Targeted mutagenesis of duplicated genes in soybean with zinc-finger nucleases

We performed targeted mutagenesis of a transgene and nine endogenous soybean (Glycine max) genes using zinc-finger nucleases (ZFNs). A suite of ZFNs were engineered by the recently described context-dependent assembly platform--a rapid, open-source method for generating zinc-finger arrays. Specific ZFNs targeting dicer-like (DCL) genes and other genes involved in RNA silencing were cloned into a vector under an estrogen-inducible promoter. A hairy-root transformation system was employed to investigate the efficiency of ZFN mutagenesis at each target locus. Transgenic roots exhibited somatic mutations localized at the ZFN target sites for seven out of nine targeted genes. We next introduced a ZFN into soybean via whole-plant transformation and generated independent mutations in the paralogous genes DCL4a and DCL4b. The dcl4b mutation showed efficient heritable transmission of the ZFN-induced mutation in the subsequent generation. These findings indicate that ZFN-based mutagenesis provides an efficient method for making mutations in duplicate genes that are otherwise difficult to study due to redundancy. We also developed a publicly accessible Web-based tool to identify sites suitable for engineering context-dependent assembly ZFNs in the soybean genome.     

Design, synthesis, and testing of an 6-O-linked series of benzimidazole based inhibitors of CDK5/p25

Alzheimer’s disease (AD) is a progressive neurodegenerative disease resulting in cognitive and behavioral impairment. The two classic pathological hallmarks of AD include extraneuronal deposition of amyloid ?? (A??) and intraneuronal formation of neurofibrillary tangles (NFTs). NFTs contain hyperphosphorylated tau. Tau is the major microtubule-associated protein in neurons and stabilizes microtubules (MTs). Cyclin dependent kinase 5 (CDK5), when activated by the regulatory binding protein p25, phosphorylates tau at a number of proline-directed serine/threonine residues, resulting in formation of phosphorylated tau as paired helical filaments (PHFs) then in subsequent deposition of PHFs as NFTs. Beginning with the structure of Roscovitine, a moderately selective CDK5 inhibitor, we sought to conduct structural modifications to increase inhibitory potency of CDK5 and increase selectivity over a similar enzyme, cyclin dependent kinase 2 (CDK2). The design, synthesis, and testing of a series of 1-isopropyl-4-aminobenzyl-6-ether-linked benzimidazoles is presented.     

Visual ecology of Indian carpenter bees I: Light intensities and flight activity

Bees are mostly active during the daytime, but nocturnality has been reported in some bee families. We studied temporal flight activity in three species of carpenter bees (genus Xylocopa) in relation to light intensities. X. leucothorax is diurnal, X. tenuiscapa is largely diurnal being only occasionally crepuscular, while X. tranquebarica is truly nocturnal. Occasional forays into dim light by X. tenuiscapa are likely to be due to the availability of richly rewarding Heterophragma quadriloculare (Bignoniaceae) flowers, which open at night. X. tranquebarica can fly even during the moonless parts of nights when light intensities were lower than 10⁻⁵ cd m⁻², which makes this species the only truly nocturnal bee known so far. Other known dim-light species fly during crepuscular or moonlit periods. We compare eye and body sizes with other known diurnal and dim-light bees. We conclude that while extremely large ocellar diameters, large eye size:body size ratio, large number of ommatidia and large ommatidial diameters are all adaptations to dim-light foraging, these alone do not sufficiently explain the flights of X. tranquebarica in extremely dim light. We hypothesise that additional adaptations must confer extreme nocturnality in X. tranquebarica.     

Enzyme heterozygosity,metabolism, and developmental stability

Developmental homeostasis, measured as either fluctuating asymmetry or variance of morphological characters, increases with enzyme heterozygosity in many, but not all, natural populations. These results have been reported forDrosophila, monarch butterflies, honeybees, blue mussels, side-blotched lizards, killifish, salmonid fishes, guppies, Sonoran topminnows, herring, rufous-collared sparrows, house sparrows, brown hares, white-tailed deer, and humans. Because heterozygosity at a few loci can not predict heterozygosity of the entiry genome, these loci must be detecting localized zones that influence the developmental environment. Studies of malate dehydrogenase in honeybees,Apis mellifera, and lactate dehydrogenase in killifish,Fundulus heteroclitus, revealed that developmental homeostasis varied with heterozygosity of individual loci. Heterozygotes differed from homozygotes in fluctuating asymmetry, morphological variance, and in correlations between morphological characters. The protein loci in these studies code for enzymes, and therefore do not directly influence morphological characters. However, some enzymatic loci substantially influence metabolism, and contribute to variation in the amount of energy available for development and growth. This argument can be made most convincingly for the LDH polymorphism in killifish. LDH genotypes differ in enzyme kinetic properties that measure differences in physiological efficiency, and these differences produce measurable and predictable differences in physiology and development. Under environmental conditions which impose a stress upon development, genotypes at these loci may have different amounts of energy available for development, and consequently exhibit different levels of developmental homeostasis.     

