Pan-genome and multi-parental framework for high-resolution trait dissection in melon (Cucumis melo).

Linking genotype with phenotype is a fundamental goal in biology and requires robust data for both. Recent advances in plant-genome sequencing have expedited comparisons among multiple-related individuals. The abundance of structural genomic within-species variation that has been discovered indicates that a single reference genome cannot represent the complete sequence diversity of a species, leading to the expansion of the pan-genome concept.

A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants.

Alignments of multiple genomes are a cornerstone of comparative genomics, but generating these alignments remains technically challenging and often impractical. We developed the msa_pipeline workflow (https://bitbucket.org/bucklerlab/msa_pipeline) to allow practical and sensitive multiple alignment of diverged plant genomes and calculation of conservation scores with minimal user inputs.

Joint analysis of days to flowering reveals independent temperate adaptations in maize.

Domesticates are an excellent model for understanding biological consequences of rapid climate change. Maize (Zea mays ssp. mays) was domesticated from a tropical grass yet is widespread across temperate regions today.

Utility of Climatic Information via Combining Ability Models to Improve Genomic Prediction for Yield Within the Genomes to Fields Maize Project.

Genomic prediction provides an efficient alternative to conventional phenotypic selection for developing improved cultivars with desirable characteristics. New and improved methods to genomic prediction are continually being developed that attempt to deal with the integration of data types beyond genomic information. Modern automated weather systems offer the opportunity to capture continuous data on a range of environmental parameters at specific field locations.

Heavy Metals Content in Great Shearwater (Ardenna Gravis): Accumulation, Distribution and Biomarkers of Effect in Different Tissues.

The purpose of this study was to explore the usefulness of Great Shearwater (Ardenna gravis) as a bioindicator for biomonitoring programs for metal pollution. Three different metals were analysed in liver, kidney, and feathers, including cadmium, lead, and zinc. Glutathione-S-transferase, malondialdehyde, reduced glutathione, and catalase were assessed as oxidative stress biomarkers.

The importance of dominance and genotype-by-environment interactions on grain yield variation in a large-scale public cooperative maize experiment.

High-dimensional and high-throughput genomic, field performance, and environmental data are becoming increasingly available to crop breeding programs, and their integration can facilitate genomic prediction within and across environments and provide insights into the genetic architecture of complex traits and the nature of genotype-by-environment interactions. To partition trait variation into additive and dominance (main effect) genetic and corresponding genetic-by-environment variances, and to identify specific environmental factors that influence genotype-by-environment interactions, we curated and analyzed genotypic and phenotypic data on 1918 maize (Zea mays L.) hybrids and environmental data from 65 testing environments.

First record of a freshwater bryozoan species in Cuba: (Linnaeus, 1758) (Phylactolaemata, Bryozoa).

The discovery of floatoblasts in wetlands of the La Niña Bonita Reservoir and the Ciénaga de Zapata Swamp, Cuba, constitutes the first record of a freshwater bryozoan species on the island and extends the distribution range of the species in the insular Caribbean. Unlike the inland waters of the Lesser Antilles the greater availability of water and lower salinity are likely the main factors that determine the distribution of in the Greater Antilles.

Diverse Chromosomal Locations of Quantitative Trait Loci for Tolerance to Maize chlorotic mottle virus in Five Maize Populations.

The recent rapid emergence of maize lethal necrosis (MLN), caused by coinfection of maize with Maize chlorotic mottle virus (MCMV) and a second virus usually from the family Potyviridae, is causing extensive losses for farmers in East Africa, Southeast Asia, and South America. Although the genetic basis of resistance to potyviruses is well understood in maize, little was known about resistance to MCMV. The responses of five maize inbred lines (KS23-5, KS23-6, N211, DR, and Oh1VI) to inoculation with MCMV, Sugarcane mosaic virus, and MLN were characterized.

The effect of artificial selection on phenotypic plasticity in maize.

