Estimating effects of a single gene and polygenes on quantitative traits from a diallel design

A genetic model is developed with additive and dominance effects of a single gene and polygenes as well as general and specific reciprocal effects for the progeny from a diallel mating design. The methods of ANOVA, minimum norm quadratic unbiased estimation (MINQUE), restricted maximum likelihood estimation (REML), and maximum likelihood estimation (ML) are suggested for estimating variance components, and the methods of generalized least squares (GLS) and ordinary least squares (OLS) for fixed effects, while best linear unbiased prediction, linear unbiased prediction (LUP), and adjusted unbiased prediction are suggested for analyzing random effects. Monte Carlo simulations were conducted to evaluate the unbiasedness and efficiency of statistical methods involving two diallel designs with commonly used sample sizes, 6 and 8 parents, with no and missing crosses, respectively. Simulation results show that GLS and OLS are almost equally efficient for estimation of fixed effects, while MINQUE (1) and REML are better estimators of the variance components and LUP is most practical method for prediction of random effects. Data from a Drosophila melanogaster experiment (Gilbert 1985a, Theor appl Genet 69:625–629) were used as a working example to demonstrate the statistical analysis. The new methodology is also applicable to screening candidate gene(s) and to other mating designs with multiple parents, such as nested (NC Design I) and factorial (NC Design II) designs. Moreover, this methodology can serve as a guide to develop new methods for detecting indiscernible major genes and mapping quantitative trait loci based on mixture distribution theory. The computer program for the methods suggested in this article is freely available from the authors.     

YajL, prokaryotic homolog of parkinsonism-associated protein DJ-1, functions as a covalent chaperone for thiol proteome

YajL is the closest Escherichia coli homolog of the Parkinsonism-associated protein DJ-1, a multifunctional oxidative stress response protein whose biochemical function remains unclear. We recently reported the aggregation of proteins in a yajL mutant in an oxidative stress-dependent manner and that YajL exhibits chaperone activity. Here, we show that YajL displays covalent chaperone and weak protein oxidoreductase activities that are dependent on its exposed cysteine 106. It catalyzes reduced RNase oxidation and scrambled RNase isomerization and insulin reduction and forms mixed disulfides with many cellular proteins upon oxidative stress. The formation of mixed disulfides was detected by immunoblotting bacterial extracts with anti-YajL antibodies under nonreducing conditions. Disulfides were purified from bacterial extracts on a YajL affinity column, separated by nonreducing-reducing SDS-PAGE, and identified by mass spectrometry. Covalent YajL substrates included ribosomal proteins, aminoacyl-tRNA synthetases, chaperones, catalases, peroxidases, and other proteins containing cysteines essential for catalysis or FeS cluster binding, such as glyceraldehyde-3-phosphate dehydrogenase, aldehyde dehydrogenase, aconitase, and FeS cluster-containing subunits of respiratory chains. In addition, we show that DJ-1 also forms mixed disulfides with cytoplasmic proteins upon oxidative stress. These results shed light on the oxidative stress-dependent chaperone function of YajL and identify YajL substrates involved in translation, stress protection, protein solubilization, and metabolism. They reveal a crucial role for cysteine 106 and suggest that DJ-1 also functions as a covalent chaperone. These findings are consistent with several defects observed in yajL or DJ-1 mutants, including translational defects, protein aggregation, oxidative stress sensitivity, and metabolic deficiencies.     

Ca<Superscript>2+</Superscript> channel currents of cortical neurons from pure and mixed cultures

Voltage-gated Ca²⁺ channels (VGCCs) are key regulators of many neuronal functions, and involved in multiple central nervous system diseases. In the last 30 years, a large number of injury and disease models have been established based on cultured neurons. Culture with serum develops a mixture of neurons and glial cells, while culture without serum develops pure neurons. Both of these neuronal-culture methods are widely used. However, the properties of Ca²⁺ currents in neurons from these two cultures have not been compared. In this study, we cultured rat cortical neurons in serum-containing or -free medium and then recorded the Ca²⁺ channel currents using patch-clamp technique. Our results showed that there were significant differences in the amplitude and activation properties of whole-cell Ca²⁺ channel currents, and of non-L-type Ca²⁺ channel currents between the neurons from these two culture systems. Our data suggested that the difference of whole-cell Ca²⁺ currents may result from the differences in non-L-type currents. Understanding of these properties will considerably advance studies of VGCCs in neurons from pure or mixed culture.     

