sucker encodes a zebrafish Endothelin-1 required for ventral pharyngeal arch development

Mutation of sucker (suc) disrupts development of the lower jaw and other ventral cartilages in pharyngeal segments of the zebrafish head. Our sequencing, cosegregation and rescue results indicate that suc encodes an Endothelin-1 (Et-1). Like mouse and chick Et-1, suc/et-1 is expressed in a central core of arch paraxial mesoderm and in arch epithelia, both surface ectoderm and pharyngeal endoderm, but not in skeletogenic neural crest. Long before chondrogenesis, suc/et-1 mutant embryos have severe defects in ventral arch neural crest expression of dHAND, dlx2, msxE, gsc, dlx3 and EphA3 in the anterior arches. Dorsal expression patterns are unaffected. Later in development, suc/et-1 mutant embryos display defects in mesodermal and endodermal tissues of the pharynx. Ventral premyogenic condensations fail to express myoD, which correlates with a ventral muscle defect. Further, expression of shh in endoderm of the first pharyngeal pouch fails to extend as far laterally as in wild types. We use mosaic analyses to show that suc/et-1 functions nonautonomously in neural crest cells, and is thus required in the environment of postmigratory neural crest cells to specify ventral arch fates. Our mosaic analyses further show that suc/et-1 nonautonomously functions in mesendoderm for ventral arch muscle formation. Collectively our results support a model for dorsoventral patterning of the gnathostome pharyngeal arches in which Et-1 in the environment of the postmigratory cranial neural crest specifies the lower jaw and other ventral arch fates.     

PHOTOINHIBITION OF TEMPERATE LAKE PHYTOPLANKTON BY NEAR-SURFACE IRRADIANCE: EVIDENCE FROM VERTICAL PROFILES AND FIELD EXPERIMENTS1

To evaluate the in situ occurrence of phytoplankton photoinhibition, the light-mediated depression of chlorophyll in vivo fluorescence (IVF) and of the cellular fluorescence capacity (CFC) of phytoplankton was determined in three southeastern United States reservoirs. Vertical profiles of a fluorescence depression index (FDI) and of the CFC for reservoir phytoplankton showed that near-surface photoinhibition of fluorescence properties occurred in association with high surface irradiance and weak vertical mixing of the water column. To characterize the time scales of photochemical and photosynthetic responses to and recovery from exposure to supraoptimal light intensity, phytoplankton IVF responses and ¹⁴C-fixation rates were measured infield experiments. Phytoplankton chlorophyll IVF, CFC, and photosynthetic ¹⁴C fixation were rapidly (20–40 min) depressed when reservoir phytoplankton were exposed to surface irradiances (1700–2000 μE·m^?2·s^?1). Light-mediated increases in the FDI declined rapidly (20–40 min) to pre-exposure levels during a subsequent low-light (75–200 μE·m^?2·s^?1) period, but CFC and ¹⁴C fixation recovered more slowly (>40 min). Exposure of reservoir phytoplankton to a light-intensity gradient revealed both intensity and time thresholds for IVF and CFC depression. Phytoplankton photochemical responses to bright light operate on time scales that, in conjunction with vertical mixing, should limit the occurrence of photoinhibition to extreme irradiance environments. Our results support the hypothesis that the photoinhibition of phytoplankton productivity occurs less commonly than is indicated by fixed-depth incubation measurements.     

Reaction-diffusion approach to modeling of the spread of early tumors along linear or tubular structures

We consider a system composed of a tubular sheet of early tumor cells, occupying the surface of a structure existing in the organism. We assume that the cells have a potential for proliferation in response to a growth factor. This model can be thought of as representing an early stage (pre-in situ) of tumor evolution. A biomedical example of such process might be the atypical adenomatous hyperplasia in the lung. Destabilization of the equilibrium in such system represents initial invasion of cancer. We are looking for a transition from a slightly perturbed equilibrium state to uncontrolled and irregular growth. We examine a mathematical model of a population of cells distributed over a linear or tubular structure. Growth of cells is regulated by a growth factor, which can diffuse over the structure. Aside from this, production of cells and of the growth factor is governed by a pair of ordinary differential equations. Equation for the cell number follows from an accepted model of cell cycle. Equation for the bounded receptor particle number follows from a time-continuous Markov process. We demonstrate existence of the solutions of the complete model, using the method of invariant rectangles. We find conditions under which diffusion causes destabilization of the spatially homogeneous steady state, leading to exponential growth and apparently chaotic spatial patterns, following a period of almost constancy. This phenomenon may serve as a mathematical explanation of "unexpected" rapid growth and invasion of temporarily stable structures composed of cancer cells.     

