Detection of Gambierdiscus and Fukuyoa single cells using recombinase polymerase amplification combined with a sandwich hybridization assay

Dinoflagellates of the genera Gambierdiscus and Fukuyoa are known to produce several bioactive compounds including the potent neurotoxic ciguatoxins (CTXs) which are able to accumulate in fish and through the food web. When humans ingest fish contaminated with CTXs, it can result in an intoxication named ciguatera. Although not all the currently recognized species are able to produce toxins, G. australes and G. excentricus have been highlighted to be the most abundant and toxic among the species present in the Atlantic. Even though the genera Gambierdiscus and Fukuyoa are endemic to tropical areas, recently their presence was recorded in subtropical and temperate regions. In this work, the development of three molecular assays for the detection of the Gambierdiscus and Fukuyoa genera and for G. australes and G. excentricus species, based on the combination of recombinase polymerase amplification with detection via hybridization, is successfully described. Furthermore, a remarkable limit of detection of a single cell was achieved. Additionally, six different species have been used to check the ability of each primer set to give an amplified product, even in presence of potentially interfering non-target DNAs. Therefore, these developments provide a rapid and cost-effective strategy for detection of both genera and two of the most toxic species, which will undoubtedly contribute to reliable screening of samples and ciguatera risk assessment, guaranteeing seafood safety and protection of human health.

     

The Role of Backbone Hydrogen Bonds in the Transition State for Protein Folding of a PDZ Domain

Backbone hydrogen bonds are important for the structure and stability of proteins. However, since conventional site-directed mutagenesis cannot be applied to perturb the backbone, the contribution of these hydrogen bonds in protein folding and stability has been assessed only for a very limited set of small proteins. We have here investigated effects of five amide-to-ester mutations in the backbone of a PDZ domain, a 90-residue globular protein domain, to probe the influence of hydrogen bonds in a β-sheet for folding and stability. The amide-to-ester mutation removes NH-mediated hydrogen bonds and destabilizes hydrogen bonds formed by the carbonyl oxygen. The overall stability of the PDZ domain generally decreased for all amide-to-ester mutants due to an increase in the unfolding rate constant. For this particular region of the PDZ domain, it is therefore clear that native hydrogen bonds are formed after crossing of the rate-limiting barrier for folding. Moreover, three of the five amide-to-ester mutants displayed an increase in the folding rate constant suggesting that the hydrogen bonds are involved in non-native interactions in the transition state for folding.     

High-Resolution Genetic Mapping of Complex Traits from a Combined Analysis of F2 and Advanced Intercross Mice

Genetic influences on anxiety disorders are well documented; however, the specific genes underlying these disorders remain largely unknown. To identify quantitative trait loci (QTL) for conditioned fear and open field behavior, we used an F₂ intercross (n = 490) and a 34th-generation advanced intercross line (AIL) (n = 687) from the LG/J and SM/J inbred mouse strains. The F₂ provided strong support for several QTL, but within wide chromosomal regions. The AIL yielded much narrower QTL, but the results were less statistically significant, despite the larger number of mice. Simultaneous analysis of the F₂ and AIL provided strong support for QTL and within much narrower regions. We used a linear mixed-model approach, implemented in the program QTLRel, to correct for possible confounding due to familial relatedness. Because we recorded the full pedigree, we were able to empirically compare two ways of accounting for relatedness: using the pedigree to estimate kinship coefficients and using genetic marker estimates of “realized relatedness.” QTL mapping using the marker-based estimates yielded more support for QTL, but only when we excluded the chromosome being scanned from the marker-based relatedness estimates. We used a forward model selection procedure to assess evidence for multiple QTL on the same chromosome. Overall, we identified 12 significant loci for behaviors in the open field and 12 significant loci for conditioned fear behaviors. Our approach implements multiple advances to integrated analysis of F₂ and AILs that provide both power and precision, while maintaining the advantages of using only two inbred strains to map QTL.     