EFFECTS OF CONE COLOR DIMORPHISM ON REPRODUCTIVE OUTPUT OF WHITE FIR GROWING ALONG ELEVATIONAL GRADIENTS

White fir can produce cones that are either green or purple, and the color is genetically determined. The purpose of this study was to determine the effects of elevation and cone color on the cone and seed characters of this species. We collected cones from trees along two elevational gradients, Red Mountain Pass (1981 and 1983) and Cucharas Pass (1983). Over 600 cones were measured for length, diameter, number of viable seeds, mass of five viable seeds, and percent successful seed set. There was a strong overall effect due to elevation, although the Cucharas and Red Mtn. locations showed somewhat different effects on the reproductive characters. Seed mass decreased with elevation in all three samples. There was significant interaction between cone color and elevation for both 1983 samples, suggesting the presence of genotype-environment interaction. A large difference was seen between the Red Mtn. and Cucharas locations, and the cone colors behaved differently at the two locations. The consistently large differences between the seed characters of green and purple cones suggested that cone color, which is presumably determined by a single gene, may profoundly affect the reproductive potential of individual trees. This appears to be an example of influential coloration in plants which is not associated with pollination or dispersal.     

Production and Characterization of Polymeric Lignin Degradation Intermediates from Two Different Streptomyces spp.

Previous investigations have identified a quantitatively major intermediate of lignin degradation by Streptomyces viridosporus. The intermediate, a modified lignin polymer, acid-precipitable polymeric lignin (APPL), is released as a water-soluble catabolite and has been recovered in amounts equivalent to 30% of the lignin originally present in a corn stover lignocellulose substrate after degradation by this actinomycete. In the present work, APPLs were collected at various time intervals from cultures of two highly ligninolytic Streptomyces sp. strains, S. viridosporus T7A and S. badius 252, growing on corn stover lignocellulose. APPL production was measured over time, and the chemistry of APPLs produced by each organism after different time intervals was compared. Chemical characterizations included assays for lignin, carbohydrate, and ash contents, molecular weight distributions by gel permeation chromatography, and chemical degradation analyses by permanganate oxidation, acidolysis, and alkaline ester hydrolysis. Differences between the organisms were observed in the cultural conditions required for APPL production and in the time courses of APPL accumulation. S. viridosporus produced APPL in solid-state fermentation over a 6- to 8-week incubation period, whereas S. badius produced as much or more APPL, but only in liquid culture and over a 7- to 8-day incubation period. The chemistry of the APPLs produced also differed. S. viridosporus APPL was more lignin-like than that of S. badius and was slowly modified further over time, although no change in molecular weight distribution over time was observed. In contrast, S. badius APPL was less lignin-like and increased substantially in average molecular weight over time. Results indicated that differing mechanisms of lignin metabolism may exist in these two Streptomyces sp. strains. S. viridosporus APPL probably originates from the heart of the lignin and is released largely as the result of β-ether cleavage and other oxidative reactions. S. badius APPL probably originates in the same manner; however, after release as a water-soluble catabolite, lower-molecular-weight intermediates of lignin degradation are repolymerized with APPL in a reaction catalyzed by an extracellular phenol oxidase. The chemical analyses and the presence of extracellular phenol oxidase in S. badius, but not in S. viridosporus, support this conclusion.     

Lipid Droplets in Schwann Cells During Tellurium Neuropathy Are Derived from Newly Synthesized Lipid

Exposure of weanling rats to a diet containing elemental tellurium results in a peripheral neuropathy characterized by segmental demyelination and minimal axonal degeneration. One of the earliest ultrastructural abnormalities in tellurium neuropathy is an increased number of cytoplasmic lipid droplets in myelinating Schwann cells. The pathogenesis of these lipid droplets was investigated using light and electron microscopic autoradiography. Nerve lipids were either "prelabeled" with [3H]acetate via in vivo intraneural injection 3 days before a 2-day exposure to tellurium, or "postlabeled" via in vivo intraneural injection or in vitro incubation with [3H]acetate following a 2-day exposure to tellurium. In the prelabeled nerves, myelin became heavily labeled, but the tellurium-induced cytoplasmic lipid droplets were rarely labeled. In the postlabeled nerves, the tellurium-induced cytoplasmic lipid droplets were the most heavily labeled structures within the nerve. These data indicate that the tellurium-induced lipid droplets in Schwann cells are derived from newly synthesized lipid rather than from the early breakdown and internalization of myelin lipids. The earliest biochemical abnormality observed in tellurium neuropathy is an inhibition of cholesterol synthesis at the squalene epoxidase step. This leads to an accumulation of squalene within the nerve. We conclude that the cytoplasmic lipid droplets in Schwann cells contain this accumulated lipid.     

