Panpsychic Organicism: Sewall Wright’s Philosophy for Understanding Complex Genetic Systems

Sewall Wright first encountered the complex systems characteristic of gene combinations while a graduate student at Harvard’s Bussey Institute from 1912 to 1915. In Mendelian breeding experiments, Wright observed a hierarchical dependence of the organism’s phenotype on dynamic networks of genetic interaction and organization. An animal’s physical traits, and thus its autonomy from surrounding environmental constraints, depended greatly on how genes behaved in certain combinations. Wright recognized that while genes are the material determinants of the animal phenotype, operating with great regularity, the special nature of genetic systems contributes to the animal phenotype a degree of spontaneity and novelty, creating unpredictable trait variations by virtue of gene interactions. As a result of his experimentation, as well as his keen interest in the philosophical literature of his day, Wright was inspired to see genetic systems as conscious, living organisms in their own right. Moreover, he decided that since genetic systems maintain ordered stability and cause unpredictable novelty in their organic wholes (the animal phenotype), it would be necessary for biologists to integrate techniques for studying causally ordered phenomena (experimental method) and chance phenomena (correlation method). From 1914 to 1921 Wright developed his “method of path coefficient” (or “path analysis”), a new procedure drawing from both laboratory experimentation and statistical correlation in order to analyze the relative influence of specific genetic interactions on phenotype variation. In this paper I aim to show how Wright’s philosophy for understanding complex genetic systems (panpsychic organicism) logically motivated his 1914–1921 design of path analysis.     

Biosynthesis and enzymology of the Caenorhabditis elegans cuticle: identification and characterization of a novel serine protease inhibitor

Caenorhabditis elegans represents an excellent model in which to dissect the biosynthesis and assembly of the nematode cuticle. A sequenced genome, straightforward transgenesis, available mutants and practical genome-wide RNAi approaches provide an invaluable toolkit in the characterization of cuticle components. We have performed a targeted RNAi screen in an attempt to identify components of the cuticle collagen biosynthetic pathway. Collagen biosynthesis and cuticle assembly are multi-step processes that involve numerous key enzymes involved in post-translational modification, trimer folding, procollagen processing and subsequent cross-linking stages. For many of these steps, the modifications and the enzymes are unique to nematodes and may represent attractive targets for the control of parasitic nematodes. A novel serine protease inhibitor was uncovered during our targeted screen, which is involved in collagen maturation, proper cuticle assembly and the moulting process. We have confirmed a link between this inhibitor and the previously uncharacterised bli-5 locus in C. elegans. The mutant phenotype, spatial expression pattern and the over-expression phenotype of the BLI-5 protease inhibitor and their relevance to collagen biosynthesis are discussed.     

De novo 3q22.1 q24 deletion associated with multiple congenital anomalies,growth retardation and intellectual disability

We describe a boy with a de novo deletion of 15.67 Mb spanning 3q22.1q24. He has bilateral micropthalmia, ptosis, cleft palate, global developmental delay and brain, skeletal and cardiac abnormalities. In addition, he has bilateral inguinal hernia and his right kidney is absent. We compare his phenotype with seven other patients with overlapping and molecularly defined interstitial 3q deletions. This patient has some phenotypic features that are not shared by the other patients. More cases with smaller deletions defined by high resolution aCGH will enable better genotype–phenotype correlations and prioritizing of candidate genes for the identification of pathways and disease mechanisms.     

Genetic events associated with an insertion mutation in yeast

The his4-912 mutation shares similar genetic properties with mutations promoted by procaryotic insertion elements. This mutation lacks all three his4 functions. Many different classes of His+ revertants have been obtained from his4-912. The most frequent class of His+ revertants results from a site mutation which confers a cold-sensitive His- phenotype. Other classes of revertants contain translocations (one between chromosomes I and III and the other between chromosomes III and XII), a transposition of the his4 region to chromosome VIII, and an inversion of most of the left arm of chromosome III. Another class contains deletions which extend from his4-912 into the his4 region. In each of these classes of revertants, the his4 region is closely linked to the chromosomal aberration. Many of these revertants contain additional changes in chromosome structure (duplication, deletion and aneuploidy) that are unrelated to the reversion of his4-912 to His4+.     

The probabilistic determination of identity-by-descent sharing for pairs of relatives from pedigrees.

