Effect of inositol hexakisphosphate kinase 2 on transforming growth factor beta-activated kinase 1 and NF-kappaB activation

We previously showed that inositol hexakisphosphate kinase 2 (IHPK2) functions as a growth-suppressive and apoptosis-enhancing kinase during cell stress. Overexpression of IHPK2 sensitized ovarian carcinoma cell lines to the growth-suppressive and apoptotic effects of interferon beta (IFN-beta), IFN-alpha2, and gamma-irradiation. Expression of a kinase-dead mutant abrogated 50% of the apoptosis induced by IFN-beta. Because the kinase-dead mutant retained significant response to cell stressors, we hypothesized that a portion of the death-promoting function of IHPK2 was independent of its kinase activity. We now demonstrate that IHPK2 binds to tumor necrosis factor (TNF) receptor-associated factor (TRAF) 2 and interferes with phosphorylation of transforming growth factor beta-activated kinase 1 (TAK1), thereby inhibiting NF-kappaB signaling. IHPK2 contains two sites required for TRAF2 binding, Ser-347 and Ser-359. Compared with wild type IHPK2-transfected cells, cells expressing S347A and S359A mutations displayed 3.5-fold greater TAK1 activation following TNF-alpha. This mutant demonstrated a 6-10-fold increase in NF-kappaB DNA binding following TNF-alpha compared with wild type IHPK2-expressing cells in which NF-kappaB DNA binding was inhibited. Cells transfected with wild type IHPK2 or IHPK2 mutants that lacked S347A and S359A mutations displayed enhanced terminal deoxynucleotidyltransferase-mediated dUTP nick end-labeling staining following TNF-alpha. We believe that IHPK2-TRAF2 binding leads to attenuation of TAK1- and NF-kappaB-mediated signaling and is partially responsible for the apoptotic activity of IHPK2.     

Synthesis of cationic single-isomer cyclodextrins for the chiral separation of amino acids and anionic pharmaceuticals

We describe a protocol for the synthesis of mono-6(A)-(1-butyl-3-imidazolium)-6(A)-deoxy-beta-cyclodextrin chloride (BIMCD), a cationic, water-soluble cyclodextrin used in the chiral separation of amino acids and anionic pharmaceuticals by capillary electrophoresis. Starting from commercially available chemicals, BIMCD is synthesized in five steps. The first step involves a nucleophilic substitution between p-toluenesulfonyl chloride and imidazole to afford 1-(p-toluenesulfonyl)imidazole (A). In the second step, a nucleophilic substitution between beta-cyclodextrin and A affords mono-6(A)-(p-toluenesulfonyl)-6(A)-deoxy-beta-cyclodextrin (B). In the third step, a nucleophilic substitution between 1-bromobutane and imidazole affords 1-butylimidazole (C). In the fourth step, a nucleophilic addition between A and C affords BIMCD tosylate. In the final step, anion exchange using an ion-exchange resin yields BIMCD as a highly water-soluble solid. Each step takes up to 2 d, including the time required for product purification. The overall protocol requires approximately 6 d.     

True phosphorus digestibility and the endogenous phosphorus outputs associated with brown rice for weanling pigs measured by the simple linear regression analysis technique

The objectives of this study were to determine true phosphorus (P) digestibility, degradability of phytate-P complex and the endogenous P outputs associated with brown rice feeding in weanling pigs by using the simple linear regression analysis technique. Six barrows with an average initial body weight of 12.5 kg were fitted with a T-cannula and fed six diets according to a 6 × 6 Latin-square design. Six maize starch-based diets, containing six levels of P at 0.80, 1.36, 1.93, 2.49, 3.04, and 3.61 g/kg per kg dry-matter (DM) intake (DMI), were formulated with brown rice. Each experimental period lasted 10 days. After a 7-day adaptation, all faecal samples were collected on days 8 and 9. Ileal digesta samples were collected for a total of 24 h on day 10. The apparent ileal and faecal P digestibility values of brown rice were affected ( P < 0.01) by the P contents in the assay diets. The apparent ileal and faecal P digestibility values increased from − 48.0 to 36.7% and from − 35.6 to 40.0%, respectively, as P content increased from 0.80 to 3.61 g/kg DMI. Linear relationships ( P < 0.05), expressed as g/kg DMI, between the apparent ileal and faecal digestible P and dietary levels of P, suggested that true P digestibility and the endogenous P outputs associated with brown rice feeding could be determined by using the simple regression analysis technique. There were no differences ( P>0.05) in true P digestibility values (57.7 ± 5.4 v. 58.2 ± 5.9%), phytate P degradability (76.4 ± 6.7 v. 79.0 ± 4.4%) and the endogenous P outputs (0.812 ± 0..096 v. 0.725 ± 0.083 g/kg DMI) between the ileal and the faecal levels. The endogenous faecal P output represented 14 and 25% of the National Research Council (1998) recommended daily total and available P requirements in the weanling pig, respectively. About 58% of the total P in brown rice could be digested and absorbed by the weanling pig. Our results suggest that the large intestine of the weanling pigs does not play a significant role in the digestion of P in brown rice. Diet formulation on the basis of total or apparent P digestibility with brown rice may lead to P overfeeding and excessive P excretion in pigs.     

