Phytochrome-Based Extracellular Matrix with Reversibly Tunable Mechanical Properties

Interrogation and control of cellular fate and function using optogenetics is providing revolutionary insights into biology. Optogenetic control of cells is achieved by coupling genetically encoded photoreceptors to cellular effectors and enables unprecedented spatiotemporal control of signaling processes. Here, a fast and reversibly switchable photoreceptor is used to tune the mechanical properties of polymer materials in a fully reversible, wavelength-specific, and dose- and space-controlled manner. By integrating engineered cyanobacterial phytochrome 1 into a poly(ethylene glycol) matrix, hydrogel materials responsive to light in the cell-compatible red/far-red spectrum are synthesized. These materials are applied to study in human mesenchymal stem cells how different mechanosignaling pathways respond to changing mechanical environments and to control the migration of primary immune cells in 3D. This optogenetics-inspired matrix allows fundamental questions of how cells react to dynamic mechanical environments to be addressed. Further, remote control of such matrices can create new opportunities for tissue engineering or provide a basis for optically stimulated drug depots.

Liquid-liquid phase separation of light-inducible transcription factors increases transcription activation in mammalian cells and mice

Light-inducible gene switches represent a key strategy for the precise manipulation of cellular events in fundamental and applied research. However, the performance of widely used gene switches is limited due to low tissue penetrance and possible phototoxicity of the light stimulus. To overcome these limitations, we engineer optogenetic synthetic transcription factors to undergo liquid-liquid phase separation in close spatial proximity to promoters. Phase separation of constitutive and optogenetic synthetic transcription factors was achieved by incorporation of intrinsically disordered regions. Supported by a quantitative mathematical model, we demonstrate that engineered transcription factor droplets form at target promoters and increase gene expression up to fivefold. This increase in performance was observed in multiple mammalian cells lines as well as in mice following in situ transfection. The results of this work suggest that the introduction of intrinsically disordered domains is a simple yet effective means to boost synthetic transcription factor activity.

Optogenetic control shows that kinetic proofreading regulates the activity of the T cell receptor

The immune system distinguishes between self and foreign antigens. The kinetic proofreading (KPR) model proposes that T cells discriminate self from foreign ligands by the different ligand binding half-lives to the T cell receptor (TCR). It is challenging to test KPR as the available experimental systems fall short of only altering the binding half-lives and keeping other parameters of the interaction unchanged. We engineered an optogenetic system using the plant photoreceptor phytochrome B (PhyB) as a ligand to selectively control the dynamics of ligand binding to the TCR by light. This opto-ligand-TCR system was combined with the unique property of PhyB to continuously cycle between the binding and non-binding states under red light, with the light intensity determining the cycling rate and thus the binding duration. Mathematical modeling of our experimental datasets showed that indeed the ligand-TCR interaction half-life is the decisive factor for activating downstream TCR signaling, substantiating KPR.

Octopamine-immunoreactive neurons in the central nervous system of the cricket, Gryllus bimaculatus

The distribution of octopamine-immunoreactive neurons is described using whole-mount preparations of all central ganglia of the cricket, Gryllus bimaculatus. Up to 160 octopamine-immunoreactive somata were mapped per animal. Medial unpaired octopamine-immunoreactive neurons occur in all but the cerebral ganglia and show segment-specific differences in number. The position and form of these cells are in accordance with well-known, segmentally-organized clusters of large dorsal and ventral unpaired medial neurons demonstrated by other techniques. In addition, bilaterally arranged groups of immunoreactive somata have been labelled in the cerebral, suboesophageal and terminal ganglia. A detailed histological description of octopamine-immunoreactive elements in the prothoracic ganglion is given. Octopamine-immunoreactive somata and axons correspond to the different dorsal unpaired medial cell types identified by intracellular single-cell staining. In the prothoracic ganglion, all efferent neurons whose primary neurites are found in the fibre bundle of dorsal unpaired cells are immunoreactive. Intersegmental octopamine-immunoreactive neurons are also present. Collaterals originating from dorsal intersegmental fibres terminate in different neuropils and fibre tracts. Fine varicose fibres have been located in several fibre tracts, motor and sensory neuropils. Peripheral varicose octopamine-immunoreactive fibres found on several nerves are discussed in terms of possible neurohemal releasing sites for octopamine.

