Hormonal regulation of DNA synthesis in primary cultures of adult rat hepatocytes : Action of glucagon

Primary cultures of adult rat hepatocytes, grown in modified minimal essential medium (Eagle's) containing 10% calf serum, could be induced into DNA replication by combinations of epidermal growth factor (EGF), insulin and glucagon. The three hormones acted synergistically, and cells began entering DNA synthesis 48 h after hormone addition. The ability of the hormones to stimulate DNA synthesis was enhanced by plating cells at high cell concentrations or by conditioned medium, and was diminished by daily medium change. The contribution of glucagon to DNA synthesis was replaced by cAMP plus 1-methyl, 3-isobutyl xanthine or by adrenergic agents. Evidence is presented which suggests that all three hormones are required on the first day of culture, and that EGF and insulin are also required after the first day. This appears to be a useful system for studies on the hormonal initiation of growth in quiescent cells.     

Taxonomic Comparison of the Amino Termini of Microbial Cell Proteins

A comparison was made of the distribution of amino terminal end groups in the cellular proteins of a number of microbes. Among the procaryotes, methionine is a highly variable but virtually ubiquitous major protein end group. This is consistent with its possible role as a general amino acid initiator of protein biosynthesis in the procaryotes. Generally, however, alanine is the most abundant of the major end groups, followed in decreasing order by serine, threonine, the acidic amino acids, and occasionally lysine. No other new major end-groups were found. Among 15 representatives of the Enterobacteriaceae, retention of the initiating methionine terminus of the cellular protein varies considerably at a tribal level and is randomized at a familial level. The profiles of the five remaining end groups, however, are strikingly uniform, and are, for example, close to but significantly different from those of the Erwineae. Among the taxonomically more heterogeneous Bacillaceae, end-group profiles vary more and are sometimes unrelated. End-group analysis is thus particularly useful as a molecular criterion of taxonomy in assessing familial homogeneity. Free NH(2) termini in eucaryote cell proteins are fewer, and they have increased acidic amino acid components and no methionine; they are otherwise similar to those of the procaryotes.     

Stringent Control of Intracellular Proteolysis in Escherichia coli

Regulation of intracellular proteolysis has been compared during amino acid deficiencies in seven double auxotrophs of Escherichia coli 9723f with a common phenylalanine requirement. Individual deficiencies were either more effective than, less effective, or equal to phenylalanine deficiency in stimulating intracellular proteolysis. For each amino acid, the same relationship prevailed in inhibiting uracil incorporation into nucleic acids, a reaction series regulated by the rel gene for stringent control. The three amino acids least abundant in the cellular protein were the least effective regulators. These findings are interpreted as supportive evidence for stringent control of intracellular proteolysis by the rel gene.     

BioNetBuilder2.0: bringing systems biology to chicken and other model organisms

Background

Systems Biology research tools, such as Cytoscape, have greatly extended the reach of genomic research. By providing platforms to integrate data with molecular interaction networks, researchers can more rapidly begin interpretation of large data sets collected for a system of interest. BioNetBuilder is an open-source client-server Cytoscape plugin that automatically integrates molecular interactions from all major public interaction databases and serves them directly to the user's Cytoscape environment. Until recently however, chicken and other eukaryotic model systems had little interaction data available.

Results

Version 2.0 of BioNetBuilder includes a redesigned synonyms resolution engine that enables transfer and integration of interactions across species; this engine translates between alternate gene names as well as between orthologs in multiple species. Additionally, BioNetBuilder is now implemented to be part of the Gaggle, thereby allowing seamless communication of interaction data to any software implementing the widely used Gaggle software. Using BioNetBuilder, we constructed a chicken interactome possessing 72,000 interactions among 8,140 genes directly in the Cytoscape environment. In this paper, we present a tutorial on how to do so and analysis of a specific use case.

Conclusion

BioNetBuilder 2.0 provides numerous user-friendly systems biology tools that were otherwise inaccessible to researchers in chicken genomics, as well as other model systems. We provide a detailed tutorial spanning all required steps in the analysis. BioNetBuilder 2.0, the tools for maintaining its data bases, standard operating procedures for creating local copies of its back-end data bases, as well as all of the Gaggle and Cytoscape codes required, are open-source and freely available at http://err.bio.nyu.edu/cytoscape/bionetbuilder/.

