Evidence for formation of DNA repair centers and dose-response nonlinearity in human cells.

The concept of DNA "repair centers" and the meaning of radiation-induced foci (RIF) in human cells have remained controversial. RIFs are characterized by the local recruitment of DNA damage sensing proteins such as p53 binding protein (53BP1). Here, we provide strong evidence for the existence of repair centers. We used live imaging and mathematical fitting of RIF kinetics to show that RIF induction rate increases with increasing radiation dose, whereas the rate at which RIFs disappear decreases. We show that multiple DNA double-strand breaks (DSBs) 1 to 2 µm apart can rapidly cluster into repair centers. Correcting mathematically for the dose dependence of induction/resolution rates, we observe an absolute RIF yield that is surprisingly much smaller at higher doses: 15 RIF/Gy after 2 Gy exposure compared to approximately 64 RIF/Gy after 0.1 Gy. Cumulative RIF counts from time lapse of 53BP1-GFP in human breast cells confirmed these results. The standard model currently in use applies a linear scale, extrapolating cancer risk from high doses to low doses of ionizing radiation. However, our discovery of DSB clustering over such large distances casts considerable doubts on the general assumption that risk to ionizing radiation is proportional to dose, and instead provides a mechanism that could more accurately address risk dose dependency of ionizing radiation.

[Recognizing transparent objects for laboratory automation]. / Erkennung transparenter Objekte für die Laborautomatisierung.

While matte objects can be visually recognized well and grasped with robots, transparent objects pose new challenges. Modern color and depth cameras (RGB-D) do not deliver correct depth data but distorted images of the background. In this paper, we show which methods are suitable to detect transparent objects in color images only and to determine their pose. Using a robotic system, views of the targeted object are generated and annotated to learn methods and to obtain data for evaluation. We also show that by using an improved method for fitting the 3D pose, a significant improvement in the accuracy of pose estimation is achieved. Thus, false detections can be eliminated and for correct detections the accuracy of pose estimation is improved. This makes it possible to grasp transparent objects with a robot.

Sex differences in distribution and identity of aromatase gene expressing cells in the young adult rat brain.

BACKGROUND: Aromatase catalyzes the synthesis of estrogens from androgens. Knowledge on its regional expression in the brain is of relevance to the behavioral implications of these hormones that might be linked to sex differences in mental health. The present study investigated the distribution of cells expressing the aromatase coding gene (Cyp19a1) in limbic regions of young adult rats of both sexes, and characterized the cell types expressing this gene. METHODS: Cyp19a1 mRNA was mapped using fluorescent in situ hybridization (FISH). Co-expression with specific cell markers was assessed with double FISH; glutamatergic, gamma-aminobutyric acid (GABA)-ergic, glial, monoaminergic, as well as interneuron markers were tested. Automated quantification of the cells expressing the different genes was performed using CellProfiler. Sex differences in the number of cells expressing Cyp19a1 was tested non-parametrically, with the effect size indicated by the rank-biserial correlation. FDR correction for multiple testing was applied. RESULTS: In the male brain, the highest percentage of Cyp19a1+ cells was found in the medial amygdaloid nucleus and the bed nucleus of stria terminalis, followed by the medial preoptic area, the CA2/3 fields of the hippocampus, the cortical amygdaloid nucleus and the amygdalo-hippocampal area. A lower percentage was detected in the caudate putamen, the nucleus accumbens, and the ventromedial hypothalamus. In females, the distribution of Cyp19a1+ cells was similar but at a lower percentage. In most regions, the majority of Cyp19a1+ cells were GABAergic, except for in the cortical-like regions of the amygdala where most were glutamatergic. A smaller fraction of cells co-expressed Slc1a3, suggesting expression of Cyp19a1 in astrocytes; monoaminergic markers were not co-expressed. Moreover, sex differences were detected regarding the identity of Cyp19a1+ cells. CONCLUSIONS: Females show overall a lower number of cells expressing Cyp19a1 in the limbic brain. In both sexes, aromatase is expressed in a region-specific manner in GABAergic and glutamatergic neurons. These findings call for investigations of the relevance of sex-specific and region-dependent expression of Cyp19a1 in the limbic brain to sex differences in behavior and mental health.

