Engineering gene networks to emulate Drosophila embryonic pattern formation

Pattern formation is essential in the development of higher eukaryotes. For example, in the Drosophila embryo, maternal morphogen gradients establish gap gene expression domain patterning along the anterior-posterior axis, through linkage with an elaborate gene network. To understand the evolution and behaviour of such systems better, it is important to establish the minimal determinants required for patterning. We have therefore engineered artificial transcription-translation networks that generate simple patterns, crudely analogous to the Drosophila gap gene system. The Drosophila syncytium was modelled using DNA-coated paramagnetic beads fixed by magnets in an artificial chamber, forming a gene expression network. Transient expression domain patterns were generated using various levels of network connectivity. Generally, adding more transcription repression interactions increased the “sharpness” of the pattern while reducing overall expression levels. An accompanying computer model for our system allowed us to search for parameter sets compatible with patterning. While it is clear that the Drosophila embryo is far more complex than our simplified model, several features of interest emerge. For example, the model suggests that simple diffusion may be too rapid for Drosophila-scale patterning, implying that sublocalisation, or “trapping,” is required. Second, we find that for pattern formation to occur under the conditions of our in vitro reaction-diffusion system, the activator molecules must propagate faster than the inhibitors. Third, adding controlled protease degradation to the system stabilizes pattern formation over time. We have reconstituted transcriptional pattern formation from purified substances, including phage RNA polymerases, ribonucleotides, and an eukaryotic translation extract. We anticipate that the system described here will be generally applicable to the study of any biological network with a spatial component

Early compaction at day 3 may be a useful additional criterion for embryo transfer

PURPOSE: The reduction of the number of embryos transferred while maintaining a satisfactory rate of pregnancy (PR) with in vitro fertilization calls for a refined technique of embryonic selection. This prospective study investigates the significance of early embryonic compaction at day 3 as a marker of the chances of implantation. METHODS: We examined 317 transfers and their outcome involving 509 embryos including 91 compacted embryos. RESULTS: Early compaction seems linked with the ovarian response to stimulation and embryonic quality. The PR is significantly increased when the embryonic cohort contains at least one compacted embryo (44% versus 29.5%, p = 0.01), and when at least one compacted embryo is transferred (44% versus 31%, p < 0.05). The analysis of our single embryo transfers shows that the implantation rates are significantly better for compacted embryos (50% versus 30%, p < 0.05) (OR 2.98; CI 1.02-5.28). CONCLUSION: Thus, early compaction, sometimes observed at day 3, may serve as a useful additional criterion for selecting the embryos transferred

Molecular characterization of corona radiata cells from patients with diminished ovarian reserve using microarray and microfluidic-based gene expression profiling

BACKGROUND: Diminished ovarian reserve (DOR) is one of the causes of infertility in young women. In this prospective study, gene expression profiling (GEP) of corona radiata cells (CRC) was performed to identify genes deregulated in DOR patients. METHODS: Microarray-based GEP of CRC isolated from eight women undergoing IVF was performed to identify genes differentially expressed between patients with normal ovarian reserve and DOR patients. Microfluidic-based quantitative RT-PCR assays were used to validate selected transcripts on 40 independent patients. A principal component analysis was used to identify more homogeneous subgroups of DOR patients. In silico analyses focusing on cis-regulation were performed to refine the interactions between patient\u27s biological characteristics and their GEP. RESULTS: Forty-eight transcripts were differentially expressed, including CXXC finger protein 5 (CXXC5), forkhead box C1 (FOXC1) (down-regulated in DOR) as well as connective tissue growth factor (CTGF), follistatin-like 3 (FSTL3), prostaglandin-endoperoxide synthase 2 (PTGS2) and suppressor of cytokine signaling 2 (SOCS2) (up-regulated in DOR). According to these transcripts, two DOR patients\u27 subgroups (DOR Gr1 and Gr2) were identified. In DOR Gr2 patients, C-terminal domain 2 (CITED2), CTGF, growth arrest-specific 1 (GAS1), insulin receptor substrate 2 (IRS2), PTGS2, SOCS2 and Versican (VCAN) were expressed at significantly higher levels and CXXC5, FOXC1, guanylate-binding protein 2 (GBP2) and zinc finger MIZ-domain containing 1 (ZMIZ1) at significantly lower levels. Higher baseline estradiol (E(2)) levels were observed in DOR Gr2 patients (P < 0.006). The in silico analyses suggested that all 11 genes differentially expressed between DOR Gr1 and DOR Gr2 subgroups could be transcriptional targets of estrogen. CONCLUSIONS: Despite small sample size limitations, 12 genes deregulated in the CRC of DOR patients were identified, which could be involved in DOR pathogenesis. A DOR patient\u27s subgroup with high baseline E(2) levels and deregulated estrogen-responsive genes was also identified

Are zona pellucida genes involved in recurrent oocyte lysis observed during in vitro fertilization?