     

Intestinal barrier function in response to abundant or depleted mucosal glutathione in Salmonella-infected rats

Background  

Glutathione, the main antioxidant of intestinal epithelial cells, is suggested to play an important role in gut barrier function and prevention of inflammation-related oxidative damage as induced by acute bacterial infection. Most studies on intestinal glutathione focus on oxidative stress reduction without considering functional disease outcome. Our aim was to determine whether depletion or maintenance of intestinal glutathione changes susceptibility of rats to Salmonella infection and associated inflammation.     

Anti-Angiogenic/Vascular Effects of the mTOR Inhibitor Everolimus Are Not Detectable by FDG/FLT-PET

Noninvasive functional imaging of tumors can provide valuable early-response biomarkers, in particular, for targeted chemotherapy. Using various experimental tumor models, we have investigated the ability of positron emission tomography (PET) measurements of 2-deoxy-2-[¹⁸F]fluoro-glucose (FDG) and 3′-deoxy-3′-[¹⁸F]fluorothymidine (FLT) to detect response to the allosteric mammalian target of rapamycin (mTOR) inhibitor everolimus. Tumor models were declared sensitive (murine melanoma B16/BL6 and human lung H596) or relatively insensitive (human colon HCT116 and cervical KB31), according to the IC₅₀ values (concentration inhibiting cell growth by 50%) for inhibition of proliferation in vitro (<10 nM and >1 µM, respectively). Everolimus strongly inhibited growth of the sensitive models in vivo but also significantly inhibited growth of the insensitive models, an effect attributable to its known anti-angiogenic/vascular properties. However, although tumor FDG and FLT uptake was significantly reduced in the sensitive models, it was not affected in the insensitive models, suggesting that endothelial-directed effects could not be detected by these PET tracers. Consistent with this hypothesis, in a well-vascularized orthotopic rat mammary tumor model, other antiangiogenic agents also failed to affect FDG uptake, despite inhibiting tumor growth. In contrast, the cytotoxic patupilone, a microtubule stabilizer, blocked tumor growth, and markedly reduced FDG uptake. These results suggest that FDG/FLT-PET may not be a suitable method for early markers of response to antiangiogenic agents and mTOR inhibitors in which anti-angiogenic/vascular effects predominate because the method could provide false-negative responses. These conclusions warrant clinical testing.     

Influence of inverse dynamics methods on the calculation of inter-segmental moments in vertical jumping and weightlifting

Background  

A vast number of biomechanical studies have employed inverse dynamics methods to calculate inter-segmental moments during movement. Although all inverse dynamics methods are rooted in classical mechanics and thus theoretically the same, there exist a number of distinct computational methods. Recent research has demonstrated a key influence of the dynamics computation of the inverse dynamics method on the calculated moments, despite the theoretical equivalence of the methods. The purpose of this study was therefore to explore the influence of the choice of inverse dynamics on the calculation of inter-segmental moments.     

Effects of an extinguished CS on competition with another CS

Three experiments were conducted using a conditioned taste aversion procedure with rats to examine the effect of nonreinforced presentations of a conditioned stimulus (CS) on its ability to compete with a target stimulus for manifest conditioned responding. Two CSs (A and B) were presented in a serial compound and then paired with the unconditioned stimulus. CS A was first paired with the US and then presented without the US (i.e., extinction) prior to reinforced presentation of the AB compound. Experiment 1 showed that A was poor at competing with B for conditioned responding when given conditioning and extinction prior to reinforcement of AB relative to a group that received both A and B for the first time during compound conditioning. That is, an extinguished A stimulus allowed greater manifest acquisition to B. Experiment 2 found that extinction treatment produced a poor CR to the pretrained and extinguished CS itself following compound conditioning. Experiment 3 found that interposing a retention interval after extinction of A and prior to compound conditioning enhanced A's ability to compete with B. The results of these experiments are discussed with regard to different theories of extinction and associative competition.     

Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological features

Background  

Ensemble attribute profile clustering is a novel, text-based strategy for analyzing a user-defined list of genes and/or proteins. The strategy exploits annotation data present in gene-centered corpora and utilizes ideas from statistical information retrieval to discover and characterize properties shared by subsets of the list. The practical utility of this method is demonstrated by employing it in a retrospective study of two non-overlapping sets of genes defined by a published investigation as markers for normal human breast luminal epithelial cells and myoepithelial cells.