It is known that there are differences in the way males and females are mentally affected. These have been in part attributed to the effect of sex hormones, such as estrogen and testosterone. Within the framework of sex-specific medicine, it is therefore important to understand the biological substrates of sex-specific systems in the brain that are involved in any of these differences. The present study investigated the enzyme responsible for the synthesis of estrogen in the brain, to identify where it is expressed in the brain and to characterize the cells in which it is expressed. To this end, female and male young adult rats were studied. Brain slices including regions of relevance to, among others, emotion processing, were analyzed using fluorescent probes for the genes of interest and visualized using microscopy. Automated cell counting illustrated sex differences, with males displaying greater expression of the aromatase gene, compared with females, in several regions. The aromatase gene was expressed together with genes for the major inhibitory and excitatory neurotransmitters.

Vesicular glutamate transporter 2 expression in the ventral tegmental area of outbred male rats following exposure to nicotine and alcohol.

Background: Initiation of use/co-use of nicotine and alcohol, commonly occurring in an episodic manner during adolescence, can imprint vulnerability to the developing brain and lead to addiction. The ventral tegmental area (VTA) is a key heterogeneous region of the mesocorticolimbic circuit involved in the binge-drinking and intoxication step of the addiction circuit. Higher human post-mortem VTA expression of vesicular glutamate transporter 2 (VGLUT2), a marker of the glutamatergic phenotype also expressed in dopaminergic [Tyrosine Hydroxylase (Th)-positive] neurons, has been associated with chronic nicotine use and co-use with alcohol. Methods: The present study aimed to map and characterize the Vglut2- and Th-expressing neurons in the VTA of adolescent male rats exposed or not to prolonged (six-weeks) episodic (three consecutive days/week) nicotine and/or alcohol administration. Nicotine (0.35 mg/kg free base) was injected subcutaneously, whereas alcohol (2 g/kg 20%) was administrated via gavage. Vglut2 and Th mRNA was assessed in the anterior and posterior VTA by use of in situ hybridization. Results: The profile of neurons varied with substance-exposure among VTA subregions. Th-only expressing neurons were more abundant in the posterior VTA of the group exposed to nicotine-only, compared to controls. The same neurons were, on the contrary, less present in the anterior VTA of animals exposed to alcohol-only, who also displayed a higher number of Vglut2-expressing neurons in the lateral anterior VTA. Conclusions: VTA Vglut2- and Th-only neurons seem differentially involved in the effects of adolescent episodic nicotine and alcohol exposure in the anterior and posterior VTA.

mRNA trans-splicing dual AAV vectors for (epi)genome editing and gene therapy.

Large genes including several CRISPR-Cas modules like gene activators (CRISPRa) require dual adeno-associated viral (AAV) vectors for an efficient in vivo delivery and expression. Current dual AAV vector approaches have important limitations, e.g., low reconstitution efficiency, production of alien proteins, or low flexibility in split site selection. Here, we present a dual AAV vector technology based on reconstitution via mRNA trans-splicing (REVeRT). REVeRT is flexible in split site selection and can efficiently reconstitute different split genes in numerous in vitro models, in human organoids, and in vivo. Furthermore, REVeRT can functionally reconstitute a CRISPRa module targeting genes in various mouse tissues and organs in single or multiplexed approaches upon different routes of administration. Finally, REVeRT enabled the reconstitution of full-length ABCA4 after intravitreal injection in a mouse model of Stargardt disease. Due to its flexibility and efficiency REVeRT harbors great potential for basic research and clinical applications.

In vitro bio-functionality of gallium nitride sensors for radiation biophysics.