Methods for detecting genetic linkage are more powerful when they fully use all of the data collected from pedigrees. We first discuss a method for obtaining the probability that a pedigree member has a given genotype, conditional on the phenotypes of his relatives. We then develop a rapid method to obtain the conditional probabilities of identity-by-descent sharing of marker alleles for all related pairs of individuals from extended pedigrees. The method assumes that the individuals are noninbred and that the relationship between genotype and phenotype is known for the marker locus studied. The probabilities of identity-by-descent sharing among relative pairs, conditional on marker phenotype information, can then be used in any of the model free tests for linkage between a trait locus and a marker locus.     

Linkage studies on Gilles de la Tourette syndrome: what is the strategy of choice?

For a linkage study it is important to ascertain family material that is sufficiently informative. The statistical power of a linkage sample can be determined via computer simulation. For complex traits uncertain parameters such as incomplete penetrance, frequency of phenocopies, gene frequency and variable expression have to be taken into account. One can either include only the most severe phenotype in the analysis or apply multiple linkage tests for a gradually broadened disease phenotype. Gilles de la Tourette syndrome (GTS) is a chronic neurological disorder characterized by multiple, intermittent motor and vocal tics. Segregation analyses suggest that GTS and milder phenotypes are caused by a single dominant gene. We report here the results of an extensive simulation study on a large set of families. We compared the effectiveness of linkage tests with only the GTS phenotype versus multiple tests that included various milder phenotypes and different gene frequencies. The scenario of multiple tests yielded superior power. Our results show that computer simulation can indicate the strategy of choice in linkage studies of multiple, complex phenotypes.     

Completed Chromosomes in Thymine-Requiring Bacillus subtilis Spores

Origin:terminus genetic marker ratios (both purA: metB and purA:ilvA) were measured in extracts of spores of Bacillus subtilis strains W23 thy his and 168 thy. For strain W23 thy his, normalized to W23 spore deoxyribonucleic acid, both ratios were equal to unity and were consistent with the presence of only completed chromosomes in the spores. The same ratios in extracts of spores of 168 thy, normalized to strain 168 or the prototroph SB19, were abnormal, i.e., 2.26 +/- 0.10 and 0.71 +/- 0.06 for purA:metB and purA:ilvA, respectively. These values were unaffected by the extent of extraction of the spore deoxyribonucleic acid, the richness of the medium on which they are formed, and the thymine phenotype. The high ratio for purA:metB is in agreement with the results of earlier workers but, because of the low purA:ilvA ratio, cannot be explained simply by the presence of partially replicated chromosomes in spores of strain 168 thy. Furthermore, purA:leuA in such extracts is 1.01 +/- 0.06, consistent with the presence of only completed chromosomes. It is concluded that the abnormal origin:terminus marker ratios are only apparent and result from non-isogenicity between strains 168 thy and 168 in the metB thyB ilvA chromosome region introduced during construction of 168 thy by transformation of strain 168 with W23 thy deoxyribonucleic acid. It is concluded further that the chromosomes of strain 168 thy spores are in a completed form.     

Phenotypic evolution under gene-culture transmission in structured populations.

I consider a simple model for the evolution of a quantitative character is structured populations when an offspring's phenotype is determined partly by his or her genetic constitution and partly by cultural transmission of the parental phenotype. Analysis of the model indicates that when individual and group selection are in the same direction, phenotypic evolution always proceeds faster under gene-culture vs. purely genetic transmission. When individual and group selection are countervailing, altruistic characters evolve faster under gene-culture transmission when individual selection is weak and migration among groups is limited, with increased individual selection and migration tending to decrease the advantage of gene-culture transmission over purely genetic transmission. Given the prevalence of cultural transmission in higher species, these results suggest that contrary to what is often assumed, group selection may indeed by a potent evolutionary force in the evolution of altruistic characters.     

Genetic analysis of the cholera toxin-positive regulatory gene toxR.

