DPHL:A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

To address the increasing need for detecting and validating protein biomarkers in clinical specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the selected reaction monitoring (SRM), parallel reaction monitoring (PRM), and massively parallel data-independent acquisition (DIA), have been developed. For optimal performance, they require the fragment ion spectra of targeted peptides as prior knowledge. In this report, we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue samples. To build the spectral resource, we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on Docker. We then applied the workflow to generate DPHL, a comprehensive DIA pan-human library, from 1096 data-dependent acquisition (DDA) MS raw files for 16 types of cancer samples. This extensive spectral resource was then applied to a proteomic study of 17 prostate cancer (PCa) patients. Thereafter, PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was validated. As a second application, the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma (DLBCL) patients and 18 healthy control subjects. Differentially expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by PRM. These data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker discovery. DPHL is freely accessible at https://www.iprox.org/page/project.html?id=IPX0001400000.     

DIA-Based Proteomics Identifies IDH2 as a Targetable Regulator of Acquired Drug Resistance in Chronic Myeloid Leukemia

Drug resistance is a critical obstacle to effective treatment in patients with chronic myeloid leukemia. To understand the underlying resistance mechanisms in response to imatinib mesylate (IMA) and adriamycin (ADR), the parental K562 cells were treated with low doses of IMA or ADR for 2 months to generate derivative cells with mild, intermediate, and severe resistance to the drugs as defined by their increasing resistance index. PulseDIA-based (DIA [data-independent acquisition]) quantitative proteomics was then employed to reveal the proteome changes in these resistant cells. In total, 7082 proteins from 98,232 peptides were identified and quantified from the dataset using four DIA software tools including OpenSWATH, Spectronaut, DIA-NN, and EncyclopeDIA. Sirtuin signaling pathway was found to be significantly enriched in both ADR-resistant and IMA-resistant K562 cells. In particular, isocitrate dehydrogenase (NADP(+)) 2 was identified as a potential drug target correlated with the drug resistance phenotype, and its inhibition by the antagonist AGI-6780 reversed the acquired resistance in K562 cells to either ADR or IMA. Together, our study has implicated isocitrate dehydrogenase (NADP(+)) 2 as a potential target that can be therapeutically leveraged to alleviate the drug resistance in K562 cells when treated with IMA and ADR.     

Role of cell wall of groundnut roots in solubilizing sparingly soluble phosphorus in soil

Groundnut showed a superior ability to take up P from a soil with low P fertility compared with sorghum and soybean. This ability was not related to its better root development or production of root exudates capable of solubilizing iron-and aluminum-bound P. In efforts to determine the role of roots per se, we found that root cell walls from groundnut showed a higher P-solubilizing activity than those from soybean or sorghum. This finding corresponds well with observations in field and pot experiments using a soil with low P availability. The reaction site of P-solubilizing activity is stable against heating and enzyme digestion by cellulase and pectinase. This is probably the first evidence to demonstrate that cell walls of plant roots are involved in P-solubilizing activity. ei]Section editor: H Marschner (deceased 21 September 1996)     

The influence of environmental manipulations on inter– and intra–individual variation in food acquisition and growth performance of Arctic charr, Salvelinus alpinus

Repeated measurements of food intake made on juvenile Arctic charr, Salvelinus alpinus , held under different rearing conditions enabled examination of the effects of environmental manipulations on both intra– and inter–individual variations in food intake to be made. This permitted the assessment of the influences of differential food acquisition on individual growth rates and biomass gain. When charr were held in isolation individual fish showed relatively little day–to–day variability in food intake and inter–individual differences in intake were small ('base–fine' values). All fish exhibited positive rates of growth and the overall range was narrow. Nevertheless, there was a highly significant positive correlation between food intake and growth, indicating that those individuals that consumed the greatest quantities of food were also those that had the highest rates of weight gain. The rearing of charr in groups led to increases in both intra– and inter–individual variations in food intake to levels considerably above 'base–line'. This increased variability in food intake was reflected in rates of weight gain being more variable amongst the charr reared in groups, with fish that lost weight often being recorded. Manipulation of the rearing environment had marked influences upon intra–individual variability in food intake, inter–individual differences in food acquisition and rates of weight gain. High stocking densities and exposure of the fish to moderate water currents were most effective in reducing levels of variability to approach those observed under 'base–line' conditions.     

