMedical Research, Basel, Switzerland.

Posttranscriptional regulation and RNA metabolism have become central topics in the understanding of mammalian gene expression and cell signalling, with the 3' untranslated region emerging as the coordinating unit. The 3' untranslated region trans-acting factor Hu protein R (HuR) forms a central posttranscriptional pathway node bridging between AU-rich element-mediated processes and microRNA regulation. While (m)RNA control by HuR has been extensively characterized, the molecular mode of action still remains elusive. Here we describe the identification of the first RRM3 (RNA recognition motif 3) targeted low molecular weight HuR inhibitors from a one-bead-one-compound library screen using confocal nanoscanning. A further compound characterization revealed the presence of an ATP-binding pocket within HuR RRM3, associated with enzymatic activity. Centered around a metal-ion-coordinating DxD motif, the catalytic site mediates 3'-terminal adenosyl modification of non-polyadenylated RNA substrates by HuR. These findings suggest that HuR actively contributes to RNA modification and maturation and thereby shed an entirely new light on the role of HuR in RNA metabolism.
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http://dx.doi.org/10.1016/j.jmb.2008.12.020DOI Listing
February 2009

Identification and mechanistic characterization of low-molecular-weight inhibitors for HuR.

Nat Chem Biol 2007 Aug 15;3(8):508-15. Epub 2007 Jul 15.

Novartis Institutes for Biomedical Research, Discovery Technologies, Brunnerstr. 59, A-1235 Vienna, Austria.

Careful regulation of mRNA half-lives is a fundamental mechanism allowing cells to quickly respond to changing environmental conditions. The mRNA-binding Hu proteins are important for stabilization of short-lived mRNAs. Here we describe the identification and mechanistic characterization of the first low-molecular-weight inhibitors for Hu protein R (HuR) from microbial broths (Actinomyces sp.): dehydromutactin (1), MS-444 (2) and okicenone (3). These compounds interfere with HuR RNA binding, HuR trafficking, cytokine expression and T-cell activation. A mathematical and experimental analysis of the compounds' mode of action suggests that HuR homodimerizes before RNA binding and that the compounds interfere with the formation of HuR dimers. Our results demonstrate the chemical drugability of HuR; to our knowledge HuR is the first example of a drugable protein within the Hu family. MS-444, dehydromutactin and okicenone may become valuable tools for studying HuR function. An assessment of HuR inhibition as a central node in malignant processes might open up new conceptual routes toward combatting cancer.
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http://dx.doi.org/10.1038/nchembio.2007.14DOI Listing
August 2007

Generation of hypoallergenic DNA vaccines by forced ubiquitination: preventive and therapeutic effects in a mouse model of allergy.

J Allergy Clin Immunol 2006 Jul 11;118(1):269-76. Epub 2006 May 11.

Department of Molecular Biology, Division of Allergy and Immunology, Hellbrunnerstrasse 34, 5020 Salzburg, Austria.

Background: Hypoallergenic immunotherapy of type I allergies aims at inducing T-cell immunity while avoiding cross-linking of pre-existing IgE. DNA-based immunotherapy depends on the recruitment of antigen-specific T(H)1 cells and therefore has to provide the whole repertoire of T-cell epitopes. Ubiquitination offers a general approach for the production of hypoallergenic DNA vaccines.

Objective: A DNA-based vaccine encoding the major birch pollen allergen Bet v 1 stably linked to ubiquitin was evaluated for its antiallergic potential in a BALB/c mouse model of allergy.

Methods: Plasmid DNA was applied to mice before (preventive) or after (therapeutic) sensitization with recombinant Bet v 1. In the preventive setting, mice were exposed to aerosolized allergen in addition. Cytokine production was monitored via ELISPOT and Luminex. IgG(1), IgG(2a), and IgE subclass antibody titers were determined by ELISA. In vitro antigen-specific cross-linking of IgE was measured in a degranulation assay. Bronchoalveolar lavages were analyzed for leukocyte subsets as well as for IFN-gamma and IL-5, and paraffin sections of lungs were examined for mucus production and endothelial damage.

Results: Prevaccination with ubiquitinated Bet v 1-stimulated T(H)1-biased immune responses with concomitant suppression of functional IgE, reduction of eosinophil counts in bronchoalveolar lavages, and alleviation of lung pathology, and could also suppress an ongoing IgE response in a therapeutic setting.

Conclusion: The data clearly demonstrate that hypoallergenic DNA vaccines encoding ubiquitin fusion constructs induce effective antiallergic immune responses.

Clinical Implications: Ubiquitination of allergen gene vaccines eliminates the risk of IgE cross-linking, thereby meeting the safety requirements for clinical applications.
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http://dx.doi.org/10.1016/j.jaci.2006.03.033DOI Listing
July 2006

Strategies for the development of safe and effective DNA vaccines for allergy treatment.

