Live-cell assays to identify regulators of ER-to-Golgi trafficking

We applied fluorescence microscopy-based quantitative assays to living cells to identify regulators of endoplasmic reticulum (ER)-to-Golgi trafficking and/or Golgi complex maintenance. We first validated an automated procedure to identify factors which influence Golgi-to-ER relocalization of GalT-CFP (β1,4-galactosyltransferase I-cyan fluorescent protein) after brefeldin A (BFA) addition and/or wash-out. We then tested 14 proteins that localize to the ER and/or Golgi complex when overexpressed for a role in ER-to-Golgi trafficking. Nine of them interfered with the rate of BFA-induced redistribution of GalT-CFP from the Golgi complex to the ER, six of them interfered with GalT-CFP redistribution from the ER to a juxtanuclear region (i.e. the Golgi complex) after BFA wash-out and six of them were positive effectors in both assays. Notably, our live-cell approach captures regulator function in ER-to-Golgi trafficking, which was missed in previous fixed cell assays, as well as assigns putative roles for other less characterized proteins. Moreover, we show that our assays can be extended to RNAi and chemical screens.     

Fast Carbon Footprinting for Large Product Portfolios

Publicly Available Specification 2050‐2011 (PAS 2050), the Green House Gas Product Protocol (GHGPP) standard and forthcoming guideline 14067 from the International Organization for Standardization (ISO) have helped to propel carbon footprinting from a subdiscipline of life cycle assessment (LCA) to the mainstream. However, application of carbon footprinting to large portfolios of many distinct products and services is immensely resource intensive. Even if achieved, it often fails to inform company‐wide carbon reduction strategies because footprint data are disjointed or don't cover the whole portfolio. We introduce a novel approach to generate standard‐compliant product carbon footprints (CFs) for companies with large portfolios at a fraction of previously required time and expertise. The approach was developed and validated on an LCA dataset covering 1,137 individual products from a global packaged consumer goods company. Three novel techniques work in concert in a single approach that enables practitioners to calculate thousands of footprints virtually simultaneously: (i) a uniform data structure enables footprinting all products and services by looping the same algorithm; (ii) concurrent uncertainty analysis guides practitioners to gradually improve the accuracy of only those data that materially impact the results; and (iii) a predictive model generates estimated emission factors (EFs) for materials, thereby eliminating the manual mapping of a product or service's inventory to EF databases. These autogenerated EFs enable non‐LCA experts to calculate approximate CFs and alleviate resource constraints for companies embarking on large‐scale product carbon footprinting. We discuss implementation roadmaps for companies, including further road‐testing required to evaluate the effectiveness of the approach for other product portfolios, limitations, and future improvements of the fast footprinting methodology.     

Shared human-chimpanzee pattern of perinatal femoral shaft morphology and its implications for the evolution of hominin locomotor adaptations

Background

Acquisition of bipedality is a hallmark of human evolution. How bipedality evolved from great ape-like locomotor behaviors, however, is still highly debated. This is mainly because it is difficult to infer locomotor function, and even more so locomotor kinematics, from fossil hominin long bones. Structure-function relationships are complex, as long bone morphology reflects phyletic history, developmental programs, and loading history during an individual’s lifetime. Here we discriminate between these factors by investigating the morphology of long bones in fetal and neonate great apes and humans, before the onset of locomotion.

Methodology/Principal Findings

Comparative morphometric analysis of the femoral diaphysis indicates that its morphology reflects phyletic relationships between hominoid taxa to a greater extent than taxon-specific locomotor adaptations. Diaphyseal morphology in humans and chimpanzees exhibits several shared-derived features, despite substantial differences in locomotor adaptations. Orangutan and gorilla morphologies are largely similar, and likely represent the primitive hominoid state.