PURPOSE: Complete oocyte lysis in in vitro fertilization (IVF) is a rare event, but one against which we remain helpless. The recurrence of this phenomenon in some women in each of their IVF attempts, regardless of treatment, together with the results of animal experiments led us to investigate the possible involvement of the genes encoding for the glycoproteins constituting the zona pellucida (ZP). PATIENTS & METHODS: Over the last ten years, during which we treated over 500 women each year, three women suffered recurrent oocyte lysis during their IVF attempts in our Centre for Reproductive Biology. For each of these three cases, we sequenced the four genes and promoter sequences encoding the glycoproteins of the ZP. The sequence variations likely to cause a change in protein expression or structure, were investigated in a control group of 35 women who underwent IVF without oocyte lysis and with normal rates of fertilization. RESULTS & CONCLUSION: We found no mutations in the ZP genes sequenced. Only some polymorphisms present in the control group and in the general population were detected, excluding their specific involvement in the phenotype observed. Thus, although we suspected that complete oocyte lysis was due to a genetic cause, it did not seem possible to directly incriminate the genes encoding the proteins of the ZP in the observed phenotype. Further study of the genes involved in the processing and organization of ZP glycoproteins may allow elucidation of the mechanism underlying recurrent oocyte lysis during in vitro fertilization

Roughness at the depinning threshold for a long-range elastic string

In this paper, we compute the roughness exponent zeta of a long-range elastic string, at the depinning threshold, in a random medium with high precision, using a numerical method which exploits the analytic structure of the problem (`no-passing' theorem), but avoids direct simulation of the evolution equations. This roughness exponent has recently been studied by simulations, functional renormalization group calculations, and by experiments (fracture of solids, liquid meniscus in 4He). Our result zeta = 0.390 +/- 0.002 is significantly larger than what was stated in previous simulations, which were consistent with a one-loop renormalization group calculation. The data are furthermore incompatible with the experimental results for crack propagation in solids and for a 4He contact line on a rough substrate. This implies that the experiments cannot be described by pure harmonic long-range elasticity in the quasi-static limit.Comment: 4 pages, 3 figure

Theory of plastic vortex creep

We develop a theory for plastic flux creep in a topologically disordered vortex solid phase in type-II superconductors. We propose a detailed description of the plastic vortex creep of the dislocated, amorphous vortex glass in terms of motion of dislocations driven by a transport current $j$. The {\em plastic barriers} $U_{pl}(j)\propto j^{-\mu}$ show power-law divergence at small drives with exponents $\mu=1$ for single dislocation creep and $\mu = 2/5$ for creep of dislocation bundles. The suppression of the creep rate is a hallmark of the transition from the topologically ordered vortex lattice to an amorphous vortex glass, reflecting a jump in $\mu$ from $\mu = 2/11$, characterizing creep in the topologically ordered vortex lattice near the transition, to its plastic values. The lower creep rates explain the observed increase in apparent critical currents in the dislocated vortex glass.Comment: 4 pages, 1 figur

Mitochondrial macro-haplogroup JT may play a protective role in ovarian ageing

This study of 200 Caucasian women shows that the distribution of the mtDNA macro-haplogroups in patients with diminished ovarian reserve (DOR) differed significantly from that of patients with normal ovarian reserve (NOR) (p=0.02). The JT macro-haplogroup was significantly under-represented in DOR patients compared with NOR patients (p=0.006) and compared with the estimated frequency of 18.8% in the general French population (p=0.0012). Our findings suggest that the risk of a prematurely depleted ovarian reserve would be three times lower for patients carrying the JT macro-haplogroup than for patients with any of the other mtDNA haplogroups (odds ratio: 0.3; 95% CI: 0.13-0.74). If these preliminary results are confirmed in larger independent studies, they should lead to the better management of infertility

Computational and Mathematical Modelling of the EGF Receptor System

This chapter gives an overview of computational and mathematical modelling of the EGF receptor system. It begins with a survey of motivations for producing such models, then describes the main approaches that are taken to carrying out such modelling, viz. differential equations and individual-based modelling. Finally, a number of projects that applying modelling and simulation techniques to various aspects of the EGF receptor system are described

Velocity-force characteristics of a driven interface in a disordered medium

Using a dynamic functional renormalization group treatment of driven elastic interfaces in a disordered medium, we investigate several aspects of the creep-type motion induced by external forces below the depinning threshold $f_c$: i) We show that in the experimentally important regime of forces slightly below $f_c$ the velocity obeys an Arrhenius-type law $v\sim\exp[-U(f)/T]$ with an effective energy barrier $U(f)\propto (f_{c}-f)$ vanishing linearly when f approaches the threshold $f_c$. ii) Thermal fluctuations soften the pinning landscape at high temperatures. Determining the corresponding velocity-force characteristics at low driving forces for internal dimensions d=1,2 (strings and interfaces) we find a particular non-Arrhenius type creep $v\sim \exp[-(f_c(T)/f)^{\mu}]$ involving the reduced threshold force $f_c(T)$ alone. For d=3 we obtain a similar v-f characteristic which is, however, non-universal and depends explicitly on the microscopic cutoff.Comment: 9 pages, RevTeX, 3 postscript figure