Genetics of the quantitative Lp(a) lipoprotein trait

The Lp(a) lipoprotein is a complex particle composed of a low density lipoprotein (LDL)-like lipoprotein and the disulfide bonded Lp(a) glycoprotein. The complex represents a quantitative genetic trait. SDS gel electrophoresis under reducing conditions of sera followed by immunoblotting with affinity-purified polyclonal anti-Lp(a) demonstrated inter- and intra-individual size heterogeneity of the glycoprotein with apparent Mr in the range 400-700kDa. According to their relative mobilities compared to apo B-100 the Lp(a) patterns were categorized into phenotypes F, B, S1, S2, S3 und S4 and into the respective double-band phenotypes. This size heterogeneity seems to be controlled by multiple alleles designated LpF, LpB, LpS1, LpS2, LpS3, LpS4 and a null allele (LpO) at a single locus. Phenotype frequencies observed in 441 unrelated subjects were in good agreement with those expected from the genetic hypothesis. Comparison of Lp(a) lipoprotein concentrations in the different phenotypes revealed a highly significant association of phenotypes B, S1 and S2 with high, and phenotypes S3 und S4 with intermediate Lp(a) concentrations. A third mode is represented by the null phenotype were no Lp(a) band is detected upon immunoblotting and Lp(a) lipoprotein is low or absent. We conclude that the same gene locus is involved in determining Lp(a) glycoprotein phenotype and Lp(a) lipoprotein concentrations in plasma. This major gene seems to be the Lp(a) glycoprotein structural gene locus.     

Evolution of specialization and ecological character displacement of herbivores along a gradient of plant quality

We study the combined evolutionary dynamics of herbivore specialization and ecological character displacement, taking into account foraging behavior of the herbivores, and a quality gradient of plant types. Herbivores can adapt by changing two adaptive traits: their level of specialization in feeding efficiency and their point of maximum feeding efficiency along the plant gradient. The number of herbivore phenotypes, their levels of specialization, and the amount of character displacement among them are the result of the evolutionary dynamics, which is driven by the underlying population dynamics, which in turn is driven by the underlying foraging behavior. Our analysis demonstrates broad conditions for the diversification of a herbivore population into many specialized phenotypes, for basically any foraging behavior focusing use on highest gains while also including errors. Our model predicts two characteristic phases in the adaptation of herbivore phenotypes: a fast character-displacement phase and a slow coevolutionary niche-shift phase. This two-phase pattern is expected to be of wide relevance in various consumer-resource systems. Bringing together ecological character displacement and the evolution of specialization in a single model, our study suggests that the foraging behavior of herbivorous arthropods is a key factor promoting specialist radiation.     

Preparation and characteristics of growth and marker properties of urinary bladder mesenchymal stem cells

Mesenchymal stem cells (MSC) are able to transdifferentiate into cells with different functional phenotypes and considered as a promising resource for regenerative therapy. MSC derived from different tissues vary in their differentiation potential and in some cases express tissue specific markers indicating a kinship between mesenchymal and parenchymal phenotypes in the same tissue. It is possible that homorganic MSC can be more effectively induced to tissue specific differentiation and preferable for cell therapy of this organ as compared with bone marrow derived cells being commonly used for this purpose. Using bladder tissue explants, we prepared primary MSC cultures from the fetal (MSC-BF) and adult syngenic BALB/c mice and characterized their abilities during long-term passaging. In contrast to the cells from adult mice, the MSC-BF cells have the ability for a sustained growth in vitro, clonogenicity and differentiation into adipose and bone cells. Similar to the bone marrow MSC, MSC-BF express the mesenchymal markers CD29, CD44, CD49f, CD90, CD105 but not the leukocyte common antigen CD45. In normal conditions, MSC-BF produce such urothelial markers as CK14 and FOXA1 although their expression level is by far lower than in the bladder tissue. The hypomethylating agent, 5-azacytidine, induces in MSC-BF the expression of the urothelial differentiation activator PPARγ and the functional urothelium markers UP1a, UP1b, UP3a, UP3b. The data obtained suggest that MSC-BF can be epigenetically reprogrammed into urothelium by the 5-azacytidine treatment, and this may offer the novel strategy for cell therapy of bladder diseases.     

