Search

Mitochondria are required for energy production and even give brown adipose tissue (BAT) its characteristic color due to their high iron content and abundance The physiological function and bioenergetic capacity of mitochondria are connected to the structure, folding, and organization of its inner-membrane cristae. During the aging process, mitochondrial dysfunction is observed, and the regulatory balance of mitochondrial dynamics is often disrupted, leading to increased mitochondrial fragmentation in aging cells. Therefore, we hypothesized that the morphological changes in BAT mitochondria and cristae observed across aging would reflect alterations to energy dynamics. We developed a quantitative three-dimensional (3D) electron microscopy approach to map cristae network organization in mouse BAT to test this hypothesis. Using this methodology, we investigated the 3D morphology of mitochondrial cristae in adult (3-month) and aged (2-year) murine BAT tissue via serial block face-scanning electron microscopy (SBF-SEM) and3D reconstruction software for manual segmentation, analysis, and quantification. Upon investigation, we found increases in mitochondrial volume, surface area, and complexity and decreased sphericity in aged BAT. Cristae examination revealed decreased cristae volume, perimeter, and complexity, with cristate appearing more heterogeneous. Overall, these data define the nature of the mitochondrial structure in BAT, showing loss of cristae definition across aging, suggesting alterations in functionality and bioactivity.Graphical AbstractWorkflow overview of serial block facing-scanning electron microscopy (SBF-SEM), data segmentation, and 3D analysis of mitochondria using Amira software in murine BAT.

Today, many industrial domains rely on vision-based embedded systems. High computing performance of the embedded platform is a mandatory feature for modern image processing applications. Yet, these embedded systems have to comply with strict requirements regarding size, weight and energy efficiency. Tulipp will develop a reference platform, which defines implementation rules and interfaces to tackle power consumption issues while delivering high, energy-efficient and guaranteed computing performance. This allows developers to find the optimal solution for their image processing application, to comply with the requirements of their embedded system and to reduce the time spent on the development and iteration process. The Tulipp reference platform consists of a hardware system, supportive development utilities and a real-time operating system (RTOS) . Chained platforms provide scalability and higher processing power. The project develops and provides: a reference hardware architecture—a scalable low-power board; a low-power operating system and image processing libraries; a productivity-enhancing toolchain. In addition, Tulipp will publish a reference platform handbook, which will help developers building and using their custom instance of the reference platform. The project is use case driven, providing real-time low-power demonstrators of a medical image processing application, automotive embedded systems for driver assistance (ADAS) and applications for Unmanned Aerial Vehicles (UAVs). The close connection to its set-up ecosystem and standardization organizations will allow the Tulipp project to propose new standards derived from its reference platform and handbook to the industry.

Many industrial domains rely on vision-based applications which require to comply with severe performance and embedded requirements. TULIPP will develop a reference platform, which consists of a hardware system, a tool chain and a real-time operating system. This platform defines implementation rules and interfaces to tackle power consumption issues while delivering high, energy efficient and guaranteed computing performance for image processing applications. Using this reference platform will enable designers to develop a complete solution at a reduced cost to meet the typical embedded systems requirements: Size, Weight and Power. Moreover, for less constrained systems which performance requirements cannot be fulfilled by one instance of the platform, the reference platform will also be scalable so that the resulting boards can be chained for higher processing power. The instance of the reference platform developed during the project will be use-case driven and split between the implementation of: a reference hardware architecture - a scalable low-power board; a low-power operating system and image processing libraries; a productivityenhancing tool chain. It will lead to three proof-of-concept demonstrators across different application domains: real-time and low-power medical image processing product prototype of surgical X-ray system (mobile c-arm); embedded image processing systems within Unmanned Aerial Vehicles (UAVs); automotive real time embedded systems for driver assistance. TULIPP will set up an ecosystem and will closely work with standardization organizations to propose new standards derived from its reference platform to the industry. © 2016 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.”

Benzene, a ubiquitous human carcinogen, forms DNA adducts through its metabolites such as p-benzoquinone (p-BQ) and hydroquinone (HQ). N(2)-(4-Hydroxyphenyl)-2'-deoxyguanosine (N(2)-4-HOPh-dG) is the principal adduct identified in vivo by (32)P-postlabeling in cells or animals treated with p-BQ or HQ. To study its effect on repair specificity and replication fidelity, we recently synthesized defined oligonucleotides containing a site-specific adduct using phosphoramidite chemistry. We here report the repair of this adduct by Escherichia coli UvrABC complex, which performs the initial damage recognition and incision steps in the nucleotide excision repair (NER) pathway. We first showed that the p-BQ-treated plasmid was efficiently cleaved by the complex, indicating the formation of DNA lesions that are substrates for NER. Using a 40-mer substrate, we found that UvrABC incises the DNA strand containing N(2)-4-HOPh-dG in a dose- and time-dependent manner. The specificity of such repair was also compared with that of DNA glycosylases and damage-specific endonucleases of E. coli, both of which were found to have no detectable activity toward N(2)-4-HOPh-dG. To understand why this adduct is specifically recognized and processed by UvrABC, molecular modeling studies were performed. Analysis of molecular dynamics trajectories showed that stable G:C-like hydrogen bonding patterns of all three Watson-Crick hydrogen bonds are present within the N(2)-4-HOPh-G:C base pair, with the hydroxyphenyl ring at an almost planar position. In addition, N(2)-4-HOPh-dG has a tendency to form more stable stacking interactions than a normal G in B-type DNA. These conformational properties may be critical in differential recognition of this adduct by specific repair enzymes.

