Designing experiments that aid in the identification of regulatory networks.

Predictive mathematical models of the interactions of a genetic network can provide insight into the mechanisms of gene regulation, the role of various genes within a network and how multiple genes interact leading to complex traits. However, identification of the parameters and interactions is currently a limiting step in the development of such models. This work reviews the state of the art for design of experiments in biological systems and demonstrates the need for improved design of experiments through the use of a model system. Appropriate design of experiments has a profound impact on the ability to identify a model and on the quality of resulting identified model. Key issues include the selection of appropriate input sequences (e.g. random, independent multivariate inputs) and the selection of the sampling frequencies. This work demonstrates that these issues are especially important in the identification of biochemical networks and that the traditional biochemical approach is incapable of truly identifying the behavior present in such networks.     

SLC6A4 gene variants and temporal lobe epilepsy susceptibility: a meta-analysis

There seems to be a role for serotoninergic neuro-transmission in the pathophysiology of the epilepsies. Different groups have studied the role of regulatory variants in the SLC6A4 gene, which code for the central serotonin transporter, in the complex genetics of temporal lobe epilepsy (TLE) obtaining contradictory findings. Therefore, a systematic review and critical analysis of this topic seem to be timely. Published studies up to October 2011 of TLE and the SLC6A4 promoter and intron 2 variant number repeat polymorphisms (VNTR) were identified by searches of Medline, Scopus and ISI-Web of Sciences databases. Meta-analysis of TLE case-control data were performed to assess the association of SLC6A4 VNTRs with TLE susceptibility. Pooled odds ratios were estimated by means of a genetic-model-free approach. The quality of the included studies was assessed by a score. The studies included compared a total of 991 TLE cases and 1,202 controls. We did not find synthetic evidence of association between SLC6A4 promoter and intron 2 variants and the risk of TLE. However, the intron 2 VNTR seems to have opposite effects in different populations. In this meta-analysis our findings were inconclusive in order to associate any of the 5-HT receptor gene variants with the risk of TLE.     

Patterns of temperature sensitivity in Contrabithorax/Ultrabithorax heterozygotes of Drosophila

Contrabithorax (Cbx) is a dominant homeotic mutant of Drosophila which transforms wings to halteres, while Ultrabithorax (Ubx) is a dominant mutant which transforms halteres to wings. Therefore $\text{Cbx}\text{Ubx}$ flies carry dominant homeotic mutants engaged in opposing transformations. This article reports that $\text{Cbx}\text{TM2 Ubx}{}^{130}$ is temperature sensitive. At 29°C, flies express strong Cbx transformation of wings, and minor Ubx transformation of halteres. Larvae shifted to 17°C prior to 72 hr express strong Ubx transformation of halteres toward wings, and slight Cbx transformation of wings. Seventeen-degree temperature-pulse experiments show that the $\text{Cbx}\text{TM2 Ubx}{}^{130}$ system is temperature sensitive continuously during embryonic and larval life. Expression of the Cbx transformation in left and right wings is highly correlated in all conditions studied, as is expression of the Ubx transformation in left and right halteres, but the Cbx transformation in wings and Ubx transformation in halteres can be negatively correlated or uncorrelated. The temperature sensitivity in $\text{Cbx}\text{TM2 Ubx}{}^{130}$ is not found in $\text{Cbx}\text{Ubx}{}^{\mathrm{61D}}$, and Ubx is only weakly expressed in $\text{Sb}\text{TM2}$Ubx¹³⁰ flies. These results show that Cbx in trans to Ubx can enhance Ubx expression, although Cbx also causes an opposing transformation to Ubx; that the $\text{Cbx}\text{Ubx}$ system acts in both the mesothorax and metathorax to modulate their phenotypes; and that both transformations are broadly temperature sensitive through embryonic and larval life. This suggests that the $\text{Cbx}\text{TM2 Ubx}{}^{130}$ system functions continuously during embryonic and larval development to maintain mesothoracic and metathoracic commitments. The results are interpreted in terms of a $\text{Cbx}\text{Ubx}$ feedback loop which maintains the mesothorax in a state of low $\text{Cbx}\text{Ubx}$ activity, and metathorax in a state of high $\text{Cbx}\text{Ubx}$ activity.     

Role of tumor necrosis factor in oxygen toxicity.

mRNA from lungs of mice exposed to high-dose oxygen (greater than 95%) for 3 days demonstrated increased expression of the genes for tumor necrosis factor (TNF), interleukin-1, and interleukin-6 compared with mRNA from lungs of mice exposed to room air. Daily treatment of mice exposed to high-dose oxygen with an antibody to TNF improved survival compared with mice receiving a similar dose of control immunoglobulin G. Pretreatment of mice with repetitive sublethal intraperitoneal doses of recombinant human TNF for 3 days or a single intravenous dose followed by exposure to high-dose oxygen afforded a significant survival advantage compared with high-dose oxygen-exposed mice pretreated with vehicle or interleukin-1. The repetitive intraperitoneal TNF pretreatment reduced the development of interstitial pneumonitis, pulmonary edema, and lung weight gain associated with oxygen toxicity and enhanced expression of the gene for the free radical protective enzyme manganous superoxide dismutase in lung tissue, a gene that is augmented as mice are exposed to high-dose oxygen. Furthermore a single intravenous dose of TNF 24 h after oxygen exposure was still protective. The results suggest that the toxicity of oxygen therapy can be partially ameliorated by either treatment with anti-TNF antibody or pretreatment and early treatment with TNF. These findings are consistent with the hypothesis that oxygen exposure induces TNF, which causes part of the toxicity of high-dose oxygen, and that pretreatment or early treatment with TNF induces the gene for an enzyme that recently has been shown to be very effective in protecting mice from the toxicity of oxygen.