Protein-Protein Docking Benchmark 2.0: an update

We present a new version of the Protein-Protein Docking Benchmark, reconstructed from the bottom up to include more complexes, particularly focusing on more unbound-unbound test cases. SCOP (Structural Classification of Proteins) was used to assess redundancy between the complexes in this version. The new benchmark consists of 72 unbound-unbound cases, with 52 rigid-body cases, 13 medium-difficulty cases, and 7 high-difficulty cases with substantial conformational change. In addition, we retained 12 antibody-antigen test cases with the antibody structure in the bound form. The new benchmark provides a platform for evaluating the progress of docking methods on a wide variety of targets. The new version of the benchmark is available to the public at http://zlab.bu.edu/benchmark2.     

CHRNA7 Polymorphisms and Response to Cholinesterase Inhibitors in Alzheimer's Disease

Background

CHRNA7 encodes the α7 nicotinic acetylcholine receptor subunit, which is important to Alzheimer''s disease (AD) pathogenesis and cholinergic neurotransmission. Previously, CHRNA7 polymorphisms have not been related to cholinesterase inhibitors (ChEI) response.

Methods

Mild to moderate AD patients received ChEIs were recruited from the neurology clinics of three teaching hospitals from 2007 to 2010 (n = 204). Nine haplotype-tagging single nucleotide polymorphisms of CHRNA7 were genotyped. Cognitive responders were those showing improvement in the Mini-Mental State Examination score ≧2 between baseline and 6 months after ChEI treatment.

Results

AD women carrying rs8024987 variants [GG+GC vs. CC: adjusted odds ratio (AOR) = 3.62, 95% confidence interval (CI) = 1.47–8.89] and GG haplotype in block1 (AOR = 3.34, 95% CI = 1.38–8.06) had significantly better response to ChEIs (false discovery rate <0.05). These variant carriers using galantamine were 11 times more likely to be responders than female non-carriers using donepezil or rivastigmine.

Conclusion

For the first time, this study found a significant association between CHRNA7 polymorphisms and better ChEI response. If confirmed by further studies, CHRNA7 polymorphisms may aid in predicting ChEI response and refining treatment choice.     

High-level expression, purification, and characterization of non-tagged Aspergillus flavus urate oxidase in Escherichia coli

The entire encoding region for Aspergillus flavus uricase was cloned into pET-32a and expressed in Escherichia coli BL21 (DE3). The uricase was expressed in the E. coli cytoplasm in a completely soluble, biologically active form. A scalable process aimed to produce and purify multi-gram quantities of highly pure, recombinant urate oxidase (rUox) from E. coli was developed. The rUox protein was produced in a 30 L fermentor containing 25 L of 2x YT medium and purified to >99% purity using hydrophobic interaction, anion-exchange, and gel filtered chromatography. The final yield of purified rUox from fermentation resulted in approximately 27 g of highly pure, biologically active rUox per kg of cell paste (approximately 238 mg/8.8 g cell paste/L). The results presented here exhibit the ability to generate multi-gram quantities of rUox from E. coli that may be used for the development of pharmaceutics of reducing the hyperuricemia.     

Increment of Iodine Content in Vegetable Plants by Applying Iodized Fertilizer and the Residual Characteristics of Iodine in Soil

As a new attempt to control iodine deficiency disorder (IDD), we explored a method of iodine supplementation by raising the iodine content in vegetables. When grown in the soil supplemented with iodized fertilizer, the three experimental plant species (cucumber, aubergine, and radish) show increasing iodine levels in both leaf and fruit/rhizome tissues as the iodine content added in soil increases. Excessive iodine added to soil can be toxic to plants, whereas the tolerance limit to excessive iodine varies in the three plant species tested. The migration and volatilization of iodine in soil is correlated with the properties of the soil used. The residual iodine in soil increases as the iodine added to soil increases. The diatomite in the iodized fertilizer helps to increase the durability of the iodized fertilizer. This study potentially provides a safe and organic iodine supplementation method to control IDD.     

PA from an H5N1 highly pathogenic avian influenza virus activates viral transcription and replication and induces apoptosis and interferon expression at an early stage of infection

ABSTRACT: BACKGROUND: Although gene exchange is not likely to occur freely, reassortment between the H5N1 highlypathogenic avian influenza virus (HPAIV) and currently circulating human viruses is aserious concern. The PA polymerase subunit of H5N1 HPAIV was recently reported toactivate the influenza replicon activity. METHODS: The replicon activities of PR8 and WSN strains (H1N1) of influenza containing PA fromHPAIV A/Cambodia/P0322095/2005 (H5N1) and the activity of the chimeric RNApolymerase were analyzed. A reassortant WSN virus containing the H5N1 Cambodia PA (CPA)was then reconstituted and its growth in cells and pathogenicity in mice examined. Theinterferon promoter, TUNEL, and caspase 3, 8, and 9 activities of C-PA-infected cells werecompared with those of WSN-infected cells. RESULTS: The activity of the chimeric RNA polymerase was slightly higher than that of WSN, and CPAreplicated better than WSN in cells. However, the multi-step growth of C-PA and itspathogenicity in mice were lower than those of WSN. The interferon promoter, TUNEL, andcaspase 3, 8, and 9 activities were strongly induced in early infection in C-PA-infected cellsbut not in WSN-infected cells. CONCLUSIONS: Apoptosis and interferon were strongly induced early in C-PA infection, which protected theuninfected cells from expansion of viral infection. In this case, these classical host-virusinteractions contributed to the attenuation of this strongly replicating virus.     