Southern blot analysis with a toxR-specific gene probe indicates that Vibrio cholerae 569B has a 1.2-kilobase deletion near the toxR gene. Heterologous conjugative crosses were carried out between the EI Tor strain RV79 and 569B tox mutants. Tox+ recombinants showed the same linkage properties to the his locus as to the previously mapped tox locus of 569B. Southern blot analysis with the toxR probe of the Tox+ recombinants obtained in these heterologous crosses showed that these recombinants had replaced the V. cholerae 569B (recipient) toxR DNA with the V. cholerae RV79 (donor) toxR DNA, indicating that tox and toxR are the same locus. However, the Tox+ recombinants synthesized an amount of toxin intermediate between the level observed for wild-type RV79 and 569B strains, suggesting there is a difference in the ability of toxR genes from different strains to activate ctx. About half of the mutations which suppress the phenotype of hypertoxinogenic locus htx are unlinked to htx and in addition have a hypotoxinogenic phenotype relative to that of the wild type. Most of these hypotoxinogenic, second-site suppressors show a linkage to his similar to the linkage of toxR to his and are therefore probably mutations in toxR. These results indicate that the toxR gene product is required for ctx expression and that a functional toxR gene is required for the effect of an htx mutation to be seen.     

Hereditary recombined three-allele variant of the Gc system

A three-allele variant with Gc 2, Gc 1F and Gc 1A2 alleles was detected in both a baby and his mother during paternity testing by isoelectric focusing. His father had a normal Gc phenotype, Gc 2-1F. Further examination of his mother's relatives revealed that his grandfather also had the same three-allele variant, while his grandmother and his aunt had normal Gc 2-1F and Gc 2-2. From these results, it was considered that the Gc 1F and Gc 1A2 alleles were on the same single chromosome. It was suggested that recombination had occurred between two chromosomes that had the Gc 1F and Gc 1A2 allele, respectively, forming the variant allele Gc 1F1A2 on a single chromosome.     

An evolutionary relationship between genetic variation and phenotypic fluctuation

The relevance of phenotype fluctuations among clones (i.e., organisms with identical genes) to evolution has recently been recognized both theoretically and experimentally. By considering the stability of the distributions of genetic variations and phenotype fluctuations, we derive a general inequality between the phenotype variance due to genetic differences and the intrinsic phenotype variance of clones. For a given mutation rate, an approximately linear relationship between the two is obtained which elucidates the consistency between the fundamental theorem of natural selection by Fisher and the evolutionary fluctuation-response relationship (fluctuation dissipation theorem) proposed recently. A general condition for the error catastrophe is also derived as the violation of the inequality, which sets up the limit to the speed of stable evolution. All of these theoretical results are confirmed by a numerical evolution experiment of a cell that consists of a catalytic reaction network. Based on the relationships proposed here, relevance of the phenotypic plasticity to evolution as well as the genetic assimilation is discussed.     

The X chromosome and fragile X mental retardation

Fragile X syndrome represents the most common inherited cause of mental retardation. It is caused by a stretch of CGG repeats within the fragile X gene, which increases in length as it is transmitted from generation to generation. Once the repeat exceeds a threshold length, no protein is produced, resulting in the fragile X phenotype. Both X chromosome inactivation and inactivation of the FMR1 gene are the result of methylation. X inactivation occurs earlier than inactivation of the FMR1 gene. The instability to a full mutation is dependent on the sex of the transmitting parent and occurs only from mother to child. For most X-chromosomal diseases, female carriers do not express the phenotype. A clear exception is fragile X syndrome. It is clear that more than 50% of the neurons have to express the protein to ensure a normal phenotype in females. This means that a normal phenotype in female carriers of a full mutation is accompanied by a distortion of the normal distribution of X inactivation.     

Linkage of genes for PHI,halothane sensitivity,A-O inhibition,H red blood cell antigens and 6-PGD variants in pigs*

