Gene expression and the concept of the phenotype

While the definition of the 'genotype' has undergone dramatic changes in the transition from classical to molecular genetics, the definition of the 'phenotype' has remained for a long time within the classical framework. In addition, while the notion of the genotype has received significant attention from philosophers of biology, the notion of the phenotype has not. Recent developments in the technology of measuring gene-expression levels have made it possible to conceive of phenotypic traits in terms of levels of gene expression. We demonstrate that not only has this become possible but it has also become an actual practice. This suggests a significant change in our conception of the phenotype: as in the case of the 'genotype', phenotypes can now be conceived in quantitative and measurable terms on a comprehensive molecular level. We discuss in what sense gene expression profiles can be regarded as phenotypic traits and whether these traits are better described as a novel concept of phenotype or as an extension of the classical concept. We argue for an extension of the classical concept and call for an examination of the type of extension involved.     

Immunological relatedness of high mobility group chromosomal proteins from calf thymus.

The non-histone proteins HMG-1, HMG-2, HMG-3, HMB-8, HMG-14, and HMG-17 (Goodwin, G. H., SANDERS, C., and Johns, E. W. (1973) Eur. J. Biochem. 38, 14) were purified from calf thymus. The apparent molecular weights on polyacrylamide gels run in the presence of sodium dodecyl sulfate of the high mobility group (HMB) proteins were determined. Those for HBG-1 and HMG-2 agreed with the molecular weights determined by sedimentation; that for HMG-17 was anomalously high. Antibodies against HMG-1 were elicited in rabbits. The interaction between HMG-1 and anti-HBG-1 was measured by quantitative precipitation and by the microcomplement fixation technique. Quantitative microcomplement fixation assays revealed that the indices of dissimilarity between HMG-1 and HMG-2, HMG-3, HMG-8, HMG-14, and HMG-17 were 2.0, 1.0, 3.8, 10.0, and 6.1, respectively. These correspond to 6%, 0%, 12%, 20%, and 16% sequence difference between HMG-1 and the other five HMG proteins, although the immunological distance between HMG-1 and HMG-14 may be too large to allow a good correlation between the sequence and the immunological reaction. Antibodies to HMB-1 bind to chromatin purified from calf thymus. Therefore, we suggest that the in situ organization of HMG proteins in chromatin and chromosomes may be studied by serological techniques.     

The concept of mobility in single- and double handed manipulation

The concept of mobility describes an important property of the human body when performing manipulation tasks. It describes, in a sense, how easy it is to accelerate a link or a point on the manipulator. Most often it is calculated for the end-link or end-point of the manipulator, since these are important for the control objective of the manipulator. Mobility is the inverse of the inertia experienced by a force acting on the end-point, or a combined force and torque acting on the end-link. The concept has been used in studies of reaching tasks with one arm, but thus far not for bi-manual manipulation. We present here the concept for both single-handed and double-handed manipulation, in a general manner which includes any type of grip of the hands on the object. The use of the concept is illustrated with data on the left and right arm in a golf swing.     

Gene and genon concept: coding versus regulation

We analyse here the definition of the gene in order to distinguish, on the basis of modern insight in molecular biology, what the gene is coding for, namely a specific polypeptide, and how its expression is realized and controlled. Before the coding role of the DNA was discovered, a gene was identified with a specific phenotypic trait, from Mendel through Morgan up to Benzer. Subsequently, however, molecular biologists ventured to define a gene at the level of the DNA sequence in terms of coding. As is becoming ever more evident, the relations between information stored at DNA level and functional products are very intricate, and the regulatory aspects are as important and essential as the information coding for products. This approach led, thus, to a conceptual hybrid that confused coding, regulation and functional aspects. In this essay, we develop a definition of the gene that once again starts from the functional aspect. A cellular function can be represented by a polypeptide or an RNA. In the case of the polypeptide, its biochemical identity is determined by the mRNA prior to translation, and that is where we locate the gene. The steps from specific, but possibly separated sequence fragments at DNA level to that final mRNA then can be analysed in terms of regulation. For that purpose, we coin the new term “genon”. In that manner, we can clearly separate product and regulative information while keeping the fundamental relation between coding and function without the need to introduce a conceptual hybrid. In mRNA, the program regulating the expression of a gene is superimposed onto and added to the coding sequence in cis - we call it the genon. The complementary external control of a given mRNA by trans-acting factors is incorporated in its transgenon. A consequence of this definition is that, in eukaryotes, the gene is, in most cases, not yet present at DNA level. Rather, it is assembled by RNA processing, including differential splicing, from various pieces, as steered by the genon. It emerges finally as an uninterrupted nucleic acid sequence at mRNA level just prior to translation, in faithful correspondence with the amino acid sequence to be produced as a polypeptide. After translation, the genon has fulfilled its role and expires. The distinction between the protein coding information as materialised in the final polypeptide and the processing information represented by the genon allows us to set up a new information theoretic scheme. The standard sequence information determined by the genetic code expresses the relation between coding sequence and product. Backward analysis asks from which coding region in the DNA a given polypeptide originates. The (more interesting) forward analysis asks in how many polypeptides of how many different types a given DNA segment is expressed. This concerns the control of the expression process for which we have introduced the genon concept. Thus, the information theoretic analysis can capture the complementary aspects of coding and regulation, of gene and genon.     