Remarkable productivity has been achieved in crop species through artificial selection and adaptation to modern agronomic practices. Whether intensive selection has changed the ability of improved cultivars to maintain high productivity across variable environments is unknown. Understanding the genetic control of phenotypic plasticity and genotype by environment (G × E) interaction will enhance crop performance predictions across diverse environments.

A study of allelic diversity underlying flowering-time adaptation in maize landraces.

Landraces (traditional varieties) of domesticated species preserve useful genetic variation, yet they remain untapped due to the genetic linkage between the few useful alleles and hundreds of undesirable alleles. We integrated two approaches to characterize the diversity of 4,471 maize landraces. First, we mapped genomic regions controlling latitudinal and altitudinal adaptation and identified 1,498 genes.

Identification of genetic variants associated with maize flowering time using an extremely large multi-genetic background population.

Flowering time is one of the major adaptive traits in domestication of maize and an important selection criterion in breeding. To detect more maize flowering time variants we evaluated flowering time traits using an extremely large multi- genetic background population that contained more than 8000 lines under multiple Sino-United States environments. The population included two nested association mapping (NAM) panels and a natural association panel.

Genome-wide association analysis of seedling root development in maize (Zea mays L.).

Background: Plants rely on the root system for anchorage to the ground and the acquisition and absorption of nutrients critical to sustaining productivity. A genome wide association analysis enables one to analyze allelic diversity of complex traits and identify superior alleles. 384 inbred lines from the Ames panel were genotyped with 681,257 single nucleotide polymorphism markers using Genotyping-by-Sequencing technology and 22 seedling root architecture traits were phenotyped.

Ozone/oxygen mixture modifies the subcellular redistribution of Bax protein in renal tissue from rats treated with cisplatin.

Background: Cellular events in cisplatin-mediated nephrotoxicity include apoptosis induction, decreased protein synthesis, changes in the subcellular redistribution of Bax mitochondrial dysfunction, DNA injury, increased lipid peroxidation, depletion of glutathione and decrease in enzymatic activity of renal antioxidant enzymes. In previous papers we have shown that intra-rectal (i.r.

Lipid peroxides and antioxidant enzymes in cisplatin-induced chronic nephrotoxicity in rats.

Cisplatin (CDDP), an anticancer drug, induces remarkable toxicity in the kidneys of animals and humans and it has been well documented that reactive oxygen species and the renal antioxidant system are strongly involved in acute renal damage induced by CDDP. The aim of the present study was to investigate whether or not the renal antioxidant system plays also an important role in chronic renal damage induced by repeated doses of CDDP (1 mg/kg intraperitoneally twice weekly during 10 weeks in rats). In order to elucidate it, serum creatinine and urea levels, renal glutathione and thiobarbituric acid-reactive substances (TBARS) content, as well as renal superoxide dismutase and glutathione peroxidase activities were measured in the kidney homogenates of chronically CDDP-treated rats and additionally histological studies were performed in the rat kidneys.

Reversion by ozone treatment of acute nephrotoxicity induced by cisplatin in rats.

Background: Ozone therapy has become a useful treatment for pathological processes, in which the damage mediated by reactive oxygen species is involved. Several lines of evidence suggest that cisplatin-induced acute nephrotoxicity is partially mediated by reactive oxygen species

Aims: To analyze the effect of ozone administration after cisplatin-induced acute nephrotoxicity.

Methods: Male Sprague-Dawley rats were treated with five intra-rectal applications of ozone/oxygen mixture at 0.

Further studies on a mixture of fatty acids from sugar cane (Saccharum officinarum) wax oil in animal models of hypersensitivity.

A mixture of fatty acids obtained from sugar cane wax oil, the main components of which are palmitic, oleic, linoleic and linolenic acids, was evaluated topically in two experimental models of hypersensitivity: the ear swelling response to ovalbumin in sensitized mice (ED50 edema: 0.63 +/- 0.06 mg/ear, ED50 myeloperoxidase: 0.

