ITMSQ: A software tool for N‐ and C‐terminal fragment ion pairs based isobaric tandem mass spectrometry quantification

Tandem MS (MS2) quantification using the series of N‐ and C‐terminal fragment ion pairs generated from isobaric‐labelled peptides was recently considered an accurate strategy in quantitative proteomics. However, the presence of multiplexed terminal fragment ion in MS2 spectra may reduce the efficiency of peptide identification, resulting in lower identification scores or even incorrect assignments. To address this issue, we developed a quantitative software tool, denoted isobaric tandem MS quantification (ITMSQ), to improve N‐ and C‐terminal fragment ion pairs based isobaric MS2 quantification. A spectrum splitting module was designed to separate the MS2 spectra from different samples, increasing the accuracy of both identification and quantification. ITMSQ offers a convenient interface through which parameters can be changed along with the labelling method, and the result files and all of the intermediate files can be exported. We performed an analysis of in vivo terminal amino acid labelling labelled HeLa samples and found that the numbers of quantified proteins and peptides increased by 13.64 and 27.52% after spectrum splitting, respectively. In conclusion, ITMSQ provides an accurate and reliable quantitative solutionfor N‐ and C‐terminal fragment ion pairs based isobaric MS2 quantitative methods.     

镉离子诱导BA/F3β细胞发生奇特的细胞凋亡

细胞凋亡一般都伴随有ＤＮＡ 片段化, 活性氧含量增加, 并能被过量的Ｂｃｌ２ 所抑制。以ＢＡ／Ｆ３β细胞为模型, 利用ＭＴＴ 检测、Ｈｏｃｈｅｓｔ 染色以及透射电镜检测等技术却发现, 镉离子虽然可以诱导该细胞凋亡, 但是这种凋亡没有ＤＮＡ 片段化, 也没有活性氧含量增加。此外, 过量Ｂｃｌ２ 对这种凋亡也没有保护作用。因此, 可以确认镉离子诱导ＢＡ／Ｆ３β细胞发生了奇特的细胞凋亡。     

Mitochondrial dysfunction in platelets and hippocampi of senescence-accelerated mice

Senescence-accelerated mice (SAM) strains are useful models to understand the mechanisms of age-dependent degeneration. In this study, measurements of the mitochondrial membrane potential (Δψ_m) of platelets and the Adenosine 5^′-triphosphate (ATP) content of hippocampi and platelets were made, and platelet mitochondria were observed in SAMP8 (faster aging mice) and SAMR1 (aging resistant control mice) at 2, 6 and 9 months of age. In addition, an Aβ-induced (Amyloid beta-protein) damage model of platelets was established. After the addition of Aβ, the Δψ_m of platelets of SAMP8 at 1and 6 months of age were measured. We found that platelet Δψ_m, and hippocampal and platelet ATP content of SAMP8 mice decreased at a relatively early age compared with SAMR1. The platelets of 6 month-old SAMP8 showed a tolerance to Aβ-induced damages. These results suggest that mitochondrial dysfunction might be one of the mechanisms leading to age-associated degeneration in SAMP mice at an early age and the platelets could serve as a biomarker for detection of mitochondrial function and age related disease.     

The role of estrogen receptor-beta, in the early age-related bone gain and later age-related bone loss in female mice

