Features-Based Deisotoping Method for Tandem Mass Spectra

For high-resolution tandem mass spectra, the determination of monoisotopic masses of fragment ions plays a key role in the subsequent peptide and protein identification. In this paper, we present a new algorithm for deisotoping the bottom-up spectra. Isotopic-cluster graphs are constructed to describe the relationship between all possible isotopic clusters. Based on the relationship in isotopic-cluster graphs, each possible isotopic cluster is assessed with a score function, which is built by combining nonintensity and intensity features of fragment ions. The non-intensity features are used to prevent fragment ions with low intensity from being removed. Dynamic programming is adopted to find the highest score path with the most reliable isotopic clusters. The experimental results have shown that the average Mascot scores and F-scores of identified peptides from spectra processed by our deisotoping method are greater than those by YADA and MS-Deconv software

Genome-wide investigation of the AP2/ERF superfamily and their expression under salt stress in Chinese willow (Salix matsudana)

AP2/ERF transcription factors (TFs) play indispensable roles in plant growth, development, and especially in various abiotic stresses responses. The AP2/ERF TF family has been discovered and classified in more than 50 species. However, little is known about the AP2/ERF gene family of Chinese willow (Salix matsudana), which is a tetraploid ornamental tree species that is widely planted and is also considered as a species that can improve the soil salinity of coastal beaches. In this study, 364 AP2/ERF genes of Salix matsudana (SmAP2/ERF) were identified depending on the recently produced whole genome sequencing data of Salix matsudana. These genes were renamed according to the chromosomal location of the SmAP2/ERF genes. The SmAP2/ERF genes included three major subfamilies: AP2 (55 members), ERF (301 members), and RAV (six members) and two Soloist genes. Genes’ structure and conserved motifs were analyzed in SmAP2/ERF family members, and introns were not found in most genes of the ERF subfamily, some unique motifs were found to be important for the function of SmAP2/ERF genes. Syntenic relationships between the SmAP2/ERF genes and AP2/ERF genes from Populus trichocarpa and Salix purpurea showed that Salix matsudana is genetically more closely related to Populus trichocarpa than to Salix purpurea. Evolution analysis on paralog gene pairs suggested that progenitor of S. matsudana originated from hybridization between two different diploid salix germplasms and underwent genome duplication not more than 10 Mya. RNA sequencing results demonstrated the differential expression patterns of some SmAP2/ERF genes under salt stress and this information can help reveal the mechanism of salt tolerance regulation in Salix matsudana

Influence of the Tibetan Plateau uplift on the Asian monsoon-arid environment evolution

As one of the most important geological events in Cenozoic era, the uplift of the Tibetan Plateau (TP) has had profound influences on the Asian and global climate and environment evolution. During the past four decades, many scholars from China and abroad have studied climatic and environmental effects of the TP uplift by using a variety of geological records and paleoclimate numerical simulations. The existing research results enrich our understanding of the mechanisms of Asian monsoon changes and interior aridification, but so far there are still a lot of issues that need to be thought deeply and investigated further. This paper attempts to review the research on the influence of the TP uplift on the Asian monsoon-arid environment, summarize three types of numerical simulations including bulk-plateau uplift, phased uplift and sub-regional uplift, and especially to analyze regional differences in responses of climate and environment to different forms of tectonic uplifts. From previous modeling results, the land-sea distribution and the Himalayan uplift may have a large effect in the establishment and development of the South Asian monsoon. However, the formation and evolution of the monsoon in northern East Asia, the intensified dryness north of the TP and enhanced Asian dust cycle may be more closely related to the uplift of the main body, especially the northern part of the TP. In this review, we also discuss relative roles of the TP uplift and other impact factors, origins of the South Asian monsoon and East Asian monsoon, feedback effects and nonlinear responses of climatic and environmental changes to the plateau uplift. Finally, we make comparisons between numerical simulations and geological records, discuss their uncertainties, and highlight some problems worthy of further studying

Iron Behaving Badly: Inappropriate Iron Chelation as a Major Contributor to the Aetiology of Vascular and Other Progressive Inflammatory and Degenerative Diseases

The production of peroxide and superoxide is an inevitable consequence of aerobic metabolism, and while these particular "reactive oxygen species" (ROSs) can exhibit a number of biological effects, they are not of themselves excessively reactive and thus they are not especially damaging at physiological concentrations. However, their reactions with poorly liganded iron species can lead to the catalytic production of the very reactive and dangerous hydroxyl radical, which is exceptionally damaging, and a major cause of chronic inflammation. We review the considerable and wide-ranging evidence for the involvement of this combination of (su)peroxide and poorly liganded iron in a large number of physiological and indeed pathological processes and inflammatory disorders, especially those involving the progressive degradation of cellular and organismal performance. These diseases share a great many similarities and thus might be considered to have a common cause (i.e. iron-catalysed free radical and especially hydroxyl radical generation). The studies reviewed include those focused on a series of cardiovascular, metabolic and neurological diseases, where iron can be found at the sites of plaques and lesions, as well as studies showing the significance of iron to aging and longevity. The effective chelation of iron by natural or synthetic ligands is thus of major physiological (and potentially therapeutic) importance. As systems properties, we need to recognise that physiological observables have multiple molecular causes, and studying them in isolation leads to inconsistent patterns of apparent causality when it is the simultaneous combination of multiple factors that is responsible. This explains, for instance, the decidedly mixed effects of antioxidants that have been observed, etc...Comment: 159 pages, including 9 Figs and 2184 reference