Protection by ozone preconditioning is mediated by the antioxidant system in cisplatin-induced nephrotoxicity in rats.

Background: Acute renal failure is a dose-limiting factor of cisplatin chemotherapy. Here, we show the protective effect of ozone oxidative preconditioning against cisplatin-induced renal dysfunction in rats. Ozone oxidative preconditioning is a prophylactic approach, which favors the antioxidant-pro-oxidant balance for preservation of the cell redox state by increasing antioxidant endogenous systems in various in vivo and in vitro experimental models.

C-phycocyanin: a biliprotein with antioxidant, anti-inflammatory and neuroprotective effects.

Phycocyanin (Pc) is a phycobiliprotein that has been recently reported to exhibit a variety of pharmacological properties. In this regard, antioxidant, anti-inflammatory, neuroprotective and hepatoprotective effects have been experimentally attributed to Pc. When it was evaluated as an antioxidant in vitro, it was able to scavenge alkoxyl, hydroxyl and peroxyl radicals and to react with peroxinitrite (ONOO(-);) and hypochlorous acid (HOCl).

Aprotinin mediated antioxidant effect in Cardiosurgery with mechanical cardiorespiratory support (CMCS).

Background: Aprotinin has been used in cardiosurgery as a hemostatic agent. Considering the implication of oxygen reactive species and proteases in the pathogenesis of Systemic Inflammatory Response Syndrome, we hypothesized that aprotinin may exert an antioxidant effect. This work was designed to evaluate the antioxidant capacity of aprotinin in vitro and in vivo in child patients undergoing cardiosurgery with mechanical cardiorespiratory support.

Effects of phycocyanin extract on tumor necrosis factor-alpha and nitrite levels in serum of mice treated with endotoxin.

Phycocyanin is a biliprotein which exerts antioxidative and anti-inflammatory effects in various in vivo and in vitro experimental models. In this study phycocyanin effects on tumor necrosis factor-alpha (TNF alpha) and nitrite levels in serum of mice treated with lipopolysaccharide (LPS) was examined. TNF alpha was measured by cytotoxicity on L-929 cells and nitrite by the Griess reaction, after reduction of all nitrates to nitrites by nitrate reductase, 1 h after LPS injection (0.

Antioxidant properties of alpha-crystallin.

alpha-Crystallin is a major chaperone lens protein to which has been ascribed antioxidant functions. In the present work we have evaluated the antioxidant and free radical scavenging properties of bovine alpha-crystallin in a series of in vitro models: zimosan-induced, luminol-enhanced chemiluminescence response of polymorphonuclear leukocytes, the autoxidation of brain homogenate, bleaching of 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid)-derived radical cations, trapping of peroxyl radicals, and reactivity toward hypochloric acid. In all these systems, the reactivity of alpha-crystallin is higher than or similar to that of bovine serum albumin.

C-phycocyanin protects cerebellar granule cells from low potassium/serum deprivation-induced apoptosis.

We tested the potential cytoprotective role of C-phycocyanin in rat cerebellar granule cell cultures. Cell death was induced by potassium and serum (K/S) withdrawal. Cell viability was studied using the neutral red assay and laser scanning cytometry with propidium iodide as fluorochrome.

Effects of phycocyanin extract on prostaglandin E2 levels in mouse ear inflammation test.

Recently it was demonstrated that phycocyanin, a biliprotein isolated from microalgae Spirulina, exerts anti-inflammatory activity in several animal models of inflammation. In this report, the effects of phycocyamin on prostaglandin E2 (PGE2) concentrations and phospholipase A2 (PLA2) activity were determined in arachidonic acid (AA) and 12-O-tetradecanoyl phorbol 13-acetate (TPA)-induced mouse ear oedema, respectively. Phycocyanin (50-200 mg/kg p.

Kinetics of c-phycocyanin reaction with hypochlorite.

Hydrochlorous acid bleaches c-phycocyanin visible absorbance with a second-order rate constant (pH 7.4) of 1.3x10(3) M(-1) s(-1).