Data from one apparent crossover between S and H, two between PHI and HAL on one side and S on the other, and one between PHI on one side and HAL, S and H on the other, indicate a gene order in pigs of Phi-Hal-S-H-Pgd for genes for PHI, halothane sensitivity, inhibition of expression of A and O, H red blood cell antigens and 6-PGD types. Rasmusen et al. (1980) provided data for a gene order in pigs ofPhi-Hal-H-Pgd for genes for phosphohexose isomerase (PHI) isozyme variants, halothane sensitivity (HAL), H red cell antigens and 6-phosphogluconate dehydrogenase (6-PGD) variants, and suggested that there might be a locus for a gene for inhibition of expression of A and O separate from the locus for H. This is contrary to an earlier proposal by Rasmusen (1972) that the H-system genotype directly influences expression of A and O. Imlah (1980) suggested that the recessive gene for halothane sensitivity has a suppressant effect on the expression of A and O. Andresen (1981) proposed that the locus for inhibition of A and O (for which Rasmusen, 1964, proposed the symbol S) was between the loci for HAL and H types. Data presented in Table 1, which includes haplotypes for three recombinant offspring described by Rasmusen et al. (1980) (883-1, 233-3 and 3864-1) as well as one other recombinant (296-2) provide evidence for the gene order for five genes proposed by Andresen. Types for 6-PGD are listed for all pigs, although they do not provide evidence for gene order in these cases. Male 883-1 (Table 1, and Rasmusen et al., 1980, Table 5) provided the original evidence for recombination between S and H. His phenotype, as well as his genotype as revealed by progeny test (Rasmusen et al., 1980, Table 6) indicated that recombination had occurred between the genes for PHI, HAL and S and the gene for H type in his dam, so that the S locus mapped between H and the loci for the other three traits. The phenotype of one of his sons (233-3, Table 1, and Rasmusen et al., 1980, Table 6) indicated that there had been a recombination between genes for PHI and HAL types on one side and S and H types on the other, providing evidence that the S locus was separate from PHI and HAL as well as H. Another pig listed in Table 1,3864-1, was also described by Rasmusen et al. (1980, Table 9) as a recombinant. This pig provides evidence for recombination between PHI on one side and HAL, S and H on the other, establishing a gene order of Phi-Hal-S-H-Pgd. The last pig listed in Table 1,296-2, is a recombinant comparable to 233-3. The H type of his dam provides markers indicating the recombination was between PHI and HAL on one side and S and H on the other, although the unusual expression of HAL phenotype in both parents of 296-2 makes her haplotypes somewhat uncertain. (Recombination may have been between PHI and HAL rather than as indicated in Table 1.) In spite of incomplete penetrance for HAL (Ollivier et al., 1975; Smith & Bampton, 1977) which makes haplotypes for HAL questionable in some cases, the other genetic markers available are useful to show that recombination has taken place. Without considering the results of halothane testing, if the apparent recombinants are accepted as being as indicated, the order of the genes at the other four loci seems established. Alleles for S types appear to be separable by recombination from those for PHI and H, and the S locus appears to be between the loci for PHI and H. For the five loci, data obtained thus far are cohsistent with a gene order of Phi-Hal-S-H-Pgd.     

Analysis of the red cell membrane in a family with hereditary elliptocytosis — total or partial of protein 4.1

Summary In a 12-year-old boy carrying a clinically silent elliptocytosis, we observed a total lack of red cell membrane band 4.1. Band 4.1 was partially absent in the father who also displayed a clinically silent elliptocytosis and, remarkably, in the mother although she presented normal discocytes. Band (2 and 2.1) phosphorylation was sharply reduced in the three persons examined. In the propositus and his mother, but not in his father, a clearly phosphorylated band appeared at the level of band 4.2. We suggest that the father and the mother carry two distinct alleles affecting differently the interactions, within the spectrin-actin protein 4.1 complex. The father's allele is elliptocytogenic in the heterozygous state and, among other molecular alterations, prevents the attachment of protein 4.1. The mother's allele is morphologically silent in the heterozygous state, yet it also affects the binding of protein 4.1, possibly because the latter is shortened. The propositus, being doubly heterozygous, has the same morphological phenotype as his father, but his protein 4.1 electrophoretic phenotype is the addition of both parental phenotypes. The distinct phosphorylation patterns in the region of bands 4.1 and 4.2 are also consistent with the two-allele hypothesis.     

Alginate overproduction affects Pseudomonas aeruginosa biofilm structure and function

During the course of chronic cystic fibrosis (CF) infections, Pseudomonas aeruginosa undergoes a conversion to a mucoid phenotype, which is characterized by overproduction of the exopolysaccharide alginate. Chronic P. aeruginosa infections involve surface-attached, highly antibiotic-resistant communities of microorganisms organized in biofilms. Although biofilm formation and the conversion to mucoidy are both important aspects of CF pathogenesis, the relationship between them is at the present unclear. In this study, we report that the overproduction of alginate affects biofilm development on an abiotic surface. Biofilms formed by an alginate-overproducing strain exhibit a highly structured architecture and are significantly more resistant to the antibiotic tobramycin than a biofilm formed by an isogenic nonmucoid strain. These results suggest that an important consequence of the conversion to mucoidy is an altered biofilm architecture that shows increasing resistance to antimicrobial treatments.     