Dissection of functional domains in phage fd adsorption protein. Discrimination between attachment and penetration sites

We constructed a set of deletion mutants in the attachment protein of phage fd. These mutants lack sequences coding for sections in the amino-terminal half. All the mutants that comprise a leader sequence are incorporated into phage particles. Our data strongly suggest a bipartite organization of the amino-terminal domain with (1) a region for receptor recognition and (2) a region that is necessary for penetration of the DNA into the host cell. These regions were mapped. Some evidence suggesting different roles for gene 3 protein in penetration of the outer and inner membrane are discussed. We demonstrate that the phenotypes caused by gene 3 protein in host cells can be subdivided into two groups with different sequence requirements: (1) phenotypes related to outer membrane disturbance; and (2) phenotypes related to the tolQRA transport system.     

Hierarchical modeling in association studies of multiple phenotypes

The genetic study of disease-associated phenotypes has become common because such phenotypes are often easier to measure and in many cases are under greater genetic control than the complex disease itself. Some disease-associated phenotypes are rare, however, making it difficult to evaluate their effects due to small informative sample sizes. In addition, analyzing numerous phenotypes introduces the issue of multiple comparisons. To address these issues, we have developed a hierarchical model (HM) for multiple phenotypes that provides more accurate effect estimates with a lower false-positive rate. We evaluated the validity and power of HM in association studies of multiple phenotypes using randomly selected cases and controls from the simulated data set in the Genetic Analysis Workshop 14. In particular, we first analyzed the association between each of the 12 subclinical phenotypes and single-nucleotide polymorphisms within the known causal loci using a conventional logistic regression model (LRM). Then we added a second-stage model by regressing all of the logistic coefficients of the phenotypes obtained from LRM on a Z matrix that incorporates the clinical correlation of the phenotypes. Specially, the 12 phenotypes were grouped into 3 clusters: 1) communally shared emotions; 2) behavioral related; and 3) anxiety related. A semi-Bayes HM effect estimate for each phenotype was calculated and compared with those from LRM. We observed that using HM to evaluate the association between SNPs and multiple related phenotypes slightly increased power for detecting the true associations and also led to fewer false-positive results.     

Deletions of chromosomal regulatory boundaries are associated with congenital disease

Background

Recent data from genome-wide chromosome conformation capture analysis indicate that the human genome is divided into conserved megabase-sized self-interacting regions called topological domains. These topological domains form the regulatory backbone of the genome and are separated by regulatory boundary elements or barriers. Copy-number variations can potentially alter the topological domain architecture by deleting or duplicating the barriers and thereby allowing enhancers from neighboring domains to ectopically activate genes causing misexpression and disease, a mutational mechanism that has recently been termed enhancer adoption.

Results

We use the Human Phenotype Ontology database to relate the phenotypes of 922 deletion cases recorded in the DECIPHER database to monogenic diseases associated with genes in or adjacent to the deletions. We identify combinations of tissue-specific enhancers and genes adjacent to the deletion and associated with phenotypes in the corresponding tissue, whereby the phenotype matched that observed in the deletion. We compare this computationally with a gene-dosage pathomechanism that attempts to explain the deletion phenotype based on haploinsufficiency of genes located within the deletions. Up to 11.8% of the deletions could be best explained by enhancer adoption or a combination of enhancer adoption and gene-dosage effects.

Conclusions

Our results suggest that enhancer adoption caused by deletions of regulatory boundaries may contribute to a substantial minority of copy-number variation phenotypes and should thus be taken into account in their medical interpretation.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0423-1) contains supplementary material, which is available to authorized users.     

Seasonal cycles of assortative mating and reproductive behaviour in polymorphic populations of Harmonia axyridis in China

Abstract 1. We observed native populations of Harmonia axyridis (Pallas) around Beijing, China, over 2 years and performed choice and no‐choice mating tests between melanic and succinic (non‐melanic) beetles in the laboratory. 2. Succinic phenotypes outnumbered melanics by 5:1 in autumn, but melanics became equally abundant in spring, supporting previous inferences that melanism is advantageous in winter, but costly in summer. 3. Female H. axyridis expressed mate preference overtly, by rejecting less‐preferred phenotypes, and cryptically, by retaining their eggs for longer periods after matings with less‐preferred males, ostensibly to replace their sperm. 4. Succinic pairs formed more quickly in the spring generation, and melanic pairs in the autumn, and the time to copula was affected by both male and female phenotype. The strength of mate preference was contingent on female phenotype, suggesting melanic alleles had pleiotropic effects. 5. Whereas pair formation was under female control, the duration of copula was under male control and lasted longer in the autumn generation than in the spring. Copulations in the choice test tended to be shorter between similar phenotypes, suggesting that males invested more in dissimilar females when alternative mates were available. 6. Although spring and autumn generations were raised under identical conditions, significant contrasts were observed in their reproductive behaviour. 7. Two alternative hypotheses are advanced to explain why gender‐specific reproductive behaviours might vary between generations: maternally‐mediated epigenetic factors that influence the expression of genes in progeny as a function of maternal environment, and linkage disequilibria among alleles that cycle in frequency seasonally as a function of assortative mating.     

