NEDD8 Ultimate Buster-1 Long (NUB1L) Protein Promotes Transfer of NEDD8 to Proteasome for Degradation through the P97UFD1/NPL4 Complex

The NEDD8 protein and neddylation levels in cells are modulated by NUB1L or NUB1 through proteasomal degradation, but the underlying molecular mechanism is not well understood. Here, we report that NUB1L down-regulated the protein levels of NEDD8 and neddylation through specifically recognizing NEDD8 and P97/VCP. NUB1L directly interacted with NEDD8, but not with ubiquitin, on the key residue Asn-51 of NEDD8 and with P97/VCP on its positively charged VCP binding motif. In coordination with the P97-UFD1-NPL4 complex (P97^UFD1/NPL4), NUB1L promotes transfer of NEDD8 to proteasome for degradation. This mechanism is also exemplified by the canonical neddylation of cullin 1 for SCF (SKP1-cullin1-F-box) ubiquitin E3 ligases that is exquisitely regulated by the turnover of NEDD8.     

The extent of clonality and genetic diversity in the rare Caldesia grandis (Alismataceae): Comparative results for RAPD and ISSR markers

Genetic variation and clonal diversity of three natural populations of the rare, highly clonal marsh herb Caldesia grandis Samuelsson were investigated using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. Both of the markers worked effectively in clone identification of C. grandis. RAPD markers detected more diversity than ISSR markers in the three populations examined. Of the 60 RAPD primers screened, seven produced highly reproducible bands. Using these primers, a total of 61 DNA fragments were generated with 52 (85.25%) being polymorphic indicating considerable genetic variation at the species level. Analysis of molecular variance (AMOVA) showed that a large proportion of genetic variation (81.5%) resided within populations, while only a small proportion (18.5%) resided among populations. With the use of 52 polymorphic RAPD markers, we were able to identify 127 genets among 342 samples from three populations. The proportion of distinguishable genets (PD: mean 0.37), Simpson's diversity index (D: mean 0.91), and evenness (E: mean 0.78) exhibited high levels of clonal diversity compared to other clonal plants. These results imply that sexual reproduction has played an important role at some time during the history of these populations. Nevertheless, the high level of diversity could have been also partially generated from somatic mutations, although this is unlikely to account for the high diversity generally found among C. grandis genets.     

Distinguishing three subtypes of hematopoietic cells based on gene expression profiles using a support vector machine

Hematopoiesis is a complicated process involving a series of biological sub-processes that lead to the formation of various blood components. A widely accepted model of early hematopoiesis proceeds from long-term hematopoietic stem cells (LT-HSCs) to multipotent progenitors (MPPs) and then to lineage-committed progenitors. However, the molecular mechanisms of early hematopoiesis have not been fully characterized. In this study, we applied a computational strategy to identify the gene expression signatures distinguishing three types of closely related hematopoietic cells collected in recent studies: (1) hematopoietic stem cell/multipotent progenitor cells; (2) LT-HSCs; and (3) hematopoietic progenitor cells. Each cell in these cell types was represented by its gene expression profile among a total number of 20,475 genes. The expression features were analyzed by a Monte-Carlo Feature Selection (MCFS) method, resulting in a feature list. Then, the incremental feature selection (IFS) and a support vector machine (SVM) optimized with a sequential minimum optimization (SMO) algorithm were employed to access the optimal classifier with the highest Matthews correlation coefficient (MCC) value of 0.889, in which 6698 features were used to represent cells. In addition, through an updated program of MCFS method, seventeen decision rules can be obtained, which can classify the three cell types with an overall accuracy of 0.812. Using a literature review, both the rules and the top features used for building the optimal classifier were confirmed to be commonly used or potential biological markers for distinguishing the three cell types of HSPCs. This article is part of a Special Issue entitled: Accelerating Precision Medicine through Genetic and Genomic Big Data Analysis edited by Yudong Cai & Tao Huang.     

