Quantitative performance characterization of three-dimensional noncontact fluorescence molecular tomography

© 2016 The Authors.Fluorescent proteins and dyes are routine tools for biological research to describe the behavior of genes, proteins, and cells, as well as more complex physiological dynamics such as vessel permeability and pharmacokinetics. The use of these probes in whole body in vivo imaging would allow extending the range and scope of current biomedical applications and would be of great interest. In order to comply with a wide variety of application demands, in vivo imaging platform requirements span from wide spectral coverage to precise quantification capabilities. Fluorescence molecular tomography (FMT) detects and reconstructs in three dimensions the distribution of a fluorophore in vivo. Noncontact FMT allows fast scanning of an excitation source and noninvasive measurement of emitted fluorescent light using a virtual array detector operating in free space. Here, a rigorous process is defined that fully characterizes the performance of a custom-built horizontal noncontact FMT setup. Dynamic range, sensitivity, and quantitative accuracy across the visible spectrum were evaluated using fluorophores with emissions between 520 and 660 nm. These results demonstrate that high-performance quantitative three-dimensional visible light FMT allowed the detection of challenging mesenteric lymph nodes in vivo and the comparison of spectrally distinct fluorescent reporters in cell culture

Garnet major‑element composition as an indicator of host‑rock type: a machine learning approach using the random forest classifier

The major-element chemical composition of garnet provides valuable petrogenetic information, particularly in metamorphic rocks. When facing detrital garnet, information about the bulk-rock composition and mineral paragenesis of the initial garnet-bearing host-rock is absent. This prevents the application of chemical thermo-barometric techniques and calls for quantitative empirical approaches. Here we present a garnet host-rock discrimination scheme that is based on a random forest machine-learning algorithm trained on a large dataset of 13,615 chemical analyses of garnet that covers a wide variety of garnet-bearing lithologies. Considering the out-of-bag error, the scheme correctly predicts the original garnet host-rock in (i) > 95% concerning the setting, that is either mantle, metamorphic, igneous, or metasomatic; (ii) > 84% concerning the metamorphic facies, that is either blueschist/greenschist, amphibolite, granulite, or eclogite/ultrahigh-pressure; and (iii) > 93% concerning the host-rock bulk composition, that is either intermediate–felsic/metasedimentary, mafic, ultramafic, alkaline, or calc–silicate. The wide coverage of potential host rocks, the detailed prediction classes, the high discrimination rates, and the successfully tested real-case applications demonstrate that the introduced scheme overcomes many issues related to previous schemes. This highlights the potential of transferring the applied discrimination strategy to the broad range of detrital minerals beyond garnet. For easy and quick usage, a freely accessible web app is provided that guides the user in five steps from garnet composition to prediction results including data visualization

A Clathrin light chain A reporter mouse for in vivo imaging of endocytosis

Clathrin-mediated endocytosis (CME) is one of the best studied cellular uptake pathways and its contributions to nutrient uptake, receptor signaling, and maintenance of the lipid membrane homeostasis have been already elucidated. Today, we still have a lack of understanding how the different components of this pathway cooperate dynamically in vivo. Therefore, we generated a reporter mouse model for CME by fusing eGFP endogenously in frame to clathrin light chain a (Clta) to track endocytosis in living mice. The fusion protein is expressed in all tissues, but in a cell specific manner, and can be visualized using fluorescence microscopy. Recruitment to nanobeads recorded by TIRF microscopy validated the functionality of the Clta-eGFP reporter. With this reporter model we were able to track the dynamics of Alexa594-BSA uptake in kidneys of anesthetized mice using intravital 2-photon microscopy. This reporter mouse model is not only a suitable and powerful tool to track CME in vivo in genetic or disease mouse models it can also help to shed light into the differential roles of the two clathrin light chain isoforms in health and disease

Designing a Process Mining-Enabled Decision Support System for Business Process Standardization in ERP Implementation Projects

Process standardization allows to optimize ERP systems and is a nec-essary step prior to ERP implementation projects. Traditional approaches to standardizing business processes are based on manually created "de-jure" process models, which are distorted, error-prone, simplistic, and often deviating from process reality. Theoretically embedded in the organizational contingency theory as kernel theory, this paper employs a design science approach to design a process mining-enabled decision support system (DSS) which combines bottom-up process mining models with manually added top-down standardization infor-mation to recommend a suitable standard process specification from a repository. Extended process models of the as-is process are matched against a repository of best-practice standard process model using an attributebased process similarity matching algorithm. Thus, the DSS aims to reduce the overall costs of process standardization, to optimize the degree of fit between the organization and the implemented processes, and to minimize the degree of organizational change re-quired in standardization and ERP implementation projects. This paper imple-ments a working prototype instantiation in the open-source process analytics platform Apromore based on a real-life event log and standardization attributes for the Purchase-to-Pay and Order-to-Cash processes from three SAP R/3 ERP systems at the industry partner

