Extended haplotype analysis of ovine ADRB3 using polymerase chain reaction single strand conformational polymorphism on two regions of the gene

The β3 adrenergic receptor (ADRB3) plays a critical role in the regulation of energy metabolism in mammals. In sheep, intronic polymorphism of the ADRB3 gene has been associated with lamb survival and various production traits. This study investigates variation in the ovine ADRB3 3' untranslated region (3'UTR), a region that may impact expression of the gene. Using PCR- single strand conformational polymorphism (SSCP), six unique patterns (named a-f) were observed in an approximately 304-bp amplicon. Sequencing revealed three single-nucleotide polymorphisms (c.*233A>C, c.*271G>C, c.*357A>T) and a single-nucleotide deletion (c.*257delG). Haplotype analyses showed that the previously described allele A defined by variation in the ovine ADRB3 intron can be divided into three haplotypes (Aa, Ab, and Ac). In total, 16 haplotypes through ovine ADRB3 were detected. This study suggests that ovine ADRB3 is highly polymorphic and that the extended haplotype analysis through the promoter, 5'UTR, coding sequence, intron, and 3'UTR needs to be performed to define the full extent of variation in this gene.     

高效液相荧光法测定大鼠脑内氨基酸类神经递质方法的改良

目的 改良测定大鼠脑组织氨基酸类神经递质的反相高效液相色谱荧光法.方法 改良使用磷酸盐-甲醇-乙腈作为流动相,反相高效液相色谱洗脱,高丝氨酸作为内标,邻苯二甲醛柱前衍生和荧光检测器,检测大鼠大脑皮质、海马、纹状体、中脑、小脑和下丘脑6个脑区中天冬氨酸(Asp)、谷氨酸(Glu)、谷氨酰胺(G1n)、甘氨酸(Gly)、γ-氨基丁酸(GABA)和牛磺酸(Tau)6种氨基酸类神经递质含量.结果 6种氨基酸在20 min内洗脱完全,分离效果良好;在6.25～ 400 μmol/L浓度范围有较好的线性关系,其相关系数不低于0.99;6种氨基酸日内试验精密度范围为1.38％ ～7.59％;日间试验精密度为2.7％～8.68％;6种氨基酸回收率不低于80％.结论 改良后的反相高效液相色谱荧光法灵敏度较高、重复性好,能有效分离检测大鼠脑组织分区中氨基酸类神经递质含量.     

华山新麦草叶片的光合生理特性

对华山新麦草(Psathyrostachys huashanica Keng ex P.C.Kuo)营养叶的净光合速率(Pn)和蒸腾速率(Tr)的日变化曲线进行了分析,并在对叶温(Tl)、气孔阻力(Rs)、光合有效辐射强度(PAR)和气温(Ta)的日变化曲线进行测定的基础上分析了它们对华山新麦草Pn的影响规律。结果表明:华山新麦草Pn的日变化曲线呈"三峰"型,峰值分别为6.5、6.2和9.0μmol.m-2.s-1,依次出现在9:30、11:30和16:30,而且具有明显的"午降"现象;Tr的日变化曲线呈"单峰"型,最大值为1.7 mmol.m-2.s-1,出现在13:30;Tl、Rs、PAR和Ta的日变化曲线均呈"单峰"型,峰值分别出现在12:30、11:30、12:30和13:30。华山新麦草的Pn对Tl、PAR和Ta的响应曲线均呈"抛物线"型,Pn在一定范围内与Tl、PAR和Ta呈正相关,随着Tl、PAR和Ta的升高逐渐增加至最大值后逐渐降低;而Pn与Rs则呈负相关,Pn在一定范围内随Rs的增大逐渐降低。根据拟合方程,华山新麦草营养叶的光补偿点和光饱和点分别为1.1和531.5μmol.m-2.s-1,说明该种类具有很强的喜光性,且对光照强度的适应范围较广。研究结果表明:较大的气孔阻力是造成华山新麦草叶片净光合速率偏低的主要原因。     

Identification and analysis of the gene cluster involved in biosynthesis of paenibactin, a catecholate siderophore produced by Paenibacillus elgii B69

Bacteria belonging to the genus Paenibacillus are recognized as rich sources of bioactive natural products. To date, there are few characterized siderophores from this genus. Here, through genome analysis, we identified a non-ribosomal peptide biosynthetic gene cluster (pae) responsible for siderophore assembly in Paenibacillus elgii B69. The 12.8 kb gene cluster comprises six open reading frames encoding proteins similar to the components of the bacillibactin biosynthetic machinery and bacillibactin esterase. To examine the product of the pae gene cluster, we cultured P. elgii B69 in iron-deficient medium for siderophore expression. A novel siderophore structurally similar to bacillibactin, designated paenibactin, was purified and characterized. Its structure was determined as a cyclic trimeric lactone of 2,3-dihydroxybenzoyl-alanine-threonine. The involvement of the pae gene cluster in paenibactin biosynthesis was confirmed by the biochemical assay of adenylation domain specificity. Furthermore, we demonstrated that the pae gene cluster evolves from an ancestral bacillibactin biosynthetic gene cluster via sequence and phylogenetic analyses. The structural difference between paenibactin and bacillibactin may stem from a mutation-induced change in the adenylation domain specificity. Based on these findings and published models for bacillibactin, we proposed models for paenibactin biosynthesis, ferric-paenibactin uptake and paenibactin-bounded iron release.     

Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception

Background

Human immunodeficiency virus type one (HIV-1) is the major pathogen that causes the acquired immune deficiency syndrome (AIDS). With the availability of large-scale protein-protein interaction (PPI) measurements, comparative network analysis can provide a promising way to study the host-virus interactions and their functional significance in the pathogenesis of AIDS. Until now, there have been a large number of HIV studies based on various animal models. In this paper, we present a novel framework for studying the host-HIV interactions through comparative network analysis across different species.

Results

Based on the proposed framework, we test our hypothesis that HIV-1 attacks essential biological pathways that are conserved across species. We selected the Homo sapiens and Mus musculus PPI networks with the largest coverage among the PPI networks that are available from public databases. By using a local network alignment algorithm based on hidden Markov models (HMMs), we first identified the pathways that are conserved in both networks. Next, we analyzed the HIV-1 susceptibility of these pathways, in comparison with random pathways in the human PPI network. Our analysis shows that the conserved pathways have a significantly higher probability of being intercepted by HIV-1. Furthermore, Gene Ontology (GO) enrichment analysis shows that most of the enriched GO terms are related to signal transduction, which has been conjectured to be one of the major mechanisms targeted by HIV-1 for the takeover of the host cell.

Conclusions

This proof-of-concept study clearly shows that the comparative analysis of PPI networks across different species can provide important insights into the host-HIV interactions and the detailed mechanisms of HIV-1. We expect that comparative multiple network analysis of various species that have different levels of susceptibility to similar lentiviruses may provide a very effective framework for generating novel, and experimentally verifiable hypotheses on the mechanisms of HIV-1. We believe that the proposed framework has the potential to expedite the elucidation of the important mechanisms of HIV-1, and ultimately, the discovery of novel anti-HIV drugs.

     

Identification and evaluation of a panel of serum biomarkers for predicting response to thalidomide in multiple myeloma patients

Evaluation of: Rajpal R, Dowling P, Meiller J et al. A novel panel of protein biomarkers for predicting response to thalidomide-based therapy in newly diagnosed multiple myeloma patients. Proteomics 11(8), 1391-1402 (2011). Predicting response to thalidomide-based therapy remains a challenging task faced by clinicians in the treatment of multiple myeloma. The pioneering work reported by Rajpal et al. moves one step further towards solving this challenge. They developed a proteomics-based approach that combines immunodepletion, 2D-difference gel electrophoresis analysis and mass spectrometry to search for serum proteins with expressions that show significant correlations to thalidomide treatment. This integrated approach allowed them to identify a panel of protein biomarkers. By using ELISA-based validation and strict statistical analysis, the authors have achieved an overall 84.0% predictive accuracy, with associated sensitivity and specificity values of 81.8 and 86.2%, respectively. Their methods and significant findings are reviewed within this article. This panel of biomarkers may not only guide initial therapy, but can also provide direct implications for personalized medicine in multiple myeloma patients.     

Pharmacokinetics, Efficacy, and Safety Evaluation of Docetaxel/Hydroxypropyl-Sulfobutyl-β-Cyclodextrin Inclusion Complex

Hydroxypropyl-sulfobutyl-β-cyclodextrin (HP-SBE-β-CD) inclusion complex was developed and used as a drug delivery system for DTX (DTX/HP-SBE-β-CD). The objective of the present study was to evaluate and compare the biological properties of DTX/HP-SBE-Β-CD with Taxotere®. The pharmacokinetics, biodistribution, antitumor efficacy in vivo and in vitro, and safety evaluation of DTX/HP-SBE-β-CD were studied. The most significant finding was that it was possible to prepare a Polysorbate-80-free inclusion complex for DTX. Studies based on pharmacokinetics, biodistribution, and antitumor efficacy indicated that DTX/HP-SBE-β-CD had similar pharmacokinetic properties and antitumor efficacy both in vitro and in vivo as Taxotere®. Fortunately, this new drug delivery system attenuated the side effects when used in vivo. As a consequence, DTX/HP-SBE-β-CD may be a promising alternative to Taxotere® for cancer chemotherapy treatment with reduced side effects. The therapeutic potential against a variety of human tumors and low toxicity demonstrated in a stringent study clearly warrant clinical investigation of DTX/HP-SBE-β-CD for possible use against human tumors.Key words: antitumor efficacy, biodistribution, DTX/HP-SBE-β-CD, pharmacokinetics, safety evaluation     

