Selection Shapes the Robustness of Ligand-Binding Amino Acids

The phenotypes of biological systems are to some extent robust to genotypic changes. Such robustness exists on multiple levels of biological organization. We analyzed this robustness for two categories of amino acids in proteins. Specifically, we studied the codons of amino acids that bind or do not bind small molecular ligands. We asked to what extent codon changes caused by mutation or mistranslation may affect physicochemical amino acid properties or protein folding. We found that the codons of ligand-binding amino acids are on average more robust than those of non-binding amino acids. Because mistranslation is usually more frequent than mutation, we speculate that selection for error mitigation at the translational level stands behind this phenomenon. Our observations suggest that natural selection can affect the robustness of very small units of biological organization.     

Certain Non-Standard Coding Tables Appear to be More Robust to Error Than the Standard Genetic Code

Since the identification of the Standard Coding Table as a “universal” method to translate genetic information into amino acids, exceptions to this rule have been reported, and to date there are nearly 20 alternative genetic coding tables deployed by either nuclear genomes or organelles of organisms. Why are these codes still in use and why are new codon reassignments occurring? This present study aims to provide a new method to address these questions and to analyze whether these alternative codes present any advantages or disadvantages to the organisms or organelles in terms of robustness to error. We show that two of the alternative coding tables, The Ciliate, Dasycladacean and Hexamita Nuclear Code (CDH) and The Flatworm Mitochondrial Code (FMC), exhibit an advantage, while others such as The Yeast Mitochondrial Code (YMC) are at a significant disadvantage. We propose that the Standard Code is likely to have emerged as a “local minimum” and that the “coding landscape” is still being searched for a “global” minimum.     

Insulin and oxidative stress modulate proliferation of rat ovarian theca-interstitial cells through diverse signal transduction pathways

Insulin and moderate oxidative stress stimulate proliferation of ovarian theca-interstitial cells. The effects of these agents on selected signal transduction pathways were examined. PD98059 (inhibitor of MAP2K1, also known as MEK-1, upstream of extracellular signal-regulated protein kinases MAPK3/1, also known as ERK1/2), wortmannin (inhibitor of PIK3C2A, also known as PI3K), and rapamycin (inhibitor of FRAP1, also known as mTOR, upstream of RPS6KB1) each significantly decreased insulin and oxidative stress-induced proliferation of theca-interstitial cells. The greatest inhibition was observed in the presence of rapamycin; this effect occurred without a significant change in cell viability. Phosphorylation of AKT was stimulated by insulin only, while phosphorylation of MAPK3/1 and RPS6KB1 was increased by insulin and oxidative stress. Insulin-induced and oxidative stress-induced phosphorylation of RPS6KB1 was partly inhibited by wortmannin and partly by PD98059; the greatest inhibition was observed in the presence of a combination of wortmannin plus PD98059. Effects of insulin and oxidative stress on phosphorylation of RPS6KB1 were confirmed by kinase activity assays. These findings indicate that actions of insulin and oxidative stress converge on MAPK3/1 and RPS6KB1. Furthermore, we speculate that activation of RPS6KB1 may be in part induced via the MAPK3/1 pathway.     

Relation of Nanostructure and Recombination Dynamics in a Low‐Temperature Solution‐Processed CuInS2 Nanocrystalline Solar Cell

The understanding and control of nanostructures with regard to transport and recombination mechanisms is of key importance in the optimization of the power conversion efficiency (PCE) of solar cells based on inorganic nanocrystals. Here, the transport properties of solution‐processed solar cells are investigated using photo‐CELIV (photogenerated charge carrier extraction by linearly increasing voltage) and transient photovoltage techniques; the solar cells are prepared by an in‐situ formation of CuInS₂ nanocrystals (CIS NCs) at the low temperature of 270 °C. Structural and morphological analyses reveal the presence of a metastable CuIn₅S₈ phase and a disordered morphology in the CuInS₂ nanocrytalline films consisting of polycrystalline grains at the nanoscale range. Consistent with the disordered morphology of the CIS NC thin films, the CIS NC devices are characterized by a low carrier mobility. The carrier density dynamic indicates that the recombination kinetics in these devices follows the dispersive bimolecular recombination model and does not fully behave in a diffusion‐controlled manner, as expected by Langevin‐type recombination. The mobility–lifetime product of the charge carriers properly explains the performance of the thin (200 nm) CIS NC solar cell with a high fill‐factor of 64% and a PCE of over 3.5%.     

