Optimization of combined genetic gain and diversity for collection and deployment of seed orchard crops

Genetic gain and diversity of seed orchards’ crops are determined by the number of parents, their breeding values and relatedness, within-orchard pollination efficiency, and level of pollen contamination. These parameters can be manipulated at establishment by varying clonal representation (e.g., linear deployment), during orchard development by genetic thinning, or by selective harvesting. Since clonal fecundities are known to vary both within and among years, then each seed crop has a unique genetic composition and, therefore, crops should be treated on a yearly basis. Here we present an optimization protocol that maximizes crop’s genetic gain at any desired genetic diversity through the selection of a subset of the crop that meets both parameters. The genetic gain is maximized within the biological limit set by each clone’s seed-cone production and effective population size is used as a proxy to genetic diversity whereby any relationship among clones is considered. The optimization was illustrated using 3 years’ reproductive output data from a first-generation western larch seed orchard and was tested under various scenarios including actual male and female reproductive output and male reproductive output assumed to be either equal to that of female or a function of clonal representation. Furthermore, various levels of co-ancestry were assigned to the orchard’s clones in supplementary simulations. Following the optimization, all solutions were effective in creating custom seedlots with different gain and diversity levels and provided the means to estimate the genetic properties of composite seedlots encompassing the remaining “unused” seed from a number of years.     

Chemical composition of Cystoseira crinita Bory from the Eastern Mediterranean

The chemical composition of the brown alga Cystoseira crinita Bory from the Eastern Mediterranean was investigated. Fourteen sterols have been identified, five of them for the first time in algae. The structure of one new sterol was established. The origin of seven sterols with short side chains was discussed. In the volatile fraction 19 compounds and in the polar fraction 15 compounds were identified. The main lipid classes were isolated and their fatty acid composition was established.     

Spontaneous cytotoxicity of macrophages against pancreatic islet cells

Activated peritoneal macrophages were found to lyse syngeneic [3H]leucine-labeled pancreatic islet cells or rat insulinoma cells after 15 h of coculture at 37 degrees C. Lysis was verified by electron microscopic analysis. Islet cell lysis was dependent on the T:E ratio and was comparable with P815 and L929 tumor cells used as targets. The cytotoxic activity was localized in the adherent fraction of Corynebacterium parvum activated peritoneal cells and was destroyed by incubation of cells with macrophage-toxic silica particles. Syngeneic thyrocytes and hepatocytes were found to be resistant to the cytolytic action of activated macrophages. It has been shown previously that macrophages contribute to pancreatic islet inflammation. The present in vitro analysis demonstrates that macrophages can function as effector cells in islet destruction.     

Uncovering hidden genetic variation in photosynthesis of field‐grown maize under ozone pollution

Ozone is the most damaging air pollutant to crops, currently reducing Midwest US maize production by up to 10%, yet there has been very little effort to adapt germplasm for ozone tolerance. Ozone enters plants through stomata, reacts to form reactive oxygen species in the apoplast and ultimately decreases photosynthetic C gain. In this study, 10 diverse inbred parents were crossed in a half‐diallel design to create 45 F₁ hybrids, which were tested for ozone response in the field using free air concentration enrichment (FACE). Ozone stress increased the heritability of photosynthetic traits and altered genetic correlations among traits. Hybrids from parents Hp301 and NC338 showed greater sensitivity to ozone stress, and disrupted relationships among photosynthetic traits. The physiological responses underlying sensitivity to ozone differed in hybrids from the two parents, suggesting multiple mechanisms of response to oxidative stress. FACE technology was essential to this evaluation because genetic variation in photosynthesis under elevated ozone was not predictable based on performance at ambient ozone. These findings suggest that selection under elevated ozone is needed to identify deleterious alleles in the world's largest commodity crop.     

Pepsin Digest of Wheat Gliadin Fraction Increases Production of IL-1β via TLR4/MyD88/TRIF/MAPK/NF-κB Signaling Pathway and an NLRP3 Inflammasome Activation