Effects of food shortage and oversupply on energy utilization, histology, and function of the gut in nestling song thrushes (Turdus philomelos)

We measured food intake, digestive efficiency, body mass increments, resting metabolic rate (RMR), carcass fat content, size and histological structure of the gut, and the rate of intestinal brush border uptake of l-proline in song thrush (Turdus philomelos) nestlings subjected to food shortage or food surplus under laboratory conditions. We assigned nestlings between 3 and 7 d of age to one of the following treatments: (1) food restriction, which resulted in a slowed growth at the rate found in undernourished, wild nestlings; (2) overfeeding, which totally suppressed begging; and (3) intermediate feeding. Threefold differences in energy consumption caused fivefold differences in body mass increments of the nestlings. Despite this, body mass-corrected RMR and intestinal mass were not affected by the feeding regime. The energy content of fecal output was highest in food-restricted birds, while their carcass fat content was lowest among treatment groups. Intestinal uptake rates of l-proline were low in the overfed and intermediate-fed young but significantly increased in the food-restricted birds, who attempted to maximize their rates of growth and development within the restrictive limits set by feeding regime. We noted a marked decrease of intestinal villi height in overfed birds as compared to intermediate-fed and food-restricted nestlings. We conclude that song thrush nestlings are characterized by a limited plasticity of their developmental program, which prohibits overfed nestlings from significantly up-regulating their gut function to accommodate increased food intake. This suggests that they already grew at a rate close to their physiological maximum. We suggest two interpretations: (1) under natural conditions, song thrush nestlings do not face frequent, unpredictable fluctuations in food abundance that could select for developmental plasticity, or (2) strong selection for uniform adult phenotypes prevents flexible developmental trajectories, which would result in a diversity of adult phenotypes.     

Genetic and phenotypic models of natural selection

The following theorem is proposed: when two phenotypes differ in attributes affecting their relative fitness, selection will cease to cause further evolutionary change when the two phenotypes have the same fitness, provided that certain modes of inheritance apply; in particular, all genotypes specifying the same phenotype must have the same average fitness. If these conditions of “uniform fitness” patterns of inheritance are not met, particular genetic models of natural selection should replace an analysis of phenotypes. If the conditions are met, an analysis of the stationary conditions when the phenotypes have equal fitnesses permits quantitative statements about the outcome of selection without recourse to genetic models. Phenotypic analyses of natural selection are illustrated by models of sex ratios in plants, sexual versus asexual reproduction in plants, and parental investment by animals.     

Application of a new human cell line,F2N78, in the transient and stable production of recombinant therapeutics

Host cell lines developed by genetic engineering sometimes show instabilities in maintaining their genetically acquired phenotypes. Previously, a hybrid host cell line, designated as hybrid of kidney and B cells (HKB), capable of retaining selected phenotypes originally existing in the parental cells was developed via fusion of 293 cells and HH514‐16 cells. Although HKB did indeed successfully preserve several favorable phenotypes, the expression of Epstein‐Barr virus (EBV) specific nuclear antigen 1 (EBNA1), which should be constitutively expressed for host cells to utilize oriP expression vector in transient production of therapeutic proteins, was observed to be unstable. Here, in an attempt to obtain stable expression of EBNA1, a cell type that contains an integrated EBV genome, rather than HH514‐16 cells, which harbor an episomal EBV genome, was applied for fusion with 293 cells. Fusion of 293 cells with Namalwa cells led to the creation of a new type of hybrid, F2N, which was able to stably express EBNA1 while not producing EBV particles. One of the F2N clones, F2N78, was observed to maintain EBNA1 expression for more than 1 year under serum‐free suspension culture conditions along with human specific glycosyl phenotypes observed previously in HKB. In addition, F2N78 was demonstrated to be an appropriate host cell line for both the transient and stable production of recombinant therapeutics with the features of safety expected of production cell lines for human use. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29: 432–440, 2013     

Genetic control of autoimmunity: protection from diabetes, but spontaneous autoimmune biliary disease in a nonobese diabetic congenic strain