There is an increasing interest in the integration of hybrid bio-semiconductor systems for the non-invasive evaluation of physiological parameters. High quality gallium nitride and its alloys show promising characteristics to monitor cellular parameters. Nevertheless, such applications not only request appropriate sensing capabilities but also the biocompatibility and especially the biofunctionality of materials. Here we show extensive biocompatibility studies of gallium nitride and, for the first time, a biofunctionality assay using ionizing radiation. Analytical sensor devices are used in medical settings, as well as for cell- and tissue engineering. Within these fields, semiconductor devices have increasingly been applied for online biosensing on a cellular and tissue level. Integration of advanced materials such as gallium nitride into these systems has the potential to increase the range of applicability for a multitude of test devices and greatly enhance sensitivity and functionality. However, for such applications it is necessary to optimize cell-surface interactions and to verify the biocompatibility of the semiconductor. In this work, we present studies of mouse fibroblast cell activity grown on gallium nitride surfaces after applying external noxa. Cell-semiconductor hybrids were irradiated with X-rays at air kerma doses up to 250 mGy and the DNA repair dynamics, cell proliferation, and cell growth dynamics of adherent cells were compared to control samples. The impact of ionizing radiation on DNA, along with the associated cellular repair mechanisms, is well characterized and serves as a reference tool for evaluation of substrate effects. The results indicate that gallium nitride does not require specific surface treatments to ensure biocompatibility and suggest that cell signaling is not affected by micro-environmental alterations arising from gallium nitride-cell interactions. The observation that gallium nitride provides no bio-functional influence on the cellular environment confirms that this material is well suited for future biosensing applications without the need for additional chemical surface modification.

GaN Heterostructures as Innovative X-ray Imaging Sensors-Change of Paradigm.

Direct conversion of X-ray irradiation using a semiconductor material is an emerging technology in medical and material sciences. Existing technologies face problems, such as sensitivity or resilience. Here, we describe a novel class of X-ray sensors based on GaN thin film and GaN/AlGaN high-electron-mobility transistors (HEMTs), a promising enabling technology in the modern world of GaN devices for high power, high temperature, high frequency, optoelectronic, and military/space applications. The GaN/AlGaN HEMT-based X-ray sensors offer superior performance, as evidenced by higher sensitivity due to intensification of electrons in the two-dimensional electron gas (2DEG), by ionizing radiation. This increase in detector sensitivity, by a factor of 104 compared to GaN thin film, now offers the opportunity to reduce health risks associated with the steady increase in CT scans in today's medicine, and the associated increase in exposure to harmful ionizing radiation, by introducing GaN/AlGaN sensors into X-ray imaging devices, for the benefit of the patient.

In vivo and ex vivo electrophysiological study of the mouse heart to characterize the cardiac conduction system, including atrial and ventricular vulnerability.

The mouse is a common and cost-effective animal model for basic research, and the number of genetically engineered mouse models with cardiac phenotype is increasing. In vivo electrophysiological study in mice is similar to that performed in humans. It is indispensable for acquiring intracardiac electrocardiogram recordings and determining baseline cardiac cycle intervals. Furthermore, the use of programmed electrical stimulation enables determination of parameters such as sinoatrial conduction time, sinus node recovery time, atrioventricular-nodal conduction properties, Wenckebach periodicity, refractory periods and arrhythmia vulnerability. This protocol describes specific procedures for determining these parameters that were adapted from analogous human protocols for use in mice. We include details of ex vivo electrophysiological study, which provides detailed insights into intrinsic cardiac electrophysiology without external influences from humoral and neural factors. In addition, we describe a heart preparation with intact innervation by the vagus nerve that can be used as an ex vivo model for vagal control of the cardiac conduction system. Data acquisition for in vivo and ex vivo electrophysiological study takes ~1 h per mouse, depending on the number of stimulation protocols applied during the procedure. The technique yields highly reliable results and can be used for phenotyping of cardiac disease models, elucidating disease mechanisms and confirming functional improvements in gene therapy approaches as well as for drug and toxicity testing.

Implantation of Combined Telemetric ECG and Blood Pressure Transmitters to Determine Spontaneous Baroreflex Sensitivity in Conscious Mice.