Inducible Gene Manipulations in Brain Serotonergic Neurons of Transgenic Rats

The serotonergic (5-HT) system has been implicated in various physiological processes and neuropsychiatric disorders, but in many aspects its role in normal and pathologic brain function is still unclear. One reason for this might be the lack of appropriate animal models which can address the complexity of physiological and pathophysiological 5-HT functioning. In this respect, rats offer many advantages over mice as they have been the animal of choice for sophisticated neurophysiological and behavioral studies. However, only recently technologies for the targeted and tissue specific modification of rat genes - a prerequisite for a detailed study of the 5-HT system - have been successfully developed. Here, we describe a rat transgenic system for inducible gene manipulations in 5-HT neurons. We generated a Cre driver line consisting of a tamoxifen-inducible CreERT2 recombinase under the control of mouse Tph2 regulatory sequences. Tissue-specific serotonergic Cre recombinase expression was detected in four transgenic TPH2-CreERT2 rat founder lines. For functional analysis of Cre-mediated recombination, we used a rat Cre reporter line (CAG-loxP.EGFP), in which EGFP is expressed after Cre-mediated removal of a loxP-flanked lacZ STOP cassette. We show an in-depth characterisation of this rat Cre reporter line and demonstrate its applicability for monitoring Cre-mediated recombination in all major neuronal subpopulations of the rat brain. Upon tamoxifen induction, double transgenic TPH2-CreERT2/CAG-loxP.EGFP rats show selective and efficient EGFP expression in 5-HT neurons. Without tamoxifen administration, EGFP is only expressed in few 5-HT neurons which confirms minimal background recombination. This 5-HT neuron specific CreERT2 line allows Cre-mediated, inducible gene deletion or gene overexpression in transgenic rats which provides new opportunities to decipher the complex functions of the mammalian serotonergic system

Assessment of ecosystem services of an urbanized tropical estuary with a focus on habitats and scenarios

Tropical estuaries are one of the most valuable ecosystems on the planet because of the number of ecosystem services they provide. The increasing anthropogenic pressure to which these estuaries are subject has caused a reduction in their natural capital stock. Therefore, the application of a pragmatic and rational ecosystem-based management approach to sustainably manage the multiple ecosystem services provided by this ecosystem is necessary. The aim of our study is to present an approach that combines prospective scenarios with habitat-based perspective to assess the supply capacity of ecosystem services, plus determine the impact of protected areas in an urbanized tropical estuary. The current situation and two scenarios were generated to evaluate the capacity of habitats to supply ecosystem services. This type of assessment will allow the decision makers to visualize the effect of their choices or the occurrence of events which might produce significant changes in the estuary. Thus, over time, measures can be taken to sustain the supply of ecosystem services. We determined that the establishment of protected areas have a positive impact; however, the effect is not the same for all of them. Consequently, indicating that actions such as community participation, research, education, management planning and infrastructure development must accompany the development of a protected area

Afrikaans as Standaard Gemiddelde Europees:Wanneer ‘n lid uit sy taalarea beweeg

A recent trend in the study of Standard Average European is the extraterritorial perspective of examining the extent to which non-European languages have converged with this Sprachbund as a result of contact with one or more of its members. The present article complements this line of research in that it investigates the extent to which a European language has diverged from Standard Average European after leaving the linguistic area. The focus is on Dutch, a nuclear member of the Sprachbund, and Afrikaans, its colonial offshoot. The two languages are compared with respect to twelve of the most distinctive linguistic features of Standard Average European. Afrikaans is found to share ten of them with Dutch, including anticausative prominence and formally distinguished intensifiers and reflexives, and could therefore still be considered a core member of the Sprachbund, despite deviations in the expression of negative pronouns and the grammaticality of external possessor constructions. This relatively low degree of divergence may be attributed to the continuity from Settler Dutch to at least the variety of Afrikaans on which the standard language is based and to the important role that Dutch continued to play in the history of Afrikaans

Quantitative analysis of conditional gene inactivation using rationally designed, tetracycline-controlled miRNAs

