Effects of ssDNA sequences on non-sequence-specific protein binding

The circular dichroism (CD) spectra of single-stranded DNAs (ssDNAs) are significantly perturbed by the binding of single-stranded DNA binding proteins such as the Ff bacteriophage gene 5 protein (g5p) and the A domain of the 70 kDa subunit of human replication protein A (RPA70-A). These two proteins have similar OB-fold secondary structures, although their CD spectra at wavelengths below 250 nm differ greatly. The spectrum of g5p is dominated by a tyrosyl L(a) band at 229 nm, while that of RPA70-A is dominated by its beta secondary structure. Despite differences in their inherent spectral properties, these two proteins similarly perturb the spectra of bound nucleic acid oligomers. CD spectra of free, non-protein-bound ssDNAs are dependent on interactions of the nearest-neighboring nucleotides in the sequence. The CD spectra (per mol of nucleotide) of simple repetitive sequences 48 nucleotides in length and containing simple combinations of A and C are related by nearest-neighbor equations. For example, 3 x Deltaepsilon[d(AAC)(16)] = 3 x Deltaepsilon[d(ACC)(16)] + Deltaepsilon[d(A)(48)] - Deltaepsilon[d(C)(48)]. Moreover, nearest-neighbor equations relate the spectra of ssDNAs when they are bound by g5p, indicating that each type of perturbed nearest neighbor has a similar average structure within the binding site of the protein.     

A novel SNP of the <Emphasis Type="Italic">Hesx1</Emphasis> gene in bovine and its associations with average daily gain

As an essential repressor, the homeobox gene Hesx1/HESX1 is required within the anterior neural plate for normal forebrain development. Mutations within the Hesx1 gene have been associated with GH deficiency or combined pituitary hormone deficiency. We detected the polymorphism of Hesx1 gene by PCR-SSCP and DNA sequencing methods in 702 individuals from four Chinese cattle breeds. A novel single nucleotide polymorphism (SNP) (IVS1 + 382T > C) was detected. The frequencies of genotype TC in four breeds were 0.000–0.222. Polymorphism of the Hesx1 gene was shown to be associated with growth in the Nanyang breed. Individuals with genotype TC was significantly lower average daily gain than TT at 18 months (P < 0.05).     

Fluorine-18 labeled galactosyl-neoglycoalbumin for imaging the hepatic asialoglycoprotein receptor

Asialoglycoprotein receptors (ASGP-R) are well known to exist on the mammalian liver, situate on the surface of hepatocyte membrane. Quantitative imaging of asialoglycoprotein receptors could estimate the function of the liver. ^99mTc labeled galactosyl-neoglycoalbumin (NGA) and diethylenetriaminepentaacetic acid galactosyl human serum albumin (GSA) have been developed for SPECT imaging and clinical used in Japan. In this study, we labeled the NGA with ¹⁸F to get a novel PET tracer [¹⁸F]FNGA and evaluated its hepatic-targeting efficacy and pharmacokinetics. Methods: NGA was labeled with ¹⁸F by conjugation with N-succinimidyl-4-¹⁸F-fluorobenzoate ([¹⁸F]SFB) under a slightly basic condition. The in vivo metabolic stability of [¹⁸F]FNGA was determined. Ex vivo biodistribution of [¹⁸F]FNGA and blocking experiment was investigated in normal mice. MicroPET images were acquired in rat with and without block at 5 min and 15 min after injection of the radiotracer (3.7 MBq/rat), respectively. Results: Starting with ¹⁸F⁻ Kryptofix 2.2.2./K₂CO₃ solution, the total reaction time for [¹⁸F]FNGA is about 150 min. Typical decay-corrected radiochemical yield is about 8–10%. After rapid purified with HiTrap desalting column, the radiochemical purity of [¹⁸F]FNGA was more than 99% determined by radio-HPLC. [¹⁸F]FNGA was metabolized to produce [¹⁸F]FB-Lys in urine at 30 min. Ex vivo biodistribution in mice showed that the liver accumulated 79.18 ± 7.17% and 13.85 ± 3.10% of the injected dose per gram at 5 and 30 min after injection, respectively. In addition, the hepatic uptake of [¹⁸F]FNGA was blocked by pre-injecting free NGA as blocking agent (18.55 ± 2.63%ID/g at 5 min pi), indicating the specific binding to ASGP receptor. MicroPET study obtained quality images of rat at 5 and 15 min post-injection. Conclusion: The novel ASGP receptor tracer [¹⁸F]FNGA was synthesized with high radiochemical yield. The promising biological properties of [¹⁸F]FNGA afford potential applications for assessment of hepatocyte function in the future. It may provide quantitative information and better resolution which particularly help to the liver surgery.     

