Community robustness and limiting similarity in periodic environments

Temporal environmental variation has long been considered as one of the potential factors that could promote species coexistence. A question of particular interest is how the ecology of fluctuating environments relates to that of equilibrium systems. Equilibrium theory says that the more similar two species are in their modes of regulation, the less robust their coexistence will be; that is, the volume of external parameters for which all populations persist shrinks with increasing similarity. In this study, we will attempt to generalize these results to temporally varying situations and establish the precise mathematical relationship between the two. Our treatment considers unstructured populations in continuous time with periodic attractors of fixed period length, where the periodic behavior is due to external forcing. Within these conditions, our treatment is general. We provide a coherent theoretical framework for defining measures of species similarity and niche. Our main conclusion is that all factors that function to regulate population growth may be considered as separate regulating factors for each moment of time. In particular, a single resource becomes a resource continuum, along which species may segregate in the same manner as along classical resource continua. Therefore, we provide a mathematical underpinning for considering fluctuation-mediated coexistence as temporal niche segregation.     

Mechanisms of Gurken-dependent pipe regulation and the robustness of dorsoventral patterning in Drosophila

The restriction of Pipe, a potential glycosaminoglycan-modifying enzyme, to ventral follicle cells of the egg chamber is essential for dorsoventral axis formation in the Drosophila embryo. pipe repression depends on the TGFalpha-like ligand Gurken, which activates the Drosophila EGF receptor in dorsal follicle cells. An analysis of Raf mutant clones shows that EGF signalling is required cell-autonomously in all dorsal follicle cells along the anteroposterior axis of the egg chamber to repress pipe. However, the autoactivation of EGF signalling important for dorsal follicle cell patterning has no influence on pipe expression. Clonal analysis shows that also the mirror-fringe cassette suggested to establish a secondary signalling centre in the follicular epithelium is not involved in pipe regulation. These findings support the view that the pipe domain is directly delimited by a long-range Gurken gradient. Pipe induces ventral cell fates in the embryo via activation of the Sp?tzle/Toll pathway. However, large dorsal patches of ectopic pipe expression induced by Raf clones rarely affect embryonic patterning if they are separated from the endogenous pipe domain. This indicates that potent inhibitory processes prevent pipe dependent Toll activation at the dorsal side of the egg.     

Meiotic DSB patterning: A multifaceted process

Meiosis is a specialized two-step cell division responsible for genome haploidization and the generation of genetic diversity during gametogenesis. An integral and distinctive feature of the meiotic program is the evolutionarily conserved initiation of homologous recombination (HR) by the developmentally programmed induction of DNA double-strand breaks (DSBs). The inherently dangerous but essential act of DSB formation is subject to multiple forms of stringent and self-corrective regulation that collectively ensure fruitful and appropriate levels of genetic exchange without risk to cellular survival. Within this article we focus upon an emerging element of this control—spatial regulation—detailing recent advances made in understanding how DSBs are evenly distributed across the genome, and present a unified view of the underlying patterning mechanisms employed.     

Patterning the fly eye: the role of apoptosis

Early development in many tissues is characterized by a rapid expansion in cell number. Excess cells are removed through activation of their intrinsic apoptotic machinery. This over-expansion followed by selective removal is important for the sculpting of these tissues, and how specific cells are selected to die is one of the central questions in development. The Drosophila eye is a unique example of such patterning through cell death. Because of its remarkable reiterative design, the fly eye lends itself to studies of mutants with increased or decreased apoptosis. We know that the process of elimination of lattice cells is highly regulated. And we have learned that each ommatidial unit is involved in the life-death decision of lattice cells through cell-cell signaling. But, we have yet to understand how this signaling is regulated spatially to result in such precision. In this article, we describe and speculate on the role of selective cell death during maturation of the fly eye.     

A two-step fermentation process for efficient production of penta-N-acetyl-chitopentaose in recombinant Escherichia coli

The nodC gene from Mesorhizobium loti was cloned into E. coli, leading to production of chitin oligosaccharides (COs)—mainly penta-N-acetyl-chitopentaose. A two-step fermentation procedure was then developed which gave 930 mg CO/L with a productivity of 37 mg/l·h.     

A P22 scaffold protein mutation increases the robustness of head assembly in the presence of excess portal protein

Bacteriophage with linear, double-stranded DNA genomes package DNA into preassembled protein shells called procapsids. Located at one vertex in the procapsid is a portal complex composed of a ring of 12 subunits of portal protein. The portal complex serves as a docking site for the DNA packaging enzymes, a conduit for the passage of DNA, and a binding site for the phage tail. An excess of the P22 portal protein alters the assembly pathway of the procapsid, giving rise to defective procapsid-like particles and aberrant heads. In the present study, we report the isolation of escape mutant phage that are able to replicate more efficiently than wild-type phage in the presence of excess portal protein. The escape mutations all mapped to the same phage genome segment spanning the portal, scaffold, coat, and open reading frame 69 genes. The mutations present in five of the escape mutants were determined by DNA sequencing. Interestingly, each mutant contained the same mutation in the scaffold gene, which changes the glycine at position 287 to glutamate. This mutation alone conferred an escape phenotype, and the heads assembled by phage harboring only this mutation had reduced levels of portal protein and exhibited increased head assembly fidelity in the presence of excess portal protein. Because this mutation resides in a region of scaffold protein necessary for coat protein binding, these findings suggest that the P22 scaffold protein may define the portal vertices in an indirect manner, possibly by regulating the fidelity of coat protein polymerization.     

