Use of molecular markers for estimating breeding parameters: a case study in a Pinus pinaster Ait. progeny trial

The management of a genetic improvement program is based on the knowledge of the genetic parameters and their relationships to determine the genetic gains. Knowledge of the coefficient of coancestry (θ) is a requirement for efficient progeny testing scheme and for estimating additive variance components for any quantitative trait. When using open-pollinated families, most authors assume that the seedlings are related as half-sibs, but this is not always true. Our aim was to estimate a mean value of the coancestry coefficient of the families present in a maritime pine Pinus pinaster Ait. (maritime or cluster pine) progeny trial originating from seed collected in a clonal seed orchard and to study how deviations from the standard assumption of θ = 0.125 affect heritability estimations. Five highly polymorphic microsatellite markers were scored in 125 offspring from a subsample of five families from the progeny trial. The mean value of the coancestry coefficient of the families present in this progeny trial was 0.130. Differences between the unadjusted and adjusted heritability estimates were more pronounced in wood density (0.609 and 0.586, respectively) than in diameter (0.166 and 0.154, respectively). We conclude that in the trial, the associated error in heritability estimates due to the inclusion of full-sibs, when assuming a standard coefficient of relationship among open-pollinated sibs of 0.250, was low and that this result is robust with respect to the number of families sampled, given unbiased estimates of average relationship among offspring within sib families.     

Genetic parameters for growth, reproductive and maternal traits in a multibreed meat sheep population

The genetic parameters for growth, reproductive and maternal traits in a multibreed meat sheep population were estimated by applying the Average Information Restricted Maximum Likelihood method to an animal model. Data from a flock supported by the Programa de Melhoramento Genético de Caprinos e Ovinos de Corte (GENECOC) were used. The traits studied included birth weight (BW), weaning weight (WW), slaughter weight (SW), yearling weight (YW), weight gain from birth to weaning (GBW), weight gain from weaning to slaughter (GWS), weight gain from weaning to yearling (GWY), age at first lambing (AFL), lambing interval (LI), gestation length (GL), lambing date (LD - number of days between the start of breeding season and lambing), litter weight at birth (LWB) and litter weight at weaning (LWW). The direct heritabilities were 0.35, 0.81, 0.65, 0.49, 0.20, 0.15 and 0.39 for BW, WW, SW, YW, GBW, GWS and GWY, respectively, and 0.04, 0.06, 0.10, 0.05, 0.15 and 0.11 for AFL, LI, GL, LD, LWB and LWW, respectively. Positive genetic correlations were observed among body weights. In contrast, there was a negative genetic correlation between GBW and GWS (-0.49) and GBW and GWY (-0.56). Positive genetic correlations were observed between AFL and LI, LI and GL, and LWB and LWW. These results indicate a strong maternal influence in this herd and the presence of sufficient genetic variation to allow mass selection for growth traits. Additive effects were of little importance for reproductive traits, and other strategies are necessary to improve the performance of these animals.     

Bioprocess iterative batch-to-batch optimization based on hybrid parametric/nonparametric models

This paper presents a novel method for iterative batch-to-batch dynamic optimization of bioprocesses. The relationship between process performance and control inputs is established by means of hybrid grey-box models combining parametric and nonparametric structures. The bioreactor dynamics are defined by material balance equations, whereas the cell population subsystem is represented by an adjustable mixture of nonparametric and parametric models. Thus optimizations are possible without detailed mechanistic knowledge concerning the biological system. A clustering technique is used to supervise the reliability of the nonparametric subsystem during the optimization. Whenever the nonparametric outputs are unreliable, the objective function is penalized. The technique was evaluated with three simulation case studies. The overall results suggest that the convergence to the optimal process performance may be achieved after a small number of batches. The model unreliability risk constraint along with sampling scheduling are crucial to minimize the experimental effort required to attain a given process performance. In general terms, it may be concluded that the proposed method broadens the application of the hybrid parametric/nonparametric modeling technique to "newer" processes with higher potential for optimization.     

DFT study of the reductive decomposition of artemisinin

Artemisinin is a sesquiterpene lactone with an endoperoxide function that is essential for its antimalarial activity. The DFT B3LYP method, together with the 6-31G(d) and 6-31+G(d,p) basis set, is employed to calculate a set of radical anions and neutral species supposed to be formed during the rearrangement of artemisinin from the two radicals (C-centered and O-centered) that are supposed to play a relevant role in the mechanism of action. The B3LYP results show that the primary and the secondary radicals centered on C(4), generated by homolytic break of the C(3)-C(4) bond and by 1,5 hydrogen shift, respectively, are more stable than radicals centered on oxygen. The calculations show that the activation barriers for rearrangements are low, leading to a thermodynamically favorable process. These results reinforce our previous conclusions based on semi-empirical calculations but also give additional information on the reductive decomposition of artemisinin.     