Role of proteinaceous amino acids released in root exudates in nutrient acquisition from the rhizosphere

The role of proteinaceous amino acids in rhizosphere nutrient mobilization was assessed both experimentally and theoretically. The degree of adsorption onto the soil's solid phase was dependent on both the amino acid species and on soil properties. On addition of amino acids to both soil and freshly precipitated Fe(OH)₃, no detectable mobilization of nutrients (K, Na, Ca, Mg, Cu, Mn, Zn, Fe, S, P, Si and Al) was observed, indicating a very low complexation ability of the acidic, neutral and basic amino acids. This was supported by results from a solution equilibria computer model which also predicted low levels of amino acid complexation with solutes present in the soil solution. On comparison with the Fe(OH)₃ and equilibria data obtained for the organic acid, citrate, it was concluded that amino acids released into the rhizosphere have a limited role in the direct acquisition of nutrients by plants. The effectiveness of root exudates such as amino acids, phytosiderophores and organic acids in nutrient mobilization from the rhizosphere is discussed with reference to rhizosphere diffusion distances, microbial degradation, rate of complexation and the root's capacity to recapture exudate-metal complexes from the soil.     

Diversity of siderophore genes encoding biosynthesis of 2,3-dihydroxybenzoic acid in Aeromonas spp.

Most species of the genus Aeromonas produce the siderophore amonabactin, although two species produce enterobactin, the siderophore of many enteric bacteria. Both siderophores contain 2,3-dihydroxybenzoic acid (2,3-DHB). Siderophore genes (designated aebC, -E, -B and -A, for aeromonad enterobactin biosynthesis) that complemented mutations in the enterobactin genes of the Escherichia coli 2,3-DHB operon, entCEBA(P15), were cloned from an enterobactin-producing isolate of the Aeromonas spp. Mapping of the aeromonad genes suggested a gene order of aebCEBA, identical to that of the E. coli 2,3-DHB operon. Gene probes for the aeromonad aebCE genes and for amoA (the entC-equivalent gene previously cloned from an amonabactin-producing Aeromonas spp.) did not cross-hybridize. Gene probes for the E. coli 2,3-DHB genes entCEBA did not hybridize with Aeromonas spp. DNA. Therefore, in the genus Aeromonas, 2,3-DHB synthesis is encoded by two distinct gene groups; one (amo) is present in the amonabactin-producers, while the other (aeb) occurs in the enterobactin-producers. Each of these systems differs from (but is functionally related to) the E. coli 2,3-DHB operon. These genes may have diverged from an ancestral group of 2,3-DHB genes.     

Rank relations among sisters in semi-free-ranging Barbary macaques (Macaca sylvanus)

Although semi-free-ranging Barbary macaque females are able to outrank older females from lower-ranking matrilines (matrilineal rank acquisition), they do not systematically outrank their older sisters, as is known to be the case for semi-free-ranging rhesus monkeys (Macaca mulatta) and Japanese macaques (Macaca fuscata). We test the hypothesis that differences in the support received by younger sisters against their older sisters and against older lower-ranking females might account for this interspecific difference. Thirty-one sister dyads, members of a group of 109 Barbary macaques living at La Montagne des Singes, France, were observed during 16 months. The results indicate that (1) all females were dominant to their younger sisters, and the latter were never observed to challenge their older sisters; (2) younger sisters received as much kin support against their older sisters as against older lower-ranking females; (3) only very young females received support from their kin against their older sisters; (4) younger sisters received much more support from nonkin females against lower-ranking females than against their older sisters; and (5) Barbary macaque females appear to be supported against their older sisters less frequently than rhesus macaque females are. We conclude that the lack of nonkin support is the main factor accounting for the failure of younger sisters to outrank their older sisters in Barbary macaques. Initially this might result from kin support not being sufficient to induce younger sisters to challenge and to solicit support against their older sisters.     

Behavioral responses of a sex-role reversed pipefish to a gradient of perceived predation risk

Conspicuous behaviors such as courtship and mating often makeanimals susceptible to predation. When perceiving themselvesat an elevated level of risk, animals frequently reduce conspicuousbehaviors in tradeoff for a decrease in probability of beingpreyed upon. In the present study, we used two experiments toexamine the effect of perceived predation risk from cod (Gadusmorhud) on nonreproductive and reproductive behaviors in thesex-role reversed pipefish (Syngnathus typhle). In the firstexperiment, no differences due to predation risk were detectedin the nonreproductive behaviors of either males or females.In the second experiment, predation risk had significant effectson reproductive behaviors. Pipefish were allowed to court andcopulate at four different predation levels. We created predationlevels differing in perceived predation risk by controllingthe number of sensory modes through which pipefish could detectthe presence of a cod. As predation risk increased, pipefishcopulated and courted less frequently, swam alone (displayedand searched for conspecifics) less often, and waited longerbefore commencing courtship. These changes in behavior minimizedthe amount of time spent above the eelgrass and presumably reducedconspicuousness to visual predators. Pipefish also copulatedafter a smaller amount of courtship as predation risk increased,indicating that they may trade information concerning mate qualityfor a reduction in predation risk. No differences were foundin any response variable between males and females. The roleof operational sex ratios and intersexual competition in determiningwhich sex assumes greater costs in mate acquisition is questioned.