At least 20 insulin-dependent diabetes (Idd) loci modify the progression of autoimmune diabetes in the NOD mouse, an animal model of human type 1 diabetes. The NOD.c3c4 congenic mouse, which has multiple B6- and B10-derived Idd-resistant alleles on chromosomes 3 and 4, respectively, is completely protected from autoimmune diabetes. We demonstrate in this study, however, that NOD.c3c4 mice develop a novel spontaneous and fatal autoimmune polycystic biliary tract disease, with lymphocytic peribiliary infiltrates and autoantibodies. Strains having a subset of the Idd-resistant alleles present in the NOD.c3c4 strain show component phenotypes of the liver disease: NOD mice with B6 resistance alleles only on chromosome 3 have lymphocytic liver infiltration without autoantibody formation, while NOD mice with B10 resistance alleles only on chromosome 4 show autoantibody formation without liver infiltration. The liver disease is transferable to naive NOD.c3c4 recipients using splenocytes from affected NOD.c3c4 mice, demonstrating an autoimmune etiology. Thus, substitution of non-NOD genetic intervals into the NOD strain can prevent diabetes, but in turn cause an entirely different autoimmune syndrome, a finding consistent with a generalized failure of self-tolerance in the NOD genetic background. The complex clinical phenotypes in human autoimmune conditions may be similarly resolved into largely overlapping biochemical pathways that are then modified, potentially by alleles at a few key chromosomal regions, to produce specific autoimmune syndromes.     

草鱼线粒体型超氧化物歧化酶的生化遗传特性

超氧化物歧化酶 (SOD)是一种对生物细胞保护至关重要、在进化上比较保守的酶。因此 ,超氧化物歧化酶作为分子钟或分子标记已被广泛应用于生物进化研究、群体遗传结构分析以及品系鉴定。但鱼类SOD的生物化学和遗传学特性都尚未进行过系统和深入的研究。为使这一重要的分子标记能更好地应用于鱼类遗传育种、种质资源保护以及进化研究 ,本实验采用聚丙烯酰胺梯度凝胶垂直电泳法 ,研究了草鱼线粒体型超氧化物歧化酶 (fm SOD)的同功酶形式 ,生化遗传表型、亚基组成以及金属类型。实验结果表明 ,草鱼fm SOD有三种不同的同功酶形式 ;按从正极到负极的排列分别命名为fm SOD 1 ,fm SOD 2 ,fm SOD 3。这三种不同的fm SOD在草鱼群体中可构成 3种不同的生化遗传学表型 :表型 1个体只含有迁移率最快的fm SOD 1同功酶 ;表型3个体只含有迁移率最慢的fm SOD 3同功酶 ;而表型 2个体中含有所有三种不同形式的同功酶。在野生草鱼群体中 ,存在所有三种表现型 ;而在基因纯合型的雌核发育草鱼群体中只检测到表型 1和表型 3。野生草鱼群体中三种表现型的个体数之比符合一对等位基因分离的 1∶2∶1孟德尔遗传分离比例。由这些实验结果得出以下结论 :(1 )草鱼fm SOD是由细胞核DNA上的基因所编码而不是由线粒体DNA上的基因所编码的     

Semaphorin-1a controls receptor neuron-specific axonal convergence in the primary olfactory center of Drosophila

In the olfactory system of Drosophila, 50 functional classes of sensory receptor neurons (ORNs) project in a highly organized fashion into the CNS, where they sort out from one another and converge into distinct synaptic glomeruli. We identified the transmembrane molecule Semaphorin-1a (Sema-1a) as an essential component to ensure glomerulus-specific axon segregation. Removal of sema-1a in ORNs does not affect the pathfinding toward their target area but disrupts local axonal convergence into a single glomerulus, resulting in two distinct targeting phenotypes: axons either intermingle with adjacent ORN classes or segregate according to their odorant receptor identity into ectopic sites. Differential Sema-1a expression can be detected among neighboring glomeruli, and mosaic analyses show that sema-1a functions nonautonomously in ORN axon sorting. These findings provide insights into the mechanism by which afferent interactions lead to synaptic specificity in the olfactory system.     

Phenotypic diversity of 188 rice embryo mutants

We have identified 188 embryo mutants of rice and characterized them into six groups based on their phenotypes: (1) embryoless in mature seed, (2) deletion of embryonic organ(s), (3) abnormal position of embryonic organs, (4) abnormal embryo size, (5) defect in organ morphology, and (6) variable abnormal phenotypes in spite of single mutations. Three types of organless mutants are obtained: small globular embryo, club-shaped embryo, and large embryo. Although 12 shootless mutants derived from at least three loci are identified, only three radicleless mutants are recovered, which produce normal adventitious roots after germination. In reduced embryo mutants, every embryonic organ is reduced, in contrast to giant embryo mutants in which only scutellum is enlarged. Considerable number of mutants are categorized into (5) and (6) in the above. These diverse embryo mutants would serve as promising materials for genetic study of embryogenesis. © 1995 Wiley-Liss, Inc.