iBench: A ground truth approach for advanced validation of mass spectrometry identification method

The discovery of many noncanonical peptides detectable with sensitive mass spectrometry inside, outside, and on cells shepherded the development of novel methods for their identification, often not supported by a systematic benchmarking with other methods. We here propose iBench, a bioinformatic tool that can construct ground truth proteomics datasets and cognate databases, thereby generating a training court wherein methods, search engines, and proteomics strategies can be tested, and their performances estimated by the same tool. iBench can be coupled to the main database search engines, allows the selection of customized features of mass spectrometry spectra and peptides, provides standard benchmarking outputs, and is open source. The proof-of-concept application to tryptic proteome digestions, immunopeptidomes, and synthetic peptide libraries dissected the impact that noncanonical peptides could have on the identification of canonical peptides by Mascot search with rescoring via Percolator (Mascot+Percolator).     

Milk metabolites can characterise individual differences in animal resilience to a nutritional challenge in lactating dairy goats

The aim of this study is built in two phases: to quantify the ability of novel milk metabolites to measure between-animal variability in response and recovery profiles to a short-term nutritional challenge, then to derive a resilience index from the relationship between these individual variations. At two different stages of lactation, sixteen lactating dairy goats were exposed to a 2-d underfeeding challenge. The first challenge was in late lactation, and the second was carried out on the same goats early in the following lactation. During the entire experiment period, samples were taken at each milking for milk metabolite measures. For each metabolite, the response profile of each goat was characterised using a piecewise model for describing the dynamic pattern of response and recovery profiles after the challenge relative to the start of the nutritional challenge. Cluster Analysis identified three types of response/recovery profiles per metabolite. Using cluster membership, multiple correspondence analyses (MCAs) were performed to further characterise response profile types across animals and metabolites. This MCA analysis identified three groups of animals. Further, discriminant path analysis was able to separate these groups of multivariate response/recovery profile type based on threshold levels of three milk metabolites: β-hydroxybutyrate, free glucose and uric acid. Further analyses were done to explore the possibility of developing an index of resilience from milk metabolite measures. Different types of performance response to short-term nutritional challenge can be distinguished using multivariate analyses of a panel of milk metabolites.     

Thyroid fine needle aspiration: the morphological features on ThinPrep® slide preparations. Eighty cases with histological control

This study had several purposes: to define cytomorphological features of thyroid cells that might be modified by alcohol fixation; to optimize May-Grünwald–Giemsa (MGG) staining on ThinPrep^® (TP; Cytyc Inc., Bexborough, MA, USA) slides and to compare the diagnostic accuracy of slides prepared by a liquid-based method with those obtained by conventional technique. This study included 120 cases of ultrasound-guided fine needle aspiration (FNA) of the thyroid and 55 FNAs performed on surgically resected thyroid specimens. Histological control was available in 80 cases. In the first group of 120 FNAs, a split-sample technique was used for the TP. Three screenings were performed: first, an individual screening of the conventional smears (CS) and of the TP, a second screening to compare cells observed on the TP with the histological control and a third screening to assess the previously defined diagnostic criteria. Twenty-seven TP cases (22%) were considered unsatisfactory for diagnosis compared with 10 in CS (8%). The high rate of unsatisfactory cases with TP is likely to be due to the use of the split-sample technique. The sensitivity was 94% for CS and 81% for TP. The specificity was 67% and 60% for CS and TP, respectively. Two occult papillary carcinomas were missed by both methods. As for the MGG staining, the modified technique used for TP resulted in the same quality as the standard procedure. Conversely, TP did however induce uncommon morphological features. In this study, sensitivity and specificity levels are higher for CS than for TP; the difference may be explained by the fact that the methanol fixative used for TP induces some cytological alterations, especially in oncocytic tumours and lymphocytic thyroïditis.     

Crystal structure determination of basic phospholipase A2 from venom of Agkistrodon halys pallas by molecular replacement method

Basic phospholipase A₂ (BPLA₂) from the venom of Agkistrodon halys pallas has a strong ability to hemolyze erythrocytes. The asymmetrical unit of P2₁2₁2₁ crystal of BPLA₂ contains two molecules. Self-rotation function was used to study the orientation relationship of these two molecules. Cross-rotation and translation functions were then used to determine the orientations and positions of the two molecules in the unit cell. The model building and preliminary structure refinement were carried out. The result shows that the two molecules in the asymmetrical unit of orthorhombic crystal are related by a non-crystallographic 2-fold symmetry axis.     