Phylogenetic relatedness and the determinants of competitive outcomes

Recent hypotheses argue that phylogenetic relatedness should predict both the niche differences that stabilise coexistence and the average fitness differences that drive competitive dominance. These still largely untested predictions complicate Darwin's hypothesis that more closely related species less easily coexist, and challenge the use of community phylogenetic patterns to infer competition. We field parameterised models of competitor dynamics with pairs of 18 California annual plant species, and then related species' niche and fitness differences to their phylogenetic distance. Stabilising niche differences were unrelated to phylogenetic distance, while species' average fitness showed phylogenetic structure. This meant that more distant relatives had greater competitive asymmetry, which should favour the coexistence of close relatives. Nonetheless, coexistence proved unrelated to phylogeny, due in part to increasing variance in fitness differences with phylogenetic distance, a previously overlooked property of such relationships. Together, these findings question the expectation that distant relatives should more readily coexist.     

Maximum-likelihood estimation of relatedness

Relatedness between individuals is central to many studies in genetics and population biology. A variety of estimators have been developed to enable molecular marker data to quantify relatedness. Despite this, no effort has been given to characterize the traditional maximum-likelihood estimator in relation to the remainder. This article quantifies its statistical performance under a range of biologically relevant sampling conditions. Under the same range of conditions, the statistical performance of five other commonly used estimators of relatedness is quantified. Comparison among these estimators indicates that the traditional maximum-likelihood estimator exhibits a lower standard error under essentially all conditions. Only for very large amounts of genetic information do most of the other estimators approach the likelihood estimator. However, the likelihood estimator is more biased than any of the others, especially when the amount of genetic information is low or the actual relationship being estimated is near the boundary of the parameter space. Even under these conditions, the amount of bias can be greatly reduced, potentially to biologically irrelevant levels, with suitable genetic sampling. Additionally, the likelihood estimator generally exhibits the lowest root mean-square error, an indication that the bias in fact is quite small. Alternative estimators restricted to yield only biologically interpretable estimates exhibit lower standard errors and greater bias than do unrestricted ones, but generally do not improve over the maximum-likelihood estimator and in some cases exhibit even greater bias. Although some nonlikelihood estimators exhibit better performance with respect to specific metrics under some conditions, none approach the high level of performance exhibited by the likelihood estimator across all conditions and all metrics of performance.     

Repeated DNA sequences and species relatedness in the genusEquisetum

The kinetics with which DNA reassociates and the thermal stability of rapidly reassociating (repetitive) DNA sequences have been monitored for six species in the genusEquisetum. Using the kinetic complexity for each of two repeated DNA sequence components as the basis for comparison, species in the subgenusEquisetum (E. arvense, E. fluviatile andE. telmateia) form one group and species in the subgenusHippochaete (E. hyemale, E. laevigatum andE. scirpoides) form another group. Using the difference in thermal stability between native and reassociated repetitive DNA for comparison, the same grouping of species is obtained.     

Estimating the correlation of pairwise relatedness along chromosomes

The 'spatial' pattern of the correlation of pairwise relatedness among loci within a chromosome is an important aspect for an insight into genomic evolution in natural populations. In this article, a statistical genetic method is presented for estimating the correlation of pairwise relatedness among linked loci. The probabilities of identity-in-state (IIS) are related to the probabilities of identity-by-descent (IBS) for the two- and three-loci cases. By decomposing the joint probabilities of two- or three-loci IBD, the probability of pairwise relatedness at a single locus and its correlation among linked loci can be simultaneously estimated. To provide effective statistical methods for estimation, weighted least square (LS) and maximum likelihood (ML) methods are evaluated through extensive Monte Carlo simulations. Results show that the ML method gives a better performance than the weighted LS method with haploid genotypic data. However, there are no significant differences between the two methods when two- or three-loci diploid genotypic data are employed. Compared with the optimal size for haploid genotypic data, a smaller optimal sample size is predicted with diploid genotypic data.     

Families and the structural relatedness among globular proteins.