Blood pressure (BP) and heart rate (HR) are both controlled by the autonomic nervous system (ANS) and are closely intertwined due to reflex mechanisms. The baroreflex is a key homeostatic mechanism to counteract acute, short-term changes in arterial BP and to maintain BP in a relatively narrow physiological range. BP is sensed by baroreceptors located in the aortic arch and carotid sinus. When BP changes, signals are transmitted to the central nervous system and are then communicated to the parasympathetic and sympathetic branches of the autonomic nervous system to adjust HR. A rise in BP causes a reflex decrease in HR, a drop in BP causes a reflex increase in HR. Baroreflex sensitivity (BRS) is the quantitative relationship between changes in arterial BP and corresponding changes in HR. Cardiovascular diseases are often associated with impaired baroreflex function. In various studies reduced BRS has been reported in e.g., heart failure, myocardial infarction, or coronary artery disease. Determination of BRS requires information from both BP and HR, which can be recorded simultaneously using telemetric devices. The surgical procedure is described beginning with the insertion of the pressure sensor into the left carotid artery and positioning of its tip in the aortic arch to monitor arterial pressure followed by the subcutaneous placement of the transmitter and ECG electrodes. We also describe postoperative intensive care and analgesic management. After a two-week period of post-surgery recovery long-term ECG and BP recordings are performed in conscious and unrestrained mice. Finally, we include examples of high-quality recordings and the analysis of spontaneous baroreceptor sensitivity using the sequence method.

Boosting oncolytic adenovirus potency with magnetic nanoparticles and magnetic force.

Oncolytic adenoviruses rank among the most promising innovative agents in cancer therapy. We examined the potential of boosting the efficacy of the oncolytic adenovirus dl520 by associating it with magnetic nanoparticles and magnetic-field-guided infection in multidrug-resistant (MDR) cancer cells in vitro and upon intratumoral injection in vivo. The virus was complexed by self-assembly with core-shell nanoparticles having a magnetite core of about 10 nm and stabilized by a shell containing 68 mass % lithium 3-[2-(perfluoroalkyl)ethylthio]propionate) and 32 mass % 25 kDa branched polyethylenimine. Optimized virus binding, sufficiently stable in 50% fetal calf serum, was found at nanoparticle-to-virus ratios of 5 fg of Fe per physical virus particle (VP) and above. As estimated from magnetophoretic mobility measurements, 3,600 to 4,500 magnetite nanocrystallites were associated per virus particle. Ultrastructural analysis by electron and atomic force microscopy showed structurally intact viruses surrounded by magnetic particles that occasionally bridged several virus particles. Viral uptake into cells at a given virus dose was enhanced 10-fold compared to nonmagnetic virus when infections were carried out under the influence of a magnetic field. Increased virus internalization resulted in a 10-fold enhancement of the oncolytic potency in terms of the dose required for killing 50% of the target cells (IC(50) value) and an enhancement of 4 orders of magnitude in virus progeny formation at equal input virus doses compared to nonmagnetic viruses. Furthermore, the full oncolytic effect developed within two days postinfection compared with six days in a nonmagnetic virus as a reference. Plotting target cell viability versus internalized virus particles for magnetic and nonmagnetic virus showed that the inherent oncolytic productivity of the virus remained unchanged upon association with magnetic nanoparticles. Hence, we conclude that the mechanism of boosting the oncolytic effect by magnetic force is mainly due to the improved internalization of magnetic virus complexes resulting in potentiated virus progeny formation. Upon intratumoral injection and application of a gradient magnetic field in a murine xenograft model, magnetic virus complexes exhibited a stronger oncolytic effect than adenovirus alone. We propose that this approach would be useful during in vivo administration to tumor-feeding blood vessels to boost the efficacy of the primary infection cycle within the tumor. For systemic application, further modification of magnetic adenovirus complexes for shielding and retargeting of the whole magnetic virus complex entity is needed.

Technical note: PCR analysis of minimum target amount of ancient DNA.

The study of ancient DNA plays an important role in archaeological and palaeontological research as well as in pathology and forensics. Here, we present a new tool for ancient DNA analysis, which overcomes contamination problems, DNA degradation, and the negative effects of PCR inhibitors while reducing the amount of starting target material in the picogram range. Ancient bone samples from four Egyptian mummies were examined by combining laser microdissection, conventional DNA extraction, and low-volume PCR. Initially, several bone particles (osteons) in the micrometer range were extracted by laser microdissection. Subsequently, ancient DNA amplification was performed to verify our extraction method. Amelogenin and beta-actin gene specific fragments were amplified via low-volume PCR in a total reaction volume of 1 microl. Results of microdissected mummy DNA samples were compared to mummy DNA, which was extracted using a standard DNA extraction method based on pulverization of bone material. Our results highlight the combination of laser microdissection and low-volume PCR as a promising new technique in ancient DNA analysis.

Organic ISFET based on poly (3-hexylthiophene).