Micropropagation of apple — A review

Micropropagation of apple has played an important role in the production of healthy, disease-free plants and in the rapid multiplication of scions and rootstocks with desirable traits. During the last few decades, in apple, many reliable methods have been developed for both rootstocks and scions from a practical, commercial point of view. Successful micropropagation of apple using pre-existing meristems (culture of apical buds or nodal segments) is influenced by several internal and external factors including ex vitro (e.g. genotype and physiological state) and in vitro conditions (e.g., media constituents and light). Specific requirements during stages of micropropagation, such as the establishment of in vitro cultures, shoot multiplication, rooting of microshoots and acclimatization are summarized in this review. New approaches for increasing shoot multiplication and rooting for apple and current use of micropropagated plantlets as tools in basic and applied research are also discussed.     

Evaluation of holocellulase production by plant-degrading fungi grown on agro-industrial residues

Agaricus brasiliensis CS1, Pleurotus ostreatus H1 and Aspergillus flavus produced holocellulases when grown in solid and submerged liquid cultures containing agro-industrial residues, including sugar cane bagasse and dirty cotton residue, as substrates. These isolates proved to be efficient producers of holocellulases under the conditions used in this screening. Bromatological analysis of agro-industrial residues showed differences in protein, fiber, hemicellulose, cellulose and lignin content. Maximal holocellulase activity (hemicellulase, cellulase and pectinase) was obtained using solid-state cultivation with 10% substrate concentration. In this case, remarkably high levels of xylanase and polygalacturonase activity (4,008 and 4,548 IU/l, respectively) were produced by A. flavus when grown in media containing corn residue, followed by P. ostreatus H1 with IU/l values of 1,900 and 3,965 when cultivated on 5% and 10% sugar cane bagasse, respectively. A. brasiliensis CS1 showed the highest reducing sugar yield (11.640 mg/ml) when grown on medium containing sugar cane bagasse. A. brasiliensis was also the most efficient producer of protein, except when cultivated on dirty cotton residue, which induced maximal production in A. flavus. Comparison of enzymatic hydrolysis of sugar cane bagasse and dirty cotton residue by crude extracts of A. brasiliensis CS1, P. ostreatus H1 and A. flavus showed that the best reducing sugar yield was achieved using sugar cane bagasse as a substrate.     

Structure at 1.0 Å resolution of a high-potential iron–sulfur protein involved in the aerobic respiratory chain of Rhodothermus marinus

The aerobic respiratory chain of the thermohalophilic bacterium Rhodothermus marinus, a nonphotosynthetic organism from the Bacteroidetes/Chlorobi group, contains a high-potential iron–sulfur protein (HiPIP) that transfers electrons from a bc ₁ analog complex to a caa ₃ oxygen reductase. Here, we describe the crystal structure of the reduced form of R. marinus HiPIP, solved by the single-wavelength anomalous diffraction method, based on the anomalous scattering of the iron atoms from the [4Fe–4S]^3+/2+ cluster and refined to 1.0 Å resolution. This is the first structure of a HiPIP isolated from a nonphotosynthetic bacterium involved in an aerobic respiratory chain. The structure shows a similar environment around the cluster as the other HiPIPs from phototrophic bacteria, but reveals several features distinct from those of the other HiPIPs of phototrophic bacteria, such as a different fold of the N-terminal region of the polypeptide due to a disulfide bridge and a ten-residue-long insertion.     

Style curvature and its adaptive significance in the Malvaceae

Curvature of un-pollinated styles towards the anthers in the Malvaceae has been interpreted as different adaptive mechanisms, presenting a challenging problem for evolutionary biologists. We have surveyed different species of this family to determine in which style curvature occurs, and to determine its possible functional roles. Two distinct types of style curvature occur in 18 species distributed in eight genera of four tribes: Type I, before pollen shedding, occurs in species of the Malvavisceae, Ureneae, and Hibisceae tribes, which have highly receptive stigmas and viable pollen when curvature brings stigmas into contact with anthers; and Type II, after pollen shedding, only appears in the protandrous species of the Malveae tribe. Curvature is often associated with annual and perennial herbs. We conclude that the adaptive significance of style curvature in the Malvaceae includes delayed selfing, promotion of outcrossing, and reduction in intrafloral male–female interference, even if the frequency of two or three of these occurs in one species only. This diversity provides model plants and the opportunity for determining the evolution, relative importance, and harmony mechanism of different adaptive significance, especially when two or three functions occur simultaneously in one floral movement of one species (e.g., Kosteletzkya virginica).     

