Gel-to-gel phase transition may occur in mammalian cells: Mechanism of formation of "dark" (compacted) neurons

In the course of many diseases, individual non-apoptotic cells that are randomly distributed among undamaged cells in various mammalian tissues become shrunken and hyperbasophilic ("dark"). The light microscopic shrinkage is caused by a potentially reversible, dramatic compaction of all ultrastructural elements inside the affected cells, and escape of the excess water through apparently intact plasma membrane. In the case of neurons, the ultrastructural compaction rapidly involves the soma-dendrite domains in an all-or-nothing manner, and also mm-long axon segments. The present paper demonstrates that such ultrastructural compaction in neurons, which affects the whole soma-dendrite domain or long axon segments, can take place both immediately after an in vivo head injury and in rat brains perfusion-fixed for 30 min., and then chilled to just above the freezing point before the same kind of head injury was inflicted. This argues strongly against any enzyme-mediated compaction mechanism. On the analogy of gel-to-gel phase transitions in polymer chemistry, we hypothesize a pure physico-chemical compaction mechanism. Specifically, after initiation at a single site in each affected cell, the ultrastructural compaction is propelled throughout the whole cell on the domino principle by the free energy stored in the form of non-covalent interactions among the constituents of some cytoplasmic gel structure.     

1 July 1858: what Wallace knew; what Lyell thought he knew; what both he and Hooker took on trust; and what Charles Darwin never told them

At the Linnean Society on 1 July 1858, Charles Lyell and Joseph Hooker, using only an extract from Charles Darwin's unpublished essay of 1844, and a copy of a recent letter to Asa Gray in Boston, argued successfully that Darwin understood how species originate long before a letter from Alfred Russel Wallace outlining his own version of the theory of evolution arrived at Darwin's home. That letter from Ternate in the Malay Archipelago, however, was not the first letter Darwin received from Wallace. This article will contend that two of the three letters Wallace sent Darwin between 10 October 1856 and 9 March 1858 arrived much earlier than Darwin recorded, thereby allowing him time to assess Wallace's ideas and claim an independent understanding of how the operation of divergence and extinction in the natural world leads strongly marked varieties to be identified as new species. By the time of the Linnean meeting Darwin's new ideas had filtered into his letters and ‘big’ species book, despite the absence of any independent evidence from the natural world to justify his constant insistence to have been guided only by inductive reasoning. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 725–736.     

后腹腔镜下保留肾单位肾部分切除术后肾功能的影响因素分析

目的:分析后腹腔镜下保留肾单位肾部分切除术后患肾肾功能的影响因素。方法:回顾性分析2011年5月~2013年10月本院收治的45例行后腹腔镜下肾部分切除术肾癌患者的临床资料,采用99mTc-DTPA肾核素扫描评估术前及术后3月术侧肾的肾小球滤过率(GFR)。结果:手术时间100~240min,平均(135±33.21)min。肾动脉阻断时间(20.01±7.35)min,肿瘤大小(3.05±1.24)cm。术前及术后3月术肾GFR分别是(46.53±6.35)、(32.22±4.65)ml/min。术侧肾术后GFR下降(15.36±2.36)ml/min,与术前相比下降约34%。经随访1月-2年,无复发及转移病例,患者全部无瘤生存。影响手术前后血肌酐水平变化的相关因素主要为手术时间、阻断时间、气流量、术中失血量(P0.05);影响手术前后GFR水平变化的相关因素主要为阻断时间、气流量、手术时间(P0.01)。术前肾功能情况、缺血时间和肿瘤最大径是术侧肾功能下降程度的独立预测因子;术前肾功能情况和肿瘤最大径是总体肾功能下降程度的独立预测因子。结论:后腹腔镜下保留肾单位肾部分切除术后患肾肾功能的影响因素包括术前肾功能、手术时间、肾动脉阻断时间、气流量、术中失血量、肿瘤大小等。     

Pupylated proteins in Corynebacterium glutamicum revealed by MudPIT analysis

In a manner similar to ubiquitin, the prokaryotic ubiquitin‐like protein (Pup) has been shown to target proteins for degradation via the proteasome in mycobacteria. However, not all actinobacteria possessing the Pup protein also contain a proteasome. In this study, we set out to study pupylation in the proteasome‐lacking non‐pathogenic model organism Corynebacterium glutamicum. A defined pup deletion mutant of C. glutamicum ATCC 13032 grew aerobically as the parent strain in standard glucose minimal medium, indicating that pupylation is dispensable under these conditions. After expression of a Pup derivative carrying an aminoterminal polyhistidine tag in the Δpup mutant and Ni²⁺‐chelate affinity chromatography, pupylated proteins were isolated. Multidimensional protein identification technology (MudPIT) and MALDI‐TOF‐MS/MS of the elution fraction unraveled 55 proteins being pupylated in C. glutamicum and 66 pupylation sites. Similar to mycobacteria, the majority of pupylated proteins are involved in metabolism or translation. Our results define the first pupylome of an actinobacterial species lacking a proteasome, confirming that other fates besides proteasomal degradation are possible for pupylated proteins.     

