Towards better accuracy for missing value estimation of epistatic miniarray profiling data by a novel ensemble approach

Epistatic miniarray profiling (E-MAP) is a powerful tool for analyzing gene functions and their biological relevance. However, E-MAP data suffers from large proportion of missing values, which often results in misleading and biased analysis results. It is urgent to develop effective missing value estimation methods for E-MAP. Although several independent algorithms can be applied to achieve this goal, their performance varies significantly on different datasets, indicating different algorithms having their own advantages and disadvantages. In this paper, we propose a novel ensemble approach EMDI based on the high-level diversity to impute missing values that consists of two global and four local base estimators. Experimental results on five E-MAP datasets show that EMDI outperforms all single base algorithms, demonstrating an appropriate combination providing complementarity among different methods. Comparison results between several fusion strategies also demonstrate that the proposed high-level diversity scheme is superior to others. EMDI is freely available at www.csbio.sjtu.edu.cn/bioinf/EMDI/.     

Site-specific ¹⁹F NMR chemical shift and side chain relaxation analysis of a membrane protein labeled with an unnatural amino acid

Site‐specific ¹⁹F chemical shift and side chain relaxation analysis can be applied on large size proteins. Here, one‐dimensional ¹⁹F spectra and T₁, T₂ relaxation data were acquired on a SH3 domain in aqueous buffer containing 60% glycerol, and a nine‐transmembrane helices membrane protein diacyl‐glycerol kinase (DAGK) in dodecyl phosphochoine (DPC) micelles. The high quality of the data indicates that this method can be applied to site‐specifically analyze side chain internal mobility of membrane proteins or large size proteins.     

Characterization of a novel and selective CB1 antagonist as a radioligand for receptor occupancy studies

Obesity remains a significant public health issue leading to Type II diabetes and cardiovascular disease. CB1 antagonists have been shown to suppress appetite and reduce body weight in animal models as well as in humans. Evaluation of pre-clinical CB1 antagonists to establish relationships between in vitro affinity and in vivo efficacy parameters are enhanced by ex vivo receptor occupancy data. Synthesis and biological evaluation of a novel and highly selective radiolabeled CB1 antagonist is described. The radioligand was used to conduct ex vivo receptor occupancy studies.     

Development of insect-resistant transgenic cotton with chimeric TVip3A* accumulating in chloroplasts

An optimized vip3A gene, designated as vip3A* was chemically synthesized and a thi1 gene chloroplast transit peptide coding sequence was attached to its 5′ end to produce the tvip3A*. vip3A* and tvip3A* genes were transformed into Gossypium hirsutum cv. Zhongmiansuo35. Of 42 independent transformants, 36 were positive for the vip3A* or tvip3A* gene. Four independent transgenic T1 lines with single-copy insertions and unchanged phenotypes (CTV1 and CTV2 for tvip3A*, and CV1 and CV2 for vip3A*) were selected by Southern blotting, and subjected to an insect bioassay and field assessment. Four homozygous T2 transgenic lines were then selected and the amount of expressed Vip3A* protein was determined by western blotting and ELISA. The protein concentrations of CTV1 and CTV2 were about three-fold higher than those of CV1 and CV2. As expected, the Vip3A* protein of CTV1 and CTV2 were transported to the chloroplasts, where they accumulated. The Vip3A* protein concentration in the chloroplasts of CTV1 and CTV2 was about 15-fold of that of CV1 and CV2. All four transgenic lines showed 100% mortality against fall armyworm (Spodoptera frugiperda) and beet armyworm (Spodoptera exigua) by insect bioassay. Moreover, CTV1 and CTV2 exhibited 100% mortality against cotton bollworm (CBW, Helicoverpa zea), whereas CV1 and CV2 showed 75.0% and 72.5% mortality against CBW, respectively. The field bioassay indicated that CTV1 and CTV2 were more resistant to CBW than CV1 and CV2. Our results suggest that the two tvip3A* transgenic lines (CTV1 and CTV2) can be used to develop insect-resistant cultivars and could be used as a resource for raising multi-toxins-expressing transgenic cotton.     

