Mechanism of imidazolium ionic liquids toxicity in Saccharomyces cerevisiae and rational engineering of a tolerant, xylose-fermenting strain

Additional file 3. Fermentation profiles of Y133 and Y133-IIL in the presence of 1 % [BMIM]Cl at pH 6.5 and pH 5.0, and either aerobic or anaerobic conditions (n = 3, Mean ± S.E, except n = 2 for Y133 pH 6.5 anaerobic 72 h)

Survey of coherent ∼1 Hz waves in Mercury's inner magnetosphere from MESSENGER observations

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95559/1/jgra22073.pd

MASH Explorer: A Universal Software Environment for Top-Down Proteomics

Top-down mass spectrometry (MS)-based proteomics enable a comprehensive analysis of proteoforms with molecular specificity to achieve a proteome-wide understanding of protein functions. However, the lack of a universal software for top-down proteomics is becoming increasingly recognized as a major barrier, especially for newcomers. Here, we have developed MASH Explorer, a universal, comprehensive, and user-friendly software environment for top-down proteomics. MASH Explorer integrates multiple spectral deconvolution and database search algorithms into a single, universal platform which can process top-down proteomics data from various vendor formats, for the first time. It addresses the urgent need in the rapidly growing top-down proteomics community and is freely available to all users worldwide. With the critical need and tremendous support from the community, we envision that this MASH Explorer software package will play an integral role in advancing top-down proteomics to realize its full potential for biomedical research

Antibody landscape of C57BL/6 mice cured of B78 melanoma via a combined radiation and immunocytokine immunotherapy regimen

Sera of immune mice that were previously cured of their melanoma through a combined radiation and immunocytokine immunotherapy regimen consisting of 12 Gy of external beam radiation and the intratumoral administration of an immunocytokine (anti-GD2 mAb coupled to IL-2) with long-term immunological memory showed strong antibody-binding against melanoma tumor cell lines via flow cytometric analysis. Using a high-density whole-proteome peptide array (of 6.090.593 unique peptides), we assessed potential protein-targets for antibodies found in immune sera. Sera from 6 of these cured mice were analyzed with this high-density, whole-proteome peptide array to determine specific antibody-binding sites and their linear peptide sequence. We identified thousands of peptides that were targeted by these 6 mice and exhibited strong antibody binding only by immune (after successful cure and rechallenge), not naïve (before tumor implantation) sera and developed a robust method to detect these differentially targeted peptides. Confirmatory studies were done to validate these results using 2 separate systems, a peptide ELISA and a smaller scale peptide array utilizing a slightly different technology. To the best of our knowledge, this is the first study of the full set of germline encoded linear peptide-based proteome epitopes that are recognized by immune sera from mice cured of cancer via radio-immunotherapy. We furthermore found that although the generation of B-cell repertoire in immune development is vastly variable, and numerous epitopes are identified uniquely by immune serum from each of these 6 immune mice evaluated, there are still several epitopes and proteins that are commonly recognized by at least half of the mice studied. This suggests that every mouse has a unique set of antibodies produced in response to the curative therapy, creating an individual “fingerprint.” Additionally, certain epitopes and proteins stand out as more immunogenic, as they are recognized by multiple mice in the immune group

Wheat polar lipids: sources of variation among near-isogenic wheat lines with different endosperm hardness

Doctor of PhilosophyDepartment of Grain Science and IndustryJon M. FaubionStarch granule surface components were studied as a function of puroindoline haplotype, starch isolation method, and processing fraction. Commonly grown cultivars and near-isogenic wheat lines that varied in their wheat endosperm hardness were collected. Wheat whole-meal, flour and starch were evaluated for their polar lipid composition. Water-washed starch was isolated using a modified batter method and a dough method. Direct infusion tandem mass spectrometry was used to identify the lipid species in the extracts. A total of 155 polar lipid species in wheat meal, flour and starch were quantitatively characterized. The predominant polar lipid classes were digalactosyldiglycerides, monogalactosyldiglycerides, phosphatidylcholine, and lysophosphatidylcholine. Wheat whole-meal, flour and surface-starch contained greater concentrations of total galactolipids while internal-starch lipids contained greater concentrations of monoacyl phospholipids. Wide ranges in starch surface polar lipid concentrations were observed between the two starch isolation methods. Starch isolation methods provided a greater source of variation than did wheat kernel hardness. When dough is optimally mixed the lipids originally on the surface of wheat starch become incorporated into the gluten phase of the dough, whereas in a batter system the starch-surface lipids stay associated with the starch granule surface. The greatest quantities of polar lipids on the starch surface occurred when both puroindoline proteins were present on starch in their wild-type form. Starch surface polar lipid content decreased dramatically when one of the puroindoline proteins was null, or if the puroindoline-b (pin-b) was in the mutated form (Tryptophan-44 to Arginine). Within the hard textured samples, more polar lipids were present on the starch surface when pin-b was in its wild-type form and puroindoline-a (pin-a) was null than when pin-a was in its wild-type form and pin-b was null. The lowest amount of polar lipids were present when pin-b was mutated (Tryptophan-44 to Arginine) and pin-a was in its wild-type form. This indicates the relative importance of pin-b’s presence and structure as it relates to lipid association with the starch granule surface