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.     

The response of lichens inhabiting exposed wood of spruce logs to post-hurricane disturbances in Western Carpathian forests

We investigated which of the following environmental factors: the number of years since the windthrow of the tree (the age of dead wood), the phytocenosis (the type of forest community), altitude, exposure, wood hardness and the spatial scale of forest disturbances (small gaps with a few fallen spruces vs large-area windthrows) contributed to the diversity and abundance of lichens inhabiting the exposed wood of windthrown spruce trees in Polish Western Carpathian forests. Both Shannon H index and sum of coverage coefficients rose with increasing age of the wood, levelling off after 11–14 y (diversity) and 14–17 y (abundance). This factor appeared to be the most important for this group of lichens, but the significant positive impact of large-area windthrows on the lichen abundance was also demonstrated by using a GLM model. The age of the wood we precisely determined on the basis of data on Norway spruce mortality collected annually in permanent plots of the Gorce National Park since 2000. Using the Shore durometer we linked the course of the wood-inhabiting lichen succession with wood decay more precisely than before. The largest number of species was associated with medium hard wood, i.e., 51 < x ≤ 80 on the Shore scale. Based on the NMDS analysis, we distinguished four age groups of logs, differing in lichen abundance and defined by the dominance of distinctive species. A large number of usually corticolous lichen species used the wood of windthrown spruce logs as an optional habitat to survive large-scale, post-hurricane forest disturbances.     

Predation impact of Leptodora kindtii on population dynamics and morphology of Bosmina fatalis and B. longirostris in mesocosms

1. We assessed the impact of predation by the invertebrate predator Leptodora kindtii on Bosmina longirostris and B. fatalis, which show seasonal and reciprocal succession patterns in Lake Suwa, in a mesocosm experiment using 20‐L tanks with or without the predator under different food conditions. We also analysed morphological responses of the two Bosmina species to the predator in the tanks. 2. Bosmina fatalis dominated B. longirostris regardless of predator presence under high food density. However, the presence of Leptodora induced the dominance of B. fatalis more rapidly than its absence. On the contrary, no dominance of B. fatalis was observed in tanks with low food density, irrespective of the presence of the predator. Only B. fatalis showed morphological changes in response to the presence of Leptodora. 3. Mucrone length and antennule shape (angle between body and antennule and angle between antennules) showed marked responses at both high and low food densities, but antennule length responded only at high food density. Mucrone length seems to be a more effective defence against Leptodora. 4. The results suggest that B. fatalis is a superior competitor against B. longirostris and is more resistant to Leptodora predation, especially in good food conditions. The repeatedly observed seasonal succession of the two Bosmina species in the eutrophic Lake Suwa – the replacement of B. longirostris by B. fatalis following the occurrence of abundant Leptodora– seems to be caused by the selective predation of Leptodora on B. longirostris as well as the competitive ability of B. fatalis.     

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     

达斡尔族成人的体格,体型及半个多世纪来的变化

对内蒙古自治区莫力达瓦族３５３名（男１８７,女１６６）２０－６０岁达斡尔族进行了活体观察与测量,总结了达斡尔族的体格特征和类型。并在城乡之间和与半个世纪以前同一地区达斡尔族的体质资料之间进行了比较。