过表达Lin28a/Lin28b对let-7家族活性的影响

研究在HeLaS3细胞中过表达Lin28a/Lin28b对let-7家族miRNA表达水平和活性的影响。首先,构建Lin28a和Lin28b的表达载体pAAV2neo-Lin28a和pAAV2neo-Lin28b,分别转染HeLaS3细胞并筛选获得Lin28a和Lin28b的稳定表达细胞株HeLaS3/pAAV2neo-Lin28a和HeLaS3/pAAV2neo-Lin28b。然后,以pAAV2neo-Gluc-(Fluc)为基本骨架,构建并获得检测let-7家族miRNA活性的8种质粒型载体,并包装为相应的重组腺相关病毒(Recombinant adeno-associated virus,rAAV),作为检测miRNA靶序列介导的转录后抑制活性的传感器,命名为Asensor。在此基础上,以HeLaS3细胞为对照,用Western blot检测HeLaS3/pAAV2neo-Lin28a和HeLaS3/pAAV2neo-Lin28b细胞中Lin28a和Lin28b表达水平,用QRT-PCR测定let-7家族各成员表达水平,用Asensor检测let-7家族各成员活性。Western blot结果显示,HeLaS3/pAAV2neo-Lin28a和HeLaS3/pAAV2neo-Lin28b均能有效地表达Lin28a和Lin28b蛋白;QRT-PCR检测结果显示,相比于HeLaS3细胞,HeLaS3/pAAV2neo-Lin28a细胞中let-7家族各成员表达水平都下降(除let-7e外),但不同成员下降幅度存在差异;Asensor检测结果显示,let-7家族所有成员活性水平都下降,但不同成员下降幅度也存在差异,且同一成员活性水平与表达水平及其下降趋势也不一致。相比于HeLaS3细胞,HeLaS3/pAAV2neo-Lin28b细胞中let-7家族成员的表达和活性水平均明显下降,但表达水平的下降幅度比HeLaS3/pAAV2neo-Lin28a细胞大,而活性的下降幅度却与之相近。本研究建立了一种检测和比较miRNA靶序列介导的转录后抑制活性的方法,首次研究了过表达Lin28a和Lin28b对细胞中的let-7家族miRNA活性影响,并发现Lin28a和Lin28b对let-7家族miRNA表达水平的影响和对其相应活性的影响不一致性,说明在检测miRNA表达水平的同时检测miRNA活性能更全面揭示miRNA的调节功能,为进一步研究let-7家族的调控机制奠定了基础。     

Differences in protein expression and ultrastructure between two wheat near-isogenic lines affected by powdery mildew

Wheat powdery mildew is caused by Blumeria graminis f. sp. tritici (Bgt). Pm21 is an effective broad-spectrum powdery mildew resistance gene, which shows a considerable promise in wheat breeding. We report here a proteomic approach to investigate the resistance response proteins after fungal infection and emphasize the resistance changes induced by Pm21. Two wheat (Triticum aestivum L.) near-isogenic lines (NILs), recurrent parent ‘Bainong,’ which is susceptible to powdery mildew, and its near-isogenic line ‘W2132’ carrying resistance gene Pm21) were used to investigate some changes in their proteomes after being infected. Proteins were extracted from the leaves sampled in 48 h after inoculation, separated by two-dimensional electrophoresis, and stained with Coomassie brilliant blue. Among these proteins, a total of 56 spots differentially expressed after Bgt infection were detected. Sixteen proteins, identified by MALDI-TOF-MS, exhibited more than a 1.5-fold increase upon fungal infection. Unfortunately, three spots were not identified successfully. The predicted functions of identified proteins were related to energy metabolism and defensive responses; they were involved in many physiological resistance responses, including enhancing energy metabolism, proteins synthesis and stabilization, antioxidant reactions, cell-wall reinforcement, and lignification. Interestingly that the expression of two proteins related to the cell-wall reinforcement was enhanced in the resistant line and one protein related to photosynthesis was lost in a susceptible line. By transmission electronic microscopy, the corresponding physiological characteristics were also observed. These results provide us with the information to further reveal the resistance mechanism of Pm21 action and comprehensively investigate the physiological response to powdery mildew at the protein level.     

An artifacts removal post-processing for epiphyseal region-of-interest (EROI) localization in automated bone age assessment (BAA)

Background

Guidewire (GW) size and stenosis dimensions are the two major factors affecting the translesional pressure drop. Studying the combined effect of these parameters on the mean pressure drop (Δp) across the stenosis is of high practical importance.