1260例阴道分泌物检测分析

目的调查海宁地区女性阴道感染情况。方法采用白带常规镜检联合需氧菌阴道炎／细菌性阴道病联合测定技术对1260例阴道分泌物进行检测。结果在1260例就诊患者中,清洁度I～II度526例（41．75％）,清洁度III～IV度734例（58．25％）,检出阴道感染患者912例,单一性感染487例（占患病人数的53．4％）,混合感染患者425例（占患病人数的46．6％）。在487例单一性感染患者中,需氧菌阴道炎（AV）患者123例,细菌性阴道病（BV）患者178例,胞溶性阴道病（CV）患者8例,外阴阴道假丝酵母菌病（VVC）患者146例,滴虫性阴道炎（TV）患者32例;在425例混合感染患者中,AV＋BV患者136例,AV＋VVC患者56例,AV＋TV患者62例,BV＋VVC患者103例,BV＋TV患者48例,AV＋BV＋VVC患者13例,AV＋BV＋TV患者7例。结论阴道混合感染及AV发病率较高,值得临床高度关注。     

Experimental assessment of trophic impacts from a network model of a seagrass ecosystem: Direct and indirect effects of gulf flounder, spot and pinfish on benthic polychaetes

Trophic cascades are predicted to occur when the abundance of predators is increased, directly reducing the abundance of the intermediate prey and indirectly increasing the abundance of the prey at the base of a food web. Mixed trophic impact analysis of a network model developed for Apalachee Bay, near St. Marks, FL, USA predicted such a trophic cascade, in that increased abundance of juvenile gulf flounder Paralichthys albigutta (x¯ = 149 mm SL, effective trophic level 3.9) should have a negative impact on juvenile spot Leiostomus xanthurus (x¯ = 30 mm SL, effective trophic level 2.9) and a positive impact on benthic polychaetes (effective trophic levels 2.3 for deposit feeders and 3.0 for predatory polychaetes) in Halodule wrightii seagrass beds. We tested the predictions of the mixed trophic impact analysis by manipulating the abundance of the high trophic-level species (juvenile gulf flounder) in a cage-exclusion study in the North River, near Harkers Island, NC, USA. We compared the polychaete communities in St. Marks, FL and Harkers Island, NC, and showed that they are 51% similar (Jaccard's Index) at the family level, with the same eight dominant families (Nereidae, Capitellidae, Syllidae, Spionidae, Cirratulidae, Terebellidae, Sabellidae, and Maldanidae) present in both locations. We used 24 open-bottom cages to enclose the benthos and its seagrass-associated animal communities. We manipulated each cage by assigning it to one of the following treatments: (1) inclusion of fishes in upper and intermediate trophic levels (1 juvenile gulf flounder and 10 juvenile spot, the flounder + spot treatment); (2) inclusion of the intermediate predator (10 juvenile spot with no gulf flounder, the spot-only treatment); and (3) no fish added (unmanipulated controls). Core samples taken within the cages provided pre- and post-experimental measures of polychaete density and biomass, and the difference in density and biomass were used as response variables. At the end of the experiment, we collected, weighed, and analyzed the gut contents of all juvenile spot present in the cages. Juvenile pinfish (Lagodon rhomboides, x¯ = 30 mm SL) were present at the end of the study, having arrived as larvae or being trapped during cage set-up, and these fish were also examined, because they also eat polychaetes and their natural densities exceeded our introduced spot densities. Significant differences among treatments were detected for the polychaete family Terebellidae for both the change in density and biomass (pre-experiment − post-experiment). Densities of the Terebellidae changed in the direction predicted by the network model's impact analysis, declining in the cages with spot added compared with the control cages. Analyses of the other response variables (post-experiment spot and pinfish densities and biomass, difference between pre- and post-experiment polychaete densities and biomass for other families, and post-experiment spot and pinfish stomach content biomass) showed no significant differences among treatments. Several variables (Nereidae densities, pinfish densities and biomass, and pinfish stomach content biomass) varied between cages with low and high seagrass cover (significant blocking effect, P < 0.001). Nereidae densities declined significantly in cages with high (73%) rather than with low coverage (31% cover) of seagrass. Pinfish density and biomass were significantly greater in the high seagrass cages at the end of the experiments (P < 0.001), suggesting that dense seagrass attracted them. We conclude that the high density of pinfish in dense seagrass was responsible for the decline in density of the Nereidae. The direct effect of intermediate predators (pinfish feeding on polychaete prey) can be influenced by preferential recruitment of fishes to structurally complex habitats. The direction of change of indirect effects, but not the magnitude, in multi-trophic-level food webs can be predicted by the mixed trophic impact analysis of network models. However, these indirect effects are likely to be small in magnitude relative to direct effects and may be difficult to detect experimentally, especially in low-power experimental caging studies with natural fluctuations in recruitment rates of competitor species.     