Protein structures come in families. Are families “closely knit” or “loosely knit” entities? We describe a measure of relatedness among polymer conformations. Based on weighted distance maps, this measure differs from existing measures mainly in two respects: (1) it is computationally fast, and (2) it can compare any two proteins, regardless of their relative chain lengths or degree of similarity. It does not require finding relative alignments. The measure is used here to determine the dissimilarities between all 12, 403 possible pairs of 158 diverse protein structures from the Brookhaven Protein Data Bank (PDB). Combined with minimal spanning trees and hierarchical clustering methods, this measure is used to define structural families. It is also useful for rapidly searching a dataset of protein structures for specific substructural motifs. By using an analogy to distributions of Euclidean distances, we find that protein families are not tightly knit entities.     

Transmission,relatedness, and the evolution of cooperative symbionts

Cooperative interactions between species, termed mutualisms, play a key role in shaping natural ecosystems, economically important agricultural systems, and in influencing human health. Across different mutualisms, there is significant variation in the benefit that hosts receive from their symbionts. Empirical data suggest that transmission mode can help explain this variation: vertical transmission, where symbionts infect their host's offspring, leads to symbionts that provide greater benefits to their hosts than horizontal transmission, where symbionts leave their host and infect other hosts in the population. However, two different theoretical explanations have been given for this pattern: firstly, vertical transmission aligns the fitness interests of hosts and their symbionts; secondly, vertical transmission leads to increased relatedness between symbionts sharing a host, favouring cooperation between symbionts. We used a combination of analytical models and dynamic simulations to tease these factors apart, in order to compare their separate influences and see how they interact. We found that relatedness between symbionts sharing a host, rather than transmission mode per se, was the most important factor driving symbiont cooperation. Transmission mode mattered mainly because it determined relatedness. We also found evolutionary branching throughout much of our simulation, suggesting that a combination of transmission mode and multiplicity of infections could lead to the stable coexistence of different symbiont strategies.     

Pathogen relatedness affects the prevalence of within-host competition

Although the evolutionary consequences of within-host competition among pathogens have been examined extensively, there exists a critical gap in our understanding of factors determining the prevalence of multiple infections. Here we examine the effects of relatedness among strains of the anther-smut pathogen Microbotryum violaceum on the probability of multiple infection in its host, Silene latifolia, after sequential inoculations. We found a significantly higher probability of multiple infection when interacting strains were more closely related, suggesting mechanisms of competitive exclusion that are conditional on genotypic characteristics of the strains involved. Pathogen relatedness therefore determines the prevalence of multiple infection in addition to its outcome, with important consequences for our understanding of virulence evolution and pathogen population structure and diversity.     

Gene therapy – when a simple concept meets a complex reality

In theory, gene therapy is a simple concept which holds great promise as a cure for disease. In practice, however, considerable obstacles have to be overcome, including problems with safe and efficient gene delivery and stable gene expression. This review gives an overview on the history of gene therapy and analyses some of the problems that have so far prevented the establishment of a successful clinical protocol. The future prospects of gene therapy are discussed.     

Studies on the relatedness of bacterial fumarate reductases

Abstract A collection of 10 Gram-negative bacteria was examined for the presence of a fumarate reductase related to that of Escherichia coli K-12. When the frd genes encoding the E. coli enzyme were used as DNA:DNA hybridization probes good signals were obtained from all members of the family Enterobacteriaceae. No significant hybridization was detected, even under non-stringent conditions, with the well characterized fumarate reducer Vibrio succinogenes or with Pseudomonas aeruginosa . These findings were confirmed and extended by immuno-diffusion studies using cell membranes and antiserum against the E. coli reductase. Precipitin lines were observed in all cases where frd homologies were detected. It was concluded that the V. succinogenes enzyme differs extensively from the E. coli fumarate reductase.     

Social evolution in the shadow of asymmetrical relatedness

The persistence of altruism and spite remains an enduring problem of social evolution. It is well known that selection for these actions depends on the structure of the population—that is, on actors'' genetic relationships to recipients and to the ‘neighbourhood’ upon which the effects of their actions redound. Less appreciated, however, is that population structure can cause genetic asymmetries between partners whereby the relatedness (defined relative to the neighbourhood) of an individual i to a partner j will differ from the relatedness of j to i. Here, we introduce a widespread mechanism of kin recognition to a model of dispersal in subdivided populations. In so doing, we uncover three remarkable consequences of asymmetrical relatedness. First, altruism directed at phenotypically similar partners evolves more easily among migrant than native actors. Second, spite directed at dissimilar partners evolves more easily among native than migrant actors. Third, unlike migrants, natives can evolve to pay costs that far outstrip those they spitefully impose on others. We find that the frequency of natives relative to migrants amplifies the asymmetries between them. Taken together, our results reveal differentiated patterns of ‘phenocentrism’ that readily arise from asymmetries of relatedness.     