Absence of recurrent axon collaterals in motoneurones to the extrinsic digit extensor muscles of the cat forelimb

Forelimb alpha-motoneurones were intracellularly recorded in anaesthetized cats and iontophoretically filled with horseradish peroxidase (HRP). All motoneurones to the elbow flexors, elbow extensor and to the extensor carpi radialis muscles displayed in parallel homonymous recurrent inhibitory postsynaptic potentials (RIPSPs) and axon collaterals. Homonymous RIPSPs and axon collaterals were missing in the nuclei to the long digit extensor muscles. Two populations of motoneurones, with and without recurrent axon collaterals, seem to be present in the extensor carpi ulnaris motor nucleus. These results are consistent with the hypothesis that the motoneurones to the extrinsic digit extensors lack a recurrent axonal system. This indicates that the contribution of the recurrent Renshaw systems to motor control may be more complex than hitherto assumed.

Optogenetic control of integrin-matrix interaction

Optogenetic approaches have gathered momentum in precisely modulating and interrogating cellular signalling and gene expression. The use of optogenetics on the outer cell surface to interrogate how cells receive stimuli from their environment, however, has so far not reached its full potential. Here we demonstrate the development of an optogenetically regulated membrane receptor-ligand pair exemplified by the optically responsive interaction of an integrin receptor with the extracellular matrix. The system is based on an integrin engineered with a phytochrome-interacting factor domain (OptoIntegrin) and a red light-switchable phytochrome B-functionalized matrix (OptoMatrix). This optogenetic receptor-ligand pair enables light-inducible and -reversible cell-matrix interaction, as well as the controlled activation of downstream mechanosensory signalling pathways. Pioneering the application of optogenetic switches in the extracellular environment of cells, this OptoMatrix-OptoIntegrin system may serve as a blueprint for rendering matrix-receptor interactions amendable to precise control with light.

Structural insights into cis element recognition of non-polyadenylated RNAs by the Nab3-RRM

Transcription termination of non-polyadenylated RNAs in Saccharomyces cerevisiae occurs through the action of the Nrd1-Nab3-Sen1 complex. Part of the decision to terminate via this pathway occurs via direct recognition of sequences within the nascent transcript by RNA recognition motifs (RRMs) within Nrd1 and Nab3. Here we present the 1.6 Å structure of Nab3-RRM bound to its UCUU recognition sequence. The crystal structure reveals clear density for a UCU trinucleotide and a fourth putative U binding site. Nab3-RRM establishes a clear preference for the central cytidine of the UCUU motif, which forms pseudo-base pairing interactions primarily through hydrogen bonds to main chain atoms and one serine hydroxyl group. Specificity for the flanking uridines is less defined; however, binding experiments confirm that these residues are also important for high affinity binding. Comparison of the Nab3-RRM to other structures of RRMs bound to polypyrimidine RNAs showed that this mode of recognition is similar to what is observed for the polypyrimidine-tract binding RRMs, and that the serine residue involved in pseudo-base pairing is only found in RRMs that bind to polypyrimidine RNAs that contain a cytosine base, suggesting a possible mechanism for discriminating between cytosine and uracil bases in RRMs that bind to polypyrimidine-containing RNA.

Cytoarchitecture of histamine-, dopamine-, serotonin- and octopamine-containing neurons in the cricket ventral nerve cord

The present article provides a comparative neuroanatomical description of the cellular localization of the biogenic amines histamine, dopamine, serotonin and octopamine in the ventral nerve cord of an insect, namely the cricket, Gryllus bimaculatus. Generally, different immunocytochemical staining techniques reveal a small number of segmentally distributed immunoreactive (-IR) amine-containing neurons allowing single cell reconstruction of prominent elements. Aminergic neurons share common morphological features in that they innervate large portions of neurophil and often connect different neuromeres by intersegmental 'wide-field' projections of varicose appearance. In many cases aminergic terminals are also found on the surface of peripheral nerves suggesting additional neurohemal release sites. Despite such morphological similarities histological analysis demonstrates for any given amine functionally distinct neuron types with specific innervation patterns establishing discrete pathways. Histamine-IR interneurons are characterized by both ascending and descending projections forming central and peripheral terminals. The descending branches from dopamine-IR cells mainly converge within the terminal ganglion, whereas serotonin-IR interneurons with ascending projections often terminate within the brain. Serotonin is also present in sensory and motor neurons. In contrast to other aminergic neurons, most octopamine-IR cells represent unpaired neurons projecting through motor nerves of the soma-containing neuromere. Octopamine-IR cells with intersegmental branches are only rarely found. Based on these findings, a colocalization of different amines within the same neuron seems to be unlikely to occur in the cricket ventral nerve cord. With respect to the neuroanatomical description of amine-containing neurons known physiological effects of biogenic amines and their possible neuromodulatory functions in insects are discussed.