Functional modularity of the beta-subunit of voltage-gated Ca2+ channels

The beta-subunit of voltage-gated Ca(2+) channels plays a dual role in chaperoning the channels to the plasma membrane and modulating their gating. It contains five distinct modular domains/regions, including the variable N- and C-terminus, a conserved Src homology 3 (SH3) domain, a conserved guanylate kinase (GK) domain, and a connecting variable and flexible HOOK region. Recent crystallographic studies revealed a highly conserved interaction between the GK domain and alpha interaction domain (AID), the high-affinity binding site in the pore-forming alpha(1) subunit. Here we show that the AID-GK domain interaction is necessary for beta-subunit-stimulated Ca(2+) channel surface expression and that the GK domain alone can carry out this function. We also examined the role of each region of all four beta-subunit subfamilies in modulating P/Q-type Ca(2+) channel gating and demonstrate that the beta-subunit functions modularly. Our results support a model that the conserved AID-GK domain interaction anchors the beta-subunit to the alpha(1) subunit, enabling alpha(1)-beta pair-specific low-affinity interactions involving the N-terminus and the HOOK region, which confer on each of the four beta-subunit subfamilies its distinctive modulatory properties.     

两种常见海水鱼高温贮存过程中挥发性盐基氮和生物胺含量变化

棘头梅童鱼(Collichthys lucidus)和龙头鱼(Harpodon nehereus)是我国沿海常见的两种小型海水鱼, 常被作为水产动物饵料, 也可被人类食用。研究检测了这两种鱼在30℃下贮存48h 每隔6h 的挥发性盐基氮(T-VBN)和9 种生物胺(尸胺、腐胺、组胺、酪胺、5-羟色胺、亚精胺、精胺、多巴胺、章鱼胺)的含量变化, 并对这两种鱼的T-VBN 和生物胺含量与时间的相关性进行分析, 为水产品类饵料安全投喂和人类食品安全提供基础资料。结果表明: 两种鱼在相同贮存条件中T-VBN 和生物胺含量均存在一定差异。T-VBN 含量随着贮存时间的延长而逐渐增加, 棘头梅童鱼T-VBN 含量从0h 的8.19 mg/100 g 增加到48h 的568.05 mg/100 g,龙头鱼从0h 的13.16 mg/100 g 增加到48h 的361.34 mg/100 g, 棘头梅童鱼增长值显著高于龙头鱼(PPPP>0.05);多巴胺在两种鱼体内均未检测到。这两种鱼体内T-VBN、腐胺、尸胺、组胺、酪胺含量与时间的相关性均极其显著(P<0.01)。       

被孢霉△~9脂肪酸脱饱和酶基因保守区的cDNA克隆及结构分析

被孢霉被广泛采用用于发酵生产γ-亚麻酸、花生四烯酸和EPA等多不饱和脂肪酸。为了解决发酵产率过低等诸多问题,我们拟采用基因工程技术改造生产菌株。通过对已克隆△~9脂肪酸脱饱和酶基因的分析,合成一组简并引物,PCR扩增了被饱霉△9脂肪酸脱饱和酶基因的保守区。结果表明被抱霉△9脂肪酸脱饱和酶基因保守区由537个核苷酸组成,共编码179个氨基酸。其与迄今为止发表的微生物面△9脂肪酸脱饱和酶基因有很高的同源性。这是被饱霉△~9脂肪酸脱饱和酶基因研究的次次报道。     

Site-directed Mutagenesis Shows the Significance of Interactions with Phospholipids and the G-protein OsYchF1 for the Physiological Functions of the Rice GTPase-activating Protein 1 (OsGAP1)

The C2 domain is one of the most diverse phospholipid-binding domains mediating cellular signaling. One group of C2-domain proteins are plant-specific and are characterized by their small sizes and simple structures. We have previously reported that a member of this group, OsGAP1, is able to alleviate salt stress and stimulate defense responses, and bind to both phospholipids and an unconventional G-protein, OsYchF1. Here we solved the crystal structure of OsGAP1 to a resolution of 1.63 Å. Using site-directed mutagenesis, we successfully differentiated between the clusters of surface residues that are required for binding to phospholipids versus OsYchF1, which, in turn, is critical for its role in stimulating defense responses. On the other hand, the ability to alleviate salt stress by OsGAP1 is dependent only on its ability to bind OsYchF1 and is independent of its phospholipid-binding activity.     