Isolation and Characterization of Bacteria Resistant to Metallic Copper Surfaces

Metallic copper alloys have recently attracted attention as a new antimicrobial weapon for areas where surface hygiene is paramount. Currently it is not understood on a molecular level how metallic copper kills microbes, but previous studies have demonstrated that a wide variety of bacteria, including Escherichia coli, Staphylococcus aureus, and Clostridium difficile, are inactivated within minutes or a few hours of exposure. In this study, we show that bacteria isolated from copper alloy coins comprise strains that are especially resistant against the toxic properties exerted by dry metallic copper surfaces. The most resistant of 294 isolates were Gram-positive staphylococci and micrococci, Kocuria palustris, and Brachybacterium conglomeratum but also included the proteobacterial species Sphingomonas panni and Pseudomonas oleovorans. Cells of some of these bacterial strains survived on copper surfaces for 48 h or more. Remarkably, when these dry-surface-resistant strains were exposed to moist copper surfaces, resistance levels were close to those of control strains and MICs for copper ions were at or below control strain levels. This suggests that mechanisms conferring resistance against dry metallic copper surfaces in these newly isolated bacterial strains are different from well-characterized copper ion detoxification systems. Furthermore, staphylococci on coins did not exhibit increased levels of resistance to antibiotics, arguing against coselection with copper surface resistance traits.Copper in its ionic form is a required trace element for most pro- and eukaryotic organisms, including humans. While needed in small amounts, copper can easily become toxic when in surplus. This toxicity is caused mainly by the intrinsic properties of copper, as free copper ions undergo redox cycling reactions alternating between Cu(I) and Cu(II). This also results in the transfer of electrons to hydrogen peroxide and the concomitant generation of hydroxyl radicals that readily attack and damage cellular biomolecules. Recently, it was found that the majority of copper stress in Escherichia coli, as indicated by hydroxyl radical formation, occurs within the periplasm, away from the cytoplasmic DNA, and is thus copper-mediated oxidative stress (25). The cytoplasm might thus be better protected from copper-mediated oxidative stress, and indeed cells usually prevent accumulation of significant intracellular concentrations of free copper ions either by producing copper-binding chaperones (26, 36) or unspecific chelators such as glutathione (20, 30) or by efflux (14, 35). Nevertheless, copper ions within the cytoplasm also cause damage. Surprisingly, this damage is not related to oxidative stress but is exerted directly by the metal ions. It seems that copper ions attack and displace iron atoms from enzymes with solvent-exposed iron sulfur clusters such as those of hydratases (24). Thus, the presence of oxygen is not needed for this reaction, and there is no copper-mediated oxidative stress involved in this damage (24).While we are now gaining a more detailed picture of why copper ions are toxic to cells, we do not understand why metallic copper surfaces kill single-celled organisms such as bacteria and yeasts. Earlier studies have demonstrated that metallic copper surfaces efficiently inactivate microbes upon contact (9, 11, 32), especially when exposed to dry surfaces (10). These beneficial properties led to the official registration of copper alloys as antimicrobials through the U.S. Environmental Protection Agency in 2008. There is now great hope that metallic copper surfaces will be able to help control hospital-acquired (nosocomial) infections. Indeed, there are ongoing trials in which dry touch surfaces in hospitals around the world are replaced by copper alloys. Results from a German hospital trial indicate that copper surfaces such as door knobs, light switches, and push plates diminished the bacterial load by up to 30% compared to stainless steel control surfaces (A. Mikolay et al., unpublished data). Similar studies in Great Britain and South Africa found that the numbers of bacteria on the surfaces of copper-containing items such as trolleys, desks, toilet seats, tap handles, or push plates were 71% (28) or 90% to 100% (5) lower than those on their stainless steel, wood, or tile control equivalents.A potential challenge when applying metallic copper might be the probable emergence and spread of resistant bacteria, similar to what was observed after the introduction of antibiotics. The goal of this study was to investigate if bacteria that can withstand dry metallic copper surfaces can be isolated and if there is a link to multiple drug resistance. Where can potentially pathogenic bacteria that are in contact with both humans and metallic copper surfaces be found? Actually, people handle copper surfaces every day. Most coins around the world are made from copper or copper alloys. This includes the U.S. penny, which is composed of copper plated over a zinc core, and the nickel, dime, and quarter, which are cupronickel alloys (www.usmint.gov/). Coins of the European Union, such as the 50-cent coin, are made from an 89% copper alloy, as are the bicolored one- and two-Euro coins, which consist of different copper alloys (http://www.copperinfo.co.uk/coins/).In the present study we isolated and initiated characterization of aerobic heterotrophic bacteria from copper alloy coins as an example of heavily used copper surfaces and person-to-person vectors. We believe that knowledge of the physiology and resistance mechanisms of these microbes will help us to adapt our strategies for using metallic copper surfaces in hygiene-sensitive areas. This might not only diminish total bacterial numbers but also prevent the emergence and spread of multiple-drug-resistant strains in hospitals equipped with copper surfaces.