Modeling the effects of pelleting on the logistics of distillers grains shipping

The energy security needs of energy importing nations continue to escalate. It is clear that biofuels can help meet some of the increasing need for energy. Theoretically, these can be produced from a variety of biological materials, including agricultural residues (such as corn stover and wheat straw), perennial grasses, legumes, algae, and other biological materials. Currently, however, the most heavily utilized material is corn starch. Industrial fuel ethanol production in the US primarily uses corn, because it is readily converted into fuel at a relatively low cost compared to other biomass sources. The production of corn-based ethanol in the US is dramatically increasing. As the industry continues to grow, the amount of byproducts and coproducts also increases. At the moment, the nonfermentable residues (which are dried and sold as distillers dried grains with solubles – DDGS) are utilized only as livestock feed. The sale of coproducts provides ethanol processors with a substantial revenue source and significantly increases the profitability of the production process. Even though these materials are used to feed animals in local markets, as the size and scope of the industry continues to grow, the need to ship large quantities of coproducts grows as well. This includes both domestic as well as international transportation. Value-added processing options offer the potential to increase the sustainability of each ethanol plant, and thus the industry overall. However, implementation of new technologies will be dependent upon how their costs interact with current processing costs and the logistics of coproduct deliveries. The objective of this study was to examine some of these issues by developing a computer model to determine potential cost ramifications of using various alternative technologies during ethanol processing. This paper focuses specifically on adding a densification unit operation (i.e., pelleting) to produce value-added DDGS at a fuel ethanol manufacturing plant. We have examined the economic implications of pelleting DDGS for varying DDGS production rates (100–1000 tons/d) and pelleting rates (0–100%), for a series of DDGS sales prices ($50–$200/ton). As the proportion of pelleting increases, the cost of transporting DDGS to distant markets drastically declines, because the rail cars can be filled to capacity. For example, at a DDGS sales price of $50/ton, 100% pelleting will reduce shipping costs (both direct and indirect) by 89% compared to shipping the DDGS in bulk form (i.e., no pelleting), whereas at a DDGS sales price of $200/ton, it will reduce costs by over 96%. It is clear that the sustainability of the ethanol industry can be improved by implementing pelleting technology for the coproducts, especially at those plants that ship their DDGS via rail.     

Macrocyclic peptidomimetic β-secretase (BACE-1) inhibitors with activity in vivo

The macrocyclic peptidic BACE-1 inhibitors 2a–c show moderate enzymatic and cellular activity. By exchange of the hydroxyethylene- to ethanolamine-transition state mimetic the peptidic character was reduced, providing the highly potent and selective inhibitor 3. Variation of the P′ moiety resulted in the macrocyclic inhibitor 14. Both macrocycles show inhibition of BACE-1 in the brain of APP51/16 transgenic mice, 3 (NB-544) after intravenous and 14 (NB-533) after oral application.     

Discovery of the imidazo[1,5-a][1,2,4]-triazolo[1,5-d][1,4]benzodiazepine scaffold as a novel,potent and selective GABAA α5 inverse agonist series

Through iterative design cycles we have discovered a number of novel new classes where the imidazo[1,5-a][1,2,4]-triazolo[1,5-d][1,4]benzodiazepine was deemed the most promising GABA_A α5 inverse agonist class with potential for cognitive enhancement. This class combines a modest subtype binding selectivity with inverse agonism and has the most favourable molecular properties for further lead optimisation towards a central nervous system (CNS) acting medicine.     

Complete genome sequence of Anaerococcus prevotii type strain (PC1)

Anaerococcus prevotii (Foubert and Douglas 1948) Ezaki et al. 2001 is the type species of the genus, and is of phylogenetic interest because of its arguable assignment to the provisionally arranged family 'Peptostreptococcaceae'. A. prevotii is an obligate anaerobic coccus, usually arranged in clumps or tetrads. The strain, whose genome is described here, was originally isolated from human plasma; other strains of the species were also isolated from clinical specimen. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the genus. Next to Finegoldia magna, A. prevotii is only the second species from the family 'Peptostreptococcaceae' for which a complete genome sequence is described. The 1,998,633 bp long genome (chromosome and one plasmid) with its 1852 protein-coding and 61 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Morphine and HIV-Tat increase microglial-free radical production and oxidative stress: possible role in cytokine regulation

