Flow rates of components in digesta of pigs prepared with re-entrant cannulas in the proximal duodenum and terminal ileum, and fed semipurified, hard wheat, and soft wheat diets.

Four pigs prepared with re-entrant cannulas in the proximal duodenum and terminal ileum were used to study flow rates of total digesta, insoluble dry matter, nitrogen, and amino acids entering and leaving the small intestine. The pigs received a semipurified diet, a hard wheat diet, or a soft wheat diet. These were approximately isonitrogenous. A higher rate of passage of digesta through the proximal duodenum and terminal ileum were measured in pigs receiving the hard wheat diet. Peak flow of digesta at the duodenum of all pigs occurred at 1 h post feeding. Peak flow of digesta at the ileum occurred at 9 h post feeding on the soft wheat diet, but somewhat earlier on the hard wheat and semipurified diet. More nitrogen and essential amino acids flowed in the solid fraction of duodenal digesta during the first 2 h post feeding for the wheat diets and 4 h post feeding for the semipurified diet. It was concluded that flow rate of most nutrients from the stomach and through the small intestine of pigs is modified by the composition and texture of the food ingested. It is postulated that efficiency of mixing of digesta with digestive secretions in the stomach is a major factor influencing rate of flow.     

Infection of the heart cockle, Clinocardium nuttallii, from Yaquina Bay,Oregon, with an endosymbiotic alga

Clinocardium nuttallii from Yaquina Bay, Oregon, were found to harbor an endosymbiotic alga. Some aspects of this relationship are presented. The areas of infection include the siphon, mantle, and occasionally the foot. C. nuttallii under 2 years old are not infected; the incidence and intensity of the infection increases in the older age groups. For all ages the incidence averages 35%. Pigment composition, morphology, and growth characteristics of the alga are similar to those found in the genus Chlorella. In situ, the algae form dense, sometimes massive colonies but do not appear to cause any host reaction or enfeeblement. The thick layers surrounding the algal cells in situ, the dense colonies, and the in vitro reaction to host extract suggest the alga is parasitic. However, the presence of chloroplasts, the location of the algal cells only in illuminated tissue, the seemingly unhampered reproduction in situ, and the eventual adaptation to mineral medium suggest the alga is a facultative parasite. Experimental infection was achieved by feeding mature uninfected cockles a diet of only symbiont cells. In vitro observations found the symbiont cells readily engulfed by host blood amoebocytes. It is believed that the animal acquires the infection through phagocytosis of the symbiont cells and subsequent diapedesis across epithelial barriers by host amoebocytic cells.     

The effect of density and mutual interference by a Predator: A laboratory study of predation by the Nudibranch Coryphella rufibranchialis on the hydroid Tubularia larynx

The nudibranch Coryphella rufibranchialis (JOHNSTON) feeds on a variety of hydroids, including Tubularia larynx Ellis & Solander. Experiments in which density of prey and predators were altered showed that more prey were eaten as prey density increased. However, more prey were consumed at low predator densities, presumably because of mutual interference among nudibranchs at the higher predator densities. The number of prey consumed per nudibranch was maximal with low predator densities and a ratio of 25–50 polyps per predator. Coryphella seems to show an opportunistic feeding strategy involving solitary predators rapidly depleting hydroid colonies and moving on to new colonies.     

Steroidal saponins of Yucca filamentosa: Yuccoside C and protoyuccoside C

Two new saponins, yuccoside C and protoyuccoside C, have been isolated from the methanolic extract of Yucca filamentosa root and their structures elucidated. Yuccoside C is 3-O-[α-d-galactopyranosyl-(1 → 2)-β-d-glucopyranosyl-(1 → 4)-β-d-glucopyranosyl]-(25S)-5β-spirostan-3β-ol, whereas protoyuccoside C is 3-O-[α-d-galactopyranosyl-(1 → 2)-β-d-glucopyranosyl-(1 → 4)-β-d-glucopyranosyl]-26-O-[β-d-glucopyranosy]-(25S)-5β-furostan-3β,22α,26-triol.     

Analysis of multiple basal cell carcinomas (BCCs) arising in one individual highlights genetic tumor heterogeneity and identifies novel driver mutations

Basal cell carcinoma (BCC) is the most common human cancer, especially in individuals with light skin phototypes (i.e., Fitzpatrick I-II skin type). Many affected develop multiple BCCs during their lifetime. It is not uncommon to observe elderly patients with >5 BCCs. In this study, we explored whether for patients diagnosed with multiple BCCs, analyzing the genomic mutations in one tumor could be sufficient to derive meaningful molecular/genetic conclusions regarding the other BCC tumors. Following the Genome Analysis Toolkit (GATK) best practices we have completed the study of 6 BCCs that occurred in an 83-year-old Caucasian male due to sun exposure. We have analyzed exome sequencing data of each BCC tumor and matched normal skin samples. We identified that BCCs from the same patient shared some of the key driver mutations, but they also displayed significant intertumoral heterogeneity. This finding may in part explain the different clinical progression/evolution of BCCs observed in the same patient. This work also highlights the value of characterizing multiple BCCs in one individual to identify patient-specific genetic events with a potential link to other malignancies and implications for personalized medicine.     

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 . The most relevant networks are found when the network topology changes abruptly revealing distinct modules related to the sets of organisms to which the proteins belong. Sound biological information can be retrieved by the computational routines used in the network approach, without using biological assumptions other than those incorporated by BLAST. Usually, all the main bacterial phyla and, in some cases, also some bacterial classes corresponded totally (100%) or to a great extent (>70%) to the modules. We checked for internal consistency in the obtained results, and we scored close to 84% of matches for community pertinence when comparisons between the results were performed. To illustrate how to use the network-based method, we employed data for enzymes involved in the chitin metabolic pathway that are present in more than 100 organisms from an original data set containing 1,695 organisms, downloaded from GenBank on May 19, 2007. A preliminary comparison between the outcomes of the network-based method and the results of methods based on Bayesian, distance, likelihood, and parsimony criteria suggests that the former is as reliable as these commonly used methods. We conclude that the network-based method can be used as a powerful tool for retrieving modularity information from weighted networks, which is useful for phylogenetic analysis.