Reorganizing and Redesigning WPI Choral Music Library

This project reorganized Worcester Polytechnic Institute choral music library and redesigned some more efficient ways of sorting data for the library online website. By moving and rearranging all the boxed music pieces in increasing numbers, the WPI choral music library was organized and cleaned. By checking and correcting the excel data from previous years, a more accurate choral music library database was created. Concerns and future recommendations for potential IQP teams are included in this report along with a copy of the updated library data as appendix

A Novel Insight into Screening for Antioxidant Peptides from Hazelnut Protein: Based on the Properties of Amino Acid Residues

This study used the properties of amino acid residues to screen antioxidant peptides from hazelnut protein. It was confirmed that the type and position of amino acid residues, grand average of hydropathy, and molecular weight of a peptide could be comprehensively applied to obtain desirable antioxidants after analyzing the information of synthesized dipeptides and BIOPEP database. As a result, six peptides, FSEY, QIESW, SEGFEW, IDLGTTY, GEGFFEM, and NLNQCQRYM were identified from hazelnut protein hydrolysates with higher antioxidant capacity than reduced Glutathione (GSH) against linoleic acid oxidation. The peptides having Tyr residue at C-terminal were found to prohibit the oxidation of linoleic acid better than others. Among them, peptide FSEY inhibited the rancidity of hazelnut oil very well in an oil-in-water emulsion. Additionally, quantum chemical parameters proved Tyr-residue to act as the active site of FSEY are responsible for its antioxidation. This is the first presentation of a novel approach to excavating desired antioxidant peptides against lipid oxidation from hazelnut protein via the properties of amino acid residues

Study on Key Technology for the Discrimination of Xihu Longjing Tea Grade by Electronic Tongue

International audienceElectronic tongue has the characteristics of sensitivity and instability. However the technical specification for its research has still not been formed. In this paper, it was introduced the key technology of electronic tongue qualitative discriminant analysis to micro-difference samples. The research objects were four different grades of Xihu Longjing Tea with less difference within small producing area in Hangzhou of Zhejiang Province in China. According to the research, the stability of equipment had not been shown until the fifth repetition for the same sample by the electronic tongue. Finally, the signal from seventh repetitive test was selected to represent the intelligent taste fingerprint for this sample. The fingerprints of electronic tongue collected at different days showed linearity drifting for the same sample. The special tea samples were set into each series of experiments to be considered as the reference sample. All samples’ signals were calibrated with the difference value between the reference sample fingerprint of corresponding test to the designated reference sample. Principal component analysis (PCA) results showed that the same grade samples were clustered, while the different grades samples were more dispersion and non-overlapping. Through Mahalanobis Distance and Residual Method, the four abnormal tea samples were rejected from highest and 1st grade respectively. The electronic tongue’s Longjing Tea Grade models were built by soft independent modeling of class analogy (SIMCA). The discrimination accuracy for tea sample grade were both 100% for correction set and prediction set. Through this study, it was established the technical specification and flow for the quick detection of tea by electronic tongue, which including the determination on intelligent taste spectrum repeatability performance, system error calibration for spectrum drifting, rejection for abnormal tea sample based on taste spectrum and establishment for the quality judgment model . The technical specification provides the theoretical base for reasonable use of electronic tongue

Impact of Tetrapeptide-FSEY on Oxidative and Physical Stability of Hazelnut Oil-In-Water Emulsion

This study investigates the antioxidant behaviors of a hazelnut tetrapeptide, FSEY (Phe-Ser-Glu-Tyr), in an oil-in-water emulsion. The emulsion was prepared with stripped hazelnut oil at a ratio of 10%. O/W emulsions, both with and without antioxidants (FSEY and TBHQ), were incubated at 37 °C. The chemical stabilities, including those of free radicals and primary and secondary oxidation productions, along with the physical stabilities, which include particle size, zeta-potential, color, pH, and ΔBS, were analyzed. Consequently, FSEY displayed excellent antioxidant behaviors in the test system by scavenging free lipid radicals. Both primary and secondary oxidation products were significantly lower in the FSEY groups. Furthermore, FSEY assisted in stabilizing the physical structure of the emulsion. This antioxidant could inhibit the increase in particle size, prevent the formation of creaming, and stabilize the original color and pH of the emulsion. Consequently, FSEY may be an effective antioxidant additive to use in emulsion systems