Developmental genetics and homology: a hierarchical approach

New advances in developmental genetics are providing a bridge to connect the study of development and evolution. The successful integration of these fields, however, is dependent on having a clear understanding of the concept of homology. Therefore, developmental genetic data must be placed within the context of the comparative method to provide insight into the evolutionary and developmental origins of traits. The comparative analysis of traits derived from several hierarchical levels (genes, gene expression patterns, embryonic origins and morphology) can potentially reveal scenarios of developmental integration, opportunity and constraint. Moreover, this approach has implications for resolving modern controversies surrounding the concept of homology.     

Speciation in parasites: a population genetics approach

Parasite speciation and host-parasite coevolution should be studied at both macroevolutionary and microevolutionary levels. Studies on a macroevolutionary scale provide an essential framework for understanding the origins of parasite lineages and the patterns of diversification. However, because coevolutionary interactions can be highly divergent across time and space, it is important to quantify and compare the phylogeographic variation in both the host and the parasite throughout their geographical range. Furthermore, to evaluate demographic parameters that are relevant to population genetics structure, such as effective population size and parasite transmission, parasite populations must be studied using neutral genetic markers. Previous emphasis on larger-scale studies means that the connection between microevolutionary and macroevolutionary events is poorly explored. In this article, we focus on the spatial fragmentation of parasites and the population genetics processes behind their diversification in an effort to bridge the micro- and macro-scales.     

Chemical genetics: a small molecule approach to neurobiology

Chemical genetics, or the specific modulation of cellular systems by small molecules, has complemented classical genetic analysis throughout the history of neurobiology. We outline several of its contributions to the understanding of ion channel biology, heat and cold signal transduction, sleep and diurnal rhythm regulation, effects of immunophilin ligands, and cell surface oligosaccharides with respect to neurobiology.     

The genetics of chutes and ladders: a community genetics approach to tritrophic interactions

Community genetics research has firmly established that intraspecific genetic variation in single populations can have large extended ecological consequences for populations and entire communities of organisms. Here, we sought to understand the bottom‐up effects of plant genetic variation on herbivore preference and performance, and the top–down control of predators on herbivores and their joint effects on plant fitness and evolution. Following three ecological genetics field experiments we detected heritable variation in plant traits that influenced both the preference and performance of a specialist weevil on Oenothera biennis. However, the weevil's preference and performance were not genetically correlated among O. biennis plant genotypes. Although predators and parasitoids were abundant, predators had no detectable effect on weevil performance because high egg and larval mortality was caused by non‐predatory factors such as intraspecific competition. Finally, neither the specialist weevil nor predators influenced plant fitness. Our results suggest that the focal tritrophic community studied here is primarily shaped by the bottom–up effects of plant genetic variation on herbivores, while top–down effects have no clear impacts on O. biennis fitness or evolution. We suggest that future studies should incorporate plant intraspecific genetic variation as a fundamental part of tritrophic interactions including their eco‐evolutionary dynamics.     

The candidate gene approach in plant genetics: a review

The candidate gene (CG) approach has been applied in plant genetics in the past decade for the characterisation and cloning of Mendelian and quantitative trait loci (QTLs). It constitutes a complementary strategy to map-based cloning and insertional mutagenesis. The goal of this paper is to present an overview of CG analyses in plant genetics. CG analysis is based on the hypothesis that known-function genes (the candidate genes) could correspond to loci controlling traits of interest. CGs refer either to cloned genes presumed to affect a given trait (`functional CGs') or to genes suggested by their close proximity on linkage maps to loci controlling the trait (`positional CGs'). In plant genetics, the most common way to identify a CG is to look for map co-segregation between CGs and loci affecting the trait. Statistical association analyses between molecular polymorphisms of the CG and variation in the trait of interest have also been carried out in a few studies. The final validation of a CG will be provided through physiological analyses, genetic transformation and/or sexual complementation. Theoretical and practical applications of validated CGs in plant genetics and breeding are discussed.     