Topographical representation of shoulder motor nuclei in the cat spinal cord as revealed by retrograde fluorochrome tracers

The present investigation demonstrates the morphological relationships among the main shoulder motor nuclei within the spinal cord of the cat. The intraspinal position of these nuclei has been revealed by retrograde labelling of spinal motor neurones via their peripheral nerves supplying anatomically identified shoulder muscles. Multiple pressure injection of up to four fluorescent tracers (Bisbenzimide, Fast Blue, Fluoro-Gold, Rhodamine-b-isothiocyanate) in one experiment was used to show the longitudinal distribution and topographical relations of motor neurones projecting to muscles acting on the scapulo-humerus joint. Tracer-positive cells have been found from middle C5 to rostral Th2 in the cervical cord, forming coherent longitudinal cell clusters separated in medial and lateral projection fields in the ventral horn. The present data suggest that the anatomical organization of spinal shoulder motor neurones corresponds to the embryonic origin of their later target muscles. All medial motor nuclei project to muscles deriving from ventral embryonic origins, while those motor nuclei lying in lateral positions innervate muscles originating from dorsal muscle primordia. Therefore, the spinal topography of shoulder motor nuclei seems to be independent of both the position and the function of a given muscle in the adult animal.

Autoinhibition of serotonin cells: an intrinsic regulatory mechanism sensitive to the pattern of usage of the cells

After periods of high-frequency firing, the normal rhythmically active serotonin (5HT)-containing neurosecretory neurons of the lobster ventral nerve cord display a period of suppressed spike generation and reduced synaptic input that we refer to as "autoinhibition." The duration of this autoinhibition is directly related to the magnitude and duration of the current injection triggering the high-frequency firing. More interesting, however, is that the autoinhibition is inversely related to the initial firing frequency of these cells within their normal range of firing (0.5-3 Hz). This allows more active 5HT neurons to resume firing after shorter durations of inhibition than cells that initially fired at slower rates. Although superfused 5HT inhibits the spontaneous firing of these cells, the persistence of autoinhibition in saline with no added calcium, in cadmium-containing saline, and in lobsters depleted of serotonin suggests that intrinsic membrane properties account for the autoinhibition. A similar autoinhibition is seen in spontaneously active octopamine neurons but is absent from spontaneously active gamma-aminobutyric acid cells. Thus, this might be a characteristic feature of amine-containing neurosecretory neurons. The 5HT cells of vertebrate brain nuclei share similarities in firing frequencies, spike shapes, and inhibition by 5HT with the lobster cells that were the focus of this study. However, the mechanism suggested to underlie autoinhibition in vertebrate neurons is that 5HT released from activated or neighboring cells acts back on inhibitory autoreceptors that are found on the dendrites and cell bodies of these neurons.

Octopamine immunoreactive neurons in the fused central nervous system of spiders

Using antisera directed against octopamine (OA), we identified and mapped octopamine-immunoreactive (OA-ir) neurons and their projections in the fused, central ganglion complex of wandering spiders, Cupiennius salei. Labeled cell bodies are concentrated in the subesophageal ganglion complex (SEG) where they are arranged serially in ventral, midline clusters. OA-ir processes from these cells project dorsally. Some neurites end close to segmental septa; others merge into longitudinal tracts connecting the neuromeres. Labeled collaterals leaving these tracts project into peripheral neuropil. In the brain, OA-ir somata were found only in the two cheliceral hemiganglia, where a cluster of 4-5 relatively large cells (soma diameter 25 microns) lies next to a group of small somata (diameter < 10 microns). Neurites originating from the large somata descend into the SEG and merge into longitudinal tracts. The central body of the brain contains profuse ascending projections. Except for fine varicosities that are confined to the roots of nerves, we found no OA-ir fibers leaving the central nervous system (CNS). Within the CNS, however, OA-ir varicosities are concentrated in neuropil and near hemolymph spaces. This distribution suggests that OA acts as a neurotransmitter and/or local neuromodulator at central synapses, while it is also released into the hemolymph and presumably acts hormonally at peripheral sites. Using high-pressure liquid chromatography measurements, the hemolymph was in fact found to contain 12-40 nM of free octopamine.