Arb Paul Ehrlich Inst Bundesamt Sera Impfstoffe Frankf A M 2003 (94):279-98; discussion 299

AKH Wien Division of Immopathology, Währinger Gürtel 18-20, A-1090 Wien.

During the past ten years, a great number of studies have demonstrated that injection of plasmid DNA coding for certain genes results in the induction of humoral and cellular immune responses against the respective gene product. The features of DNA vaccines enable a broad range of applications, including the induction of protective immunity against viral, bacterial, and parasitic infections, and open up new perspectives for the treatment of cancer. Furthermore, based on their Th1-promoting properties, DNA vaccines also turned out to balance Th2-mediated immune reactions, a quality which renders them a promising alternative for immunotherapy against allergy. Their unique immunological properties offer new possibilities for the development of vaccines, which do not cause anaphylactic side effects, a major drawback of specific immunotherapy (SIT). In this review, we present approaches to avoid the translation of native allergenic determinants, thus preventing release of allergy mediators stimulated by crosslinking of pre-existing or vaccine-induced IgE antibodies on mast cells. Three approaches are described, which fulfill these requirements: (i) cutting the allergen gene into overlapping fragments, which lack any antigenic determinant of the native allergen, but display the original repertoire of T cell epitopes, (ii) using hypoallergenic derivatives or (iii) fusing the allergen with ubiquitin, thus fragmenting the antigen and destroying its native structure. The presented experiments demonstrate that DNA vaccines are suitable to balance an allergic response in a protective as well as a therapeutic experimental design, thus demonstrating their potential for allergy treatment. In addition to conventional plasmid DNA vaccines, aspects and perspectives of replicon-based DNA vaccines will be discussed.
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May 2004

Contour integration in striate cortex. Classic cell responses or cooperative selection?

Exp Brain Res 2002 Nov 1;147(2):145-52. Epub 2002 Oct 1.

FB Physik/Neurophysik, Philipps-Universität, Renthof 7, 35032 Marburg, Germany.

Psychophysics has established various rules of contour integration in gestalt perception. We tested the rule of good continuation by stimulating behaving monkeys with simple figures composed of Gabor patches, while recording from upper layer cells in visual cortex (V1). By decomposing these figures into their components and stimulating receptive field centers and surrounds separately with this stimulus set, we tested center-surround interaction for linearity. In pure-fixation tasks, the interaction was negative for the early strong evoked response, i.e., in this phase figural context rather inhibited the cells. However, in the following tonic response phase, a subgroup of neurons showed positive interaction during the whole stimulus presentation period of at least 1,000 ms. Attention to the figure in discrimination tasks only slightly improved this positive interaction between 150 and 300 ms. We interpret these results as selective cooperation and mutual facilitation of cortical V1 cells, thereby supporting the saliency of borders and contours in perception of visual scenes.
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http://dx.doi.org/10.1007/s00221-002-1178-6DOI Listing
November 2002

Perceptual grouping correlates with short synchronization in monkey prestriate cortex.

Neuroreport 2002 Oct;13(15):1881-6

Philipps-University, Physics Department, Neurophysics Group, Marburg, Germany.

Synchronization in the visual cortex at 35-80 Hz is assumed to support perceptual grouping. We tested this hypothesis in a figure-ground task in which a trained monkey indicated by a key whether he perceived a figure that was composed of the same blobs as the background distractors. The task was sufficiently difficult such that about 25% of responses were incorrect. We recorded population activity with 7 microelectrodes in prestriate cortex (V2). During a short period before the monkey's perceptual response, locations of figure-activated neurons showed increased synchronization (50-80 Hz) in correct compared to incorrect responses, while other signal measures were unrelated to perception. These are first indications that a short synchronous burst in V2 may support perceptual grouping.
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http://dx.doi.org/10.1097/00001756-200210280-00010DOI Listing
October 2002

Inter-cellular spike coincidences in visual detection tasks.

Naturwissenschaften 2002 Jul;89(7):316-8

FB Physik/Neurophysik, Philipps-Universität, Marburg, Germany.

Synchronized spike activity is discussed as a possible representational code for object integration and as a neuronal basis of attention, perception and awareness. As a byproduct of experiments in which monkeys were trained to detect simple figures composed of single Gabor patches in a noisy background of similar elements, we found in special cases increased spike synchrony above chance level specifically related to figure detection. The long latency of this effect is difficult to interpret. It may be a sign of the cognitive state of an animal when it perceives the figure.
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http://dx.doi.org/10.1007/s00114-002-0333-zDOI Listing
July 2002