Detecting network communities: an application to phylogenetic analysis.

This paper proposes a new method to identify communities in generally weighted complex networks and apply it to phylogenetic analysis. In this case, weights correspond to the similarity indexes among protein sequences, which can be used for network construction so that the network structure can be analyzed to recover phylogenetically useful information from its properties. The analyses discussed here are mainly based on the modular character of protein similarity networks, explored through the Newman-Girvan algorithm, with the help of the neighborhood matrix .

Comparative protein analysis of the chitin metabolic pathway in extant organisms: a complex network approach.

Chitin is a structural endogenous carbohydrate, which is a major component of fungal cell walls and arthropod exoskeletons. A renewable resource and the second most abundant polysaccharide in nature after cellulose, chitin is currently used for waste water clearing, cosmetics, medical, and veterinary applications. This work comprises data mining of protein sequences related to the chitin metabolic pathway of completely sequenced genomes of extant organisms pertaining to the three life domains, followed by meta-analysis using traditional sequence similarity comparison and complex network approaches.

Primary culture of venom glands from the Brazilian armed spider, Phoneutria nigriventer (Araneae, Ctenidae).

Phoneutria spider venoms are a rich source of bioactive components. The limited amounts of crude material available, however, can be considered as a major hindrance for a faster development in the field. In the present study, we attempted to establish primary cultures of venom glands of Phoneutria nigriventer as an alternative, in vitro source of venom.

Biochemical characterization and molecular cloning of a plasminogen activator proteinase (LV-PA) from bushmaster snake venom.

The protein (LV-PA) from bushmaster (Lachesis muta muta) venom is a serine proteinase which specifically activates the inactive proenzyme plasminogen. LV-PA is a single chain glycoprotein with an apparent molecular mass of 33 kDa that fell to 28 kDa after treatment with N-Glycosidase F (PNGase F). Approximately 93% of its protein sequence was determined by automated Edman degradation of various fragments derived from a digestion with trypsin.