Microbial Community Response to Seawater Amendment in Low-Salinity Tidal Sediments

Rising sea levels and excessive water withdrawals upstream are making previously freshwater coastal ecosystems saline. Plant and animal responses to variation in the freshwater–saline interface have been well studied in the coastal zone; however, microbial community structure and functional response to seawater intrusion remains relatively unexplored. Here, we used molecular approaches to evaluate the response of the prokaryotic community to controlled changes in porewater salinity levels in freshwater sediments from the Altamaha River, Georgia, USA. This work is a companion to a previously published study describing results from an experiment using laboratory flow-through sediment core bioreactors to document biogeochemical changes as porewater salinity was increased from 0 to 10 over 35 days. As reported in Weston et al. (Biogeochemistry, 77:375–408, 62), porewater chemistry was monitored, and cores were sacrificed at 0, 9, 15, and 35 days, at which time we completed terminal restriction fragment length polymorphism and 16S rRNA clone library analyses of sediment microbial communities. The biogeochemical study documented changes in mineralization pathways in response to artificial seawater additions, with a decline in methanogenesis, a transient increase in iron reduction, and finally a dominance of sulfate reduction. Here, we report that, despite these dramatic and significant changes in microbial activity at the biogeochemical level, no significant differences were found between microbial community composition of control vs. seawater-amended treatments for either Bacterial or Archaeal members. Further, taxa in the seawater-amended treatment community did not become more “marine-like” through time. Our experiment suggests that, as seawater intrudes into freshwater sediments, observed changes in metabolic activity and carbon mineralization on the time scale of weeks are driven more by shifts in gene expression and regulation than by changes in the composition of the microbial community.     

Edgetic perturbation models of human inherited disorders

Cellular functions are mediated through complex systems of macromolecules and metabolites linked through biochemical and physical interactions, represented in interactome models as ‘nodes’ and ‘edges’, respectively. Better understanding of genotype‐to‐phenotype relationships in human disease will require modeling of how disease‐causing mutations affect systems or interactome properties. Here we investigate how perturbations of interactome networks may differ between complete loss of gene products (‘node removal’) and interaction‐specific or edge‐specific (‘edgetic’) alterations. Global computational analyses of ～50 000 known causative mutations in human Mendelian disorders revealed clear separations of mutations probably corresponding to those of node removal versus edgetic perturbations. Experimental characterization of mutant alleles in various disorders identified diverse edgetic interaction profiles of mutant proteins, which correlated with distinct structural properties of disease proteins and disease mechanisms. Edgetic perturbations seem to confer distinct functional consequences from node removal because a large fraction of cases in which a single gene is linked to multiple disorders can be modeled by distinguishing edgetic network perturbations. Edgetic network perturbation models might improve both the understanding of dissemination of disease alleles in human populations and the development of molecular therapeutic strategies.     

Formulation of novel lipid-coated magnetic nanoparticles as the probe for in vivo imaging

Background  

Application of superparamagnetic iron oxide nanoparticles (SPIOs) as the contrast agent has improved the quality of magnetic resonance (MR) imaging. Low efficiency of loading the commercially available iron oxide nanoparticles into cells and the cytotoxicity of previously formulated complexes limit their usage as the image probe. Here, we formulated new cationic lipid nanoparticles containing SPIOs feasible for in vivo imaging.     