Synthetic biology as driver for the biologization of materials sciences

Materials in nature have fascinating properties that serve as a continuous source of inspiration for materials scientists. Accordingly, bio-mimetic and bio-inspired approaches have yielded remarkable structural and functional materials for a plethora of applications. Despite these advances, many properties of natural materials remain challenging or yet impossible to incorporate into synthetic materials. Natural materials are produced by living cells, which sense and process environmental cues and conditions by means of signaling and genetic programs, thereby controlling the biosynthesis, remodeling, functionalization, or degradation of the natural material. In this context, synthetic biology offers unique opportunities in materials sciences by providing direct access to the rational engineering of how a cell senses and processes environmental information and translates them into the properties and functions of materials. Here, we identify and review two main directions by which synthetic biology can be harnessed to provide new impulses for the biologization of the materials sciences: first, the engineering of cells to produce precursors for the subsequent synthesis of materials. This includes materials that are otherwise produced from petrochemical resources, but also materials where the bio-produced substances contribute unique properties and functions not existing in traditional materials. Second, engineered living materials that are formed or assembled by cells or in which cells contribute specific functions while remaining an integral part of the living composite material. We finally provide a perspective of future scientific directions of this promising area of research and discuss science policy that would be required to support research and development in this field.

Generic and reversible opto-trapping of biomolecules

Molecular traps can control activity and abundance of many biological factors. Here, we report the development of a generic opto-trap to reversibly bind and release biomolecules with high spatiotemporal control by illumination with non-invasive and cell-compatible red and far-red light. We use the Arapidopsis thaliana photoreceptor phytochrome B to regulate the release of diverse proteins from a variety of material scaffolds. Fusion of a short 100 amino acids "PIF-tag", derived from the phytochrome interacting factor 6, renders arbitrary molecules opto-trap-compatible. Reversible opto-trapping of target molecules enables novel possibilities for future developments in diagnostics, therapeutics, and basic research.

STATEMENT OF SIGNIFICANCE

The investigation of cellular signaling events or the development of complex therapeutics and integrative diagnostic devices requires the deliberate control of biomolecule abundance and activity. During recent years, the use of natural photoreceptors within cells leveraged the control of diverse cellular events, benefiting from the superior spatial and temporal control characteristics of light as compared to conventional chemical stimuli. Concurrently, biological switches entailing intrinsic compatibility toward biological environments increasingly found application in biohybrid materials. We employ the plant red/far-red photoreceptor phytochrome B, which reversibly interacts with its phytochrome interacting factors (PIFs), for developing a generic opto-trap. This platform allows the use of red and far-red light to spatiotemporally control binding and release of arbitrary PIF-fused biomolecules from various material scaffolds.

Signal-processing and adaptive prototissue formation in metabolic DNA protocells

The fundamental life-defining processes in living cells, such as replication, division, adaptation, and tissue formation, occur via intertwined metabolic reaction networks that process signals for downstream effects with high precision in a confined, crowded environment. Hence, it is crucial to understand and reenact some of these functions in wholly synthetic cell-like entities (protocells) to envision designing soft materials with life-like traits. Herein, we report on all-DNA protocells composed of a liquid DNA interior and a hydrogel-like shell, harboring a catalytically active DNAzyme, that converts DNA signals into functional metabolites that lead to downstream adaptation processes via site-selective strand displacement reactions. The downstream processes include intra-protocellular phenotype-like changes, prototissue formation via multivalent interactions, and chemical messenger communication between active sender and dormant receiver cell populations for sorted heteroprototissue formation. The approach integrates several tools of DNA-nanoscience in a synchronized way to mimic life-like behavior in artificial systems for future interactive materials.

Spatiotemporally confined red light-controlled gene delivery at single-cell resolution using adeno-associated viral vectors

Methodologies for the controlled delivery of genetic information into target cells are of utmost importance for genetic engineering in both fundamental and applied research. However, available methods for efficient gene transfer into user-selected or even single cells suffer from low throughput, the need for complicated equipment, high invasiveness, or side effects by off-target viral uptake. Here, we engineer an adeno-associated viral (AAV) vector system that transfers genetic information into native target cells upon illumination with cell-compatible red light. This OptoAAV system allows adjustable and spatially resolved gene transfer down to single-cell resolution and is compatible with different cell lines and primary cells. Moreover, the sequential application of multiple OptoAAVs enables spatially resolved transduction with different transgenes. The approach presented is likely extendable to other classes of viral vectors and is expected to foster advances in basic and applied genetic research.

