Degenerate coding in neural systems

When the dimensionality of a neural circuit is substantially larger than the dimensionality of the variable it encodes, many different degenerate network states can produce the same output. In this review I will discuss three different neural systems that are linked by this theme. The pyloric network of the lobster, the song control system of the zebra finch, and the odor encoding system of the locust, while different in design, all contain degeneracies between their internal parameters and the outputs they encode. Indeed, although the dynamics of song generation and odor identification are quite different, computationally, odor recognition can be thought of as running the song generation circuitry backwards. In both of these systems, degeneracy plays a vital role in mapping a sparse neural representation devoid of correlations onto external stimuli (odors or song structure) that are strongly correlated. I argue that degeneracy between input and output states is an inherent feature of many neural systems, which can be exploited as a fault-tolerant method of reliably learning, generating, and discriminating closely related patterns.     

简并PCR及其应用

简并PCR技术是根据同源蛋白的氨基酸序列扩增到同源基因的核苷酸序列,具有独特的优点。成功进行简并PCR的关键是设计好两组引物库和对反应条件进行优化。由于简并PCR自身的特点,在新基因的克隆、基因表达检测、病毒检测和基因组研究中有其广泛而独特的应用。     

简并PCR技术及其在基因克隆中的应用

本文简要介绍简并PCR技术,包括什么是简并引物,如何设计简并引物,进行简并PCR的反应条件,应用简并PCR获得全长基因的方法和简并PCR技术的应用范围,并对简并PCR技术的局限性及其新进展进行讨论。在此基础上,简述基因的克隆策略以及简并PCR技术在基因克隆中的应用。简并PCR技术是寻找和发现“新”基因或蛋白质家族新成员的一种非常有用的工具。 Abstract:Degenerate PCR is introduced in this paper,including what is degenerate PCR,how to design degenerate primers,how to optimize degenerate PCR parameters,how to applying degenerate PCR to obtain full-length gene and which fields can apply degenerate PCR.The limits and recent advances of degenerate PCR are also discussed.Based on this introduction,strategies of gene cloning and applications of degenerate PCR in gene cloning are summarized in brief.Degenerate PCR is a very useful tool for searching and discovering new genes and new members of a protein family.     

白腊DREB基因克隆中简并引物的设计

根据拟南芥DREB2A基因序列进行GenBank内Blastx序列同源性查询,对其中同源性较高的25个氨基酸序列进行了分析,设计简并引物,应用RT-PCR技术克隆白腊DREB2A基因,得测长2473bp,与拟南芥DREB2A同源性为96.94%的基因片段,并在GenBank登记,注册号为AY536056。     

Energetics of Ehrlich ascites mitochondria: membrane potential of isolated mitochondria and mitochondria within digitonin-permeabilized cells

Ehrlich ascites tumour cells were treated with digitonin so that they became permeable for low-molecular-weight compounds but, at certain concentrations of digitonin, retained most of their cytoplasmic proteins. Respiration of mitochondria with exogenous substrates and their membrane potential could thus be measured in situ by means of oxygen electrode and tetraphenylphosphonium-sensitive electrode, respectively. The results were compared with data from similar measurements on mitochondria isolated from such digitonin-permeabilized cells. Isolated mitochondria and mitochondria in situ oxidized succinate at similar rates and developed membrane potential of comparable magnitude. Both preparations also exhibited an identical nonlinear relationship between resting state respiration (titrated with a respiratory inhibitor) and the membrane potential. In the cells permeabilized with low concentrations of digitonin (i.e., retaining most of cytoplasmic proteins) and suspended in medium containing NaCl and other major anions and cations at concentrations close to those in mammalian plasma, anaerobiosis did not produce a decrease in the mitochondrial membrane potential, which was collapsed only after a subsequent addition of oligomycin. In this medium, glucose had little effect on either respiration or the membrane potential.     

piRNAs meet mitochondria

zuc/MitoPLD encodes a conserved enzyme that localizes to mitochondria and hydrolyzes the mitochondria-specific lipid cardiolipin. Surprisingly, zuc/MitoPLD activity is required for Piwi-interacting RNA (piRNA)-mediated silencing of transposable elements in fly and mouse germlines, suggesting that signaling from mitochondria influences the piRNA pathway.     

