SLocX: Predicting Subcellular Localization of Arabidopsis Proteins Leveraging Gene Expression Data

Despite the growing volume of experimentally validated knowledge about the subcellular localization of plant proteins, a well performing in silico prediction tool is still a necessity. Existing tools, which employ information derived from protein sequence alone, offer limited accuracy and/or rely on full sequence availability. We explored whether gene expression profiling data can be harnessed to enhance prediction performance. To achieve this, we trained several support vector machines to predict the subcellular localization of Arabidopsis thaliana proteins using sequence derived information, expression behavior, or a combination of these data and compared their predictive performance through a cross-validation test. We show that gene expression carries information about the subcellular localization not available in sequence information, yielding dramatic benefits for plastid localization prediction, and some notable improvements for other compartments such as the mitochondrion, the Golgi, and the plasma membrane. Based on these results, we constructed a novel subcellular localization prediction engine, SLocX, combining gene expression profiling data with protein sequence-based information. We then validated the results of this engine using an independent test set of annotated proteins and a transient expression of GFP fusion proteins. Here, we present the prediction framework and a website of predicted localizations for Arabidopsis. The relatively good accuracy of our prediction engine, even in cases where only partial protein sequence is available (e.g., in sequences lacking the N-terminal region), offers a promising opportunity for similar application to non-sequenced or poorly annotated plant species. Although the prediction scope of our method is currently limited by the availability of expression information on the ATH1 array, we believe that the advances in measuring gene expression technology will make our method applicable for all Arabidopsis proteins

How to obtain solderable Al/Ni:V/Ag contacts

We investigate process sequences for obtaining solderable Al/Ni:V/Ag contacts to PERC-type crystalline Si solar cells by in-line Al evaporation. For a high cell efficiency the evaporated aluminum must be annealed at 350 °C for about 5 min. We find that annealing the Al/Ni:V/Ag metallization stack at temperatures above 150 °C destroys the solderability of the wetting layer. A solution for this problem is to first deposit the 2.5 μm Al layer by evaporation, then anneal the cell at 350 °C for 10 min, and finally sputter a double layer of Ni:V/Ag with respective thickness values of 200 nm and 25 nm. This process leads to a contact resistivity lower than 1 mΩcm2. The solderablility is proven by a peel force greater than 3 N/mm. We present a solderable PERC cell with Al/Ni:V/Ag rear side metallization and an efficiency of 18.9%.BMUB/VaCoC/0325195

Novel Concept of Micro Patterned Micro Titer Plates Fabricated via UV-NIL for Automated Neuronal Cell Assay Read-Out

The UV-nanoimprint lithography(UV-NIL) fabrication of a novel network of micron-sized channels, forming an open channel microfluidic system is described. Details about the complete manufacturing process, from mastering to fabrication in small batches and in high throughput with up to 1200 micro titer plates per hour is presented. Deep insight into the evaluation of a suitable UV-curable material, mr-UVCur26SF is given, presenting cytotoxic evaluation, cell compatibility tests and finally a neuronal assay. The results indicate how the given pattern, in combination with the resist, paves the way to faster, cheaper, and more reliable drug screening.This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement NO. 646260. The research was also partially supported by NextGenMicrofluidics project under HORIZON2020 with grant agreement no 862092

Influence of Solder Pads to PERC Solar Cells for Module Integration

AbstractThe majority of screen printed solar cells has silver pads at the rear side to enable soldering for the module manufacturing. The pads increase the recombination at the silicon/metal interface due to the absence of a back surface field (BSF) at the solder pads. This reduces the efficiency of full-area Al-BSF solar cells. For passivated emitter and rear cells (PERC), a large area fraction of the rear side is covered with the passivation layer. When using specially designed Ag pastes for the rear side of PERC cells, the passivation of this layer is maintained, and the rear recombination is reduced.A comparison of solar cells with and without solder pads confirms that there is no loss in solar cell performance, both cell types achieve an efficiency of 19.6%. We investigate the influence of solder pads to PERC solar cells by calculating the effective rear surface recombination. The calculations confirm that there is a loss in open circuit voltage of less than 2mV due to the solder pads.A 54-cell PERC PV module is manufactured. The cell-to-module loss reveals that the module process is still to be optimized. Comparable modules made from 9 solar cells lost less than 1% relative in all J-V parameters after a 1000h damp-heat test