Unearthing the transition rates between photoreceptor conformers

Background

Obtaining accurate estimates of biological or enzymatic reaction rates is critical in understanding the design principles of a network and how biological processes can be experimentally manipulated on demand. In many cases experimental limitations mean that some enzymatic rates cannot be measured directly, requiring mathematical algorithms to estimate them. Here, we describe a methodology that calculates rates at which light-regulated proteins switch between conformational states. We focus our analysis on the phytochrome family of photoreceptors found in cyanobacteria, plants and many optogenetic tools. Phytochrome proteins change between active (P_A) and inactive (P_I) states at rates that are proportional to photoconversion cross-sections and influenced by light quality, light intensity, thermal reactions and dimerisation. This work presents a method that can accurately calculate these photoconversion cross-sections in the presence of multiple non-light regulated reactions.

Results

Our approach to calculating the photoconversion cross-sections comprises three steps: i) calculate the thermal reversion reaction rate(s); ii) develop search spaces from which all possible sets of photoconversion cross-sections exist, and; iii) estimate extinction coefficients that describe our absorption spectra. We confirm that the presented approach yields accurate results through the use of simulated test cases. Our test cases were further expanded to more realistic scenarios where noise, multiple thermal reactions and dimerisation are considered. Finally, we present the photoconversion cross-sections of an Arabidopsis phyB N-terminal fragment commonly used in optogenetic tools.

Conclusions

The calculation of photoconversion cross-sections has implications for both photoreceptor and synthetic biologists. Our method allows, for the first time, direct comparisons of photoconversion cross-sections and response speeds of photoreceptors in different cellular environments and synthetic tools. Due to the generality of our procedure, as shown by the application to multiple test cases, the photoconversion cross-sections and quantum yields of any photoreceptor might now, in principle, be obtained.

Electronic supplementary material

The online version of this article (doi:10.1186/s12918-016-0368-y) contains supplementary material, which is available to authorized users.

Comparative functional analysis of full-length and N-terminal fragments of phytochrome C, D and E in red light-induced signaling

Phytochromes (phy) C, D and E are involved in the regulation of red/far-red light-induced photomorphogenesis of Arabidopsis thaliana, but only limited data are available on the mode of action and biological function of these lesser studied phytochrome species. We fused N-terminal fragments or full-length PHYC, D and E to YELLOW FLUORESCENT PROTEIN (YFP), and analyzed the function, stability and intracellular distribution of these fusion proteins in planta. The activity of the constitutively nuclear-localized homodimers of N-terminal fragments was comparable with that of full-length PHYC, D, E-YFP, and resulted in the regulation of various red light-induced photomorphogenic responses in the studied genetic backgrounds. PHYE-YFP was active in the absence of phyB and phyD, and PHYE-YFP controlled responses, as well as accumulation, of the fusion protein in the nuclei, was saturated at low fluence rates of red light and did not require functional FAR-RED ELONGATED HYPOCOTYL1 (FHY-1) and FHY-1-like proteins. Our data suggest that PHYC-YFP, PHYD-YFP and PHYE-YFP fusion proteins, as well as their truncated N-terminal derivatives, are biologically active in the modulation of red light-regulated photomorphogenesis. We propose that PHYE-YFP can function as a homodimer and that low-fluence red light-induced translocation of phyE and phyA into the nuclei is mediated by different molecular mechanisms.

Synthetic Biology Makes Polymer Materials Count

Synthetic biology applies engineering concepts to build cellular systems that perceive and process information. This is achieved by assembling genetic modules according to engineering design principles. Recent advance in the field has contributed optogenetic switches for controlling diverse biological functions in response to light. Here, the concept is introduced to apply synthetic biology switches and design principles for the synthesis of multi-input-processing materials. This is exemplified by the synthesis of a materials system that counts light pulses. Guided by a quantitative mathematical model, functional synthetic biology-derived modules are combined into a polymer framework resulting in a biohybrid materials system that releases distinct output molecules specific to the number of input light pulses detected. Further demonstration of modular extension yields a light pulse-counting materials system to sequentially release different enzymes catalyzing a multistep biochemical reaction. The resulting smart materials systems can provide novel solutions as integrated sensors and actuators with broad perspectives in fundamental and applied research.