Monte Carlo simulation of the spatial distribution of energy deposition for an electron microbeam

Dosimetry calculations characterizing the spatial variation of the energy deposited by the slowing and stopping of energetic electrons are reported and compared with experimental measurements from an electron microbeam facility. The computations involve event-by-event, detailed-histories Monte Carlo simulations of low-energy electrons interacting in water vapor. Simulations of electron tracks with starting energies from 30 to 80 keV are used to determine energy deposition distributions in thin cylindrical rings as a function of penetration and radial distance from a beam source. Experimental measurements of the spatial distribution of an electron microbeam in air show general agreement with the density-scaled simulation results for water vapor at these energies, yielding increased confidence in the predictions of Monte Carlo track-structure simulations for applications of the microbeam as a single-cell irradiator.     

A simple model of linkage disequilibrium and genetic drift in human genomic SNPs: importance of demography and SNP age

We propose a simple model of evolution at a pair of SNP loci, under mutation, genetic drift and recombination. The developed model allows to consider evolution of SNPs under different demographic scenarios. We applied it to SNP data containing polymorphisms spanning 19 gene regions. We initially matched the linkage disequilibrium (LD) data only, and then we reconciled both LD and heterozygosity data. The imbalance between LD and heterozygosity data, observed for some of the analyzed genomic regions, may be a signature of selection acting in these regions. However, assuming neutrality, we obtain estimates of the age of population expansion of modern humans, which are consistent with the consensus estimates. In addition, we are able to estimate the ages of the polymorphisms observed in different genomic regions and we find that they vary widely with respect to their age. Polymorphisms at loci implicated in human disease, seem to be younger than average. Our results supplement the conclusions originally obtained by Reich and co-workers for the same set of data.     

A fast method for computing high-significance disease association in large population-based studies

Because of rapid progress in genotyping techniques, many large-scale, genomewide disease-association studies are now under way. Typically, the disorders examined are multifactorial, and, therefore, researchers seeking association must consider interactions among loci and between loci and other factors. One of the challenges of large disease-association studies is obtaining accurate estimates of the significance of discovered associations. The linkage disequilibrium between SNPs makes the tests highly dependent, and dependency worsens when interactions are tested. The standard way of assigning significance (P value) is by a permutation test. Unfortunately, in large studies, it is prohibitively slow to compute low P values by this method. We present here a faster algorithm for accurately calculating low P values in case-control association studies. Unlike with several previous methods, we do not assume a specific distribution of the traits, given the genotypes. Our method is based on importance sampling and on accounting for the decay in linkage disequilibrium along the chromosome. The algorithm is dramatically faster than the standard permutation test. On data sets mimicking medium-to-large association studies, it speeds up computation by a factor of 5,000-100,000, sometimes reducing running times from years to minutes. Thus, our method significantly increases the problem-size range for which accurate, meaningful association results are attainable.     

Selective formation of glycosidic linkages of N-unsubstituted 4-hydroxyquinolin-2-(1H)-ones