The molecular and cellular mechanism of estrogen action in skeletal tissue remains unclear. The purpose of this study was to understand the role of estrogen receptor-beta, (ERbeta) on cortical and cancellous bone during growth and aging by comparing the bone phenotype of 6- and 13-month-old female mice with or without ERbeta. Groups of 11-14 wild-type (WT) controls and ERbeta knockout (BERKO) female mice were necropsied at 6 and 13 months of age. At both ages, BERKO mice did not differ significantly from WT controls in uterine weight and uterine epithelial thickness, indicating that ERbeta does not regulate the growth of uterine tissue. Femoral length increased significantly by 5.5% at 6 months of age in BERKO mice compared with WT controls. At 6 months of age, peripheral quantitative computerized tomography (pQCT) analysis of the distal femoral metaphysis (DFM) and femoral shafts showed that BERKO mice had significantly higher cortical bone content and periosteal circumference as compared with WT controls at both sites. In contrast to the findings in cortical bone, at 6 months of age, there was no difference between BERKO and WT mice in trabecular density, trabecular bone volume (TBV), or formation and resorption indices at the DFM. In 13-month-old WT mice, TBV (-41%), trabecular density (-27%) and cortical thickness decreased significantly. while marrow cavity and endocortical circumference increased significantly compared with 6-month-old WT mice. These age-related decreases in cancellous and endocortical bone did not occur in BERKO mice. At 13 months of age, BERKO mice had significantly higher total, trabecular and cortical bone, while having significantly lower bone resorption, bone formation and bone turnover in DFM compared with WT mice. These results indicate that deleting ERbeta protected against age-related bone loss in both the cancellous and endocortical compartments by decreasing bone resorption and bone turnover in aged female mice. These data demonstrate that in female mice, ERbeta plays a role in inhibiting periosteal bone formation, longitudinal and radial bone growth during the growth period, while it plays a role in stimulating bone resorption, bone turnover and bone loss on cancellous and endocortical bone surfaces during the aging process.     

Expression Profiling and Validation of Potential Reference Genes During <Emphasis Type="Italic">Paralichthys olivaceus</Emphasis> Embryogenesis

Differential expression of genes is crucial to embryogenesis. The analysis of gene expression requires appropriate references that should be minimally regulated during the embryonic development. To select the most stable genes for gene normalization, the expression profiles of eight commonly used reference genes (ACTB, GAPDH, rpL17, α-Tub, EF1-α, UbcE, B2M, and 18S rRNA) were examined during Japanese flounder (Paralichthys olivaceus) embryonic development using quantitative real-time polymerase chain reaction. It was found that all seven mRNA genes appeared to be developmentally regulated and exhibited significant variation of expression. However, further analyses revealed the stage-specific expression stability. Hence when normalization using these mRNA genes, the differential and stage-related expression should be considered. 18S rRNA gene, on the other hand, showed the most stable expression and could be recommended as a suitable reference gene during all embryonic developmental stages in P. olivaceus. In summary, our results provided not only the appropriate reference gene for embryonic development research in P. olivaceus, but also possible guidance to reference gene selection for embryonic gene expression analyses in other fish species.     

Climate‐driven speedup of alpine treeline forest growth in the Tianshan Mountains,Northwestern China

Forest growth is sensitive to interannual climatic change in the alpine treeline ecotone (ATE). Whether the alpine treeline ecotone shares a similar pattern of forest growth with lower elevational closed forest belt (CFB) under changing climate remains unclear. Here, we reported an unprecedented acceleration of Picea schrenkiana forest growth since 1960s in the ATE of Tianshan Mountains, northwestern China by a stand‐total sampling along six altitudinal transects with three plots in each transect: one from the ATE between the treeline and the forest line, and the other two from the CFB. All the sampled P. schrenkiana forest patches show a higher growth speed after 1960 and, comparatively, forest growth in the CFB has sped up much slower than that in the ATE. The speedup of forest growth at the ATE is mainly accounted for by climate factors, with increasing temperature suggested to be the primary driver. Stronger water deficit as well as more competition within the CFB might have restricted forest growth there more than that within the ATE, implying biotic factors were also significant for the accelerated forest growth in the ATE, which should be excluded from simulations and predictions of warming‐induced treeline dynamics.     