Excitation of identified serotonergic neurons by escape command neurons in lobsters

Serotonin-containing neurosecretory neurons in the first abdominal ganglion (A1 5-HT cells) of the lobster (Homarus americanus) ventral nerve cord have been shown previously to function as 'gain setters' in postural, slow muscle, command neuron circuitries. Here we show that these same amine neurons receive excitatory input from lateral (LG) and medial (MG) giant axons, which are major interneurons in phasic, fast muscle systems. Activation of either LG or MG axons elicits short-latency, non-fatiguing, long-lasting excitatory postsynaptic potentials (EPSPs) in A1 5-HT cells which follow stimulus frequencies of up to 100 Hz in a 1:1 fashion. Single spikes triggered in either giant axon can produce EPSPs in the A1 5-HT cells of sufficient magnitude to cause the cells to spike and to fire additional action potentials after variable latencies; action potentials elicited in this way reset the endogenous spontaneous spiking rhythm of the A1 5-HT neurons. The giant-axon-evoked EPSP amplitudes show substantial variation from animal to animal. In individual preparations, the variation of EPSP size from stimulus to stimulus was small over the first 25 ms of the response, but increased considerably in the later, plateau phase of each response. When tested in the same preparation, EPSPs in A1 5-HT cells evoked by firing the LG axons were larger, longer-lasting and more variable than those triggered by firing the MGs. Firing A1 5-HT cells through an intracellular electrode, prior to activation of the giant fiber pathway, significantly reduced the size of LG-evoked EPSPs in A1 5-HT cells. Finally, morphological and physiological results suggest that similarities exist between giant fiber pathways in lobsters and crayfish. The possible functional significance of an involvement of these large amine-containing neurosecretory neurons in both tonic and phasic muscle circuitries will be discussed.

The distribution of histamine-immunoreactive neurons in the ventral nerve cord of the cricket, Gryllus bimaculatus

The present study demonstrates the immunocytochemical localisation of the biogenic amine, histamine (HA), in interneurons within the ventral nerve cord of the cricket, Gryllus bimaculatus. Analysis of whole-mount preparations combined with histology of serial sections reveals a constant number of HA-immunoreactive (HA-ir) neurons in the suboesophageal (n=8), thoracic (n=4) and abdominal ganglia (females/males n=24/20). Except for the suboesophageal and prothoracic ganglion, each thoracic and abdominal neuromere contains one pair of bilateral-symmetric HA-ir somata in a medio-ventral position. Axons from HA-ir cells in the thorax extend anteriorly and share common projection areas in thoracic associative neuropils; they terminate in the brain. HA-ir cells also display efferent descending axons. Extending posteriorly, these axons give rise to varicose HA-ir fibre plexuses on the surface of nerve 1 of the abdominal ganglia. In the suboesophageal ganglion, processes from a bilateral symmetric group of clustered HA-ir cells ascend into the tritocerebrum of the brain and further project into the frontal ganglion and the recurrent nerve. Ultrastructural analysis reveals dense-core vesicles, indicative of non-synaptic secretion, in HA-ir elements within the stomatogastric nervous system. Arborisations of HA-ir neurons are present in all major neuropil regions of the ventral nerve cord and display characteristic varicose structures also detected in other types of amine-containing cells. Central HA-ir varicose projections in dorsal and ventral neuropils are located in close apposition to the ganglionic surface. The wide-spread innervation of all neuromeres by HA-ir interneurons and the identification of possible neurohemal release sites suggest a general role of HA as a neuroactive substance, including neuromodulatory and neurohormonal functions.

Short-term triple therapy with lansoprazole 30 mg or 60 mg, amoxycillin and clarithromycin to eradicate Helicobacter pylori

BACKGROUND

We investigated the efficacy of 30 vs. 60 mg lansoprazole daily in a 1-week triple therapy for eradication of Helicobacter pylori in a prospective randomized study.

METHODS

Two hundred and fifteen consecutive out-patients with peptic ulcer disease or non-ulcer dyspepsia, in whom H. pylori infection was confirmed by histology and/or a urease biopsy test, were randomly assigned to a 1-week treatment with either 15 mg lansoprazole b.d. (LAC15 group) or 30 mg lansoprazole b.d. (LAC30 group) in combination with 1 g amoxycillin b.d. and 500 mg clarithromycin b.d.

