Identification of archaeal proteins that affect the exosome function in vitro

Background  

The archaeal exosome is formed by a hexameric RNase PH ring and three RNA binding subunits and has been shown to bind and degrade RNA in vitro. Despite extensive studies on the eukaryotic exosome and on the proteins interacting with this complex, little information is yet available on the identification and function of archaeal exosome regulatory factors.     

Modulation of humoral immune response to oral BCG vaccination by Mycobacterium bovis BCG Moreau Rio de Janeiro (RDJ) in healthy adults

We hypothesize that the energy strategy of a cell is a key factor for determining how, or if, the immune system interacts with that cell. Cells have a limited number of metabolic states, in part, depending on the type of fuels the cell consumes. Cellular fuels include glucose (carbohydrates), lipids (fats), and proteins. We propose that the cell's ability to switch to, and efficiently use, fat for fuel confers immune privilege. Additionally, because uncoupling proteins are involved in the fat burning process and reportedly in protection from free radicals, we hypothesize that uncoupling proteins play an important role in immune privilege. Thus, changes in metabolism (caused by oxidative stresses, fuel availability, age, hormones, radiation, or drugs) will dictate and initiate changes in immune recognition and in the nature of the immune response. This has profound implications for controlling the symptoms of autoimmune diseases, for preventing graft rejection, and for targeting tumor cells for destruction.     

Anti-Inflammatory and Anti-Rheumatic Potential of Selective Plant Compounds by Targeting TLR-4/AP-1 Signaling: A Comprehensive Molecular Docking and Simulation Approaches

Plants are an important source of drug development and numerous plant derived molecules have been used in clinical practice for the ailment of various diseases. The Toll-like receptor-4 (TLR-4) signaling pathway plays a crucial role in inflammation including rheumatoid arthritis. The TLR-4 binds with pro-inflammatory ligands such as lipopolysaccharide (LPS) to induce the downstream signaling mechanism such as nuclear factor κappa B (NF-κB) and mitogen activated protein kinases (MAPKs). This signaling activation leads to the onset of various diseases including inflammation. In the present study, 22 natural compounds were studied against TLR-4/AP-1 signaling, which is implicated in the inflammatory process using a computational approach. These compounds belong to various classes such as methylxanthine, sesquiterpene lactone, alkaloid, flavone glycosides, lignan, phenolic acid, etc. The compounds exhibited different binding affinities with the TLR-4, JNK, NF-κB, and AP-1 protein due to the formation of multiple hydrophilic and hydrophobic interactions. With TLR-4, rutin had the highest binding energy (−10.4 kcal/mol), poncirin had the highest binding energy (−9.4 kcal/mol) with NF-κB and JNK (−9.5 kcal/mol), respectively, and icariin had the highest binding affinity (−9.1 kcal/mol) with the AP-1 protein. The root means square deviation (RMSD), root mean square fraction (RMSF), and radius of gyration (RoG) for 150 ns were calculated using molecular dynamic simulation (MD simulation) based on rutin’s greatest binding energy with TLR-4. The RMSD, RMSF, and RoG were all within acceptable limits in the MD simulation, and the complex remained stable for 150 ns. Furthermore, these compounds were assessed for the potential toxic effect on various organs such as the liver, heart, genotoxicity, and oral maximum toxic dose. Moreover, the blood–brain barrier permeability and intestinal absorption were also predicted using SwissADME software (Lausanne, Switzerland). These compounds exhibited promising physico-chemical as well as drug-likeness properties. Consequently, these selected compounds portray promising anti-inflammatory and drug-likeness properties.     

Potential of Potassium Hydroxide Pretreatment of Switchgrass for Fermentable Sugar Production

Chemical pretreatment of lignocellulosic biomass has been extensively investigated for sugar generation and subsequent fuel production. Alkaline pretreatment has emerged as one of the popular chemical pretreatment methods, but most attempts thus far have utilized NaOH for the pretreatment process. This study aimed at investigating the potential of potassium hydroxide (KOH) as a viable alternative alkaline reagent for lignocellulosic pretreatment based on its different reactivity patterns compared to NaOH. Performer switchgrass was pretreated at KOH concentrations of 0.5–2 % for varying treatment times of 6–48 h, 6–24 h, and 0.25–1 h at 21, 50, and 121 °C, respectively. The pretreatments resulted in the highest percent sugar retention of 99.26 % at 0.5 %, 21 °C, 12 h while delignification up to 55.4 % was observed with 2 % KOH, 121 °C, 1 h. Six pretreatment conditions were selected for subsequent enzymatic hydrolysis with Cellic CTec2® for sugar generation. The pretreatment condition of 0.5 % KOH, 24 h, 21 °C was determined to be the most effective as it utilized the least amount of KOH while generating 582.4 mg sugar/g raw biomass for a corresponding percent carbohydrate conversion of 91.8 %.     