Regulatory Mutants at the his1 Locus of Yeast

The his1 gene in Saccharomyces cerevisiae codes for phosphoribosyl transferase, an allosteric enzyme that catalyzes the initial step in histidine biosynthesis. Mutants that specifically alter the feedback regulatory function were isolated by selecting his1 prototrophic revertants that overproduce and excrete histidine. The prototrophs were obtained from diploids homoallelic for his1--7 and heterozygous for the flanking markers thr3 and arg6. Among six independently derived mutant isolates, three distinct levels of histidine excretion were detected. The mutants were shown to be second-site alterations mapping at the his1 locus by recovery of the original auxotrophic parental alleles. The double mutants, HIS1--7e, are dominant with respect to catalytic function but recessive in regulatory function. When removed from this his1--7 background, the mutant regulatory site (HIS1-e) still confers prototrophy but not histidine excretion. To yield the excretion phenotype, the primary and altered secondary sites are required in cis array. Differences in histidine excretion levels correlate with resistance to the histidine analogue, triazoalanine.     

Early life of fathers affects offspring fitness in a wild rodent

Intergenerational fitness effects on offspring due to the early life of the parent are well studied from the standpoint of the maternal environment, but intergenerational effects owing to the paternal early life environment are often overlooked. Nonetheless, recent laboratory studies in mammals and ecologically relevant studies in invertebrates predict that paternal effects can have a major impact on the offspring's phenotype. These nongenetic, environment‐dependent paternal effects provide a mechanism for fathers to transmit environmental information to their offspring and could allow rapid adaptation. We used the bank vole Myodes glareolus, a wild rodent species with no paternal care, to test the hypothesis that a high population density environment in the early life of fathers can affect traits associated with offspring fitness. We show that the protein content in the diet and/or social environment experienced during the father's early life (prenatal and weaning) influence the phenotype and survival of his offspring and may indicate adaptation to density‐dependent costs. Furthermore, we show that experiencing multiple environmental factors during the paternal early life can lead to a different outcome on the offspring phenotype than stimulated by experience of a single environmental factor, highlighting the need to study developmental experiences in tandem rather than independent of each other.     

Deletion and allelic exchange of the Aspergillus fumigatus veA locus via a novel recyclable marker module

Detailed evaluation of gene functions in an asexual fungus requires advanced methods of molecular biology. For the generation of targeted gene deletions in the opportunistic pathogen Aspergillus fumigatus we designed a novel blaster module allowing dominant selection of transformants due to resistance to phleomycin as well as dominant (counter)selection of a Cre recombinase-mediated marker excision event. For validation purposes we have deleted the A. fumigatus pabaA gene in a wild-type isolate by making use of this cassette. The resulting pabaA::loxP strain served as the recipient for subsequent targeting of the velvet locus. Homologous reconstitution of the deleted gene was performed by an allele whose expression is driven in a nitrogen source-dependent manner, as validated by Northern analyses. Overexpression of the veA locus in A. fumigatus does not result in any obvious phenotype, whereas the sporulation capacities of the veA null mutant are reduced on nitrate-containing medium, a phenotype that is completely restored in the reconstituted strain.     

26S and 18S rRNA synthesis in bobbed mutants of Drosophila melanogaster

For the most part, bobbed mutations of Drosophila melanogaster consist of deletions of 26S and 18S rDNA located on the X and Y chromosomes. Studies on the synthesis of rRNA of third instar larvae and one day old adult females of three severe bobbed genotypes, indicate that no decrease can be detected, compared ot wild type strains. One of the bobbed mutants studied was a rather unusual type: these flies possess a quantity of rDNA that should confer upon them a near wild type phenotype whereas they actually show an extreme bobbed phenotype. The two other bobbed mutants are of a classical type: their severe bobbed phenotype corresponds to large deletions of rDNA. Two hypotheses can be proposed to explain the extreme bobbed phenotype of the flies, in spite of the fact that rRNA synthesis occurs normally. A regulatory phenomenon may interfere at the stages studied, but in earlier stages a net decrease in rRNA synthesis may have occurred producing an irreversible effect in the tissues affected by bobbed mutations (abdominal cuticle, bristles). The second hypothesis is that the rRNA produced may not be functional, perhaps because it is specific of earlier stages.