A fluorescence assay for elucidating the substrate specificities of deubiquitinating enzymes

Ubiquitin C-terminal hydrolases (UCHs) are a representative family of deubiquitinating enzymes (DUBs), which specifically cleave ubiquitin (Ub) chains or extensions. Here we present a convenient method for characterizing the substrate specificities of various UCHs by fluorescently mutated Ub-fusion proteins (Ub(F45W)-Xaa) and di-ubiquitin chains (Ub(F45W)-diUb). After removal of the intact substrate by Ni(2+)-NTA affinity, the enzymatic activities of UCHs were quantitatively determined by recording fluorescence of the Ub(F45W) product. The results show that three UCHs, i.e. UCH-L1, UCH-L3 and UCH37/UCH-L5, are distinct in their substrate specificities for the Ub-fusions and diUb chains. This assay method may also be applied to study the enzymatic activities and substrate specificities of other DUBs.     

Serum S100β is a Better Biomarker than Neuron-Specific Enolase for Sepsis-Associated Encephalopathy and Determining Its Prognosis: A Prospective and Observational Study

S100β and neuron-specific enolase (NSE) are brain injury biomarkers, mainly used in brain trauma, cerebral stroke and hypoxic ischemia encephalopathy. The aim of this study was to study the clinical significance of serum S100β and NSE in diagnosing sepsis-associated encephalopathy (SAE) and predicting its prognosis. This was a prospective and observational study. Clinical data of septic patients were collected within 24 h after ICU admission from May 2012 to April 2013. We evaluated the level of consciousness twice per day. SAE was defined as cerebral dysfunction in the presence of sepsis that fulfilled the exclusion criteria. The infection biochemical indicators, Glasgow coma scale (GCS) score, acute physiology and chronic health evaluation score II, serum NSE and S100β were newly measured or evaluated for SAE patients. Finally, hospital mortality, bacteriological categories, length of ICU stay and length of hospital stay were also recorded for all enrolled patients. The data was analyzed with the Chi square test, two-sample t test or Mann–Whitney U test between two groups. The correlation between two factors was analyzed using the Pearson or Spearman analysis. Receiver operating characteristic (ROC) curves were used to determine the ability of S100β and NSE in diagnosing SAE and predicting the hospital mortality. In addition, cut-off points were obtained from the curves to determine the highest sum of sensitivity and specificity. Of 112 enrolled patients, 48 patients were diagnosed with SAE. The serum S100β and NSE concentrations in SAE patients were both significantly higher than in non-SAE patients 0.306 (IQR 0.157–0.880) μg/L vs. 0.095 (IQR 0.066–0.177) μg/L, 24.87 (IQR 31.73–12.73) ng/mL vs. 15.49 (IQR 9.88–21.46) ng/mL, P < 0.01]. GCS scores were related more closely to S100β than NSE (?0.595 vs. ?0.337). S100β levels of 0.131 μg/L diagnosed SAE with 67.2 % specificity and 85.4 % sensitivity in the ROC curve, the area under the curve was 0.824 (95 % confidence interval 0.750–0.898). NSE levels of 24.15 ng/mL diagnosed SAE with 82.8 % specificity and 54.2 % sensitivity, and the area under the curve was 0.664 (95 % confidence interval 0.561–0.767). In addition, the area under the curve for S100β for predicting hospital mortality was larger than for NSE (0.730 vs. 0.590). Serum S100β concentrations in SAE patients were significantly higher than in non-SAE patients. These may be related to the severity of SAE and may predict the outcome of sepsis. The efficacy and sensitivity of serum S100β in diagnosing SAE were high, but it had a low specificity. Moreover, compared to NSE, serum S100β was better for both diagnosing SAE and predicting the outcome of sepsis.