一例智力低下患者7q~ 标记染色体的来源鉴定

以人类染色体显微切割、PCR技术构建的现有人类染色体特异性和染色体区带特异性探针池作为绘画探针,采用正向染色体绘画技术,结合染色体筛查方法,查明了一例7q~ 标记染色体患者的染色体附加片段来源于3q26→3qter。确定该患者的核型为46,XX,-7, der(7)t(7;3)(7pter→7q32::3q26→3qter)。应用这个策略,能够快速有效地鉴定标记染色体的来源。     

Chemical shift assignments and secondary structure of the Grb2 SH2 domain by heteronuclear NMR spectroscopy

Summary The growth factor receptor-bound protein-2 (Grb2) is an adaptor protein that mediates signal transduction pathways. Chemical shift assignments were obtained for the SH2 domain of Grb2 by heteronuclear NMR spectroscopy, employing the uniformly ¹³C-/¹⁵N-enriched protein as well as the protein containing selectively ¹⁵N-enriched amino acids. Using the Chemical Shift Index (CSI) method, the chemical shift indices of four nuclei, ¹H, ¹³C, ¹³C and ¹³CO, were used to derive the secondary structure of the protein. Nuclear Overhauser enhancements (NOEs) were then employed to confirm the secondary structure. The CSI results were compared to the secondary structural elements predicted for the Grb2 SH2 domain from a sequence alignment [Lee et al. (1994) Structure, 2, 423–438]. The core structure of the SH2 domain contains an antiparallel -sheet and two -helices. In general, the secondary structural elements determined from the CSI method agree well with those predicted from the sequence alignment.Abbreviations crk viral p47^gag-crk - EGF epidermal growth factor - GAP GTPase-activating protein - PI3K phosphatidylinositol-3-kinase - PLC- phospholipase-C-, shc, src homologous and collagen - src sarcoma family of nonreceptor tyrosine kinase     

适用于获取最优化配方的一种算法

本文应用印楝种仁提取物（F3）与敌敌畏混配为例,以斜纹夜蛾（Spodopteralitura）为目标害虫,介绍一种适用于获取最优化配方的算法,在二次通用回归旋转组合设计的基础上,经参数辨识,获取二次回归方程,经失拟性、回归显著性检验,本方程基本能够反映杀虫剂用量与斜纹夜蛾幼虫死亡机率值之间的关系．在害虫防治实践中,要求在防治费用最小的基础上,目标害虫有最大的死亡率.因此,以防治目标害虫的费用作为优化算法的目标函数,以害虫死亡机率值最大作为约束条件,有如下的一组优化算式为目标函数约束条件式中a1,a2分别为参试杀虫剂1,2最低用量,b1,b2则为相应的最高用量．C1,C2分别为杀虫剂1,2的单价,N1,N2为杀虫剂l,2的用量．Y为目标害虫死亡机率值回归方程．本文所依据的试验设计中,以对数函数关系变换编码值与使用浓度之间的关系,所以应用拉格朗日求极值原理求取最优化配方．由计算所得的混配比例与其他方法所获结果一致．     

细菌巨大质粒的快速检测

本文报道了一种快速检测微生物巨大质粒的方法．该方法是通过对Ｅｃｋｈａｒｄｔ所报道的方法加以改进,使之能对根瘤菌、大肠杆菌、甚至链霉菌的大质粒进行快速检测．     

双单抗的免疫层析一步法用于早妊诊断的研究

在试管式、微孔式和斑点式的酶免测定法测定人绒毛膜促性腺激素（ＨＣＧ）的基础上,发展了应用双单克隆抗体的免疫层析一步法测定ＨＣＧ。此法用胶体金标记抗βＨＣＧ单克隆抗体,将抗αＨＣＧ单克隆抗体包被在硝酸纤维素膜上。无需分离步骤,特别是在进行测定时除加入样品外无需再加任何试剂,此方法特别迅速、简便,２～５ｍｉｎ即可得结果。凡ＨＣＧ浓度＞２５ＩＵ／Ｌ的样品可得到阳性结果。在人体血或尿中可能出现的高浓度的干扰物质,如抗坏血酸、乙酰水杨酸、雌二醇、蛋白质、胆红素、甘油三酯等对本测定均无干扰作用,在促黄体激素（ＬＨ）浓度高达５００ＩＵ／Ｌ时仍与ＨＣＧ没有交叉反应。能进行测定的最高值大于３００ＩＵ／ｍｌ,这表示,当ＨＣＧ浓度达到妊娠期的最高值时仍不会有假阴性结果。