Design constraints on a synthetic metabolism

A metabolism is a complex network of chemical reactions that converts sources of energy and chemical elements into biomass and other molecules. To design a metabolism from scratch and to implement it in a synthetic genome is almost within technological reach. Ideally, a synthetic metabolism should be able to synthesize a desired spectrum of molecules at a high rate, from multiple different nutrients, while using few chemical reactions, and producing little or no waste. Not all of these properties are achievable simultaneously. We here use a recently developed technique to create random metabolic networks with pre-specified properties to quantify trade-offs between these and other properties. We find that for every additional molecule to be synthesized a network needs on average three additional reactions. For every additional carbon source to be utilized, it needs on average two additional reactions. Networks able to synthesize 20 biomass molecules from each of 20 alternative sole carbon sources need to have at least 260 reactions. This number increases to 518 reactions for networks that can synthesize more than 60 molecules from each of 80 carbon sources. The maximally achievable rate of biosynthesis decreases by approximately 5 percent for every additional molecule to be synthesized. Biochemically related molecules can be synthesized at higher rates, because their synthesis produces less waste. Overall, the variables we study can explain 87 percent of variation in network size and 84 percent of the variation in synthesis rate. The constraints we identify prescribe broad boundary conditions that can help to guide synthetic metabolism design.     

Zebrafish xenografts as a tool for in vivo studies on human cancer

The zebrafish has become a powerful vertebrate model for genetic studies of embryonic development and organogenesis and increasingly for studies in cancer biology. Zebrafish facilitate the performance of reverse and forward genetic approaches, including mutagenesis and small molecule screens. Moreover, several studies report the feasibility of xenotransplanting human cells into zebrafish embryos and adult fish. This model provides a unique opportunity to monitor tumor-induced angiogenesis, invasiveness, and response to a range of treatments in vivo and in real time. Despite the high conservation of gene function between fish and humans, concern remains that potential differences in zebrafish tissue niches and/or missing microenvironmental cues could limit the relevance and translational utility of data obtained from zebrafish human cancer cell xenograft models. Here, we summarize current data on xenotransplantation of human cells into zebrafish, highlighting the advantages and limitations of this model in comparison to classical murine models of xenotransplantation.     

APC/C-Cdc20 mediates deprotection of centromeric cohesin at meiosis II in yeast

Cells undergoing meiosis produce haploid gametes through one round of DNA replication followed by 2 rounds of chromosome segregation. This requires that cohesin complexes, which establish sister chromatid cohesion during S phase, are removed in a stepwise manner. At meiosis I, the separase protease triggers the segregation of homologous chromosomes by cleaving cohesin's Rec8 subunit on chromosome arms. Cohesin persists at centromeres because the PP2A phosphatase, recruited by the shugoshin protein, dephosphorylates Rec8 and thereby protects it from cleavage. While chromatids disjoin upon cleavage of centromeric Rec8 at meiosis II, it was unclear how and when centromeric Rec8 is liberated from its protector PP2A. One proposal is that bipolar spindle forces separate PP2A from Rec8 as cells enter metaphase II. We show here that sister centromere biorientation is not sufficient to “deprotect” Rec8 at meiosis II in yeast. Instead, our data suggest that the ubiquitin-ligase APC/C^Cdc20 removes PP2A from centromeres by targeting for degradation the shugoshin Sgo1 and the kinase Mps1. This implies that Rec8 remains protected until entry into anaphase II when it is phosphorylated concurrently with the activation of separase. Here, we provide further support for this model and speculate on its relevance to mammalian oocytes.