Sphingolipids in mitochondria

Sphingolipids are bioactive lipids found in cell membranes that exert a critical role in signal transduction. In recent years, it has become apparent that sphingolipids participate in growth, senescence, differentiation and apoptosis. The anabolism and catabolism of sphingolipids occur in discrete subcellular locations and consist of a strictly regulated and interconnected network, with ceramide as the central hub. Altered sphingolipid metabolism is linked to several human diseases. Hence, an advanced knowledge of how and where sphingolipids are metabolized is of paramount importance in order to understand the role of sphingolipids in cellular functions. In this review, we provide an overview of sphingolipid metabolism. We focus on the distinct pathways of ceramide synthesis, highlighting the mitochondrial ceramide generation, transport of ceramide to mitochondria and its role in the regulation of mitochondrial-mediated apoptosis, mitophagy and implications to disease. We will discuss unanswered questions and exciting future directions. This article is part of a Special Issue entitled: Lipids of Mitochondria edited by Guenther Daum.     

Calcium and mitochondria

The literature suggests that the physiological functions for which mitochondria sequester Ca(2+) are (1). to stimulate and control the rate of oxidative phosphorylation, (2). to induce the mitochondrial permeability transition (MPT) and perhaps apoptotic cell death, and (3). to modify the shape of cytosolic Ca(2+) pulses or transients. There is strong evidence that intramitochondrial Ca(2+) controls both the rate of ATP production by oxidative phosphorylation and induction of the MPT. Since the results of these processes are so divergent, the signals inducing them must not be ambiguous. Furthermore, as pointed out by Balaban [J. Mol. Cell. Cardiol. 34 (2002 ) 11259-11271], for any repetitive physiological process dependent on intramitochondrial free Ca(2+) concentration ([Ca(2+)](m)), a kind of intramitochondrial homeostasis must exist so that Ca(2+) influx during the pulse is matched by Ca(2+) efflux during the period between pulses to avoid either Ca(2+) buildup or depletion. In addition, mitochondrial Ca(2+) transport modifies both spatial and temporal aspects of cytosolic Ca(2+) signaling. Here, we look at the amounts of Ca(2+) necessary to mediate the functions of mitochondrial Ca(2+) transport and at the mechanisms of transport themselves in order to set up a hypothesis about how the mechanisms carry out their roles. The emphasis here is on isolated mitochondria and on general mitochondrial properties in order to focus on how mitochondria alone may function to fulfill their physiological roles even though the interactions of mitochondria with other organelles, particularly with endoplasmic and sarcoplasmic reticulum [Sci. STKE re1 (2004) 1-9], may also influence this story.     

Photodesorption of mitochondria

Photodesorption of mitochondria absorbed on a quartz plate was discovered. The rate of photodesorption of mitochondria from the plate into solution depends on the wavelength, intensity, and irradiation period. The maximum rate of photodesorption was detected upon irradiation with UV light at the mitochondrial protein tryptophan absorption band. UV photodesorption is presumably caused by a local photothermal effecth—eating of photoexcited proteins at the membrane surface that attach mitochondria to the plate. Preliminary fixation of a smear with isopropanol or acetone drastically decreased photodesorption and spontaneous desorption. No photodesorption of either mitochondria or formazan was observed upon illumination with green light of formazan granules formed in mitochondria as a product of reductase reaction. These data are important for elaborating a technique of immobilizing mitochondria for enzyme assays and biosensors.     

Biogenesis of mitochondria

Summary The action of ethidium bromide and berenil on the mitochondrial genome of Saccharomyces cerevisiae has been compared in three types of study: (i) early kinetics (up to 4 h) of petite induction by the drugs in the presence or absence of sodium dodecyl sulphate; (ii) genetic consequences of long-term (8 cell generations) exposure to the drugs; (iii) inhibition of mitochondrial DNA replication, both in whole cells and in isolated mitochondria.The results have been interpreted as follows. Firstly, the early events in petite induction differ markedly for the two drugs, as indicated by differences in the short-term kinetics. After some stage a common pathway is apparently followed because the composition of the population of petite cells induced after long-term exposure are very similar for both ethidium bromide and berenil. Secondly, both drugs probably act at the same site to inhibit mitochondrial DNA replication, in view of the fact that a petite strain known to be resistant to ethidium bromide inhibition of mitochondrial DNA replication was found to have simultaneously acquired resistance to berenil. From consideration of the drug concentrations needed to inhibit mitochondrial DNA replication in vivo and in vitro it is suggested that in vivo permeability barriers impede the access of ethidium bromide to the site of inhibition of mitochondrial DNA replication, whilst access of berenil to this site is facilitated. The site at which the drugs act to inhibit mitochondrial DNA replication may be different from the site(s) involved in early petite induction. Binding of the drugs at the latter site(s) is considered to initiate a series of events leading to the fragmentation of yeast mitochondrial DNA and petite induction.