Influence of metabolic syndrome on biomarkers of oxidative stress and inflammation in obese adults

Objective: Both obesity and the metabolic syndrome (MetS) have been independently linked with increased oxidative and inflammatory stress. This study tested the hypothesis that obesity with MetS is associated with greater oxidative and inflammatory burden compared with obesity alone. Research Methods and Procedures: Forty‐eight normal‐weight and 40 obese (20 without MetS; 20 with MetS) adults were studied. MetS was defined according to National Cholesterol Education Program Adult Treatment Panel III criteria. Plasma concentrations of oxidized low‐density lipoprotein, C‐reactive protein, tumor necrosis factor‐α, interleukin (IL)‐6, and IL‐18 were determined by enzyme immunoassay. Results: Plasma biomarkers of oxidative stress and inflammation were lowest in normal‐weight controls. Of note, obese MetS adults demonstrated significantly higher plasma concentrations of oxidized low‐density lipoprotein (62.3 ± 3.2 vs. 54.0 ± 4.0 U/L; p < 0.05), C‐reactive protein (3.0 ± 0.6 vs. 1.5 ± 0.3 mg/L; p < 0.01), tumor necrosis factor‐α (2.1 ± 0.1 vs. 1.6 ± 0.1 pg/mL; p < 0.05), IL‐6 (2.8 ± 0.4 vs. 1.4 ± 0.2 pg/mL; p < 0.01), and IL‐18 (253 ± 16 vs. 199 ± 16 pg/mL; p < 0.01), compared with obese adults without MetS. Discussion: These results suggest that MetS heightens oxidative stress and inflammatory burden in obese adults. Increased oxidative and inflammatory stress may contribute to the greater risk of coronary heart disease and cerebrovascular disease in obese adults with MetS.     

Genome-Wide Association Studies and the Problem of Relatedness Among Advanced Intercross Lines and Other Highly Recombinant Populations

Model organisms offer many advantages for the genetic analysis of complex traits. However, identification of specific genes is often hampered by a lack of recombination between the genomes of inbred progenitors. Recently, genome-wide association studies (GWAS) in humans have offered gene-level mapping resolution that is possible because of the large number of accumulated recombinations among unrelated human subjects. To obtain analogous improvements in mapping resolution in mice, we used a 34th generation advanced intercross line (AIL) derived from two inbred strains (SM/J and LG/J). We used simulations to show that familial relationships among subjects must be accounted for when analyzing these data; we then used a mixed model that included polygenic effects to address this problem in our own analysis. Using a combination of F₂ and AIL mice derived from the same inbred progenitors, we identified genome-wide significant, subcentimorgan loci that were associated with methamphetamine sensitivity, (e.g., chromosome 18; LOD = 10.5) and non-drug-induced locomotor activity (e.g., chromosome 8; LOD = 18.9). The 2-LOD support interval for the former locus contains no known genes while the latter contains only one gene (Csmd1). This approach is broadly applicable in terms of phenotypes and model organisms and allows GWAS to be performed in multigenerational crosses between and among inbred strains where familial relatedness is often unavoidable.SUSCEPTIBILITY to diseases such as drug abuse is partially determined by genetic factors. The identification of the alleles that underlie disease susceptibility is an immensely important goal that promises to revolutionize both the diagnosis and the treatment of human disease. Genome-wide association studies (GWAS) in humans can locate common alleles with great precision. However, GWAS may be unable to identify the bulk of the heritable variability for common genetic diseases; some of this “missing heritability” is thought to be due to rare alleles (Manolio et al. 2009). Model organisms are complementary to human genetic studies and offer unique advantages including the ability to control the environment, perform dangerous or invasive procedures, and test hypotheses by manipulating genes via genetic engineering; a final advantage is that crosses between two inbred strains avoid many of the difficulties associated with rare alleles.Studies in model organisms have frequently employed intercrosses (F₂''s) to identify quantitative trait loci (QTL) that underlie phenotypic variability. F₂ crosses are easy to produce and easy to analyze; however, due to a lack of recombination they can identify only larger genomic regions and are thus unsuitable for identifying the genes that cause QTL (Flint et al. 2005; Peters et al. 2007). This is a serious limitation that can be addressed by using populations with greater numbers of accumulated recombinations. Darvasi and Soller (1995) suggested the creation of advanced intercross lines (AILs) by successive generations of random mating after the F₂ generation to produce additional recombinations. An AIL offers vastly improved mapping resolution while maintaining the desirable property that all polymorphic alleles are common.We used an AIL to study sensitivity to methamphetamine, which is a genetically complex trait that may be useful for identifying genetic factors influencing the subjectively euphoric response to stimulant drugs and susceptibility to drug abuse (Palmer et al. 2005; Phillips et al. 2008; Bryant et al. 2009). For example, a prior study suggested that the gene Casein Kinase 1 Epsilon (Csnk1e) might influence sensitivity to the acute locomotor response to methamphetamine in mice (Palmer et al. 2005). This conclusion has been bolstered by additional pharmacological (Bryant et al. 2009) and genetic studies. In addition, we have shown that polymorphisms in this gene are associated with sensitivity to the euphoric effects of amphetamine in humans (Veenstra-Vanderweele et al. 2006). Another group has subsequently reported that this same gene is associated with heroine addiction (Levran et al. 2008). Thus, genes that modulate the acute locomotor response to a drug in mice may also be important for sensitivity to similar drugs in humans as well as the risk for developing drug abuse.The purpose of this study was to develop a framework for rapid identification of high precision QTL and ideally specific genes that influence sensitivity to methamphetamine in mice by employing an AIL. We produced an F₂ cross (n = 490) and a corresponding 34th generation AIL (n = 688) derived from the inbred strains SM/J and LG/J. This allowed us to compare and integrate the results from F₂ and AIL mice. We examined the locomotor stimulant response to a 2-mg/kg dose of methamphetamine, which is extremely disparate in the two progenitor strains. We performed a GWAS using either simple regression, which ignored relatedness, or a mixed model that accounted for relatedness by using identity coefficients that were calculated from the pedigree. We also explored two methods to estimate significance: simple permutation and gene dropping. We discuss the performance of a mixed model that includes polygenic effects vs. simple regression and the performance of permutation vs. gene dropping. The methods used in this study are applicable to a variety of other phenotypes and populations.     

