Using Fluorescence in situ hybridization to study maize lines genetically predicted to have chromosomal abnormalities [abstract]

Abstract only availableSince the 1960s, genetic evidence has indicated chromosome damage and nondisjunction in lines of maize containing knob heterochromatin-bearing chromosomes and at least two B chromosomes. However, at that time researchers lacked the technology to visualize these occurrences. Now, using Fluorescence in situ Hybridization to "paint" and photograph the chromosomes, it is possible to accurately karyotype and identify broken, missing, or extra chromosomes. A line with a very large number of heterochromatic knobs had been crossed with another line containing supernumerary B chromosomes. This F1 hybrid that had been self pollinated (B73+B/K10) was chosen for study by the FISH method because it contains both knobs and B chromosomes, as well as exhibiting abnormalities such as irregular rows, ovule abortion, and defective kernels. This material combined a high knob number with B chromosomes and exhibited properties suggestive of chromosome breakage or nondisjunction. Metaphase spreads from the root tips were prepared and hybridized to fluorescent probes. Spreads were observed using fluorescence microscopy. The majority of the plants studied possessed the normal content of 20 A chromosomes plus varying numbers of B chromosomes. One individual was found with 21 chromosomes that might have resulted from nondisjunction. No chromosomal breakage was evident in this background. FISH proved to be a powerful cytogenetic tool in observing these plants; however, further research on this topic is needed to provide insight into the cause of the genetic abnormalities

Evaluating the Applicability of the Fokker-Planck Equation in Polymer Translocation: A Brownian Dynamics Study

Brownian dynamics (BD) simulations are used to study the translocation dynamics of a coarse-grained polymer through a cylindrical nanopore. We consider the case of short polymers, with a polymer length, N, in the range N=21-61. The rate of translocation is controlled by a tunable friction coefficient, gamma_{0p}, for monomers inside the nanopore. In the case of unforced translocation, the mean translocation time scales with polymer length N as ~ (N-N_p)^alpha, where N_p is the average number of monomers in the nanopore. The exponent approaches the value alpha=2 when the pore friction is sufficiently high, in accord with the prediction for the case of the quasi-static regime where pore friction dominates. In the case of forced translocation, the polymer chain is stretched and compressed on the cis and trans sides, respectively, for low gamma_{0p}. However, the chain approaches conformational quasi-equilibrium for sufficiently large gamma_{0p}. In this limit the observed scaling of with driving force and chain length supports the FP prediction that is proportional to N/f_d for sufficiently strong driving force. Monte Carlo simulations are used to calculate translocation free energy functions for the system. The free energies are used with the Fokker-Planck equation to calculate translocation time distributions. At sufficiently high gamma_{0p}, the predicted distributions are in excellent agreement with those calculated from the BD simulations. Thus, the FP equation provides a valid description of translocation dynamics for sufficiently high pore friction for the range of polymer lengths considered here. Increasing N will require a corresponding increase in pore friction to maintain the validity of the FP approach. Outside the regime of low N and high pore friction, the polymer is out of equilibrium, and the FP approach is not valid.Comment: 13 pages, 11 figure

Polymer Translocation Dynamics in the Quasi-Static Limit

Monte Carlo (MC) simulations are used to study the dynamics of polymer translocation through a nanopore in the limit where the translocation rate is sufficiently slow that the polymer maintains a state of conformational quasi-equilibrium. The system is modeled as a flexible hard-sphere chain that translocates through a cylindrical hole in a hard flat wall. In some calculations, the nanopore is connected at one end to a spherical cavity. Translocation times are measured directly using MC dynamics simulations. For sufficiently narrow pores, translocation is sufficiently slow that the mean translocation time scales with polymer length N according to \propto (N-N_p)^2, where N_p is the average number of monomers in the nanopore; this scaling is an indication of a quasi-static regime in which polymer-nanopore friction dominates. We use a multiple-histogram method to calculate the variation of the free energy with Q, a coordinate used to quantify the degree of translocation. The free energy functions are used with the Fokker-Planck formalism to calculate translocation time distributions in the quasi-static regime. These calculations also require a friction coefficient, characterized by a quantity N_{eff}, the effective number of monomers whose dynamics are affected by the confinement of the nanopore. This was determined by fixing the mean of the theoretical distribution to that of the distribution obtained from MC dynamics simulations. The theoretical distributions are in excellent quantitative agreement with the distributions obtained directly by the MC dynamics simulations for physically meaningful values of N_{eff}. The free energy functions for narrow-pore systems exhibit oscillations with an amplitude that is sensitive to the nanopore length. Generally, larger oscillation amplitudes correspond to longer translocation times.Comment: 13 pages, 13 figure

