Electron transfer dissociation of iTRAQ labeled peptide ions

Triply and doubly charged iTRAQ ( isobaric tagging for relative and absolute quantitation) labeled peptide cations from a tryptic peptide mixture of bovine carbonic anhydrase II were subjected to electron transfer ion/ion reactions to investigate the effect of charge bearing modifications associated with iTRAQ on the fragmentation pattern. It was noted that electron transfer dissociation (ETD) of triply charged or activated ETD (ETD and supplemental collisional activation of intact electron transfer species) of doubly charged iTRAQ tagged peptide ions yielded extensive sequence information, in analogy with ETD of unmodified peptide ions. That is, addition of the fixed charge iTRAQ tag showed relatively little deleterious effect on the ETD performance of the modified peptides. ETD of the triply charged iTRAQ labeled peptide ions followed by collision-induced dissociation (CID) of the product ion at m/ z 162 yielded the reporter ion at m/ z 116, which is the reporter ion used for quantitation via CID of the same precursor ions. The reporter ion formed via the two-step activation process is expected to provide quantitative information similar to that directly produced from CID. A 103 Da neutral loss species observed in the ETD spectra of all the triply and doubly charged iTRAQ labeled peptide ions is unique to the 116 Da iTRAQ reagent, which implies that this process also has potential for quantitation of peptides/proteins. Therefore, ETD with or without supplemental collisional activation, depending on the precursor ion charge state, has the potential to directly identify and quantify the peptides/proteins simultaneously using existing iTRAQ reagents.     

Visualization of comparative genomic analyses by BLAST score ratio

Background  

The first microbial genome sequence, Haemophilus influenzae, was published in 1995. Since then, more than 400 microbial genome sequences have been completed or commenced. This massive influx of data provides the opportunity to obtain biological insights through comparative genomics. However few tools are available for this scale of comparative analysis.     

GeneKeyDB: A lightweight,gene-centric,relational database to support data mining environments

Background  

The analysis of biological data is greatly enhanced by existing or emerging databases. Most existing databases, with few exceptions are not designed to easily support large scale computational analysis, but rather offer exclusively a web interface to the resource. We have recognized the growing need for a database which can be used successfully as a backend to computational analysis tools and pipelines. Such database should be sufficiently versatile to allow easy system integration.     

Effects of single amino acid substitution on the collision-induced dissociation of intact protein ions: Turkey ovomucoid third domain

Expanded understanding of the factors that direct polypeptide ion fragmentation can lead to improved specificity in the use of tandem mass spectrometry for the identification and characterization of proteins. Like the fragmentation of peptide cations, the dissociation of whole protein cations shows several preferred cleavages, the likelihood for which is parent ion charge dependent. While such cleavages are often observed, they are far from universally observed, despite the presence of the residues known to promote them. Furthermore, cleavages at residues not noted to be common in a variety of proteins can be dominant for a particular protein or protein ion charge state. Motivated by the ability to study a small protein, turkey ovomucoid third domain, for which a variety of single amino acid variants are available, the effects of changing the identity of one amino acid in the protein sequence on its dissociation behavior were examined. In particular, changes in amino acids associated with C-terminal aspartic acid cleavage and N-terminal proline cleavage were emphasized. Consistent with previous studies, the product ion spectra were found to be dependent upon the parent ion charge state. Furthermore, the fraction of possible C-terminal aspartic acid cleavages observed to occur for this protein was significantly larger than the fraction of possible N-terminal proline cleavages. In fact, very little N-terminal proline cleavage was noted for the wild-type protein despite the presence of three proline residues in the protein. The addition/removal of proline and aspartic acids was studied along with changes in selected residues adjacent to proline residues. Evidence for inhibition of proline cleavage by the presence of nearby basic residues was noted, particularly if the basic residue was likely to be protonated.     

Microbial production and consumption of dimethyl sulfide (DMS) in a sea grass (Zostera noltii)-dominated marine intertidal sediment ecosystem (Bassin d'Arcachon, France)