Spatial scale dependence of the species diversityin Tianmu Mountain and its relationship with spatial patterns by using multifractal analysis

This study took the Tianmu Mountain National Natural Preservation Area in western Zhejiang Province as an example 1) to quantify the species diversity with selected species indices including Shannon-Wiener index (H), Margalef index (K) and Evenness index (E) at different spatial scales, 2) to analyze the spatial distribution patterns of the species diversity by multifractal parameters such as the singularity index α, its fractal dimension f(α), the f(α)–α spectrum range (SR) and its symmetry (Dist) using the multifractal theory, and 3) to determine their relationships. Results of nonlinear regression analysis with power functions showed that increasing spatial scale resulted in increasing H but decreasing E and K, indicating that the scale dependence of species diversity existed. By using the multifractal method, it was indicated that species spatial distribution had multifractal features. Moreover, strong linear relationships of the diversity indices H, E and K with α_min and clear nonlinear associations of the diversity indices H, E and K with power functions for SR and Dist were found. Since interactions of the species diversity and the spatial characteristics are very complex, the above mentioned relationships need further validation along with precise explanations of any correlations among their ecological processes.     

The temperature-sensitive role of Cryptococcus neoformans ROM2 in cell morphogenesis

ROM2 is associated with Cryptococcus neoformans virulence. We examined additional roles of ROM2 in C. neoformans and found that ROM2 plays a role in several cell functions specifically at high temperature conditions. Morphologically rom2 mutant cells demonstrated a "tear"-like shape and clustered together. A sub-population of cells had a hyperelongated phenotype at restrictive growth conditions. Altered morphology was associated with defects in actin that was concentrated at the cell periphery and with abnormalities in microtubule organization. Interestingly, the ROM2 associated defects in cell morphology, location of nuclei, and actin and microtubule organization were not observed in cells grown at temperatures below 37 degrees C. These results indicate that in C. neoformans, ROM2 is important at restrictive temperature conditions and is involved in several cell maintenance functions.     

Whole-genome sequencing and assembly with high-throughput, short-read technologies

While recently developed short-read sequencing technologies may dramatically reduce the sequencing cost and eventually achieve the $1000 goal for re-sequencing, their limitations prevent the de novo sequencing of eukaryotic genomes with the standard shotgun sequencing protocol. We present SHRAP (SHort Read Assembly Protocol), a sequencing protocol and assembly methodology that utilizes high-throughput short-read technologies. We describe a variation on hierarchical sequencing with two crucial differences: (1) we select a clone library from the genome randomly rather than as a tiling path and (2) we sample clones from the genome at high coverage and reads from the clones at low coverage. We assume that 200 bp read lengths with a 1% error rate and inexpensive random fragment cloning on whole mammalian genomes is feasible. Our assembly methodology is based on first ordering the clones and subsequently performing read assembly in three stages: (1) local assemblies of regions significantly smaller than a clone size, (2) clone-sized assemblies of the results of stage 1, and (3) chromosome-sized assemblies. By aggressively localizing the assembly problem during the first stage, our method succeeds in assembling short, unpaired reads sampled from repetitive genomes. We tested our assembler using simulated reads from D. melanogaster and human chromosomes 1, 11, and 21, and produced assemblies with large sets of contiguous sequence and a misassembly rate comparable to other draft assemblies. Tested on D. melanogaster and the entire human genome, our clone-ordering method produces accurate maps, thereby localizing fragment assembly and enabling the parallelization of the subsequent steps of our pipeline. Thus, we have demonstrated that truly inexpensive de novo sequencing of mammalian genomes will soon be possible with high-throughput, short-read technologies using our methodology.     