Fluorine-18 labeled galactosylated chitosan for asialoglycoprotein-receptor-mediated hepatocyte imaging

Galactosylated chitosan (GC) was prepared by reacting lactobionic acid with water-soluble chitosan. GC was labeled with fluorine-18 by conjugation with N-succinimidyl-4-¹⁸F-fluorobenzoate ([¹⁸F]SFB) under a slightly basic condition. After rapid purification with HiTrap desalting column, [¹⁸F]FB-GC was obtained with high radiochemical purity (>97%) determined by radio-HPLC. The total reaction time for [¹⁸F]FB-GC was about 150 min. Typical decay-corrected radiochemical yield was about 4–8%. Ex vivo biodistribution in normal mice showed that [¹⁸F]FB-GC had moderate activity accumulation in liver with very good retention (11.13 ± 1.63, 10.97 ± 1.90 and 10.77 ± 0.95% ID/g at 10, 60, 120 min after injection, respectively). The other tissues except kidney showed relative low radioactivity accumulation. The high liver/background ratio affords promising biological properties to get clear images. The specific binding of this radiotracer to the ASGP receptor was confirmed by blocking experiment in mice. Compared with the non-blocking group the hepatic uptake of [¹⁸F]FB-GC significantly declined in all selected time points. The better liver retention properties of [¹⁸F]FB-GC than that of albumin based imaging agents may improve imaging quality and simplify pharmacokinetic model of liver function in the future application with PET imaging.     

枣疯病植原体tuf和rp基因的克隆与序列分析

【目的】枣疯病是一种重要的植原体病害,本研究旨在明确北京及河北地区枣疯病植原体的分类地位,为枣疯病在亚组水平上分类提供一定的参考依据。【方法】利用植原体通用引物fTufu/rTufu和rp(v)F1A/rp(v)R1A对北京和河北地区枣疯病植原体延伸因子tuf基因和核糖体蛋白基因(rp)进行PCR扩增并进行核苷酸序列测定及相似性分析。【结果】获得北京地区JWB-XFSZ株系、JWB-XFDO株系以及河北地区JWB-TXSZ株系的tuf基因片段均为824 bp;北京地区JWB-XFSZ株系的rp基因片段为1196 bp。经序列相似性比较表明:tuf基因与16SrV组的葡萄黄叶病(Flavescence dorée)相似性最高,为92.84%,而与已经公布的其它地区(陕西杨凌)的枣疯病植原体tuf基因相似性较低,为57.29%;关于rp基因,北京地区枣疯病JWB-XFSZ株系与16SrV组的枣疯病泰山株系(JWB-Taishan)以及大麻丛枝病植原体(HFWB)相似性最高,均为99.83%,与16SrV组的成员相似性均在96%以上。【结论】北京与河北地区枣疯病植原体具有较高的相似性,而在tuf基因水平上,与陕西地区枣疯病植原体具有较大的差异;本研究中北京与河北两地区枣疯病植原体归属于16SrV组。     

Spectroscopic investigation on the toxic interaction of melamine with herring sperm DNA

The toxic interaction of melamine with herring sperm DNA (hs‐DNA) was investigated by using fluorescence and UV–vis absorption spectra techniques. The experimental results showed that the toxic interaction between melamine and hs‐DNA occurred. Fluorescence quenching experiments indicated the existence of electrostatic binding between melamine and hs‐DNA. The binding constants K_A and the binding site numbers were calculated by means of the Stern–Volmer equation and were 9.8 × 10⁴ L mol^?1 and 1.3, respectively. Both the results of fluorescence spectra and UV–vis absorption spectra verified that there are electrostatic binding between melamine and hs‐DNA. The possibility in the presence of a classical intercalation binding mode could be ruled out by using DNA unwinding experiments. © 2010 Wiley Periodicals, Inc. J Biochem Mol Toxicol 24:323–329, 2010; View this article online at wileyonlinelibrary.com . DOI 10.1002/jbt.20341