RESULTS

Eradication of H. pylori was successful in 87% (per protocol) and 82% (intention-to-treat) of the patients with LAC15 and in 94% (per protocol) and 87% (intention-to-treat) of the patients with LAC30. The difference was not significant. In both treatment groups, all peptic ulcers were healed at the check-up. Adverse effects were seen in 11 patients of the LAC15 group and 10 patients of the LAC30 group: they caused discontinuation of the therapy in four of the LAC15 group and two patients of the LAC 30 group.

CONCLUSIONS

A 7-day triple therapy using lansoprazole (LAC15) is an efficient and economical regimen for the eradication of H. pylori.

Rewiring and dosing of systems modules as a design approach for synthetic mammalian signaling networks

Modularly structured signaling networks coordinate the fate and function of complex biological systems. Each component in the network performs a discrete computational operation, but when connected to each other intricate functionality emerges. Here we study such an architecture by connecting auxin signaling modules and inducible protein biotinylation systems with transcriptional control systems to construct synthetic mammalian high-detect, low-detect and band-detect networks that translate overlapping gradients of inducer molecules into distinct gene expression patterns. Guided by a mathematical model we apply fundamental computational operations like conjunction or addition to rewire individual building blocks to qualitatively and quantitatively program the way the overall network interprets graded input signals. The design principles described in this study might serve as a conceptual blueprint for the development of next-generation mammalian synthetic gene networks in fundamental and translational research.

Human Atrial Fibroblast Adaptation to Heterogeneities in Substrate Stiffness

Fibrosis is associated with aging and many cardiac pathologies. It is characterized both by myofibroblast differentiation and by excessive accumulation of extracellular matrix proteins. Fibrosis-related tissue remodeling results in significant changes in tissue structure and function, including passive mechanical properties. This research area has gained significant momentum with the recent development of new tools and approaches to better characterize and understand the ability of cells to sense and respond to their biophysical environment. We use a novel hydrogel, termed CyPhyGel, to provide an advanced in vitro model of remodeling-related changes in tissue stiffness. Based on light-controlled dimerization of a Cyanobacterial Phytochrome, it enables contactless and reversible tuning of hydrogel mechanical properties with high spatial and temporal resolution. Human primary atrial fibroblasts were cultured on CyPhyGels. After 4 days of culturing on stiff (~4.6 kPa) or soft (~2.7 kPa) CyPhyGels, we analyzed fibroblast cell area and stiffness. Cells grown on the softer substrate were smaller and softer, compared to cells grown on the stiffer substrate. This difference was absent when both soft and stiff growth substrates were combined in a single CyPhyGel, with the resulting cell areas being similar to those on homogeneously stiff gels and cell stiffnesses being similar to those on homogeneously soft substrates. Using CyPhyGels to mimic tissue stiffness heterogeneities in vitro, our results confirm the ability of cardiac fibroblasts to adapt to their mechanical environment, and suggest the presence of a paracrine mechanism that tunes fibroblast structural and functional properties associated with mechanically induced phenotype conversion toward myofibroblasts. In the context of regionally increased tissue stiffness, such as upon scarring or in diffuse fibrosis, such a mechanism could help to prevent abrupt changes in cell properties at the border zone between normal and diseased tissue. The light-tunable mechanical properties of CyPhyGels and their suitability for studying human primary cardiac cells make them an attractive model system for cardiac mechanobiology research. Further investigations will explore the interactions between biophysical and soluble factors in the response of cardiac fibroblasts to spatially and temporally heterogeneous mechanical cues.

Optogenetic control of focal adhesion kinase signaling

Focal adhesion kinase (FAK) integrates signaling from integrins, growth factor receptors and mechanical stress to control cell adhesion, motility, survival and proliferation. Here, we developed a single-component, photo-activatable FAK, termed optoFAK, by using blue light-induced oligomerization of cryptochrome 2 (CRY2) to activate FAK-CRY2 fusion proteins. OptoFAK functions uncoupled from physiological stimuli and activates downstream signaling rapidly and reversibly upon blue light exposure. OptoFAK stimulates SRC creating a positive feedback loop on FAK activation, facilitating phosphorylation of paxillin and p130Cas in adherent cells. In detached cells or in mechanically stressed adherent cells, optoFAK is autophosphorylated upon exposure to blue light, however, downstream signaling is hampered indicating that the accessibility to these substrates is disturbed. OptoFAK may prove to be a useful tool to study the biological function of FAK in growth factor and integrin signaling, tension-mediated focal adhesion maturation or anoikis and could additionally serve as test system for kinase inhibitors.