Conclusions/Significance

These findings are compatible with two possible evolutionary scenarios. Diaphyseal morphology may reflect retained adaptive traits of ancestral taxa, hence human-chimpanzee shared-derived features may be indicative of the locomotor behavior of our last common ancestor. Alternatively, diaphyseal morphology might reflect evolution by genetic drift (neutral evolution) rather than selection, and might thus be more informative about phyletic relationships between taxa than about locomotor adaptations. Both scenarios are consistent with the hypothesis that knuckle-walking in chimpanzees and gorillas resulted from convergent evolution, and that the evolution of human bipedality is unrelated to extant great ape locomotor specializations.     

Self-organizing ontology of biochemically relevant small molecules

Background  

The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while providing new challenges, the biggest being the curation, annotation, and classification of this information to facilitate useful biochemical pattern analysis. Unfortunately, the human resources currently employed by the organizations supporting these efforts (e.g. ChEBI) are expanding linearly, while new useful scientific information is being released in a seemingly exponential fashion. Compounding this, currently existing chemical classification and annotation systems are not amenable to automated classification, formal and transparent chemical class definition axiomatization, facile class redefinition, or novel class integration, thus further limiting chemical ontology growth by necessitating human involvement in curation. Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest.     

A new species of <Emphasis Type="Italic">Pustula</Emphasis> (Oomycetes,Albuginales) is the causal agent of sunflower white rust

White blister rust of sunflower is an emerging disease that is among the most important diseases in this crop in South Africa and has recently spread to Europe. For the genus Albugo, it has been demonstrated that species are mostly at least host genus specific and that several previously overlooked species are present on Brassicaceae. It thus seems likely that previously unrecognised species are also present in the genus Pustula. Based on previous phylogenetic reconstruction in combination with differences in oospore ornamentation, it is revealed that Pustula on sunflower, previously attributed to Pustula tragopogonis (syn. Albugo tragopogonis), is distinct from Pustula on Tragopogon. Therefore, this pathogen is described as a new species, Pustula helianthicola. In addition, taxonomic observations revealed that Pustula tragopogonis is an incorrect name and is replaced by the new combination, Pustula obtusata.     

Synthesis and evaluation of N(1)-alkylindole-3-ylalkylammonium compounds as nicotinic acetylcholine receptor ligands

In this study thirty-three novel indole derivatives were designed and synthesized based on the structure of deformylflustrabromine B (1), a metabolite isolated from the marine bryozoan Flustra foliacea L. The syntheses were carried out using standard methodologies and in good yields. The molecules were tested for their affinities for the α4β2¹, α3β4¹, α7¹ and (α1)₂β1γδ nicotinic acetylcholine receptor (nAChR) subtypes. Binding assays showed that, among these ligands, compound 7c exhibited the highest affinity with K_i = 136.1, 93.9 and 862.4 nM for the α4β2¹, α3β4¹, and α7¹ nAChRs subtypes, respectively. These results indicated that the indole core might be a useful scaffold for the development of new potent and selective nAChR ligands.     

Detecting and investigating substrate cycles in a genome-scale human metabolic network

Substrate cycles, also known as futile cycles, are cyclic metabolic routes that dissipate energy by hydrolysing cofactors such as ATP. They were first described to occur in the muscles of bumblebees and brown adipose tissue in the 1970s. A popular example is the conversion of fructose?6-phosphate to fructose?1,6-bisphosphate and back. In the present study, we analyze a large number of substrate cycles in human metabolism that consume ATP and discuss their statistics. For this purpose, we use two recently published methods (i.e. EFMEvolver and the K-shortest EFM method) to calculate samples of 100?000 and 15?000 substrate cycles, respectively. We find an unexpectedly high number of substrate cycles in human metabolism, with up to 100 reactions per cycle, utilizing reactions from up to six different compartments. An analysis of tissue-specific models of liver and brain metabolism shows that there is selective pressure that acts against the uncontrolled dissipation of energy by avoiding the coexpression of enzymes belonging to the same substrate cycle. This selective force is particularly strong against futile cycles that have a high flux as a result of thermodynamic principles.