The role of mass spectrometry in plant systems biology

Large-scale analyses of proteins and metabolites are intimately bound to advancements in MS technologies. The aim of these non-targeted "omic" technologies is to extend our understanding beyond the analysis of only parts of the system. Here, metabolomics and proteomics emerged in parallel with the development of novel mass analyzers and hyphenated techniques such as gas chromatography coupled to time-of-flight mass spectrometry (GC-TOF-MS) and multidimensional liquid chromatography coupled to mass spectrometry (LC-MS). The analysis of (i) proteins (ii) phosphoproteins, and (iii) metabolites is discussed in the context of plant physiology and environment and with a focus on novel method developments. Recently published studies measuring dynamic (quantitative) behavior at these levels are summarized; for these works, the completely sequenced plants Arabidopsis thaliana and Oryza sativa (rice) have been the primary models of choice. Particular emphasis is given to key physiological processes such as metabolism, development, stress, and defense. Moreover, attempts to combine spatial, tissue-specific resolution with systematic profiling are described. Finally, we summarize the initial steps to characterize the molecular plant phenotype as a corollary of environment and genotype.     

Data Dependence Analysis of Assembly Code

Determination of data dependences is a task typically performed with high-level language source code in today's optimizing and parallelizing compilers. Very little work has been done in the field of data dependence analysis on assembly language code, but this area will be of growing importance, e.g., for increasing instruction-level parallelism. A central element of a data dependence analysis in this case is a method for memory reference disambiguation which decides whether two memory operations may access (or definitely access) the same memory location. In this paper we describe a new approach for the determination of data dependences in assembly code. Our method is based on a sophisticated algorithm for symbolic value propagation, and it can derive value-based dependences between memory operations instead of just address-based dependences. We have integrated our method into the Salto system for assembly language optimization. Experimental results show that our approach greatly improves the precision of the dependence analysis in many cases.     

HiL simulation in biomechanics: a new approach for testing total joint replacements

Instability of artificial joints is still one of the most prevalent reasons for revision surgery caused by various influencing factors. In order to investigate instability mechanisms such as dislocation under reproducible, physiologically realistic boundary conditions, a novel test approach is introduced by means of a hardware-in-the-loop (HiL) simulation involving a highly flexible mechatronic test system. In this work, the underlying concept and implementation of all required units is presented enabling comparable investigations of different total hip and knee replacements, respectively. The HiL joint simulator consists of two units: a physical setup composed of a six-axes industrial robot and a numerical multibody model running in real-time. Within the multibody model, the anatomical environment of the considered joint is represented such that the soft tissue response is accounted for during an instability event. Hence, the robot loads and moves the real implant components according to the information provided by the multibody model while transferring back the position and resisting moment recorded. Functionality of the simulator is proved by testing the underlying control principles, and verified by reproducing the dislocation process of a standard total hip replacement. HiL simulations provide a new biomechanical testing tool for analyzing different joint replacement systems with respect to their instability behavior under realistic movements and physiological load conditions.     

Quantifying the Benefits of SSA-Based Mobile Code

High-performance just-in-time compilers for Java need to invest considerable effort before actual code generation can commence. This is in part due to the very nature of the Java Virtual Machine, which is not well matched to the requirements of optimizing code generators. Alternative transportation formats based on Static Single Assignment form should theoretically be superior to virtual machines, but this claim has not previously been validated in practice. This paper revisits the topic and attempts to quantify the effect of using an SSA-based mobile code representation (IR) instead of a virtual-machine based one.To this end, we have integrated full support for a verifiable SSA-based IR into Jikes RVM, an existing Java execution environment. The resulting system is capable of loading and executing Java programs represented in either format, traditional JVM bytecode as well as the SSA-based representation, and it can even execute programs made up of a mixture of the two formats. In our implementation, the two alternative just-in-time compilation pipelines share a common low-level code generator.Performance results are encouraging and show simultaneous improvements in both compilation time and code quality relative to Jikes RVM's standard optimizing compiler for JVM class files. They support the hypothesis that SSA-based intermediate representations offer advantages in the context of just-in-time compilation.     

Zur Synthese und Funktionalisierung neuer Poly[(silylen)‐2,5‐thiophene]

Treatment of 2,5‐dilithiothiophene with (dimethylamino) methylsilylbis(triflates) gave poly[(dimethylamino‐silylene)‐2,5‐thiophene] 4 in high yield. The amino–silyl bond was cleaved selectively by triflic acid leading to triflate substituted poly[(silylene)‐2,5‐thiophene] 5 . Conversions of this polymers with nucleophiles gave other functionalized derivatives 6 – 9 . Hydrosilylation reaction between silicon–vinyl and silicon–hydrogen derivatives results in polymer networks which may serve as interesting preceramic materials. The structures of the polymers were proven by NMR spectroscopy (²⁹Si, ¹³C, ¹H).     

Origin,metabolism, and adverse health effects of cholesterol oxidation products

Cholesterol oxidation products (COP), also called oxysterols, enter the organism by intake of COP-containing foodstuff or are generated in vivo by enzymatic or non-enzymatic oxidation (peroxidation) of cholesterol. COP are transported in lymph and blood with lipoproteins (mainly fatty acyl monoesters at the 3β-position) or bound to albumin. As being substrates for acyl CoA: cholesterol acyltransferase (ACAT), lecithin:cholesterol acyltransferase (LCAT), and cholesteryl ester transfer protein (CETP), COP are esterified and exchanged between lipoproteins and are distributed in the whole organism. Kupffer cells and hepatocytes are the target cells for COP transformation and excretion via bile secretion. Regarding biological activities, COP reveal widespread effects on cholesterol metabolism as well as on structure and function of cellular membranes. Throughout their actions, COP were shown to be cytotoxic but they were also suggested to be regulatory agents. Their detrimental part in atherogenesis seems to be still underestimated, while valid data on the role of COP in carcinogenesis are still missing.     

Lessons Learned from the Studies of Roots Shaded from Direct Root Illumination

The root is the below-ground organ of a plant, and it has evolved multiple signaling pathways that allow adaptation of architecture, growth rate, and direction to an ever-changing environment. Roots grow along the gravitropic vector towards beneficial areas in the soil to provide the plant with proper nutrients to ensure its survival and productivity. In addition, roots have developed escape mechanisms to avoid adverse environments, which include direct illumination. Standard laboratory growth conditions for basic research of plant development and stress adaptation include growing seedlings in Petri dishes on medium with roots exposed to light. Several studies have shown that direct illumination of roots alters their morphology, cellular and biochemical responses, which results in reduced nutrient uptake and adaptability upon additive stress stimuli. In this review, we summarize recent methods that allow the study of shaded roots under controlled laboratory conditions and discuss the observed changes in the results depending on the root illumination status.