The effect of data scaling on dual prices and sensitivity analysis in linear programs

In many practical situations scaling the data is necessary to solve linear programs. This note explores the relationships in translating the sensitivity analysis between the original and the scaled problems.     

Ensiling Agricultural Residues for Bioethanol Production

The potential of using ensiling, with and without supplemental enzymes, as a cost-effective pretreatment for bioethanol production from agricultural residues was investigated. Ensiling did not significantly affect the lignin content of barley straw, cotton stalk, and triticale hay ensiled without enzyme, but slightly increased the lignin content in triticale straw, wheat straw, and triticale hay ensiled with enzyme. The holocellulose (cellulose plus hemicellulose) losses in the feedstocks, as a result of ensiling, ranged from 1.31 to 9.93%. The percent holocellulose loss in hays during ensiling was lower than in straws and stalks. Ensiling of barley, triticale, wheat straws, and cotton stalk significantly increased the conversion of holocellulose to sugars during subsequent hydrolysis with two enzyme combinations. Enzymatic hydrolysis of ensiled and untreated feedstocks by Celluclast 1.5 L-Novozyme 188 enzyme combination resulted in equal or higher saccharification than with Spezyme CP-xylanase combination. Enzyme loadings of 40 and 60 FPU/g reducing sugars gave similar sugar yields. The percent saccharification with Celluclast 1.5 L-Novozyme 188 at 40 FPU/g reducing sugars was 17.1 to 43.6%, 22.4 to 46.9%, and 23.2 to 32.2% for untreated feedstocks, feedstocks ensiled with, and without enzymes, respectively. Fermentation of the hydrolysates from ensiled feedstocks resulted in ethanol yields ranging from 0.21 to 0.28 g/g reducing sugars.     

Potential of Agricultural Residues and Hay for Bioethanol Production

Production of bioethanol from agricultural residues and hays (wheat, barley, and triticale straws, and barley, triticale, pearl millet, and sweet sorghum hays) through a series of chemical pretreatment, enzymatic hydrolysis, and fermentation processes was investigated in this study. Composition analysis suggested that the agricultural straws and hays studied contained approximately 28.62-38.58% glucan, 11.19-20.78% xylan, and 22.01-27.57% lignin, making them good candidates for bioethanol production. Chemical pretreatment with sulfuric acid or sodium hydroxide at concentrations of 0.5, 1.0, and 2.0% indicated that concentration and treatment agent play a significant role during pretreatment. After 2.0% sulfuric acid pretreatment at 121 degrees C/15 psi for 60 min, 78.10-81.27% of the xylan in untreated feedstocks was solubilized, while 75.09-84.52% of the lignin was reduced after 2.0% sodium hydroxide pretreatment under similar conditions. Enzymatic hydrolysis of chemically pretreated (2.0% NaOH or H2SO4) solids with Celluclast 1.5 L-Novozym 188 (cellobiase) enzyme combination resulted in equal or higher glucan and xylan conversion than with Spezyme(R) CP- xylanase combination. The glucan and xylan conversions during hydrolysis with Celluclast 1.5 L-cellobiase at 40 FPU/g glucan were 78.09 to 100.36% and 74.03 to 84.89%, respectively. Increasing the enzyme loading from 40 to 60 FPU/g glucan did not significantly increase sugar yield. The ethanol yield after fermentation of the hydrolyzate from different feedstocks with Saccharomyces cerevisiae ranged from 0.27 to 0.34 g/g glucose or 52.00-65.82% of the theoretical maximum ethanol yield.     

Modulation of humoral immune response to oral BCG vaccination by Mycobacterium bovis BCG Moreau Rio de Janeiro (RDJ) in healthy adults

Background  

Oral administration of BCG was the route initially used by Calmette and Guérin, but was replaced by intradermal administration in virtually all countries after the Lubeck accident. However, Brazil continued to administer oral BCG Moreau RDJ, which was maintained until the mid-1970s when it was substituted by the intradermal route. Although BCG vaccination has been used in humans since 1921, little is known of the induced immune response. The aim of this study was to analyse immunological responses after oral vaccination with M. bovis BCG Moreau RDJ.