Methods

In this study, time averaged mass and momentum conservation equations are solved analytically to obtain pressure drop-flow, Δp-Q, curves for three different percentage area blockages corresponding to moderate (64%), intermediate (80%), and severe (90%) stenoses. Stenosis is considered to be axisymmetric consisting of three different sections namely converging, throat, and diverging regions. Analytical expressions for pressure drop are obtained for each of these regions separately. Using this approach, effects of lesion length and GW insertion on the mean translesional pressure drop and its component (loss due to momentum change and viscous loss) are analyzed.

Results and Conclusion

It is observed that for a given percent area stenosis (AS), increase in the throat length only increases the viscous loss. However, increase in the severity of stenosis and GW insertion increase both loss due to momentum change and viscous loss. GW insertion has greater contribution to the rise in viscous loss (increase by 2.14 and 2.72 times for 64% and 90% AS, respectively) than loss due to momentum change (1.34% increase for 64% AS and 25% decrease for 90% AS). It also alters the hyperemic pressure drop in moderate (48% increase) to intermediate (30% increase) stenoses significantly. However, in severe stenoses GW insertion has a negligible effect (0.5% increase) on hyperemic translesional pressure drop. It is also observed that pressure drop in a severe stenosis is less sensitive to lesion length variation (4% and 14% increase in Δp for without and with GW, respectively) as compared to intermediate (10% and 30% increase in Δp for without and with GW, respectively) and moderate stenoses (22% and 48% increase in Δp for without and with GW, respectively). Based on the contribution of pressure drop components to the total translesional pressure drop, it is found that viscous losses are dominant in moderate stenoses, while in severe stenoses losses due to momentum changes are significant. It is also shown that this simple analytical solution can provide valuable information regarding interpretation of coronary diagnostic parameters such as fractional flow reserve (FFR).     

Stroke intervention pathways: NMDA receptors and beyond

Despite abundant evidence from basic/preclinical research that excessive NMDAR (N-methyl-d-aspartate receptor) stimulation is a crucial step required for brain damage following a stroke, clinical trials for NMDAR blockers have all ended with disappointments. The past decade of stroke research has revealed distinct NMDAR subpopulations and many specific effectors downstream of these receptors that are differentially responsible for neuronal survival and death. These new advancements provide promising targets for the development of novel NMDAR-based neuroprotective stroke therapies that could have greater therapeutic windows and reduced side effects. In this review, we discuss these advancements with a particular emphasis on the identification of novel signaling effectors downstream of proneuronal death NMDARs and the potential implications of these findings for the development of stroke therapeutics.     

An inducible transgenic Cre mouse line for the study of hippocampal development and adult neurogenesis

The hippocampus is crucial for higher brain functions, such as learning, memory, and emotion. Many diseases like epilepsy and Down's syndrome are associated with abnormalities in early hippocampal development. In addition, adult dentate neurogenesis is thought to be defective in several classes of psychiatric disorders. However, the mechanisms regulating hippocampal development and adult neurogenesis remain unclear. One of the limitations to studying these processes is the scarcity of available specific mouse tools. Here, we report an inducible transgenic Cre mouse line, Frizzled 9‐CreER?, in which tamoxifen administration induces Cre recombinant. Our data show that Cre is expressed in the developing hippocampal primordium, confined to the granule cell layer at P20 and further limited to the subgranular zone in the adult dentate gyrus. Cre recombinase shows very high activity in all of these regions. Thus, this transgenic line will be a powerful tool in understanding the mechanisms of hippocampal development, adult neurogenesis, and associated diseases. genesis 49:919–926, 2011. © 2011 Wiley Periodicals, Inc.     

Rheb1 is required for mTORC1 and myelination in postnatal brain development

mTor kinase is involved in cell growth, proliferation, and differentiation. The roles of mTor activators, Rheb1 and Rheb2, have not been established in?vivo. Here, we report that Rheb1, but not Rheb2, is critical for embryonic survival and mTORC1 signaling. Embryonic deletion of Rheb1 in neural progenitor cells?abolishes mTORC1 signaling in developing brain and increases mTORC2 signaling. Remarkably, embryonic and early postnatal brain development appears grossly normal in these Rheb1f/f,Nes-cre mice with the notable exception of deficits of myelination. Conditional expression of Rheb1 transgene in neural progenitors increases mTORC1 activity and promotes myelination in the brain. In addition the Rheb1 transgene rescues mTORC1 signaling and hypomyelination in the Rheb1f/f,Nes-cre mice. Our study demonstrates that Rheb1 is essential for mTORC1 signaling and myelination in the brain, and suggests that mTORC1 signaling plays a role in selective cellular adaptations, rather than general cellular viability.