Intraspecific genotypic richness and relatedness predict the invasibility of microbial communities

Biological invasions can lead to extinction events in resident communities and compromise ecosystem functioning. We tested the effect of two widespread biodiversity measurements, genotypic richness and genotypic dissimilarity on community invasibility. We manipulated the genetic structure of bacterial communities (Pseudomonas fluorescens) and submitted them to invasion by Serratia liquefaciens. We show that the two diversity measures impact on invasibility via distinct and additive mechanisms. Genotypic dissimilarity of the resident communities linearly increased productivity and in parallel decreased invasion success, indicating that high dissimilarity prevents invasion through niche pre-emption. By contrast, genotypic richness exerted a hump-shaped effect on invasion and was linked to the production of toxins antagonistic to the invader. This effect peaked at intermediate richness, suggesting that high richness levels may increase invasibility. Invasibility could be well predicted by the combination of these two mechanisms, documenting that both genotypic richness and dissimilarity need to be considered, if we are to understand the biotic properties determining the susceptibility of ecosystems to biological invasions.     

Immunological relatedness of annelid extracellular hemoglobins and chlorocruorins

1. The immunological relatedness of several annelid extracellular hemoglobins and chlorocruorins was investigated using ELISAs and Western blotting to determine the binding of purine polyclonal and monoclonal antibodies to Lumbricus terrestris hemoglobin with the hemoglobins of Tubifex tubifex, Tylorrhynchus heterochaetus, Arenicola marina and Macrobdella decora and the chlorocruoins of Myxicola infundibulum and Eudistylia vancouverii. 2. Polyclonal antibodies to Lumbricus terrestris hemoglobin bound to all the other hemoglobins and chlorocruorins. However, the titers were in all cases one to several orders of magnitude smaller than with Lumbricus terrestris hemoglobin. 3. Polyclonal antibodies to Eudistylia vancouverii chlorocruorin bound to the hemoglobins of Lumbricus terrestris, Tubifex tubifex, Arenicola marina, Tylorrhynchus heterochaetus and Macrobdella decora. 4. Of the nine monoclonal antibodies to Lumbricus terrestris hemoglobin isolated, two (No. 24 and No. 26) bound to the other hemoglobins and to Myxicola chlorocruorin, but the binding was again weaker than with Lumbricus hemoglobin. Antibody No. 26 also bound to Eudistylia chlorocruorin. Although antibody No. 24 appears to recognize a conformation-dependent epitope, antibody No. 26 recognizes a common epitope in each of the four subunits M, D1, D2, and T of unreduced Lumbricus hemoglobin. 4. An additional two monoclonal antibodies to Lumbricus hemoglobin (No. 21 and No. 25) bound also only to Tubifex hemoglobin. Antibody No. 21 recognizes subunits D1 and M of Lumbricus hemoglobin and No. 25 appears to recognize a conformation-dependent epitope.     

Inferred relatedness and heritability in malaria parasites

Malaria parasites vary in phenotypic traits of biomedical or biological interest such as growth rate, virulence, sex ratio and drug resistance, and there is considerable interest in identifying the genes that underlie this variation. An important first step is to determine trait heritability (H²). We evaluate two approaches to measuring H² in natural parasite populations using relatedness inferred from genetic marker data. We collected single-clone Plasmodium falciparum infections from 185 patients from the Thailand–Burma border, monitored parasite clearance following treatment with artemisinin combination therapy (ACT), measured resistance to six antimalarial drugs and genotyped parasites using 335 microsatellites. We found strong relatedness structure. There were 27 groups of two to eight clonally identical (CI) parasites, and 74 per cent of parasites showed significant relatedness to one or more other parasites. Initially, we used matrices of allele sharing and variance components (VC) methods to estimate H². Inhibitory concentrations (IC₅₀) for six drugs showed significant H² (0.24 to 0.79, p = 0.06 to 2.85 × 10⁻⁹), demonstrating that this study design has adequate power. However, a phenotype of current interest—parasite clearance following ACT—showed no detectable heritability (H² = 0–0.09, ns) in this population. The existence of CI parasites allows the use of a simple ANOVA approach for quantifying H², analogous to that used in human twin studies. This gave similar results to the VC method and requires considerably less genotyping information. We conclude (i) that H² can be effectively measured in malaria parasite populations using minimal genotype data, allowing rational design of genome-wide association studies; and (ii) while drug response (IC₅₀) shows significant H², parasite clearance following ACT was not heritable in the population studied.