Opiate abuse alters the progression of human immunodeficiency virus and may increase the risk of neuroAIDS. As neuroAIDS is associated with altered microglial reactivity, the combined effects of human immunodeficiency virus-Tat and morphine were determined in cultured microglia. Specifically, experiments determined the effects of Tat and morphine on microglial-free radical production and oxidative stress, and on cytokine release. Data show that combined Tat and morphine cause early and synergistic increases in reactive oxygen species, with concomitant increases in protein oxidation. Furthermore, combined Tat and morphine, but not Tat or morphine alone, cause reversible decreases in proteasome activity. The effects of morphine on free radical production and oxidative stress are prevented by pre-treatment with naloxone, illustrating the important role of opioid receptor activation in these phenomena. While Tat is well known to induce cytokine release from cultured microglia, morphine decreases Tat-induced release of the cytokines tumor necrosis factor-α and interleukin-6, as well as the chemokine monocyte chemoattractant protein-1 (MCP-1). Finally, experiments using the reversible proteasome inhibitor MG115 show that temporary, non-cytotoxic decreases in proteasome activity increase protein oxidation and decrease tumor necrosis factor-α, interleukin-6, and MCP-1 release from microglia. Taken together, these data suggest that oxidative stress and proteasome inhibition may be involved in the immunomodulatory properties of opioid receptor activation in microglia.     

Prolectin, a Glycan-binding Receptor on Dividing B Cells in Germinal Centers

Prolectin, a previously undescribed glycan-binding receptor, has been identified by re-screening of the human genome for genes encoding proteins containing potential C-type carbohydrate-recognition domains. Glycan array analysis revealed that the carbohydrate-recognition domain in the extracellular domain of the receptor binds glycans with terminal α-linked mannose or fucose residues. Prolectin expressed in fibroblasts is found at the cell surface, but unlike many glycan-binding receptors it does not mediate endocytosis of a neoglycoprotein ligand. However, compared with other known glycan-binding receptors, the receptor contains an unusually large intracellular domain that consists of multiple sequence motifs, including phosphorylated tyrosine residues, that allow it to interact with signaling molecules such as Grb2. Immunohistochemistry has been used to demonstrate that prolectin is expressed on a specialized population of proliferating B cells in germinal centers. Thus, this novel receptor has the potential to function in carbohydrate-mediated communication between cells in the germinal center.Membrane-bound mammalian glycan-binding receptors, often referred to as lectins, are believed to play multiple distinct roles in the immune system, decoding information in complex oligosaccharide structures on cell surfaces and soluble glycoproteins (1, 2). A host of glycan-binding receptors on dendritic cells and macrophages function in pathogen recognition, often resulting in uptake of microbes through endocytic mechanisms. Examples include the mannose receptor, DC-SIGN,³ langerin, and the macrophage galactose receptor. Glycan-binding receptors can also recognize glycans found on the surfaces of mammalian cells. Some of these receptors, such as the selectins, mediate adhesion between leukocytes and endothelia (3, 4). A small number of receptors, notably members of the siglec family, bind mammalian-type glycans and have been shown to have potential signaling functions (5). While multiple glycan-binding receptors have been described on cells of the myeloid lineage, the complement of such receptors on lymphocytes is much more restricted. The best characterized examples are the T-cell adhesion molecule L-selectin (4) and the B-cell receptor CD22, also designated siglec-2 (5).Genomic screening for potential glycan-binding receptors has usually been undertaken by initially searching for the presence of one of the several types of structural domains that are known to support sugar-binding activity (6). Knowledge of the structures of multiple families of modular carbohydrate-recognition domains (CRDs) has facilitated identification of proteins with potential sugar-binding activity and can lead to predictions of what types of ligands might be bound. Although the human genome has been extensively screened with profile-recognition algorithms that identify common sequence motifs associated with CRDs, refinements to the genome sequence and improvements in gene-recognition algorithms occasionally result in detection of novel proteins that contain putative CRDs.We describe a previously undetected glycan-binding receptor identified by re-screening of the human genome and provide characterization of its molecular and cellular properties. Based on its expression in a specialized population of proliferating B cells in germinal centers, we propose that it be designated prolectin. Our results suggest that prolectin functions in carbohydrate-mediated communication between cells in the germinal center.     

