The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype–phenotype maps

Biological information is stored in DNA, RNA and protein sequences, which can be understood as genotypes that are translated into phenotypes. The properties of genotype–phenotype (GP) maps have been studied in great detail for RNA secondary structure. These include a highly biased distribution of genotypes per phenotype, negative correlation of genotypic robustness and evolvability, positive correlation of phenotypic robustness and evolvability, shape-space covering, and a roughly logarithmic scaling of phenotypic robustness with phenotypic frequency. More recently similar properties have been discovered in other GP maps, suggesting that they may be fundamental to biological GP maps, in general, rather than specific to the RNA secondary structure map. Here we propose that the above properties arise from the fundamental organization of biological information into ‘constrained'' and ‘unconstrained'' sequences, in the broadest possible sense. As ‘constrained'' we describe sequences that affect the phenotype more immediately, and are therefore more sensitive to mutations, such as, e.g. protein-coding DNA or the stems in RNA secondary structure. ‘Unconstrained'' sequences, on the other hand, can mutate more freely without affecting the phenotype, such as, e.g. intronic or intergenic DNA or the loops in RNA secondary structure. To test our hypothesis we consider a highly simplified GP map that has genotypes with ‘coding'' and ‘non-coding'' parts. We term this the Fibonacci GP map, as it is equivalent to the Fibonacci code in information theory. Despite its simplicity the Fibonacci GP map exhibits all the above properties of much more complex and biologically realistic GP maps. These properties are therefore likely to be fundamental to many biological GP maps.     

Behavioral Phenotype of the Reeler Mutant Mouse: Effects of Reln Gene Dosage and Social Isolation.

Reeler (rl/rl) and reeler/wild-type (+/rl) mice synthesize Reln at subnormal rates, as do patients with schizophrenia, bipolar disorder, and autism, thereby forming the basis for a Reln hypothesis for vulnerability to these psychopathologies and justifying attention to the behavioral phenotypes of Reln-deficient mice. Tests of gait, emotionality, social aggression, spatial working memory, novel-object detection, fear conditioning, and sensorimotor reflex modulation revealed the behavioral phenotype of rl/rl, but not +/rl, mice to be different from that of wild-type (+/+) mice. These results reveal no effect of Reln gene dosage and provide significant challenges to both the Reln and the neurodevelopmental hypotheses of the etiology of major psychopathologies. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

INTROGRESSING PHEROMONE QTL BETWEEN SPECIES: TOWARDS AN EVOLUTIONARY UNDERSTANDING OF DIFFERENTIATION IN SEXUAL COMMUNICATION

As a first step toward understanding how noctuid moths evolve species-specific pheromone communication systems, we hybridized and backcrossed two closely related moth species, Heliothis virescens (Hv) and H. subflexa (Hs), which differ qualitatively and quantitatively in their multi-component sex pheromone blends. We used amplified fragment length polymorphism (AFLP) marker-based mapping of backcross families to determine which of the 30 autosomes in these moths contained quantitative trait loci (QTL) controlling the percentages of specific chemical components in the pheromone blends. In two previous backcrosses to Hs, we found a strong depressive effect of Hv-chromosome 22 on the percentage of three acetate components in the pheromone gland. These acetates are present in Hs and absent in Hv. Here, we describe how we introgressed Hv-chromosome 22 into the genomic background of Hs. Selection for Hv-chromosome 22 started from backcross 3 (BC₃) females. All females that had Hv-chromosome 22 and a low percentage of acetates (< 3% of the total amount of pheromone components present) were backcrossed to Hs males. In BC₅ to BC₈, we determined whether Hv-chromosome 22 was present by a) running only the primer pairs that would yield the markers for that chromosome, and/or b) determining the relative percentages of acetates in the pheromone glands. Either or both genotype and phenotype were used as a criterion to continue to backcross these females to Hs males. In BC₉, we confirmed the isolation of Hv-chromosome 22 in the Hs genomic background, and backcrossed the males to Hs females to eliminate the Hv-sex chromosome as well as mitochondrial DNA. The pheromone composition was determined in BC₃, BC₅, and BC₁₁ females with and without Hv-chromosome 22. All backcross females with Hv-chromosome 22 contained significantly less acetates than females without this chromosome. In addition, BC₃ females with Hv-chromosome 22 contained significantly more Z11-16:OH than BC₃ females without Hv-chromosome 22. However, in BC₅ and BC₁₁ females, the correlation between Z11-16:OH and Hv-chromosome 22 was lost, suggesting that there are separate QTL for the acetates and for Z11-16:OH, and that the relative amount of the alcohol component is only affected in epistasis with other (minor) QTL. Now that we have succeeded in isolating the chromosome that has a major effect on acetate production, we can test in behavioral experiments whether the presence of acetates may have been a driving force for a shift in pheromone composition. Such tests are necessary to move towards an evolutionary understanding of the differentiation in sexual communication in Heliothis spp. moths.     

Online phenotype discovery based on minimum classification error model

Identifying and validating novel phenotypes from images inputting online is a major challenge against high-content RNA interference (RNAi) screening. Newly discovered phenotypes should be visually distinct from existing ones and make biological sense. An online phenotype discovery method featuring adaptive phenotype modeling and iterative cluster merging using improved gap statistics is proposed. Clustering results based on compactness criteria and Gaussian mixture models (GMM) for existing phenotypes iteratively modify each other by multiple hypothesis test and model optimization based on minimum classification error (MCE). The method works well on discovering new phenotypes adaptively when applied to both of synthetic datasets and RNAi high content screen (HCS) images with ground truth labels.     