Roll-to-Roll pilot line for large-scale manufacturing of microfluidic devices

Roll-to-roll (R2R) technologies with roller-based nanoimprinting methods enable manufacturing of highly cost-effective and large-scale sheets of flexible polymer film with precise structures on a micro- and nanoscale 1. Areas that can benefit strongly from such large scale technologies are microfluidics, biosensors, and lab-on-chip products for point of care diagnostics, drug discovery and food control. Here, R2R fabrication could greatly reduce production costs and increase manufacturing capacity with respect to currently used products. A pilot line with this technology is investigated in the European Horizon 2020 project R2R Biofluidics and its capabilities are tested on two Demonstrators: - Demonstrator 1: In-vitro diagnostic chip with imprinted microfluidic channels based on optical chemiluminescence measurement by photodetectors. - Demonstrator 2: Neuronal cell culture plate with imprinted cavities and channels for controlled culturing and fluorescence imaging of neurons, for high throughput drug screening. Please click Additional Files below to see the full abstract

High-throughput roll-to-roll production of polymer biochips for multiplexed DNA detection in point-of-care diagnostics

Roll-to-roll UV nanoimprint lithography has superior advantages for high-throughput manufacturing of micro- or nano-structures on flexible polymer foils with various geometries and configurations. Our pilot line provides large-scale structure imprinting for cost-effective polymer biochips (4500 biochips/hour), enabling rapid and multiplexed detections. A complete high-volume process chain of the technology for producing structures like μ-sized, triangular optical out-couplers or capillary channels (width: from 1 μm to 2 mm, height: from 200 nm up to 100 μm) to obtain biochips (width: 25 mm, length: 75 mm, height: 100 μm to 1.5 mm) was described. The imprinting process was performed with custom-developed resins on polymer foils with resin thicknesses ranging between 125–190 μm. The produced chips were tested in a commercial point-of-care diagnostic system for multiplexed DNA analysis of methicillin resistant Staphylococcus aureus (e.g., mecA, mecC gene detections). Specific target DNA capturing was based on hybridisation between surface bound DNA probes and biotinylated targets from the sample. The immobilised biotinylated targets subsequently bind streptavidin–horseradish peroxidase conjugates, which in turn generate light upon incubation with a chemiluminescent substrate. To enhance the light out-coupling thus to improve the system performance, optical structures were integrated into the design. The limits-of-detection of mecA (25 bp) for chips with and without structures were calculated as 0.06 and 0.07 μM, respectively. Further, foil-based chips with fluidic channels were DNA functionalised in our roll-to-roll micro-array spotter following the imprinting. This straightforward approach of sequential imprinting and multiplexed DNA functionalisation on a single foil was also realised for the first time. The corresponding foil-based chips were able to detect mecA gene DNA sequences down to a 0.25 μM concentration.This research was supported by R2R BIOFLUIDICS project (http://www.r2r-biofluidics.eu/) under Horizon 2020 European Union (EU) Research and Innovation Programme with grant agreement no 646260. The research was also partially supported by NextGenMicrofluidics project (https:// www. nextgenmicrofluidics.eu/) under HORIZON2020 with grant agreement no 862092. The authors cordially thank Gerburg Schider & Gerhard Mohr, Markus Postl, Paul Patter and Alexander Wheeldon (JOANNEUM RESEARCH – Materials, Weiz, Austria) for revising the manuscript, preparing all the chip and R2R pilot line illustrations, taking the photographs and providing technical support, respectively. The authors are also grateful to Christian Wolf and Johannes Götz (JOANNEUM RESEARCH – Materials, Weiz, Austria) for their supports in the fluidic design and R2R UV-NIL structuring, respectively. We further kindly thank Alba Simon Munoz and Robert Fay (SCIENION AG, Berlin, Germany) for providing the illustration of the R2R micro-spotting line. PT specially thanks Ege Ozgun (NANOTAM, Bilkent University, Ankara, Turkey) for critically reading the manuscript