Predictive Mapping of Plant Species and Communities Using GIS and Landsat Data in a Southern Mongolian Mountain Range

We assessed presence/absence prediction of plant species and communities in a southern Mongolian mountain range from geospatial data using a randomized sampling approach. One hundred randomized vegetation samples (3?×?3 m) were collected within the 2?×?2 km summit region of the Dund Saykhan range, which forms part of the core zone of the Gobi Gurvan Saykhan National Park in arid southern Mongolia. Using logistic regression, habitat preference models for all abundant species (n?=?52) and communities (n?=?5) were constructed; predictors were derived from Landsat 5 imagery and a digital elevation model. Nagelkerkes r ² was used for an initial data mining, and all significant models were validated by splitting the data and using one half for accuracy assessment based on the AUC (Area Under the receiver operating characteristic Curve)-values. Significant models could be built for half of the species. Altitude proved to be the most important predictor followed by variables derived from Landsat data. The clear altitudinal distribution patterns most definitely reflect precipitation; overall biodiversity in this arid environment is widely controlled by moisture availability. The chosen approach may prove valuable for applied studies wherever spatial data on species distributions are required for conservation efforts.     

A role for the 30S subunit E site in maintenance of the translational reading frame

The exit (E) site has been implicated in several ribosomal activities, including translocation, decoding, and maintenance of the translational reading frame. Here, we target the 30S subunit E site by introducing a deletion in rpsG that truncates the β-hairpin of ribosomal protein S7. This mutation (S7ΔR77–Y84) increases both −1 and +1 frameshifting but does not increase miscoding, providing evidence that the 30S E site plays a specific role in frame maintenance. Mutation S7ΔR77–Y84 also stimulates +1 programmed frameshifting during prfB′-lacZ translation in many synthetic contexts. However, no effect is seen when the E codon of the frameshift site corresponds to those found in nature, suggesting that E-tRNA release does not normally limit the rate of prfB frameshifting. Ribosomes containing S7ΔR77–Y84 exhibit an elevated rate of spontaneous reverse translocation and an increased K_1/2 for E-tRNA. These effects are of similar magnitude, suggesting that both result from destabilization of E-tRNA. Finally, this mutation of the 30S E site does not inhibit EF-G-dependent translocation, consistent with a primary role for the 50S E site in the mechanism.     