Inflorescence architecture: A developmental genetics approach

We are characterizing a suiteof Pisum sativum mutants that alter inflorescence architecture to construct a model for the genetic regulation of inflorescence development in a plant with a compound raceme. Such a model, when compared with those created forAntirrhinum majus andArabidopsis thaliana, both of which have simple racemes, should provide insight into the evolution of the development of inflorescence architecture. The highly conserved nature of cloned genes that regulate reproductive development in plants and the morphological similarities among our mutants and those identified inA. majus andA. thaliana enhance the probability that a developmental genetics approach will be fruitful. Here we describe sixP. sativum mutants that affect morphologically and architecturally distinct aspects of the inflorescence, and we analyze interactions among these genes. Both vegetative and inflorescence growth of the primary axis is affected byUNIFOLIA TA, which is necessary for the function ofDETERMINATE (DET).DET maintains indeterminacy in the first-order axis. In its absence, the meristem differentiates as a stub covered with epidermal hairs.DET interacts withVEGETATIVE1 (VEG1).VEG1 appears essential for second-order inflorescence (I₂) development.veg1 mutants fail to flower or differentiate the I₂ meristem into a rudimentary stub,det veg1 double mutants produce true terminal flowers with no stubs, indicating that two genes must be eliminated for terminal flower formation inP. sativum, whereas elimination of a single gene accomplishes this inA. thaliana andA. majus. NEPTUNE also affects I₂ development by limiting to two the number of flowers produced prior to stub formation. Its role is independent ofDET, as indicated by the additive nature of the double mutantdet nep. UNI, BROC, and PIM all play roles in assigning floral meristem identity to the third-order branch.pim mutants continue to produce inflorescence branches, resulting in a highly complex architecture and aberrant flowers.uni mutants initiate a whorl of sepals, but floral organogenesis is aberrant beyond that developmental point, and the double mutantuni pim lacks identifiable floral organs. A wild-type phenotype is observed inbroc plants, butbroc enhancesthe pim phenotype in the double mutant, producing inflorescences that resemble broccoli. Collectively these genes ensure that only the third-order meristem, not higher- or lower-order meristems, generates floral organs, thus precisely regulating the overall architecture of the plant. Gene symbols used in this article: For clarity a common symbolization is used for genes of all species discussed in this article. Genes are symbolized with italicized capital letters. Mutant alleles are represented by lowercase, italicized letters. In both cases, the number immediately following the gene symbol differentiates among genes with the same symbol. If there are multiple alleles, a hyphen followed by a number is used to distinguish alleles. Protein products are represented by capital letters without italics.     

Personalized peptide vaccination: a new approach for advanced cancer as therapeutic cancer vaccine

Since both tumor cells and host immune cell repertoires are diverse and heterogeneous, immune responses against tumor-associated antigens should differ substantially among individual cancer patients. Selection of suitable peptide vaccines for individual patients based on the preexisting host immunity before vaccination could induce potent anti-tumor responses that provide clinical benefit to cancer patients. We have developed a novel immunotherapeutic approach of personalized peptide vaccination (PPV) in which a maximum of four human leukocyte antigen (HLA) class IA-matched peptides are selected for vaccination among pooled peptides on the basis of both HLA class IA type and the preexisting host immunity before vaccination. In this review, we discuss our recent results of preclinical and clinical studies of PPV for various types of advanced cancer.     

Personalized neoantigen vaccines: A new approach to cancer immunotherapy

Neoantigens arise from somatic mutations that differ from wild-type antigens and are specific to each individual patient, which provide tumor specific targets for developing personalized cancer vaccines. Decades of work has increasingly shown the potential of targeting neoantigens to generate effective clinical responses. Current clinical trials using neoantigen targeting cancer vaccines, including in combination with checkpoint blockade monoclonal antibodies, have demonstrated potent T-cell responses against those neoantigens accompanied by antitumor effects in patients. Personalized neoantigen vaccines represent a potential new class of cancer immunotherapy.     