We have fabricated organic field-effect transistors (OFETs) with regioregular poly(3-hexylthiophene) (P3HT) operable at low-voltages in liquid solutions, suitable for in vitro biosensing applications. Measurements in electrolytes have shown that the performance of the transistors did not deteriorate and they can be directly used as ion-sensitive transducers. Furthermore, more complex media have been tested, with the perspective of cell analysis. Degradation effects acting on the device operating in liquid could be partly compensated by adopting an alternate current measuring mode.

Single particle adsorbing transfer system.

Here we present a novel approach for horizontal transfer of single particles after laser microdissection. The developed technique is a single particle adsorbing system for highly selective and gentle horizontal transfer of microdissected fixed and living material. As mediated via low-pressure technology, the transfer process can be precisely controlled, thus facilitating horizontal particle transfer of any isolated material, e.g. tissue material, single cells or chromosomes, in addition to precise positioning for sample release. This collection method allows one to predefine target positions and enables material transfer without contamination to any planar microchip device. This contamination free transfer is indispensable for novel lab-on-a-chip systems performing nanoscale polymerase chain reaction analyses. Using virtual reaction chamber microdevices, small amounts of microdissected material--as little as one single cell--can be directly transmitted and immediately used for single cell analysis.

Single cell analysis of mutations in the APC gene.

INTRODUCTION: Mutation analysis of inherited monogenic diseases is an important aspect of preimplantation genetic diagnosis. Familial adenomatous polyposis of the colon is an autosomal dominant inherited disorder caused by mutations in the tumor suppressor gene adenomatous polyposis coli (APC). A characteristic of this severe disease is the development of thousands of polyps in the colon which untreated evolve into malignant colon carcinomas. Here we present a novel approach for the establishment of mutation detection in the APC gene in single cells applicable for preimplantation genetic diagnosis. METHODS: Single fixed lymphocytes were isolated via laser microdissection and transferred to reaction centers of planar chemically structured glass slides via a recently developed horizontal low-pressure single particle adsorbing transfer system (SPATS). A multiplex nested polymerase chain reaction protocol in a 1-microl reaction volume, followed by sequencing and fragment length analysis was applied in order to detect mutations in the APC gene. RESULTS: Reliable isolation and transfer of single lymphocytes was demonstrated. High amplification efficiency and low allelic drop out (ADO) rates for polymorphic microsatellite markers and mutation specific amplification products of various mutations in the APC gene were obtained from fixed single cells. CONCLUSIONS: This novel nanotechnological downscaling approach enables a reliable validation of genetic testing using diploid single lymphocytes, and will open a wide range of single cell diagnostics.

Dynamic force microscopy imaging of plasmid DNA and viral RNA.

Plasmid DNA and viral RNA were imaged in a liquid environment by dynamic force microscopy (DFM) and fine structures of DNA with heights of 1.82+/-0.66 nm were obtained in topographical images. In simultaneously acquired phase images, DNA could be imaged with better contrast at lower imaging forces. By splitting the cantilever oscillation signal into lower and upper parts, the contribution of the adhesion between tip and sample to the topographical images was eliminated, resulting in better signal-to-noise ratio. DFM of the single stranded RNA genome of a human rhinovirus showed loops protruding from a condensed RNA core, 20-50 nm in height. The mechanical rigidity of the RNA was determined by single molecule pulling experiments. From fitting RNA stretching curves to the Worm-Like-Chain (WLC) model a persistence length of 1.0+/-0.17 nm was obtained.

Live cell catapulting and recultivation.

Laser micromanipulation systems are used worldwide in the field of life science research. Most of their applications focus on the isolation of specific cells from different types of tissue and the manipulation of subcellular structures within fixed or living cells. Using the PALM MicroBeam, it is possible to microdissect living cells from a cell culture, to catapult them into collection devices, and to re-cultivate the isolated cells. For this purpose, new protocols and special equipment were developed. It has also been demonstrated that Laser Microdissection and Pressure Catapulting (LMPC) have no influence on the proliferation rate of the cells. Even re-cultivated cell colonies, trypsinized and seeded out again, are still viable after a second LMPC-procedure. This new approach opens a wide field of interesting applications in cell biology, molecular pathology, and pharmacology.

Immunospot assay based on fluorescent nanoparticles for Dengue fever detection.