Waist circumference and BMI cut-off based on 10-year cardiovascular risk: evidence for "central pre-obesity"

Objective: The objective was to assess the waist circumference (WC) cut‐off point that best identifies a level of 10‐year cardiovascular disease (CVD) risk with optimal balance of sensitivity and specificity in Chinese subjects according to their predicted 10‐year CVD risk. Research Methods and Procedures: A community‐based cross‐sectional observational study involving 14,919 Hong Kong Chinese subjects. The 10‐year CVD risk based on various prediction models was calculated. The projected WC cut‐off points were then determined. Results: There were 4837 (32.4%) men and 10,082 (67.6%) women (mean age ± standard deviation, 47.3 ± 13.5 years; age range, 18 to 93 years; median age, 45.0 years). The mean optimal WC or BMI predicting a 15% to 30% 10‐year CVD risk were 83 to 88 cm and 25 kg/m² for men, and 76 cm and 23 kg/m² for women, respectively. With WC ≥90 cm in men and ≥80 cm in women, the likelihood ratio at various WC cut‐off points to develop a ≥20% 10‐year CVD risk is 1.5 to 2.0 in men and 3.0 in women. The likelihood ratio was 1.5 in men with WC at 84 cm and in women at 70 cm. Discussion: Our results agree with the present guidelines on the definition of general and central obesity in Asia‐Pacific regions. We propose the creation of an intermediate state of high WC, the “central pre‐obesity” for Chinese men with WC ≥84 to 90 cm (≥33 to 36 inches) and women with WC ≥74 to 80 cm (≥29 to 32 inches). People with central pre‐obesity, similar to those with overweight (BMI ≥23 to 25 kg/m²), already have an increased risk of co‐morbidities.     

Sexually dimorphic SCAMP1 expression in the forebrain motor pathway for song production of juvenile zebra finches

Mechanisms regulating sexual differentiation of the zebra finch song system are not well understood. The present study was designed to more fully characterize secretory carrier membrane protein 1 (SCAMP1), which was identified in a cDNA microarray screen as showing increased expression in the forebrains of developing male compared with female zebra finches. We completed the sequence of the open reading frame and used in situ hybridization to compare mRNA in song control regions of juvenile (25-day-old) individuals. Expression was significantly greater in the HVC (used as a proper name) and robust nucleus of the arcopallium (RA) in males than in females. Immunohistochemistry revealed that SCAMP1 protein is also expressed in these two brain regions, and qualitatively appears greater in males. Western analysis confirmed that the protein is increased in the telencephalon of males when compared with females at 25 days of age. These results are consistent with the idea that SCAMP1 is involved in masculinization of these brain areas, perhaps facilitating the survival of cells within them.     

Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A

Optimization of a serotype-selective, small-molecule inhibitor of botulinum neurotoxin serotype A (BoNTA) endopeptidase is a formidable challenge because the enzyme-substrate interface is unusually large and the endopeptidase itself is a large, zinc-binding protein with a complex fold that is difficult to simulate computationally. We conducted multiple molecular dynamics simulations of the endopeptidase in complex with a previously described inhibitor (K(i) (app) of 7+/-2.4 microM) using the cationic dummy atom approach. Based on our computational results, we hypothesized that introducing a hydroxyl group to the inhibitor could improve its potency. Synthesis and testing of the hydroxyl-containing analog as a BoNTA endopeptidase inhibitor showed a twofold improvement in inhibitory potency (K(i) (app) of 3.8+/-0.8 microM) with a relatively small increase in molecular weight (16 Da). The results offer an improved template for further optimization of BoNTA endopeptidase inhibitors and demonstrate the effectiveness of the cationic dummy atom approach in the design and optimization of zinc protease inhibitors.     

Validation of Zebrafish （Danio redo） Reference Genes for Quantitative Real-time RT-PCR Normalization

The normalization of quantitative real time RT-PCR （qRT-PCR） is important to obtain accurate gene expression data. The most common method for qRT-PCR normalization is to use reference, or housekeeping genes. However, there is emerging evidence that even reference genes can be regulated under different conditions, qRT-PCR has only recently been used in terms of zebrafish gene expression studies and there is no validated set of reference genes. This study characterizes the expression of nine possible reference genes during zebrafish embryonic development and in a zebrafish tissue panel. All nine reference genes exhibited variable expression. The fl-actin, EFlot and Rpll3ot genes comprise a validated reference gene panel for zebrafish developmental time course studies, and the EF1 or, Rpll3α and 18S rRNA genes are more suitable as a reference gene panel for zebrafish tissue analysis. Importantly, the zebrafish GAPDH gene appears unsuitable as reference gene for both types of studies.