Pattern formation of reaction-diffusion system having self-determined flow in the amoeboid organism of Physarum plasmodium

The amoeboid organism, the plasmodium of Physarum polycephalum, behaves on the basis of spatio-temporal pattern formation by local contraction-oscillators. This biological system can be regarded as a reaction-diffusion system which has spatial interaction by active flow of protoplasmic sol in the cell. Paying attention to the physiological evidence that the flow is determined by contraction pattern in the plasmodium, a reaction-diffusion system having self-determined flow arises. Such a coupling of reaction-diffusion-advection is a characteristic of the biological system, and is expected to relate with control mechanism of amoeboid behaviours. Hence, we have studied effects of the self-determined flow on pattern formation of simple reaction-diffusion systems. By weakly nonlinear analysis near a trivial solution, the envelope dynamics follows the complex Ginzburg-Landau type equation just after bifurcation occurs at finite wave number. The flow term affects the nonlinear term of the equation through the critical wave number squared. Contrary to this, wave number isn't explicitly effective with lack of flow or constant flow. Thus, spatial size of pattern is especially important for regulating pattern formation in the plasmodium. On the other hand, the flow term is negligible in the vicinity of bifurcation at infinitely small wave number, and therefore the pattern formation by simple reaction-diffusion will also hold. A physiological role of pattern formation as above is discussed.Comment: REVTeX, one column, 7 pages, no figur

Electromagnetic wave diffraction by periodic planar metamaterials with nonlinear constituents

We present a theory which explains how to achieve an enhancement of nonlinear effects in a thin layer of nonlinear medium by involving a planar periodic structure specially designed to bear a trapped-mode resonant regime. In particular, the possibility of a nonlinear thin metamaterial to produce the bistable response at a relatively low input intensity due to a large quality factor of the trapped-mode resonance is shown. Also a simple design of an all-dielectric low-loss silicon-based planar metamaterial which can provide an extremely sharp resonant reflection and transmission is proposed. The designed metamaterial is envisioned for aggregating with a pumped active medium to achieve an enhancement of quantum dots luminescence and to produce an all-dielectric analog of a 'lasing spaser'.Comment: 18 pages, 13 figure

Sequential analysis of global gene expression profiles in immature and in vitro matured bovine oocytes: potential molecular markers of oocyte maturation

Abstract Background Without intensive selection, the majority of bovine oocytes submitted to in vitro embryo production (IVP) fail to develop to the blastocyst stage. This is attributed partly to their maturation status and competences. Using the Affymetrix GeneChip Bovine Genome Array, global mRNA expression analysis of immature (GV) and in vitro matured (IVM) bovine oocytes was carried out to characterize the transcriptome of bovine oocytes and then use a variety of approaches to determine whether the observed transcriptional changes during IVM was real or an artifact of the techniques used during analysis. Results 8489 transcripts were detected across the two oocyte groups, of which ~25.0% (2117 transcripts) were differentially expressed (p < 0.001); corresponding to 589 over-expressed and 1528 under-expressed transcripts in the IVM oocytes compared to their immature counterparts. Over expression of transcripts by IVM oocytes is particularly interesting, therefore, a variety of approaches were employed to determine whether the observed transcriptional changes during IVM were real or an artifact of the techniques used during analysis, including the analysis of transcript abundance in oocytes in vitro matured in the presence of α-amanitin. Subsets of the differentially expressed genes were also validated by quantitative real-time PCR (qPCR) and the gene expression data was classified according to gene ontology and pathway enrichment. Numerous cell cycle linked (CDC2, CDK5, CDK8, HSPA2, MAPK14, TXNL4B), molecular transport (STX5, STX17, SEC22A, SEC22B), and differentiation (NACA) related genes were found to be among the several over-expressed transcripts in GV oocytes compared to the matured counterparts, while ANXA1, PLAU, STC1and LUM were among the over-expressed genes after oocyte maturation. Conclusion Using sequential experiments, we have shown and confirmed transcriptional changes during oocyte maturation. This dataset provides a unique reference resource for studies concerned with the molecular mechanisms controlling oocyte meiotic maturation in cattle, addresses the existing conflicting issue of transcription during meiotic maturation and contributes to the global goal of improving assisted reproductive technology

Model study of dissipation of jets in deep wells

This paper presents an experimental investigation of a submerged round jet discharging vertically into a deep well. The research work was concentrated on two positions of the jet: (a) impingement at the centre of the well; and (b) impingement near the upstream side of the well. Square and rectangular shaped wells were tested for various pipe heights and well dimensions. Using a laser Doppler anemometer, velocity distributions were measured in the vertical and horizontal planes inside the well and compared with those for the free jet and the wall jet. The flow pattern and velocity decay of the jet were studied while varying the ratios of well height to pipe diameter between the practical limits of 6 to 16. Based on these results, an optimum size for a deep well has been indicated, with satisfactory prototype performance. </jats:p

215 INVESTIGATION OF A PREFERENTIALLY UPREGULATED GENE CLUSTER IN DAY 7 BOVINE EMBRYOS DERIVED FROM RNA SEQUENCING DATA

Successful establishment and maintenance of pregnancy requires optimum conceptus-maternal cross talk. Despite significant progress in our understanding of the temporal changes in the transcriptome of the uterine endometrium, we have only a rudimentary knowledge of the genes and pathways governing growth and development of the bovine conceptus. A recent RNA sequencing study from our group (Mamo et al. 2011 Biol. Reprod. 85, 1143–1151) described the global transcriptome profile of the bovine conceptus at 5 key stages of its pre- and peri-implantation growth (Days 7, 10, 13, 16, and 19) using RNA sequencing techniques. One cluster of genes (n = 1680 transcripts) was preferentially upregulated at Day 7 and subsequently downregulated, suggesting that these genes might be markers of blastocyst formation. The objective of this study was to characterise the pattern of expression of these genes before Day 7 (i.e. from the zygote to blastocyst stage). The list of genes was submitted to DAVID (Database for Annotation, Visualisation, and Integrated Discovery) to take advantage of available ontology information contained therein. The expression of 9 genes belonging to ontologies specifically related to embryo developmental (GINS1, TAF8, ESRRB, NCAPG2, SP1, XAB2, CDC2L1, MSX1, and AQP3) plus Na/K ATPase, a gene previously known to be involved in blastocoe formation, was studied by quantitative real-time PCR (QPCR) in 6 replicate pools of 5 embryos produced by maturation, fertilization, and embryo culture in vitro. Stages studies included immature and mature oocyte, zygote, 2- cell, 4-cell, 8-cell, 16-cell, morula, blastocyst, and hatched blastocyst. In addition, in vivo derived Day 13 and Day 16 embryos were included as controls to confirm down-regulation after Day 7. Data were analysed using the GLM procedure of SAS. The QPCR expression data supported the RNA Seq data in that expression of all transcripts was downregulated after the blastocyst stage. Expression before the blastocyst stage was characterised by 1 of 3 broad patterns: (1) the expression was of maternal origin where the expression was very high up to 8-cell stage and decreased subsequently (MSX1), (2) the expression was of embryonic origin being low up to the 8-cell stage and increasing thereafter (TAF8, ESRRB, AQP3, and Na/K ATPase), or (3) static or decreased expression from oocyte to the maternal-zygotic transition followed by increased expression from the 16-cell stage (GINS1, NCAPG2, SP1, XAB2, and CDC2L1). In conclusion, the genes identified in this cluster, despite having different patterns of expression before the blastocyst stage, may represent markers of blastocyst formation in cattle given their downregulation subsequently. Supported by Science Foundation Ireland (07/SRC/B1156). </jats:p