A comparative study for selective glucosylation of N-unsubstituted 4-hydroxyquinolin-2(1H)-ones into 4-(tetra-O-acetyl-β-d-glucopyranosyloxy)quinolin-2(1H)-ones is reported. Four glycosyl donors including tetra-O-acetyl-α-d-glucopyranosyl bromide, β-d-glucose pentaacetate, glucose tetraacetate and tetra-O-acetyl-α-d-glucopyranosyl trichloroacetimidate were tested, along with different promoters and reaction conditions. The best results were obtained with tetra-O-acetyl-α-d-glucopyranosyl bromide with Cs₂CO₃ in CH₃CN. In some cases the 4-O-glucosylation of the quinolinone ring was accompanied by 2-O-glucosylation yielding the corresponding 2,4-bis(tetra-O-acetyl-β-d-glucopyranosyloxy)quinoline. Next, 4-(tetra-O-acetyl-β-d-glucopyranosyloxy)quinolin-2(1H)-ones were deacetylated into 4-(β-d-glucopyranosyloxy)quinolin-2(1H)-ones with Et₃N in MeOH. In some instances the deacetylation was accompanied by the sugar-aglycone bond cleavage. Structure elucidation, complete assignment of proton and carbon resonances as well as assignment of anomeric configuration for all the products under investigation were performed by 1D and 2D NMR spectroscopy.     

Moz-dependent Hox expression controls segment-specific fate maps of skeletal precursors in the face

Development of the facial skeleton depends on interactions between intrinsic factors in the skeletal precursors and extrinsic signals in the facial environment. Hox genes have been proposed to act cell-intrinsically in skeletogenic cranial neural crest cells (CNC) for skeletal pattern. However, Hox genes are also expressed in other facial tissues, such as the ectoderm and endoderm, suggesting that Hox genes could also regulate extrinsic signalling from non-CNC tissues. Here we study moz mutant zebrafish in which hoxa2b and hoxb2a expression is lost and the support skeleton of the second pharyngeal segment is transformed into a duplicate of the first-segment-derived jaw skeleton. By performing tissue mosaic experiments between moz(-) and wild-type embryos, we show that Moz and Hox genes function in CNC, but not in the ectoderm or endoderm, to specify the support skeleton. How then does Hox expression within CNC specify a support skeleton at the cellular level? Our fate map analysis of skeletal precursors reveals that Moz specifies a second-segment fate map in part by regulating the interaction of CNC with the first endodermal pouch (p1). Removal of p1, either by laser ablation or in the itga5(b926) mutant, reveals that p1 epithelium is required for development of the wild-type support but not the moz(-) duplicate jaw-like skeleton. We present a model in which Moz-dependent Hox expression in CNC shapes the normal support skeleton by instructing second-segment CNC to undergo skeletogenesis in response to local extrinsic signals.     

Mitochondrial dynamics in chondrocytes and their connection to the mechanical properties of the cytoplasm

BACKGROUND: The motion and redistribution of intracellular organelles is a fundamental process in cells. Organelle motion is a complex phenomenon that depends on a large number of variables including the shape of the organelle, the type of motors with which the organelles are associated, and the mechanical properties of the cytoplasm. This paper presents a study that characterizes the diffusive motion of mitochondria in chondrocytes seeded in agarose constructs and what this implies about the mechanical properties of the cytoplasm. METHOD OF APPROACH: Images showing mitochondrial motion in individual cells at 30 s intervals for 15 min were captured with a confocal microscope. Digital image correlation was used to quantify the motion of the mitochondria, and the mean square displacement (MSD) was calculated. Statistical tools for testing whether the characteristic motion of mitochondria varied throughout the cell were developed. Calculations based on statistical mechanics were used to establish connections between the measured MSDs and the mechanical nature of the cytoplasm. RESULTS: The average MSD of the mitochondria varied with time according to a power law with the power term greater than 1, indicating that mitochondrial motion can be viewed as a combination of diffusion and directional motion. Statistical analysis revealed that the motion of the mitochondria was not uniform throughout the cell, and that the diffusion coefficient may vary by over 50%, indicating intracellular heterogeneity. High correlations were found between movements of mitochondria when they were less than 2 microm apart. The correlation is probably due to viscoelastic properties of the cytoplasm. Theoretical analysis based on statistical mechanics suggests that directed diffusion can only occur in a material that behaves like a fluid on large time scales. CONCLUSIONS: The study shows that mitochondria in different regions of the cell experience different characteristic motions. This suggests that the cytoplasm is a heterogeneous viscoelastic material. The study provides new insight into the motion of mitochondria in chondrocytes and its connection with the mechanical properties of the cytoplasm.