Accelerating aging by mouse reverse genetics: a rational approach to understanding longevity

Investigating the molecular basis of aging has been difficult, primarily owing to the pleiotropic and segmental nature of the aging phenotype. There are many often interacting symptoms of aging, some of which are obvious and appear to be common to every aged individual, whereas others affect only a subset of the elderly population. Although at first sight this would suggest multiple molecular mechanisms of aging, there now appears to be almost universal consensus that aging is ultimately the result of the accumulation of somatic damage in cellular macromolecules, with reactive oxygen species likely to be the main damage-inducing agent. What remains significant is unravelling how such damage can give rise to the large variety of aging symptoms and how these can be controlled. Although humans, with over a century of clinical observations, remain the obvious target of study, the mouse, with a relatively short lifespan, easy genetic accessibility and close relatedness to humans, is the tool par excellence to model aging-related phenotypes and test strategies of intervention. Here we present the argument that mouse models with engineered defects in genome maintenance systems are especially important because they often exhibit a premature appearance of aging symptoms. Confirming studies on human segmental progeroid syndromes, most of which are based on heritable mutations in genes involved in genome maintenance, the results thus far obtained with mouse models strongly suggest that lifespan and onset of aging are directly related to the quality of DNA metabolism. This may be in keeping with the recent discovery of a possible 'universal survival' pathway that improves antioxidant defence and genome maintenance and simultaneously extends lifespan in the mouse and several invertebrate species.     

A macroscopic approach to population genetics

Conventional population genetics uses as primitive variables the frequencies and fitnesses of individual genes. This paper develops a formalism whose primitive variables are the frequencies and fitnesses of genotypes and environmental histories in a population. From the mathematical relation that describes genetic variation and selection of genotypes and environmental histories we derive a sequence of more specialized equations, including those of the conventional theory. Some familiar formulas of the conventional theory (including Fisher's fundamental theorem, the formula relating the rate of change of a metric character to selection pressure, and the definitions of broad and narrow heritability) are shown to be special cases of simpler and more general formulas. It is shown that the “genotypic value” of a trait, together with its heritability, may depend strongly on genotype-environment correlations.A generalization of Fisher's fundamental theorem shows that the rate of evolution of a trait depends on the skewness of its fitness distribution. An equation relating the second derivative of the mean fitness to the skewness is derived.Finally, the formalism is applied in a preliminary way to a recent theory of genetic variation (Layzer,1978a), according to which the genetic variability of a trait is selected along with the trait itself. It is shown that there is positive feedback between the two kinds of selection.     

Tsetse fly population genetics: an indirect approach to dispersal

Tsetse populations are distributed discontinuously, particularly the morsitans group. Dispersal among diverse populations cannot easily be measured directly because the geographical distances between them can be too great to have a reasonable expectation of recapturing experimentally released flies. Moreover, reproductive success of widely dispersed flies might be poor. The question of dispersal rates in tsetse is immediately important because area-wide eradication plans involving the sterile insect technique are under consideration. Dispersal and gene flow are important from evolutionary and historical viewpoints. An indirect method of estimating dispersal is to measure gene flow. Genetic data indicate surprisingly low rates of gene flow in the morsitans and palpalis groups studied to date. The underlying assumptions in making such estimates need to be examined carefully, however, before accepting firm conclusions, and further research is needed. Of particular interest is the question of tsetse adaptation to local environments.     

Quantitative genetics: a promising approach for the assessment of genetic variation in endangered species

The measurement of genetic variation is often an important component of endangered species management programs. Each of several tools available to measure genetic diversity has positive and negative attributes. Quantitative genetic techniques have not received much attention in the conservation field, yet they are likely to reveal variation that is most closely associated with components of fitness. In addition, quantitative genetics may not be as logistically difficult for threatened populations as was once thought. Finally, quantitative genetic models provide a better outlook for conservation programs than single-locus models.     