Cellular retinoic acid-binding proteins are essential for hindbrain patterning and signal robustness in zebrafish

The vitamin A derivative retinoic acid (RA) is a morphogen that patterns the anterior-posterior axis of the vertebrate hindbrain. Cellular retinoic acid-binding proteins (Crabps) transport RA within cells to both its nuclear receptors (RARs) and degrading enzymes (Cyp26s). However, mice lacking Crabps are viable, suggesting that Crabp functions are redundant with those of other fatty acid-binding proteins. Here we show that Crabps in zebrafish are essential for posterior patterning of the hindbrain and that they provide a key feedback mechanism that makes signaling robust as they are able to compensate for changes in RA production. Of the four zebrafish Crabps, Crabp2a is uniquely RA inducible and depletion or overexpression of Crabp2a makes embryos hypersensitive to exogenous RA. Computational models confirm that Crabp2a improves robustness within a narrow concentration range that optimizes a 'robustness index', integrating spatial information along the RA morphogen gradient. Exploration of signaling parameters in our models suggests that the ability of Crabp2a to transport RA to Cyp26 enzymes for degradation is a major factor in promoting robustness. These results demonstrate a previously unrecognized requirement for Crabps in RA signaling and hindbrain development, as well as a novel mechanism for stabilizing morphogen gradients despite genetic or environmental fluctuations in morphogen availability.     

A two-step EMG-and-optimization process to estimate muscle force during dynamic movement

The present study proposed a two-step EMG-and-optimization method for muscle force estimation in dynamic condition. Considering the strengths and the limitations of existing methods, the proposed approach exploited the advantages of min/max optimization with constraints on the contributions of the flexor and extensor muscle groups to the net joint moment estimated through an EMG-to-moment approach. Our methodology was tested at the knee joint during dynamic half squats, and was compared with traditional min/max optimization. In general, results showed significant differences in muscle force estimates from EMG-and-optimization method when compared with those from traditional min/max optimization. Muscle forces were higher – especially in the antagonist muscles – and more consistent with EMG patterns because of the ability of the proposed approach to properly account for agonist/antagonist cocontraction. In addition, muscle forces agree with mechanical constraints regarding the net, the agonist, and the antagonist moments, thus greatly improving the confidence in muscle force estimates. The proposed two-step EMG-and-optimization method for muscle force estimation is easy to implement with relatively low computational requirements and, thus, could offer interesting advantages for various applications in many fields, including rehabilitation, clinical, and sports biomechanics.     

The conditional medaka mutation eyeless uncouples patterning and morphogenesis of the eye

In early vertebrate eye development, the retinal anlage is specified in the anterior neuroectoderm. During neurulation, the optic vesicles evaginate from the lateral wall of the prosencephalon. Here we describe the temperature-sensitive mutation eyeless in the Japanese medakafish. Marker gene analysis indicates that, whereas, specification of two retinal primordia and proximodistal patterning takes place in the mutant embryo, optic vesicle evagination does not occur and subsequent differentiation of the retinal primordia is not observed. The mutation eyeless thus uncouples patterning and morphogenesis at early steps of retinal development. Temperature-shift experiments indicate a requirement for eyeless activity prior to optic vesicle evagination. Cell transplantation shows that eyeless acts cell autonomously.     

Dynamic-module redundancy confers robustness to the gene regulatory network involved in hair patterning of Arabidopsis epidermis

Redundancy among dynamic modules is emerging as a potentially generic trait in gene regulatory networks. Moreover, module redundancy could play an important role in network robustness to perturbations. We explored the effect of dynamic-module redundancy in the networks associated to hair patterning in Arabidopsis root and leaf epidermis. Recent studies have put forward several dynamic modules belonging to these networks. We defined these modules in a discrete dynamical framework that was previously reported. Then, we addressed whether these modules are sufficient or necessary for recovering epidermal cell types and patterning. After defining two quantitative estimates of the system's robustness, we also compared the robustness of each separate module with that of a network coupling all the leaf or root modules. We found that, considering certain assumptions, all the dynamic modules proposed so far are sufficient on their own for pattern formation, but reinforce each other during epidermal development. Furthermore, we found that networks of coupled modules are more robust to perturbations than single modules. These results suggest that dynamic-module redundancy might be an important trait in gene regulatory networks and point at central questions regarding network evolution, module coupling, pattern robustness and the evolution of development.     

A role for wingless in an early pupal cell death event that contributes to patterning the Drosophila eye

Programmed cell death (PCD) is utilized in a wide variety of tissues to refine structure in developing tissues and organs. However, little is understood about the mechanisms that, within a developing epithelium, combine signals to selectively remove some cells while sparing essential neighbors. One popular system for studying this question is the developing Drosophila pupal retina, where excess interommatidial support cells are removed to refine the patterned ommatidial array. In this paper, we present data indicating that PCD occurs earlier within the pupal retina than previously demonstrated. As with later PCD, this death is dependent on Notch activity. Surprisingly, altering Drosophila Epidermal Growth Factor Receptor or Ras pathway activity had no effect on this death. Instead, our evidence indicates a role for Wingless signaling to provoke this cell death. Together, these signals regulate an intermediate step in the selective removal of unneeded interommatidial cells that is necessary for a precise retinal pattern.