Rapid microwave fixation of cell monolayers preserves microtubule-associated cell structures.

Microwave (MW) fixation has been suggested as a method to rapidly immobilize cellular dynamics for fine structural studies in the electron microscope. To show its suitability for studies on cell monolayers, one has to apply MW fixation systematically in correlation with samples on the light microscopy level. Examples for MW fixation of cell monolayers, however, are still rare. MW-accelerated fixation for relatively long periods of time (1-2 min) has been reported without showing its suitability at the fine structural level. Here, we provide a rapid MW fixation protocol for cell monolayers on a subminute time scale. The impact of the MW-accelerated glutaraldehyde fixation on temperature-sensitive cytoskeletal components such as microtubules was evaluated. For testing the effectiveness of MW-assisted primary fixation, saponin treatment of the monolayers was included. Simultaneous MW-accelerated fixation and extraction by saponin was necessary to achieve a gradual improvement in visualization of cytoskeletal aspects in association with cell junctions, mitochondria, and centrioles. To establish a valuable routine program for fine structural studies of resin-embedded cell models on substrata, a protocol combining MW fixation with automatic processing in a tissue processor is provided.     

Strategies for PHA production by mixed cultures and renewable waste materials

Production of polyhydroxyalkanoates (PHA) by mixed cultures has been widely studied in the last decade. Storage of PHA by mixed microbial cultures occurs under transient conditions of carbon or oxygen availability, known respectively as aerobic dynamic feeding and anaerobic/aerobic process. In these processes, PHA-accumulating organisms, which are quite diverse in terms of phenotype, are selected by the dynamic operating conditions imposed to the reactor. The stability of these processes during long-time operation and the similarity of the polymer physical/chemical properties to the one produced by pure cultures were demonstrated. This process could be implemented at industrial scale, providing that some technological aspects are solved. This review summarizes the relevant research carried out with mixed cultures for PHA production, with main focus on the use of wastes or industrial surplus as feedstocks. Basic concepts, regarding the metabolism and microbiology, and technological approaches, with emphasis on the kind of feedstock and reactor operating conditions for culture selection and PHA accumulation, are described. Challenges for the process optimization are also discussed.     

Facies development of a Late Ordovician mixed carbonate-siliciclastic ramp proximal to the developing Taconic orogen: Lourdes Formation, Newfoundland, Canada

The Upper Ordovician (late Whiterockian to Mohawkian) Lourdes Formation represents a narrow (tens of kilometers), short-lived [∼5–7 million years (my)], open-ocean (high-energy) mixed siliciclastic-carbonate ramp that onlapped allochthonous strata along the orogen side of the local Taconic foreland basin. Platform development followed a 6–8 my hiatus during which weathering had concentrated chemically mature siliciclastics that were admixed with initial carbonate sediments. A cross-platform facies gradient contains paleokarst and peritidal carbonates and sandstones, shallow-ramp carbonate bioherms and skeletal shoals, and deeper ramp calcareous shales. Transgressive systems tracts are marked by ramp-wide sheets and shoals of skeletal grainstone and low accumulation rates, and highstand systems tracts are marked by significant admixture and interbedding of siliciclastics with cross-ramp carbonate facies. Platform demise coincides with increased siliciclastic input, which is likely tectonically influenced. The Lourdes platform is equivalent to epicontinental foreland ramps along eastern Laurentia, but its narrower width precluded formation of oceanographically restricted platform-interior facies.     

Mixed self-assembly of polydiacetylenes for highly specific and sensitive strip biosensors

Polydiacetylenes (PDAs), which possess unique properties that allow them to change color in response to environmental changes such as variations in pH, temperature, and molecular binding, have been widely investigated as signal transducers in biosensor applications. Most PDA-based sensors reported to date have been evaluated largely on the basis of their ability to detect purified samples, however, and their specificity has rarely been tested. In this study, novel PDAs fabricated on polyvinylidene fluoride (PVDF) strips by photoreaction of composite diacetylene self-assemblies were developed as biosensors, and nonspecific binding to off-target biomolecules was assessed. A mixed PDA surface containing biotin and ethanolamide bound the target, i.e., streptavidin, more specifically than did biotin alone. The optimized PDA biosensor exhibited approximately 2850-fold higher selectivity for streptavidin relative to bovine serum albumin controls. A PDA biosensor that was further prepared showed distinctive signals for the urine of diabetic patients compared to urine samples from healthy/non-diabetic person due to the concentration of microalbuminuria. To our knowledge, this is the first strip-type biosensor fabricated with PDAs and the first PDA-based biosensor that can effectively overcome the problem of nonspecific binding.