Cooperativity and Frustration in Protein-Mediated Parallel Actin Bundles

We examine the mechanism of bundling of cytoskeletal actin filaments by two representative bundling proteins, fascin and espin. Small-angle X-ray studies show that increased binding from linkers drives a systematic \textit{overtwist} of actin filaments from their native state, which occurs in a linker-dependent fashion. Fascin bundles actin into a continuous spectrum of intermediate twist states, while espin only allows for untwisted actin filaments and fully-overtwisted bundles. Based on a coarse-grained, statistical model of protein binding, we show that the interplay between binding geometry and the intrinsic \textit{flexibility} of linkers mediates cooperative binding in the bundle. We attribute the respective continuous/discontinous bundling mechanisms of fascin/espin to differences in the stiffness of linker bonds themselves.Comment: 5 pages, 3 figures, figure file has been corrected in v

Turkey diseases : cause, prevention, and control

Cover title

Identification of chloroplast DNA insertions in nuclear chromosomes of maize B73 line using the FISH procedure

Abstract only availableIt is known that chloroplast DNA can incorporate itself into the nuclear genome of plants. However, the sites of chloroplast (ct) DNA integration into chromosomes of maize have not yet been analyzed. This project is the first attempt to find the location of the ctDNA on the maize chromosomes. Fluorescent in situ hybridization is a technique that has proved useful in karyotyping and chromosomal mapping in maize. The FISH procedure is being used in this study to discover the location of the ctDNA in the nuclear genome of the inbred line B37. In order to develop ctDNA “probes” for FISH analysis, we have used the polymerase chain reaction (PCR) to produce fragments of ctDNA. Primers were chosen to amplify fragments of 10 kb or larger. The amplified DNAs were purified and labeled with fluorescent dyes and these probes were subsequently hybridized to chromosomes. The probes recognize and bind to the corresponding DNA sequences within the chromosomes. Root tip cells were used to prepare the slides for hybridization. Because the cells are collected during the metaphase stage of division, the chromosomes are compact and more easily visible. Chromosomes that contain ctDNA can be detected using a compound microscope with fluorescent attachments. The location of the ctDNA on the chromosomes is made visible by the fluorescent labeling of the probe. Eight of eleven regions of the chloroplast genome of the B73 line have been specifically amplified and have been observed under the microscope for FISH analysis. This information will contribute to an understanding of the extent and mechanism of transfer of organellar genomes to the nucleus.MU Monsanto Undergraduate Research Fellowshi

Expected climate change impacts on land and natural resource use in Namibia: exploring economically efficient responses

Abstract This paper informs policy over the efficiency of investments on Namibia's rangelands both now and under future expected climate change. It is in this setting that Namibia's pastoralist communities, communal conservancies and increasing numbers of wildlife reside, and their economic activity dominates. We bring the principles of economics to decision-making. We analyse primary land uses, livestock production and wildlife viewing tourism in three ecologically different biomes -the southern Karoo Biome, the central Savanna Biome and the northeastern Woodland Biome. We analyse how expected climate change will impact these investments to 2080. From an economic perspective, pastoralism and wildlife-based tourism developed within common property management systems can be sound investments across Namibia's communal lands. Furthermore, as climate changes, the existing economic benefits to the Namibian economy associated with pastoralism and wildlife-based tourism should be magnified, as capital-intensive commercial fenced ranching systems become less economic. Recent research indicates that adoption of good rangeland management principles involving flexible herding, economies of scale and commercially viable utilisation of invasive bush can significantly increase profits and economic returns on investment for livestock systems in Namibia. Furthermore, under conditions of expected climate change, our results indicate that income from natural resource use will be more resilient than livestock and other agricultural investments. Estimated losses in economic contribution will be highest in the agricultural sector, and in particular with commercial fenced ranching, and rainfed cropping. Climate change poses considerable challenges for pastoralists and other economic activity on Namibia's rangelands. Global climate modelling suggests that by 2080, Namibia's temperatures will have increased by some 3°C and rainfall decreased by 5% to 20%. Our results suggest that gradual change in climate over the next 70 years will see the potential national value of livestock income halved and that of tourism income reduced by one quarter. Active interventions should include shifts in livestock and rangeland policy, encouraging the adoption of more flexible and resilient systems and including efforts to make rangeland use less rigid and more able to change and adapt. Adaptation to climate change should include promotion of natural resource-based land uses such as continued expansion of the Community Based Natural Resource Management programme. Furthermore, national policy now recognises this, and implementation of the Namibia Rangeland Management Policy will provide incentives to invest in sound rangeland management. (Continued on next page