Processing and selection of surgically-retrieved sperm for ICSI: a review

Although the technique of intracytoplasmic sperm injection (ICSI) has been a revolution in the alleviation of male infertility, the use of testicular sperm for ICSI was a formerly unseen breakthrough in the treatment of the azoospermic man with primary testicular failure. At the clinical level, different procedures of testicular sperm retrieval (conventional TESE, micro-TESE, FNA/TESA, MESA, PESA) are being performed, the choice is mainly based on the cause of azoospermia (obstructive versus non-obstructive) and the surgeon’s skills. At the level of the IVF laboratory, mechanical procedures to harvest the sperm from the tissue may be combined with enzymatic treatment in order to increase the sperm recovery rates. A number of techniques have been developed for viable sperm selection in males with only immotile testicular sperm available. However, large, well-designed studies on the benefit and safety of one over the other technique are lacking. Despite all the available methods and combinations of laboratory procedures which have a common goal to maximize sperm recovery from testicular samples, a large proportion of NOA patients fail to father a genetically own child. Advanced technology application may improve recovery rates by detection of the testicular foci with active spermatogenesis and/or identification of the rare individual sperm in the testicular suspensions. On the other hand, in vitro spermatogenesis or sperm production from embryonic stem cells or induced pluripotent stem cells might be future options. The present review summarizes the available strategies which aim to maximize sperm recovery from surgically retrieved samples.     

PlexinA4-Semaphorin3A-mediated crosstalk between main cortical interneuron classes is required for superficial interneuron lamination

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Temperature profile of oxygen activation and defense against oxygen toxicity in a psychrophilic member of the Bacteroidaceae

Abstract The temperature profiles have been determined for O₂ reduction by activating substrates for whole cells and cell extracts of the psychrophilic, obligately anaerobic bacterium, strain B6, belonging to the Bacteroidaceae. The profiles were similar whether the cells were grown at 15 or 1°C, and also for cells harvested in the exponential or stationary phase. The H₂O producing pyruvate oxidase displayed in cell-free extracts a considerably higher activity than the H₂O₂ producing NADH and NADPH oxidases at all temperatures in the range 30–1°C, and characteristically makes up a larger proportion of the total O₂ reduction capacity the lower the temperature. It thus seems that the O₂ scavenging property of the pyruvate oxidase, postulated to be utilized in a defense mechanism against the detrimental effects of the H₂O₂ producing pyridine nucleotide oxidases, is particularly well adapted to function at the low temperatures of the Barents Sea, from which this obligately anaerobic organism originates.