In Silico Screening for Palmitoyl Substrates Reveals a Role for DHHC1/3/10 (zDHHC1/3/11)-mediated Neurochondrin Palmitoylation in Its Targeting to Rab5-positive Endosomes

Protein palmitoylation, a common post-translational lipid modification, plays an important role in protein trafficking and functions. Recently developed palmitoyl-proteomic methods identified many novel substrates. However, the whole picture of palmitoyl substrates has not been clarified. Here, we performed global in silico screening using the CSS-Palm 2.0 program, free software for prediction of palmitoylation sites, and selected 17 candidates as novel palmitoyl substrates. Of the 17 candidates, 10 proteins, including 6 synaptic proteins (Syd-1, transmembrane AMPA receptor regulatory protein (TARP) γ-2, TARP γ-8, cornichon-2, Ca²⁺/calmodulin-dependent protein kinase IIα, and neurochondrin (Ncdn)/norbin), one focal adhesion protein (zyxin), two ion channels (TRPM8 and TRPC1), and one G-protein-coupled receptor (orexin 2 receptor), were palmitoylated. Using the DHHC palmitoylating enzyme library, we found that all tested substrates were palmitoylated by the Golgi-localized DHHC3/7 subfamily. Ncdn, a regulator for neurite outgrowth and synaptic plasticity, was robustly palmitoylated by the DHHC1/10 (zDHHC1/11; z1/11) subfamily, whose substrate has not yet been reported. As predicted by CSS-Palm 2.0, Cys-3 and Cys-4 are the palmitoylation sites for Ncdn. Ncdn was specifically localized in somato-dendritic regions, not in the axon of rat cultured neurons. Stimulated emission depletion microscopy revealed that Ncdn was localized to Rab5-positive early endosomes in a palmitoylation-dependent manner, where DHHC1/10 (z1/11) were also distributed. Knockdown of DHHC1, -3, or -10 (z11) resulted in the loss of Ncdn from Rab5-positive endosomes. Thus, through in silico screening, we demonstrate that Ncdn and the DHHC1/10 (z1/11) and DHHC3/7 subfamilies are novel palmitoyl substrate-enzyme pairs and that Ncdn palmitoylation plays an essential role in its specific endosomal targeting.     

Cysteine Racemization on IgG Heavy and Light Chains

Under basic pH conditions, the heavy chain 220-light chain 214 (H220-L214) disulfide bond, found in the flexible hinge region of an IgG1, can convert to a thioether. Similar conditions also result in racemization of the H220 cysteine. Here, we report that racemization occurs on both H220 and L214 on an IgG1 with a λ light chain (IgG1λ) but almost entirely on H220 of an IgGl with a κ light chain (IgG1κ) under similar conditions. Likewise, racemization was detected at significant levels on H220 and L214 on endogenous human IgG1λ but only at the H220 position on IgG1κ. Low but measurable levels of d-cysteines were found on IgG2 cysteines in the hinge region, both with monoclonal antibodies incubated under basic pH conditions and on antibodies isolated from human serum. A simplified reaction mechanism involving reversible β-elimination on the cysteine is presented that accounts for both base-catalyzed racemization and thioether formation at the hinge disulfide.     

Regulation of connexin‐ and pannexin‐based channels by post‐translational modifications

Connexin (Cx) and pannexin (Panx) proteins form large conductance channels, which function as regulators of communication between neighbouring cells via gap junctions and/or hemichannels. Intercellular communication is essential to coordinate cellular responses in tissues and organs, thereby fulfilling an essential role in the spreading of signalling, survival and death processes. The functional properties of gap junctions and hemichannels are modulated by different physiological and pathophysiological stimuli. At the molecular level, Cxs and Panxs function as multi‐protein channel complexes, regulating their channel localisation and activity. In addition to this, gap junctional channels and hemichannels are modulated by different post‐translational modifications (PTMs), including phosphorylation, glycosylation, proteolysis, N‐acetylation, S‐nitrosylation, ubiquitination, lipidation, hydroxylation, methylation and deamidation. These PTMs influence almost all aspects of communicating junctional channels in normal cell biology and pathophysiology. In this review, we will provide a systematic overview of PTMs of communicating junction proteins and discuss their effects on Cx and Panx‐channel activity and localisation.