Aberrant promoter methylation and associated chromatin changes are primarily studied in human malignancies. Thus far, mouse models for human cancer have been rarely utilized to study the role of DNA methylation in tumor onset and progression. It would be advantageous to use mouse tumor models to a greater extent to study the role and mechanism of DNA methylation in cancer because mouse models allow manipulation of the genome, study of samples/populations with a homogeneous genetic background, the possibility of modulating gene expression in vivo, the statistical power of using large numbers of tumor samples, access to various tumor stages, and the possibility of preclinical trials. Therefore, it is likely that the mouse will emerge as an increasingly utilized model to study DNA methylation in cancer. To foster the use of mouse models, we developed an arrayed mouse NotI-EcoRV genomic library, with clones from three commonly used mouse strains (129SvIMJ, FVB/NJ, and C57BL/6J). A total of 23,040 clones representing an estimated three- to fourfold coverage of the mouse genome were arrayed in 60 x 384-well plates. We developed restriction landmark genomic scanning (RLGS) mixing gels with 32 plates to enable the cloning of methylated sequences from RLGS profiles run with NotI-EcoRV-HinfI. RLGS was used to study aberrant methylation in two mouse models that overexpressed IL-15 or c-Myc and developed either T/NK-cell leukemia or T-cell lymphomas, respectively. Careful analysis of 198 sequences showed that 188 (94.9%) identified CpG-island sequences, 132 sequences (66.7%) had homology to the 5' regions of known genes or mRNAs, and all 132 NotI-EcoRV clones were located at the same CpG islands with the predicted promoter sequences. We have also developed a modified pGL3-based luciferase vector that now contains the NotI, AscI, and EcoRV restriction sites and allows the rapid cloning of NotI-EcoRV library fragments in both orientations. Luciferase assays using NotI-EcoRV clones confirmed that the library is enriched for promoter sequences. Thus, this library will support future genetic and epigenetic studies in mouse models.

A complex production mask-house faces the issue of handling and understanding the logistics information from the production process of the masks. We managed to control key performance indicators like cycle-time, flow-factor, line-speed, WIP, etc. To improve the line flow, we set-up rules for optimising batching at operations and forbid batching between operations, we defined maximum and minimum WIP at the operations, scheduled urgency of the different lots and built rules for bottleneck management. Also we restricted the number of “hot lots”. By migrating to the modern MES (manufacturing execution system) MaTISSe, which manages the shopfloor control, and a reporting database, we are able to eliminate the time deviations within our data, caused by data-extraction for different reports at different moments. This gives us a better understanding of our fixed bottleneck and a faster recognition of the temporarily bottlenecks caused by missing availability of machines or men. In this paper we describe the features and advantages of our new MES, as well as the migration process. We have already achieved considerable benefits. Our plan is to extend decision support within the MES, to help both managers and operators to make the right decisions. The project behind this paper reaped major benefits described here and we are looking forward to further challenges and successes.

Semiconductor manufacturing has become a global business, in which companies of different size unite in virtual enterprises to meet new opportunities. Therefore Mask manufacturing is a key business, but mask ordering is a complex process and is always critical regarding design to market time, even though mask complexity and customer base are increasing using a wide variety of different mask order forms which are frequently faulty and very seldom complete. This is effectively blocking agile manufacturing and can tie wafer fabs to a single mask The goal of the project is elimination of the order verification through paperless, electronically linked information sharing/exchange between chip design, mask production and production stages, which will allow automation of the mask preparation. To cover these new techniques and their specifications as well as the common ones with automated tools a special generic Meta-model will be generated, based on the current standards for mask specifications, including the requirements from the involved partners (Alcatel Microelectronics, Altis, Compugraphics, Infineon, Nimble, Sigma-C), the project works out a pre-normative standard. The paper presents the current status of work. This work is partly funded by the Commission of the European Union under the Fifth Framework project IST-1999-10332 AutoMOPS.

Through application of modern supply chain concepts in combination with state-of-the-art information technology, mask manufacturing performance and customer satisfaction can be improved radically. The AutoMOPS solution emphasizes on the elimination of the order verification through paperless, electronically linked information sharing/exchange between chip design, mask production and prototype production stages.