Evolutionary morphogenesis for multi-cellular systems

With a gene required for each phenotypic trait, direct genetic encodings may show poor scalability to increasing phenotype length. Developmental systems may alleviate this problem by providing more efficient indirect genotype to phenotype mappings. A novel classification of multi-cellular developmental systems in evolvable hardware is introduced. It shows a category of developmental systems that up to now has rarely been explored. We argue that this category is where most of the benefits of developmental systems lie (e.g. speed, scalability, robustness, inter-cellular and environmental interactions that allow fault-tolerance or adaptivity). This article describes a very simple genetic encoding and developmental system designed for multi-cellular circuits that belongs to this category. We refer to it as the morphogenetic system. The morphogenetic system is inspired by gene expression and cellular differentiation. It focuses on low computational requirements which allows fast execution and a compact hardware implementation. The morphogenetic system shows better scalability compared to a direct genetic encoding in the evolution of structures of differentiated cells, and its dynamics provides fault-tolerance up to high fault rates. It outperforms a direct genetic encoding when evolving spiking neural networks for pattern recognition and robot navigation. The results obtained with the morphogenetic system indicate that this “minimalist” approach to developmental systems merits further study.

Executive Self, Self-Esteem, and Negative Affectivity: Relations at the Phenotypic and Genotypic Level.

Complementary approaches examined the relations among executive self, self-esteem, and negative affectivity. A cross-sectional (N = 4,242) and a longitudinal (N = 158) study established that self-esteem mediated the relation between executive self and negative affectivity. A 3rd study (N = 878 twin pairs) replicated this pattern and examined genetic and environmental influences underlying all 3 phenotypes. Covariation among the 3 phenotypes reflected largely common genetic influences, although unique genetic effects explained variability in both executive self and negative affectivity. Executive self was influenced by shared environmental influences unique from those affecting self-esteem and negative affectivity. Nonshared environmental influences accounted for the majority of variance in each construct and were primarily unique to each. The unique genetic and nonshared environmental influences support the proposition that the executive self, self-esteem, and negative affectivity capture distinct and important differences between people. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Hereditary Prostate Cancer: Genes Related,Target Therapy and Prevention

Prostate cancer (PCa) is globally the second most diagnosed cancer type and the most common cause of cancer-related deaths in men. Family history of PCa, hereditary breast and ovarian cancer (HBOC) and Lynch syndromes (LS), are among the most important risk factors compared to age, race, ethnicity and environmental factors for PCa development. Hereditary prostate cancer (HPCa) has the highest heritability of any major cancer in men. The proportion of PCa attributable to hereditary factors has been estimated in the range of 5–15%. To date, the genes more consistently associated to HPCa susceptibility include mismatch repair (MMR) genes (MLH1, MSH2, MSH6, and PMS2) and homologous recombination genes (BRCA1/2, ATM, PALB2, CHEK2). Additional genes are also recommended to be integrated into specific research, including HOXB13, BRP1 and NSB1. Importantly, BRCA1/BRCA2 and ATM mutated patients potentially benefit from Poly (ADP-ribose) polymerase PARP inhibitors, through a mechanism of synthetic lethality, causing selective tumor cell cytotoxicity in cell lines. Moreover, the detection of germline alterations in MMR genes has therapeutic implications, as it may help to predict immunotherapy benefits. Here, we discuss the current knowledge of the genetic basis for inherited predisposition to PCa, the potential target therapy, and the role of active surveillance as a management strategy for patients with low-risk PCa. Finally, the current PCa guideline recommendations are reviewed.     

甜菜叶片表型与其产质量的关系

甜菜生产用种主要依靠进口,来源不同的品种表型各异,甜菜高产高糖的表型特征,是育种和栽培管理最直观和简捷的指标.本研究利用丰产和高糖两种类型的2对甜菜品种为材料,通过连续两年对不同类型甜菜营养生长期叶片的形态指标进行比较,分析各指标与甜菜产量和含糖的关系.研究结果表明,丰产型甜菜品种在整个生育期的叶片长度和生育前期叶面积...     

Frequency and Spectrum of Mutations Induced by Gamma Rays Revealed by Phenotype Screening and Whole-Genome Re-Sequencing in Arabidopsis thaliana

Genetic variations are an important source of germplasm diversity, as it provides an allele resource that contributes to the development of new traits for plant breeding. Gamma rays have been widely used as a physical agent for mutation creation in plants, and their mutagenic effect has attracted extensive attention. However, few studies are available on the comprehensive mutation profile at both the large-scale phenotype mutation screening and whole-genome mutation scanning. In this study, biological effects on M₁ generation, large-scale phenotype screening in M₂ generation, as well as whole-genome re-sequencing of seven M₃ phenotype-visible lines were carried out to comprehensively evaluate the mutagenic effects of gamma rays on Arabidopsis thaliana. A total of 417 plants with visible mutated phenotypes were isolated from 20,502 M₂ plants, and the phenotypic mutation frequency of gamma rays was 2.03% in Arabidopsis thaliana. On average, there were 21.57 single-base substitutions (SBSs) and 11.57 small insertions and deletions (InDels) in each line. Single-base InDels accounts for 66.7% of the small InDels. The genomic mutation frequency was 2.78 × 10⁻¹⁰/bp/Gy. The ratio of transition/transversion was 1.60, and 64.28% of the C > T events exhibited the pyrimidine dinucleotide sequence; 69.14% of the small InDels were located in the sequence with 1 to 4 bp terminal microhomology that was used for DNA end rejoining, while SBSs were less dependent on terminal microhomology. Nine genes, on average, were predicted to suffer from functional alteration in each re-sequenced line. This indicated that a suitable mutation gene density was an advantage of gamma rays when trying to improve elite materials for one certain or a few traits. These results will aid the full understanding of the mutagenic effects and mechanisms of gamma rays and provide a basis for suitable mutagen selection and parameter design, which can further facilitate the development of more controlled mutagenesis methods for plant mutation breeding.