An Algorithm for Finding Functional Modules and Protein Complexes in Protein-Protein Interaction Networks

Biological processes are often performed by a group of proteins rather than by individual proteins, and proteins in a same biological group form a densely connected subgraph in a protein-protein interaction network. Therefore, finding a densely connected subgraph provides useful information to predict the function or protein complex of uncharacterized proteins in the highly connected subgraph. We have developed an efficient algorithm and program for finding cliques and near-cliques in a protein-protein interaction network. Analysis of the interaction network of yeast proteins using the algorithm demonstrates that 59% of the near-cliques identified by our algorithm have at least one function shared by all the proteins within a near-clique, and that 56% of the near-cliques show a good agreement with the experimentally determined protein complexes catalogued in MIPS

Redox signaling in aging kidney and opportunity for therapeutic intervention through natural products.

Kidney diseases are serious public problems with high morbidity and mortality in the general population and heavily retard renal function with aging regardless of the cause. Although myriad strategies have been assigned to prevent or harness disease progression, unfortunately, thus far, there is a paucity of effective therapies partly due to an insufficient knowledge of underlying pathological mechanisms, indicating deeper studies are urgently needed. Additionally, natural products are increasingly recognized as an alternative source for disease intervention owing to the potent safety and efficacy, which might be exploited for novel drug discovery. In this review, we primarily expatiate the new advances on mediators that might be amenable to targeting aging kidney and kidney diseases, including nicotinamide adenine dinucleotide phosphate oxidase (NOX), transforming growth factor-β (TGF-β), renin-angiotensin system (RAS), nuclear factor-erythroid 2 related factor 2 (Nrf2), peroxisome proliferator-activated γ receptor (PPARγ), advanced glycation endproducts (AGEs) as well as microRNAs and vitagenes. Of note, we conclude by highlighting some natural products which have the potential to facilitate the development of novel treatment for patients with myriad renal diseases

Draft genome sequence of Acidithiobacillus ferrooxidans YQH-1

AbstractAcidithiobacillus ferrooxidans YQH-1 is a moderate acidophilic bacterium isolated from a river in a volcano of Northeast China. Here, we describe the draft genome of strain YQH-1, which was assembled into 123 contigs containing 3,111,222bp with a G+C content of 58.63%. A large number of genes related to carbon dioxide fixation, dinitrogen fixation, pH tolerance, heavy metal detoxification, and oxidative stress defense were detected. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no. LJBT00000000