Influence of substrate/inoculum ratio, inoculum source and ammonia inhibition on anaerobic digestion of poultry waste

Poultry wastes are rich in organic matter, allowing their use as substrates for biogas production by anaerobic digestion (AD). The major difficulty in the anaerobic digestion of this protein-rich waste is ammonia inhibition. Different results of biochemical methane potential (BMP) were obtained after the mesophilic anaerobic digestion of different avian waste in batch mode. It was shown that using two different inoculum (Liger and Saint-Brieuc) sources and different substrate-to-inoculum (S/I) ratios does not have a significant effect on the biochemical methane potential of organic laying hen droppings (OLHD); an average of 0.272 Nm3 CH4·kg-1·VS was obtained with both inocula. Otherwise, it affects the hydrolysis constant KH, and it decreases when the substrate-to-inoculum ratio increases. Furthermore, Liger is the most suitable inoculum for our substrate because it shows stability during the process even with different organic loads. Comparing the biochemical methane potential of multiple avian wastes such as organic laying hen droppings and different slaughterhouse waste highlights the importance of slaughterhouse waste in the anaerobic digestion process because of the high methane yield observed especially with the viscera (0.779 Nm3 CH4·kg-1 VS, SD = 0.027 Nm3 CH4·kg-1 VS). Moreover, methane production was affected by increasing the ammonia concentrations; when [N-NH3] > 9.8 g·N-NH3·L-1, the biochemical methane potential decreases and the lag phase increases (λ > 30 days); a total inhibition of the process was observed when ammonia concentration is above 21.8 g·L-1.

Cloning and functional characterization of an NAD(+)-dependent DNA ligase from Staphylococcus aureus

A Staphylococcus aureus mutant conditionally defective in DNA ligase was identified by isolation of complementing plasmid clones that encode the S. aureus ligA gene. Orthologues of the putative S. aureus NAD(+)-dependent DNA ligase could be identified in the genomes of Bacillus stearothermophilus and other gram-positive bacteria and confirmed the presence of four conserved amino acid motifs, including motif I, KXDG with lysine 112, which is believed to be the proposed site of adenylation. DNA sequence comparison of the ligA genes from wild type and temperature-sensitive S. aureus strain NT64 identified a single base alteration that is predicted to result in the amino acid substitution E46G. The S. aureus ligA gene was cloned and overexpressed in Escherichia coli, and the enzyme was purified to near homogeneity. NAD(+)-dependent DNA ligase activity was demonstrated with the purified enzyme by measuring ligation of (32)P-labeled 30-mer and 29-mer oligonucleotides annealed to a complementary strand of DNA. Limited proteolysis of purified S. aureus DNA ligase by thermolysin produced products with apparent molecular masses of 40, 22, and 21 kDa. The fragments were purified and characterized by N-terminal sequencing and mass analysis. The N-terminal fragment (40 kDa) was found to be fully adenylated. A fragment from residues 1 to 315 was expressed as a His-tagged fusion in E. coli and purified for functional analysis. Following deadenylation with nicotinamide mononucleotide, the purified fragment could self-adenylate but lacked detectable DNA binding activity. The 21- and 22-kDa C-terminal fragments, which lacked the last 76 amino acids of the DNA ligase, had no adenylation activity or DNA binding activity. The intact 30-kDa C terminus of the S. aureus LigA protein expressed in E. coli did demonstrate DNA binding activity. These observations suggest that, as in the case with the NAD(+)-dependent DNA ligase from B. stearothermophilus, two independent functional domains exist in S. aureus DNA ligase, consisting of separate adenylation and DNA binding activities. They also demonstrate a role for the extreme C terminus of the ligase in DNA binding. As there is much evidence to suggest that DNA ligase is essential for bacterial survival, its discovery in the important human pathogen S. aureus indicates its potential as a broad-spectrum antibacterial target for the identification of novel antibiotics.

Activation of human liver glycogen phosphorylase by alteration of the secondary structure and packing of the catalytic core

Glycogen phosphorylases catalyze the breakdown of glycogen to glucose-1-phosphate, which enters glycolysis to fulfill the energetic requirements of the organism. Maintaining control of blood glucose levels is critical in minimizing the debilitating effects of diabetes, making liver glycogen phosphorylase a potential therapeutic target. To support inhibitor design, we determined the crystal structures of the active and inactive forms of human liver glycogen phosphorylase a. During activation, forty residues of the catalytic site undergo order/disorder transitions, changes in secondary structure, or packing to reorganize the catalytic site for substrate binding and catalysis. Knowing the inactive and active conformations of the liver enzyme and how each differs from its counterpart in muscle phosphorylase provides the basis for designing inhibitors that bind preferentially to the inactive conformation of the liver isozyme.

Inhibition of MMP-1 and MMP-13 with phosphinic acids that exploit binding in the S2 pocket

Through the use of empirical and computational methods, phosphinate-based inhibitors of MMP-1 and MMP-13 that bind into the S2 pocket of these enzymes were designed. The synthesis and testing of 2 suggested that binding was occurring as hypothesized. Structure determination of a co-crystal of 2 bound to the catalytic domain of MMP-1 confirmed the binding mode. Substituents binding into S2, S1', S2' and S3', were optimized yielding compounds with low double-digit nM IC50's against these enzymes.