The relation between net dimethyl sulfide (DMS) production and changes in near surface (0-5 mm) oxygen concentrations in a sea grass (Zostera noltii Hornem)-covered intertidal sediment ecosystem was examined during a diel cycle. Sediment covered with Zostera was found to be more oxygenated than uncovered sediment during the period of photosynthesis. This phenomenon was probably caused by radial oxygen loss of the Zostera root-rhizome system. The population sizes of the three functional groups of microbes mainly responsible for the concentration of DMS, the dimethylsulfoniopropionate (DMSP)-demethylating, DMSP-cleaving and DMS-oxidizing bacteria, were quantified by most probable number (MPN) methodologies. Sediments with Zostera supported substantially higher populations of both aerobic (149x10(6) cm(-3) DMSP-utilizing and 0.4x10(6) cm(-3) DMS-oxidizing) and anaerobic (43x10(6) cm(-3) DMSP-utilizing and 0.4x10(6) cm(-3) DMS-oxidizing) microorganisms than sediments without Zostera (DMSP-utilizing aerobes and anaerobes both 2x10(6) cm(-3) and DMS-oxidizing aerobes and anaerobes both 0.2x10(6) cm(-3)). Experiments conducted with sediment cores and sediment slurries suggested that the net production of DMS in these sediments was significantly lower during oxic periods than during anoxic periods. Intact sediment cores with and without Zostera produced DMS when incubated under anoxic/dark conditions (97.0 and 53.6 nmol DMS m(-2) h(-1), respectively), while oxic/light-incubated cores did not produce detectable amounts of DMS. In addition, kinetic parameter values (V(max) and K(m)) for DMSP degradation in cell suspensions of isolated DMSP-demethylating and DMSP-cleaving bacteria were measured and compared to documented values for other strains. Both V(max) and K(m) values for DMSP-demethylating organisms were found to be relatively low (14.4-20.1 nmol DMSP mg protein(-1) min(-1) and 4.1-15.5 μM, respectively) while these parameter values varied widely in the group of the DMSP-cleaving organisms (6.7-1000 nmol DMSP mg protein(-1) min(-1) and 2-2000 μM, respectively). It was hypothesized that a diel rhythm in DMS emission occurred, with a relatively low net production during the day and a high net production during the night. Environmental changes which result in increased anoxic conditions in coastal sediments, such as an increase in eutrophication, may therefore result in increased atmospheric DMS emission rates.     

外源亚精胺对盐胁迫下白刺幼苗叶片抗氧化酶系统的影响

为进一步阐明盐生植物白刺耐盐性与多胺的关系,通过水培试验研究了叶面喷施亚精胺(Spd)对不同浓度NaCl胁迫下西伯利亚白刺幼苗叶片丙二醛(MDA)和超氧阴离子(O2)产生速率,以及抗氧化物酶系统和根系活力的影响.结果表明:叶面喷施0.1 mmol·L1 Spd 5 d后,可显著提高100和200 mmol·L1 NaCl胁迫下白刺幼苗叶片超氧化物歧化酶(SOD)、过氧化物酶(POD)和过氧化氢酶(CAT)的活性以及根系活力,降低了叶片MDA含量和O2的产生速率;而在0、50、300 mmol·L-1 NaC1处理下,外施Spd对白刺幼苗叶片上述指标无显著影响.研究结果证实,在100～200 mmol·L-1 NaCl胁迫范围内,外施亚精胺可能通过增强体内保护酶活性来显著降低活性氧水平,有效减轻盐胁迫对盐生植物白刺幼苗造成的过氧化伤害,从而增强白刺对盐环境的适应性.     

昆仑岩黄耆(豆科)在中国的分布

报道了豆科Leguminosae昆仑岩黄耆Hedysarum krassnovii B．Fedtsch．在中国的分布。昆仑岩黄耆与近缘种红花岩黄耆H.multijugum Maxim.形态易混淆,但以其小叶3-9×3-7mm;旗瓣倒卵形,顶端凹陷约2mm深;翼瓣狭披针形;龙骨瓣近半圆形或矩圆形;花萼二唇彤;荚果具1-2节荚等性状易于区分。另外,此二种的物候期、生境及地理分布亦有区别。     

Selective disulfide bond cleavage in gold(I) cationized polypeptide ions formed via gas-phase ion/ion cation switching

Gaseous multiply protonated disulfide-linked peptides have been subjected to reactions with AuCl2(-) ions to explore the possibility of effecting cation switching of Au+ for two protons and to determine whether cationization by Au+ ions affords selective dissociation of disulfide linkages. The incorporation of Au+ into several model disulfide-linked peptides proved to be straightforward. The primary ion/ion reaction channels were proton transfer, which does not lead to Au+ incorporation, and attachment of AuCl2(-) ions to the polypeptide cation, which does incorporate Au+. Fragmentation of the attachment product, the extent of which varied with peptide and charge state, led to losses of one or more molecules of HCl and, to some extent, cleavage of polypeptides at the disulfide linkage into its two constituent chains. Collisional activation of the intact metal-ion-incorporated peptides showed cleavage of the disulfide linkage to be a major, and in some cases exclusive, process. Cations with protons as the only cationizing agents showed only small contributions from cleavage of the disulfide linkage. These results indicate that Au+ incorporation into a disulfide-linked polypeptide ion is a promising way to effect selective dissociation of disulfide bonds. Cation switching via ion/ion reactions is a convenient means for incorporating gold and is attractive because it avoids the requirement of adding metal salts to the analyte solution.