最大信息熵原理与群体遗传平衡

建立了用最大信息熵原理推导群体遗传平衡定律的统一数学模型,并给出了模型的统一解,此解正是Hardy-Weinberg定律所给出的平衡群体的基因型频率,说明当群体信息熵达到最大时,群体基因型频率不再变化,即达到“平衡”。这证明了最大熵分布就是Hardy-Weinberg平衡分布。Hardy-Weinberg平衡定律与最大信息熵原理的内在一致性说明,杂交和随机交配是一个不可逆过程,使群体基因型信息熵增大,无序性增,是选择和近亲交配使群体的信息熵降低,有序性增加,育种过程实际就是调节群体信息熵的过程。过程信息熵的含义是表示一个概率分布的不确定性,最大熵原理意味着在一定的约束条件,选择具有最大不确定性的分布,从而其分布是最为随机的。最大熵原理在信息,工程,天文,地理,图像处理,模式识别等自然科学和社会科学领域都有广泛的成功应用,本文从群体遗传学角度证明了这一原理具有普遍适用性。熵是描述系统状态的函数,而最大熵原理则表明了系统发展变化的趋势,系统的最终状态必然是熵增加至最大值的状态,对于任何系统都是如此。因此,群体遗传系统的平衡定律可以统一用最大熵原理进行判定和描述;任意群体的基因型信息熵在随机交配世代传递时有不断增加的趋势;在一定约束条件下基因型信息熵达到最大值时,就称之为达到遗传平衡。本文将信息论原理应用于群体遗传学研究,揭示了基因信息熵的生物学意义,并表明可以用信息学和控制论的原理和方法来研究群体遗传学问题。     

The Expression and Significance of Neuronal Iconic Proteins in Podocytes

Growing evidence suggests that there are many common cell biological features shared by neurons and podocytes; however, the mechanism of podocyte foot process formation remains unclear. Comparing the mechanisms of process formation between two cell types should provide useful guidance from the progress of neuron research. Studies have shown that some mature proteins of podocytes, such as podocin, nephrin, and synaptopodin, were also expressed in neurons. In this study, using cell biological experiments and immunohistochemical techniques, we showed that some neuronal iconic molecules, such as Neuron-specific enolase, nestin and Neuron-specific nuclear protein, were also expressed in podocytes. We further inhibited the expression of Neuron-specific enolase, nestin, synaptopodin and Ubiquitin carboxy terminal hydrolase-1 by Small interfering RNA in cultured mouse podocytes and observed the significant morphological changes in treated podocytes. When podocytes were treated with Adriamycin, the protein expression of Neuron-specific enolase, nestin, synaptopodin and Ubiquitin carboxy terminal hydrolase-1 decreased over time. Meanwhile, the morphological changes in the podocytes were consistent with results of the Small interfering RNA treatment of these proteins. The data demonstrated that neuronal iconic proteins play important roles in maintaining and regulating the formation and function of podocyte processes.     

Biological characteristics of dengue virus and potential targets for drug design

Dengue infection is a major cause of morbidity in tropical and subtropical regions, bringing nearly 40% of the world population at risk and causing more than 20,000 deaths per year. But there is neither a vaccine for dengue disease nor antivirai drugs to treat the infection. In recent years, dengue infection has been particularly prevalent in India, Southeast Asia, Brazil, and Guangdong Province, China. In this article, we present a brief summary of the biological characteristics of dengue virus and associated flaviviruses, and outline the prowess on studies of vaccines and drugs based on potential targets of the dengue virus.     

Hydrolase-catalyzed Michael addition of 1,3-dicarbonyl compounds to α,β-unsaturated compounds in organic solvent

A novel strategy to perform Michael additions between 1,3-dicarbonyl compounds and α,β-unsaturated compounds was developed by the catalysis of hydrolase. We found that 11 hydrolase could catalyze the enzymatic Michael addition reaction to form the carbon–carbon bond. In 2-methyl-2-butanol d-aminoacylase showed high Michael addition activity. The influence of substrate and Michael acceptor structure on Michael addition was evaluated systematically. Some control experiments demonstrated that the active site of d-aminoacylase was responsible for the enzymatic Michael addition reaction. This novel Michael addition activity of hydrolase is of practical significance in expanding the application of enzymes and in the evolution of new biocatalysts.