Elucidation of the biosynthesis of carnosic acid and its reconstitution in yeast

Rosemary extracts containing the phenolic diterpenes carnosic acid and its derivative carnosol are approved food additives used in an increasingly wide range of products to enhance shelf-life, thanks to their high anti-oxidant activity. We describe here the elucidation of the complete biosynthetic pathway of carnosic acid and its reconstitution in yeast cells. Cytochrome P450 oxygenases (CYP76AH22-24) from Rosmarinus officinalis and Salvia fruticosa already characterized as ferruginol synthases are also able to produce 11-hydroxyferruginol. Modelling-based mutagenesis of three amino acids in the related ferruginol synthase (CYP76AH1) from S. miltiorrhiza is sufficient to convert it to a 11-hydroxyferruginol synthase (HFS). The three sequential C20 oxidations for the conversion of 11-hydroxyferruginol to carnosic acid are catalysed by the related CYP76AK6-8. The availability of the genes for the biosynthesis of carnosic acid opens opportunities for the metabolic engineering of phenolic diterpenes, a class of compounds with potent anti-oxidant, anti-inflammatory and anti-tumour activities

Cognitive Trajectories in Preclinical and Prodromal Alzheimer's Disease Related to Amyloid Status and Brain Atrophy:A Bayesian Approach

Background: Cognitive decline is a key outcome of clinical studies in Alzheimer’s disease (AD). Objective: To determine effects of global amyloid load as well as hippocampus and basal forebrain volumes on longitudinal rates and practice effects from repeated testing of domain specific cognitive change in the AD spectrum, considering non-linear effects and heterogeneity across cohorts. Methods: We included 1,514 cases from three cohorts, ADNI, AIBL, and DELCODE, spanning the range from cognitively normal people to people with subjective cognitive decline and mild cognitive impairment (MCI). We used generalized Bayesian mixed effects analysis of linear and polynomial models of amyloid and volume effects in time. Robustness of effects across cohorts was determined using Bayesian random effects meta-analysis. Results: We found a consistent effect of amyloid and hippocampus volume, but not of basal forebrain volume, on rates of memory change across the three cohorts in the meta-analysis. Effects for amyloid and volumetric markers on executive function were more heterogeneous. We found practice effects in memory and executive performance in amyloid negative cognitively normal controls and MCI cases, but only to a smaller degree in amyloid positive controls and not at all in amyloid positive MCI cases. Conclusions: We found heterogeneity between cohorts, particularly in effects on executive functions. Initial increases in cognitive performance in amyloid negative, but not in amyloid positive MCI cases and controls may reflect practice effects from repeated testing that are lost with higher levels of cerebral amyloid

Novelty-Related fMRI Responses of Precuneus and Medial Temporal Regions in Individuals at Risk for Alzheimer Disease

BACKGROUND AND OBJECTIVES: We assessed whether novelty-related fMRI activity in medial temporal lobe regions and the precuneus follows an inverted U-shaped pattern across the clinical spectrum of increased Alzheimer disease (AD) risk as previously suggested. Specifically, we tested for potentially increased activity in individuals with a higher AD risk due to subjective cognitive decline (SCD) or mild cognitive impairment (MCI). We further tested whether activity differences related to diagnostic groups were accounted for by CSF markers of AD or brain atrophy. METHODS: We studied 499 participants aged 60-88 years from the German Center for Neurodegenerative Diseases Longitudinal Cognitive Impairment and Dementia Study (DELCODE) who underwent task-fMRI. Participants included 163 cognitively normal (healthy control, HC) individuals, 222 SCD, 82 MCI, and 32 patients with clinical diagnosis of mild AD. CSF levels of β-amyloid 42/40 ratio and phosphorylated-tau181 were available from 232 participants. We used region-based analyses to assess novelty-related activity (novel > highly familiar scenes) in entorhinal cortex, hippocampus, and precuneus as well as whole-brain voxel-wise analyses. First, general linear models tested differences in fMRI activity between participant groups. Complementary regression models tested quadratic relationships between memory impairment and activity. Second, relationships of activity with AD CSF biomarkers and brain volume were analyzed. Analyses were controlled for age, sex, study site, and education. RESULTS: In the precuneus, we observed an inverted U-shaped pattern of novelty-related activity across groups, with higher activity in SCD and MCI compared with HC, but not in patients with AD who showed relatively lower activity than MCI. This nonlinear pattern was confirmed by a quadratic relationship between memory impairment and precuneus activity. Precuneus activity was not related to AD biomarkers or brain volume. In contrast to the precuneus, hippocampal activity was reduced in AD dementia compared with all other groups and related to AD biomarkers. DISCUSSION: Novelty-related activity in the precuneus follows a nonlinear pattern across the clinical spectrum of increased AD risk. Although the underlying mechanism remains unclear, increased precuneus activity might represent an early signature of memory impairment. Our results highlight the nonlinearity of activity alterations that should be considered in clinical trials using functional outcome measures or targeting hyperactivity