Prion Protein-Detergent Micelle Interactions Studied by NMR in Solution

Cellular prion proteins, PrP^C, carrying the amino acid substitutions P102L, P105L, or A117V, which confer increased susceptibility to human transmissible spongiform encephalopathies, are known to form structures that include transmembrane polypeptide segments. Herein, we investigated the interactions between dodecylphosphocholine micelles and the polypeptide fragments 90–231 of the recombinant mouse PrP variants carrying the amino acid replacements P102L, P105L, A117V, A113V/A115V/A118V, K110I/H111I, M129V, P105L/M129V, and A117V/M129V. Wild-type mPrP-(90–231) and mPrP[M129V]-(91–231) showed only weak interactions with dodecylphosphocholine micelles in aqueous solution at pH 7.0, whereas discrete interaction sites within the polypeptide segment 102–127 were identified for all other aforementioned mPrP variants by NMR chemical shift mapping. These model studies thus provide evidence that amino acid substitutions within the polypeptide segment 102–127 affect the interactions of PrP^C with membranous structures, which might in turn modulate the physiological function of the protein in health and disease.Transmissible spongiform encephalopathies (TSEs),² such as Creutzfeldt-Jakob disease and the Gerstmann-Sträussler-Scheinker syndrome in humans, are accompanied by the appearance in the brain of an aggregated “scrapie” isoform of the host-encoded prion protein, PrP^Sc (1–3). The cellular form, PrP^C, consists of an unstructured N-terminal “tail” of residues 23–125 and a globular domain of residues 126–231, and is attached by a C-terminal glycosylphosphatidylinositol (GPI) anchor to the outer plasma membrane. This structure ensures a role of membrane interactions in the physiological function of PrP^C and probably also in the disease-related events leading to TSEs. For example, transgenic mice expressing a prion protein variant lacking the GPI membrane anchor did not develop the typical clinical signs of TSE after inoculation with infectious brain homogenate, although significant amounts of PrP^Sc accumulated in the brain (4). This finding led to the conclusion that membrane-association of PrP^C is necessary for the development of a TSE. Independent evidence for the importance of membrane interactions for the onset of prion diseases was derived from cell-free conversion assays and cell culture experiments (5, 6).Data have also been presented that indicate that in addition to the normal form with the C terminus linked to a GPI anchor and the C-terminal domain located on the cell surface, PrP^C can adopt two different transmembrane topologies, ^CtmPrP and ^NtmPrP, which have the C-terminal polypeptide segment located in the lumen of the endoplasmic reticulum (^CtmPrP) or in the cytoplasm (^NtmPrP) (7–9). The population of the ^CtmPrP variant is <10% of the total wild-type prion protein present during cellular biosynthesis but is increased to 20–30% for the pathogenic mutations P102L, P105L, and A117V of human PrP and the designed variant mouse PrPs obtained with the amino acid exchanges A113V/A115V/A118V and K110I/H111I (10–13). The population of ^CtmPrP was further increased when an additional mutation, L9R, was present in the N-terminal signal sequence (14), so that ∼50% of the PrP was synthesized as the ^CtmPrP variant in granule neurons obtained from transgenic mice expressing a prion protein construct carrying the four amino acid replacements L9R, A113V, A115V, and A118V (15). Quite generally, an increase in the population of ^CtmPrP was also shown to be associated with severe neurodegeneration in transgenic mice, and it has been suggested that ^CtmPrP may be the proximate cause of neuronal death in certain prion disorders (10, 11, 15).In vitro studies on interactions of full-length and N-terminally truncated forms of recombinant PrP showed that acidic membranes caused the N-terminal part of the protein to become more structured, whereas the C-terminal domain was destabilized (16–19). Furthermore, zwitterionic gel-phase dipalmitoylphosphatidylcholine or raft-like membranes were shown to induce increased α-helical structure in recombinant Syrian hamster PrP-(90–231) at pH 7.0 (18, 19). Membrane interactions of polypeptides representing sequence motifs found in the prion protein have also been studied (20–23).In this report we describe investigations of PrP interactions with a membrane mimetic and focus on the mutations P102L, P105L, and A117V, which have been linked with familial Gerstmann-Sträussler-Scheinker syndrome in humans (2, 24, 25). Our interest in these variant proteins is related to open questions about the mechanisms by which pathogenic mutations predispose humans for prion diseases. We studied the interactions of a recombinant wild-type mouse prion protein fragment, mPrP-(90–231), and the variants mPrP[P102L]-(91–231), mPrP[P105L]-(91–231), mPrP[A117V]-(90–231), mPrP[A113V,A115V,A118V]-(90–231), and mPrP[K110I,H111I]-(90–231). For these studies, we used the N-terminally truncated protein composed of residues 90–231. This region contains the transmembrane segment, all known disease-associated point mutations, the entire polypeptide fragment with proteinase K-resistance in PrP^Sc, which is also sufficient to transmit disease (1, 25, 26). The amino acid substitutions in these variant PrPs are located either within a hydrophobic stretch of residues 112–127, which is highly conserved in mammalian PrPs (27, 28), or in the positively charged segment of residues 95–111 (Fig. 1, B and C). We also included the M129V polymorphism into this study, which was reported to have a significant influence on the susceptibility of humans to prion diseases and on the disease phenotype. For example, the mutations P105L and A117V are only pathogenic in the presence of valine at position 129 (2, 24). The zwitterionic detergent dodecylphosphocholine (DPC, Fig. 1A) was used as a biomembrane mimetic model system, and NMR spectroscopy was employed to screen for protein-detergent micelle interactions, and for the structural characterization of the various prion protein constructs interacting with the detergent micelles.Open in a separate windowFIGURE 1.Detergent and proteins used in this study. A, zwitterionic form of DPC. B, schematic diagram of the mPrP-(90–231) polypeptide indicating the locations of the regular secondary structures, i.e. three α-helices and two strands of an antiparallel β-sheet, a “positively charged cluster” (CC) of amino acid residues in positions 95–111, and a “hydrophobic polypeptide segment” (HPS) comprising residues 112–127. C, amino acid sequence alignment of residues 90–135 for wild-type mPrP-(90–231) and the protein variants studied in this paper, where for each variant mPrP the amino acid replacements are given and identical residues are indicated by dots; the numbering is according to Schätzl et al. (27).