Investigation of aggregation and assembly of alkali lignin using iodine as a probe

Molecular iodine has been introduced into the alkali lignin (AL) solutions to adjust the π-π aggregation, and the effect of lignin-iodine complexes on the aggregation and assembly characteristics of AL have been investigated by using fluorescence, UV-vis spectroscopy, light scattering, and viscometric techniques. Results show that AL form π-π aggregates (i.e., J-aggregates) in THF driven by the π-π interaction of the aromatic groups in AL, and the π-π aggregates undergo disaggregation in THF-I(2) media because of the formation of lignin-iodine charge-transfer complexes. By using iodine as a probe to investigate the aggregation behaviors and assembly characteristics, it is estimated that about 18 mol % aromatic groups of AL form π-π aggregates in AL molecular aggregates. When molecular iodine is introduced into the AL solutions, lignin-iodine complexes occur with charge-transfer transition from HOMO of the aromatic groups of AL to the LUMO of iodine. The formation of lignin-iodine complexes reduces the affinity of the aromatic groups approaching each other due to the electrostatic repulsion and then eliminates the π-π interaction of the aromatic groups. The disaggregation of the π-π aggregates brings a dissociation behavior of AL chains and a pronounced molecular expansion. This dissociation behavior and molecular expansion of AL in the dipping solutions induce a decrease in the adsorbed amount and an increase in the adsorption rate, when AL is transferred from the dipping solution to the self-assembled adsorbed films. Consequently, the adsorption behavior of AL can be controlled by adjusting the π-π aggregation. Above observations give insight into the occurrence of J-aggregation of the aromatic groups in the AL molecular aggregates and the disaggregation mechanism of AL aggregates induced by the lignin-iodine complexes for the first time. The understanding can provide an academic instruction in the efficient utilization of the alkali lignin from the waste liquor and also leads to further development in expanding functionalities of the aromatic compounds through manipulation of the π-π aggregation.     

DeltAMT: a statistical algorithm for fast detection of protein modifications from LC-MS/MS data

Identification of proteins and their modifications via liquid chromatography-tandem mass spectrometry is an important task for the field of proteomics. However, because of the complexity of tandem mass spectra, the majority of the spectra cannot be identified. The presence of unanticipated protein modifications is among the major reasons for the low spectral identification rate. The conventional database search approach to protein identification has inherent difficulties in comprehensive detection of protein modifications. In recent years, increasing efforts have been devoted to developing unrestrictive approaches to modification identification, but they often suffer from their lack of speed. This paper presents a statistical algorithm named DeltAMT (Delta Accurate Mass and Time) for fast detection of abundant protein modifications from tandem mass spectra with high-accuracy precursor masses. The algorithm is based on the fact that the modified and unmodified versions of a peptide are usually present simultaneously in a sample and their spectra are correlated with each other in precursor masses and retention times. By representing each pair of spectra as a delta mass and time vector, bivariate Gaussian mixture models are used to detect modification-related spectral pairs. Unlike previous approaches to unrestrictive modification identification that mainly rely upon the fragment information and the mass dimension in liquid chromatography-tandem mass spectrometry, the proposed algorithm makes the most of precursor information. Thus, it is highly efficient while being accurate and sensitive. On two published data sets, the algorithm effectively detected various modifications and other interesting events, yielding deep insights into the data. Based on these discoveries, the spectral identification rates were significantly increased and many modified peptides were identified.     

MtDNA haplogroups M7 and B in southwestern Han Chinese at risk for acute mountain sickness

We conducted a case-control study to investigate the association of mitochondrial DNA (mtDNA) haplogroups with acute mountain sickness (AMS) in Han Chinese from southwestern (SW) China. Pearson's chi-square test or Fisher's exact test revealed significant reduction of mtDNA haplogroups D and M9, while a significant increase of haplogroup M7 in AMS subjects compared with non-AMS subjects. The multivariate logistic regression analysis after adjustment for body mass index (BMI), a risk factor of AMS in the present study, showed that both D and M9 were associated with significantly decreased risk of AMS, while M7 was associated with a significantly increased risk of AMS (OR=0.605, p=0.000; OR=0.037, p=0.001, and OR=2.419, p=0.001, respectively). In addition, further analysis stratified by the AMS severities indicated that haplogroup B was correlated with a 2.41-folds increased risk of developing severe AMS (95%C.I=1.288-4.514, p=0.006). Our findings provide evidence that, in SW Han Chinese, mtDNA haplogroups D and M9 are related to individual tolerance to AMS, while haplogroups M7 and B are risk factors for AMS.