Fatty Acids from Degenerating Myelin Lipids Are Conserved and Reutilized for Myelin Synthesis During Regeneration in Peripheral Nerve

Abstract: Following nerve crush, cholesterol from degenerating myelin is conserved and reutilized for new myelin synthesis during nerve regeneration. The possibility that other myelin lipids are salvaged and reutilized has not been investigated previously. We examined the fate of myelin phospholipids and their fatty acyl moieties following nerve crush by electron microscopic autoradiography of myelin lipids prelabeled with [³H]oleate or [2-³H]-glycerol. Both precursors were incorporated predominantly (>90%) into phospholipids; >85% of the [³H]oleate was incorporated as oleate, with the remainder in longer-chain fatty acids. Before nerve crush, both labels were restricted to myelin sheaths. Following nerve crush and subsequent regeneration, over half the label from [³H]oleate, but little from [2-³H]glycerol, remained in nerve. The oleate label was present as fatty acyl moieties in phospholipids and was localized to newly formed myelin sheaths. Among the extracellular soluble lipids within the degenerating nerve, the bulk of the labeled phospholipids floated at the same density as lipoprotein particles. These data indicate that myelin phospholipids are completely hydrolyzed during nerve degeneration, that at least half the resultant free fatty acids are salvaged and reutilized for new myelin synthesis, and that these salvaged fatty acids are transported by a lipoprotein-mediated mechanism similar to that functioning in cholesterol reutilization.     

Creatine kinase kinetics,ATP turnover,and cardiac performance in hearts depleted of creatine with the substrate analogue β-guanidinopropionic acid

Rats were fed a diet containing 1% of the creatine substrate analogue β-guanidinopropionic acid for 6–10 weeks. ³¹P-NMR investigation of isolated, glucose-perfused working hearts showed a 90% reduction in [phosphocreatine] from 22.2 to 2.5 μmol/g dry wt in guanidinopropionic acid-fed animals but no change in [P_i], [ATP], or intracellular pH. The unidirectional exchange flux in the creatine kinase reaction (direction phosphocreatine → ATP) was measured by saturation transfer NMR in hearts working against a perfusion pressure of 70 cm of water. This exchange was 10 μmol/g dry wt per s in control hearts and decreased 4-fold to 2.5–2.8 μmol/g dry wt per s in hearts from guanidinopropionic acid-fed animals. Oxygen consumption and cardiac performance were measured in parallel experiments at two perfusion pressures, 70 and 140 cm. No significant differences were observed in oxygen uptake or in any of the performance criteria between hearts from control and guanidinopropionic acid-fed rats at either workload. Assuming an ADP:O ratio of 3, the oxygen consumption measurements correspond to ATP turnover rates of 4.2–7.8 μmol/g dry per s. These rates are 1.5–3-times greater than the rate of the phosphocreatine → ATP exchange in hearts from guanidinopropionic acid-fed rats. These data suggest that phosphocreatine cannot be an obligate intermediate of energy transduction in the heart.     

Chemical bonding in carborane/aromatic co-polymers: a first-principles analysis of experimental photoemission spectra

First-principles density functional theory calculations have been used to study the relative stability and analyse the chemical bonding of novel cross-linked carborane polymers. Atomic charges with several population analysis methods based on fully relaxed structures were calculated to interpret the chemical binding energy shifts of XPS spectra of these boron carbide polymers. The results indicate that a base structure with one aromatic linking unit with carborane is energetically favoured. The linear relationship between experimental core-level photoemission binding energies and computational partial atomic charges from four population analysis methods (Mulliken, Hirshfeld, atoms-in-molecules (AIM) and natural bond order (NBO)) were analysed and the results indicate that cross-linking occurs at icosahedral B sites non-adjacent to icosahedral carbon sites, in agreement with recently reported experimental results. The role of basis set size in determining partial atomic charges was found to vary with population analysis method. Best linear correlations were identified with the more robust population analysis methods (Hirshfeld, AIM and NBO) with the AIM methods noted as being particularly sensitive to basis set size.