Celiac disease (CD) is a gluten-responsive, chronic inflammatory enteropathy. IL-1 cytokine family members IL-1β and IL-18 have been associated with the inflammatory conditions in CD patients. However, the mechanisms of IL-1 molecule activation in CD have not yet been elucidated. We show in this study that peripheral blood mononuclear cells (PBMC) and monocytes from celiac patients responded to pepsin digest of wheat gliadin fraction (PDWGF) by a robust secretion of IL-1β and IL-1α and a slightly elevated production of IL-18. The analysis of the upstream mechanisms underlying PDWGF-induced IL-1β production in celiac PBMC show that PDWGF-induced de novo pro-IL-1β synthesis, followed by a caspase-1 dependent processing and the secretion of mature IL-1β. This was promoted by K+ efflux and oxidative stress, and was independent of P2X7 receptor signaling. The PDWGF-induced IL-1β release was dependent on Nod-like receptor family containing pyrin domain 3 (NLRP3) and apoptosis-associated speck like protein (ASC) as shown by stimulation of bone marrow derived dendritic cells (BMDC) from NLRP3^−/− and ASC^−/− knockout mice. Moreover, treatment of human PBMC as well as MyD88^−/− and Toll-interleukin-1 receptor domain-containing adaptor-inducing interferon-β (TRIF)^−/− BMDC illustrated that prior to the activation of caspase-1, the PDWGF-triggered signal constitutes the activation of the MyD88/TRIF/MAPK/NF-κB pathway. Moreover, our results indicate that the combined action of TLR2 and TLR4 may be required for optimal induction of IL-1β in response to PDWGF. Thus, innate immune pathways, such as TLR2/4/MyD88/TRIF/MAPK/NF-κB and an NLRP3 inflammasome activation are involved in wheat proteins signaling and may play an important role in the pathogenesis of CD.     

Diversity,migration routes,and worldwide population genetic structure of Lecanosticta acicola,the causal agent of brown spot needle blight

Lecanosticta acicola is a pine needle pathogen causing brown spot needle blight that results in premature needle shedding with considerable damage described in North America, Europe, and Asia. Microsatellite and mating type markers were used to study the population genetics, migration history, and reproduction mode of the pathogen, based on a collection of 650 isolates from 27 countries and 26 hosts across the range of L. acicola. The presence of L. acicola in Georgia was confirmed in this study. Migration analyses indicate there have been several introduction events from North America into Europe. However, some of the source populations still appear to remain unknown. The populations in Croatia and western Asia appear to originate from genetically similar populations in North America. Intercontinental movement of the pathogen was reflected in an identical haplotype occurring on two continents, in North America (Canada) and Europe (Germany). Several shared haplotypes between European populations further suggests more local pathogen movement between countries. Moreover, migration analyses indicate that the populations in northern Europe originate from more established populations in central Europe. Overall, the highest genetic diversity was observed in south‐eastern USA. In Europe, the highest diversity was observed in France, where the presence of both known pathogen lineages was recorded. Less than half of the observed populations contained mating types in equal proportions. Although there is evidence of some sexual reproduction taking place, the pathogen spreads predominantly asexually and through anthropogenic activity.     

Identifying uniformly mutated segments within repeats

Given a long string of characters from a constant size alphabet we present an algorithm to determine whether its characters have been generated by a single i.i.d. random source. More specifically, consider all possible n-coin models for generating a binary string S, where each bit of S is generated via an independent toss of one of the n coins in the model. The choice of which coin to toss is decided by a random walk on the set of coins where the probability of a coin change is much lower than the probability of using the same coin repeatedly. We present a procedure to evaluate the likelihood of a n-coin model for given S, subject a uniform prior distribution over the parameters of the model (that represent mutation rates and probabilities of copying events). In the absence of detailed prior knowledge of these parameters, the algorithm can be used to determine whether the a posteriori probability for n=1 is higher than for any other n>1. Our algorithm runs in time O(l4logl), where l is the length of S, through a dynamic programming approach which exploits the assumed convexity of the a posteriori probability for n. Our test can be used in the analysis of long alignments between pairs of genomic sequences in a number of ways. For example, functional regions in genome sequences exhibit much lower mutation rates than non-functional regions. Because our test provides means for determining variations in the mutation rate, it may be used to distinguish functional regions from non-functional ones. Another application is in determining whether two highly similar, thus evolutionarily related, genome segments are the result of a single copy event or of a complex series of copy events. This is particularly an issue in evolutionary studies of genome regions rich with repeat segments (especially tandemly repeated segments).     

Levels of zinc and lipid peroxidation in acute coronary syndrome

The present study was carried out on 20 female patients diagnosed with acute coronary syndrome (ACS). The control group was composed of 20 healthy female volunteers. Plasma malondialdehyde (MDA) levels and serum zinc (Zn), total cholesterol, low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, and VLDL-cholesterol, Lp(a), Apo-A₁, and Apo-B were determined in all patients and controls. Plasma MDA levels were determined to be significantly high in patients with ACS compared to the controls (1.75±0.27 vs 0.8±0.43 nmol/mL; p<0.05). On the other hand, Zn levels in patients with ACS were determined to be significantly low compared to the control group (67.9±14.8 vs 101.8±22.4 mg/dL; p<0.05). There was a statistically significant negative correlation between MDA and Zn levels in patients with ACS (r=−0.678, p<0.05). Other lipid parameters were significantly altered in patients with ACS compared to the controls (p<0.05). In conclusion, Zn and lipid peroxidation levels are important in patients with ACS and they must be monitored during diagnosis and treatment of these patients.