传染性脾肾坏死病毒（ISKNV）感染途径,宿主范围及对温度敏感性的研究

传染性脾肾坏死病毒（ISKNV）无细菌滤液通过肌肉注射、划痕浸泡、腹腔注射和口服等四种感染途径,人工感染健康鳜鱼（Sinipercachuatsi）,四种途径都能引起典型的传染性脾肾坏死病毒病。通过腹腔注射感染途径,病毒滤液在25～34℃条件下,能引起健康鳜鱼发病。另外,用病毒滤液感染尼罗非鲫（Oreochromis。niloticus）、草鱼（Ctenopharyngodonidellus）、乌鳢（Ophiocephalusargus）、大口黑鲈（Micropterussalmoides）和尖吻鲈（Latescalcarifer）五种鱼,大口黑鲈能够感染成功,为ISKNV的宿主,而其它鱼不能感染成功,不是ISKNV的宿主。     

小鼠胚胎及生后发育的肾上腺皮质的组织学与组织化学研究

胚龄１３日小鼠肾上腺结构尚未形成,在肾附近可见两群细胞。１５日两群细胞融合,呈一新月形小体,外包被膜,内含两类细胞,一类胞体较大,染色较深,另一类胞体较小,染色浅。１７日,胞体大染色深的细胞形成团索状,发育成皮质细胞;另一类细胞则迁移至中央,形成髓质。组织化学研究显示,胎龄１５日及以后的肾上腺皮质细胞３β－羟甾体脱氢酶（３β－ＨＳＤＨ）、脂类、酸性磷酸酶（ＡＣＰ）、亮氨酸氨基肽酶（ＬＮＡｓｅ）均为阳性。以上一些酶活性的出现提示１５日及其后胚鼠,生后１～６０天小鼠的肾上腺皮质都有分泌甾体激素之功能。     

PARK6 PINK1 mutants are defective in maintaining mitochondrial membrane potential and inhibiting ROS formation of substantia nigra dopaminergic neurons

Mutations in PTEN-induced kinase 1 (PINK1) gene cause recessive familial type 6 of Parkinson's disease (PARK6). PINK1 is believed to exert neuroprotective effect on SN dopaminergic cells by acting as a mitochondrial Ser/Thr protein kinase. Autosomal recessive inheritance indicates the involvement of loss of PINK1 function in PARK6 pathogenesis. In the present study, confocal imaging of cultured SN dopaminergic neurons prepared from PINK1 knockout mice was performed to investigate physiological importance of PINK1 in maintaining mitochondrial membrane potential (ΔΨ_m) and mitochondrial morphology and test the hypothesis that PARK6 mutations cause the loss of PINK1 function. PINK1-deficient SN dopaminergic neurons exhibited a depolarized ΔΨ_m. In contrast to long thread-like mitochondria of wild-type neurons, fragmented mitochondria were observed from PINK1-null SN dopaminergic cells. Basal level of mitochondrial superoxide and oxidative stressor H₂O₂-induced ROS generation were significantly increased in PINK1-deficient dopaminergic neurons. Overexpression of wild-type PINK1 restored hyperpolarized ΔΨ_m and thread-like mitochondrial morphology and inhibited ROS formation in PINK1-null dopaminergic cells. PARK6 mutant (G309D), (E417G) or (CΔ145) PINK1 failed to rescue mitochondrial dysfunction and inhibit oxidative stress in PINK1-deficient dopaminergic neurons. Mitochondrial toxin rotenone-induced cell death of dopaminergic neurons was augmented in PINK1-null SN neuronal culture. These results indicate that PINK1 is required for maintaining normal ΔΨ_m and mitochondrial morphology of cultured SN dopaminergic neurons and exerts its neuroprotective effect by inhibiting ROS formation. Our study also provides the evidence that PARK6 mutant (G309D), (E417G) or (CΔ145) PINK1 is defective in regulating mitochondrial functions and attenuating ROS production of SN dopaminergic cells.     

Infectious spleen and kidney necrosis virus (a fish iridovirus) enters Mandarin fish fry cells via caveola-dependent endocytosis

Infectious spleen and kidney necrosis virus (ISKNV) is the type species of the genus Megalocytivirus from the family Iridoviridae. Megalocytiviruses have been implicated in more than 50 fish species infections and currently threaten the aquaculture industry, causing great economic losses in China, Japan, and Southeast Asia. However, the cellular entry mechanisms of megalocytiviruses remain largely uncharacterized. In this study, the main internalization mechanism of ISKNV was investigated by using mandarin fish fry (MFF-1) cells. The progression of ISKNV infection is slow, and infection is not inhibited when the cells are treated with ammonium chloride (NH(4)Cl), chloroquine, sucrose, and chlorpromazine, which are inhibitors of clathrin-dependent endocytosis. The depletion of cellular cholesterol by methyl-β-cyclodextrin results in the significant inhibition of ISKNV infection; however, the infection is resumed with cholesterol replenishment. Inhibitors of caveolin-1-involved signaling events, including phorbol 12-myristate 13-acetate (PMA), genistein, and wortmannin, impair ISKNV entry into MFF-1 cells. Moreover, ISKNV entry is dependent on dynamin and the microtubule cytoskeleton. Cofraction analysis of ISKNV and caveolin-1 showed that ISKNV colocates with caveolin-1 during virus infection. These results indicate that ISKNV entry into MFF-1 cells proceeds via classical caveola-mediated endocytosis and is dependent on the microtubules that serve as tracks along which motile cavicles may move via a caveola-caveosome-endoplasmic reticulum (ER) pathway. As a fish iridovirus, ISKNV entry into MFF-1 cells is different from the clathrin-mediated endocytosis of frog virus 3 entry into mammalian cells (BHK-21) at 28°C, which has been recognized as a model for iridoviruses. Thus, our work may help further the understanding of the initial steps of iridovirus infection.