The combination of RNA interference (RNAi) with the tetracycline-controlled transcription activation (tet) system promises to become a powerful method for conditional gene inactivation in cultured cells and in whole organisms. Here, we tested critical sequence elements that originated from miRNA mR-30 for optimal efficiency of RNAi-based gene knockdown in mammalian cells. Rationally designed miRNAs, expressed conditionally via the tet system, led to an efficient knockdown of the expression of both reporter genes and the endogenous mitotic spindle protein TPX2 in HeLa cells. Quantitative studies of the tet-controlled gene inactivation revealed that the residual expression of the target gene is an intrinsic attribute of all cells that cannot be eliminated either by increasing the miRNA to target mRNA ratio or by simultaneous expression of miRNAs targeting different sequences within the transcript. The kinetic analysis of the reversibility of the miRNA mediated knockdown suggests that the recovery of target gene expression is primarily driven by cell division. Our miRNA design provides a useful tool for conditional gene inactivation in combination with the RNA-polymerase II based tet system. The identified characteristics of the conditional RNAi-mediated knockdown need to be considered for its application in cell culture or in vivo

Reversible Disruption of Pre-Pulse Inhibition in Hypomorphic-Inducible and Reversible CB1-/- Mice

Although several genes are implicated in the pathogenesis of schizophrenia, in animal models for such a severe mental illness only some aspects of the pathology can be represented (endophenotypes). Genetically modified mice are currently being used to obtain or characterize such endophenotypes. Since its cloning and characterization CB1 receptor has increasingly become of significant physiological, pharmacological and clinical interest. Recently, its involvement in schizophrenia has been reported. Among the different approaches employed, gene targeting permits to study the multiple roles of the endocannabinoid system using knockout (-/-) mice represent a powerful model but with some limitations due to compensation. To overcome such a limitation, we have generated an inducible and reversible tet-off dependent tissue-specific CB1-/- mice where the CB1R is re-expressed exclusively in the forebrain at a hypomorphic level due to a mutation (IRh-CB1-/-) only in absence of doxycycline (Dox). In such mice, under Dox+ or vehicle, as well as in wild-type (WT) and CB1-/-, two endophenotypes motor activity (increased in animal models of schizophrenia) and pre-pulse inhibition (PPI) of startle reflex (disrupted in schizophrenia) were analyzed. Both CB1-/- and IRh-CB1-/- showed increased motor activity when compared to WT animals. The PPI response, unaltered in WT and CB1-/- animals, was on the contrary highly and significantly disrupted only in Dox+ IRh-CB1-/- mice. Such a response was easily reverted after either withdrawal from Dox or haloperidol treatment. This is the first Inducible and Reversible CB1-/- mice model to be described in the literature. It is noteworthy that the PPI disruption is not present either in classical full CB1-/- mice or following acute administration of rimonabant. Such a hypomorphic model may provide a new tool for additional in vivo and in vitro studies of the physiological and pathological roles of cannabinoid system in schizophrenia and in other psychiatric disorders

New Mouse Lines for the Analysis of Neuronal Morphology Using CreER(T)/loxP-Directed Sparse Labeling

BACKGROUND: Pharmacologic control of Cre-mediated recombination using tamoxifen-dependent activation of a Cre-estrogen receptor ligand binding domain fusion protein [CreER(T)] is widely used to modify and/or visualize cells in the mouse. METHODS AND FINDINGS: We describe here two new mouse lines, constructed by gene targeting to the Rosa26 locus to facilitate Cre-mediated cell modification. These lines should prove particularly useful in the context of sparse labeling experiments. The R26rtTACreER line provides ubiquitous expression of CreER under transcriptional control by the tetracycline reverse transactivator (rtTA); dual control by doxycycline and tamoxifen provides an extended dynamic range of Cre-mediated recombination activity. The R26IAP line provides high efficiency Cre-mediated activation of human placental alkaline phosphatase (hPLAP), complementing the widely used, but low efficiency, Z/AP line. By crossing with mouse lines that direct cell-type specific CreER expression, the R26IAP line has been used to produce atlases of labeled cholinergic and catecholaminergic neurons in the mouse brain. The R26IAP line has also been used to visualize the full morphologies of retinal dopaminergic amacrine cells, among the largest neurons in the mammalian retina. CONCLUSIONS: The two new mouse lines described here expand the repertoire of genetically engineered mice available for controlled in vivo recombination and cell labeling using the Cre-lox system