Tagged library approach facilitates forward chemical genetics

Forward chemical genetics has been highlighted as a new method for the study of various biological pathways using exogenous ligands. However, limited success in the field has demonstrated that, in many cases, it is not feasible to determine the protein targets of small-molecule probes. Identifying protein targets is an integral part of forward chemical genetics and is also the most challenging. Over the past decade, several biochemical and genetic methods have been developed to facilitate target identification processes. Even so, one of the major difficulties is that these methods require the chemical modification of active compounds, with a significant amount of structure-activity relationship (SAR) study to ensure that the small-molecule tags do not compromise bioactivity. In this article, we will highlight a new strategy for small molecule libraries that have built-in linkers in order to avoid this well-known problem and demonstrate their successful use in forward chemical genetics.     

Focus: Personalized Medicine: Crowdfunding for Personalized Medicine Research

Given the current funding situation of the National Institutes of Health, getting funding for rare disease research is extremely difficult. In light of the enormous potential for research in the rare diseases and the scarcity of research funding, we provide a case study of a novel successful crowdfunding approach at a non-profit organization called Rare Genomics Institute. We partner with biotechnology companies willing to donate their products, such as mouse models, gene editing software, and sequencing services, for which researchers can apply. First, we find that personal stories can be powerful tools to seek funding from sympathetic donors who do not have the same rational considerations of impact and profit. Second, for foundations facing funding restrictions, company donations can be a valuable tool in addition to crowdfunding. Third, rare disease research is particularly rewarding for scientists as they proceed to be pioneers in the field during their academic careers. Overall, by connecting donors, foundations, researchers, and patients, crowdfunding has become a powerful alternative funding mechanism for personalized medicine.     

Trafficking and postsecretory events responsible for the formation of secreted human salivary peptides: a proteomics approach

To elucidate the localization of post-translational modifications of different classes of human salivary proteins and peptides (acidic and basic proline-rich proteins (PRPs), Histatins, Statherin, P-B peptide, and "S type" Cystatins) a comparative reversed phase HPLC-ESI-MS analysis on intact proteins of enriched granule preparations from parotid and submandibular glands as well as parotid, submandibular/sublingual (Sm/Sl), and whole saliva was performed. The main results of this study indicate the following. (i) Phosphorylation of all salivary peptides, sulfation of Histatin 1, proteolytic cleavages of acidic and precursor basic PRPs occur before granule storage. (ii) In agreement with previous studies, basic PRPs are secreted by the parotid gland only, whereas all isoforms of acidic PRPs (aPRPs) are secreted by both parotid and Sm/Sl glands. (iii) Phosphorylation levels of aPRPs, Histatin 1, and Statherin are higher in the parotid gland, whereas the extent of cleavage of aPRP is higher in Sm/Sl glands. (iv) O-Sulfation of tyrosines of Histatin 1 is a post-translational modification specific for the submandibular gland. (v) The concentration of Histatin 3, Histatin 5, and Histatin 6, but not Histatin 1, is higher in parotid saliva. (vi) Histatin 3 is submitted to the first proteolytic cleavage (generating Histatins 6 and 5) during granule maturation, and it occurs to the same relative extent in both glands. (vii) The proteolytic cleavages of Histatin 5 and 6, generating a cascade of Histatin 3 fragments, take place after granule secretion and are more extensive in parotid secretion. (viii) Basic PRPs are cleaved in the oral cavity by unknown peptidases, generating various small proline-rich peptides. (ix) C-terminal removal from Statherin is more extensive in parotid saliva. (x) P-B peptide is secreted by both glands, and its relative quantity is higher in submandibular/sublingual secretion. (xi) In agreement with previous studies, S type Cystatins are mainly the product of Sm/Sl glands.