Dengue fever is one of the most neglected tropical diseases and of highest international public health importance, with 50 million cases worldwide every year. Early detection can decrease mortality rates from more than 20% to less than 1% and the relevant early diagnosis analyte is the viral non-structural glycoprotein, NS1. Currently, enzyme linked immunosorbent assay (ELISA) is the method of choice to detect NS1. However, this is a time consuming method, requiring 3-5h, and it is the bottleneck for routine of clinical analysis laboratory in epidemic periods, when hundreds of samples should be tested. Here we describe an easy method combining principles of fluorophore linked immunosorbent assay (FLISA) and enzyme linked immunospotting (ELISPOT). For detection, we used mouse anti-NS1 IgG labeled with fluorescent nanoparticles. The presented procedure needs only 4 µL of serum samples and requires 45-60 min. The detection limit, 5.2 ng/mL, is comparable to ELISA tests. The comparison of 83 samples with a commercial ELISA revealed a sensitivity of 81% and specificity of 88%. The use of fluorescent nanoparticles provides a higher sensitivity than an assay using usual fluorescent dye molecules, besides avoiding bleaching effects. Based on the results, the proposed method provides fast, specific and sensitive results, and proves to be a suitable method for Dengue NS1 detection in impoverished regions or epidemic areas.

Development of a disposable and highly sensitive paper-based immunosensor for early diagnosis of Asian soybean rust.

Soybean is one of the most important crops and plays a key role in the whole food chain production. Soybean crops are very susceptible to the fungus Phakopsora Pachyrhizi, the agent responsible by the Asian soybean rust. The spore of the fungus is easily disseminated by wind with adequate environment, leaf wetness, high humidity and temperatures, the crop can be totally lost within few days. A high sensitive, specific and easy test is the key for early diagnosing the soybean rust and therefore save the crop. Here we present a paper-based immunosensor for early stage diagnosis of soybean rust that can be performed by unskilled operators on-site. Nitrocellulose membrane was chosen as the substrate to stick the antigen due to its high binding properties. Polyclonal antibodies labeled with fluorescent nanoparticles were employed as the recognizers. An analytical curve with spiked samples shows a linear response range from 0.0032 to 3.2 µg/mL. This immunosensor presents a very low detection limit of 2.2 ng/mL, which corresponds approximately to 8-12 spores/mL. The paper-based sensor reachs the detection range of ELISA and PCR based test systems, and outranges the available commercial test kits by two order of magnitude. We believe this immunosensor has a great potential as a point-of-care device for the early diagnosis of Asian soybean rust.

One-step synthesis of polymer core-shell particles with a carboxylated ruthenium complex: a potential tool for biomedical applications.

Luminescent core-shell particles are structures widely applied to biomedical purposes with the potential of combining multiple features within one single particle. The development of particles that are easily synthesised and tunable for each application, combining biocompatibility, easy bioconjugation and a high detection signal as a label, is highly desired. In this work, we describe a one-step synthesis of poly[styrene-co-(2-hydroxyethyl methacrylate)], PSHEMA, core-shell particles containing [Ru(4,4'-dicarboxilate-2,2'-bpy)3] luminescent complexes. These particles show monodispersity, biocompatibility, easy functionalization and dye incorporation to focus on bioapplications, such as cell-tracking and diagnostics. The monomers assemble during the polymerization and produce core-shell structures with hydrophilic-hydrophobic character. This allows the concentration of hydrophilic ruthenium complexes onto the shell and incorporation of hydrophobic molecules (e.g. diphenylanthracene) due to the hydrophobic character of styrene. The incorporation of the Ru complex resulted in higher photostability compared to the free dye. Furthermore, carboxylic groups on the particle surface originated from carboxylated ligands of Ru complexes were used to immobilize biomolecules. The particles were successfully used as a diagnostic label for dengue fever (DF) infection. Using the complexes in the immunospot assay the test provided a detection limit (DL) of 187 ng mL-1 for the viral non-structural glycoprotein NS1. The particles showed a considerable decrease in the DL and allowed the diagnosis of the infection 24 hours earlier compared to common available assays based on gold nanoparticles. In addition, the particles were tested with an adherent grown fibroblast cell line and showed potential biocompatibility.