Somatic immunoglobulin sequence divergence and its implications for studies of evolutionary divergence

The divergence of immunoglobulin genes due to somatic mutation provides a natural example of DNA sequence divergence. This divergence was examined to gain insight into the processes of evolution and the determinants of the variance-to-mean ratio of sequence divergence. Normally, this ratio is found to be larger than expected (1.0 under Poisson assumptions) for the evolutionary divergence or most genes. Although not significantly less than one, all seven groups of immunoglobulin amino acid sequences have ratios smaller than expected, contrary to the evolutionary pattern generally observed. The substitutions in the immunoglobulin genes appear to be highly nonrandom and an excess of parallel changes (the major nonrandom feature of these mutations) is shown to cause smaller ratios. Because convergent or parallel mutations are often observed in the evolutionary divergence of genes, this suggests that forces causing the large observed ratios may actually have to be more powerful than previously expected. Further, since selection is one of the likely causes of parallel mutations, it should be noted that selection could significantly decrease the variance-to-mean ratio. The high frequency of parallel mutations and their resulting effects, as observed in the immunoglobulin genes, suggest that only poor inferences of sequence divergence can be made without actual knowledge of the ancestral sequence.     

The discovery of two novel archosaur diseases with implications for future paleopathological exploration

Two novel bone diseases from the archosaur record were noted during the course of a survey of archosaur oral pathology. These abnormalities, pertaining to abnormal suturing of the crocodilian palate and ventral mandibular muscle scarring in tyrannosaurs, are classified within this paper according to a new classification system for ancient bone pathology. Standardization of this type is suggested for future disease exploration.     

Structural divergence among genomes of closely related baculoviruses and its implications for baculovirus evolution

Baculoviruses are members of a large, well-characterized family of dsDNA viruses that have been identified from insects of the orders Lepidoptera, Hymenoptera, and Diptera. Baculovirus genomes from different virus species generally exhibit a considerable degree of structural diversity. However, some sequenced baculovirus genomes from closely related viruses are structurally very similar and share overall nucleotide sequence identities in excess of 95%. This review focuses on the comparative analysis of partial and complete nucleotide sequences from two groups of closely related baculoviruses with broad host ranges: (a) group I multiple nucleopolyhedroviruses (MNPVs) from a cluster including Autographa californica (Ac)MNPV, Rachiplusia ou (Ro)MNPV, and Plutella xylostella (Plxy)MNPV; and (b) granuloviruses (GVs) from a cluster including Xestia c-nigrum (Xecn)GV and Helicoverpa armigera (Hear)GV. Even though the individual viruses in these clusters share high nucleotide sequence identities, a significant degree of genomic rearrangement (in the form of insertions, deletions, and homologous recombination resulting in allelic replacement) is evident from alignments of their genomes. These observations suggest an important role for recombination in the early evolution and biological characteristics of baculoviruses of these two groups.     

Hidden mitochondrial DNA divergence in the Lake Biwa endemic goby Gymnogobius isaza: implications for its evolutionary history

The gobiid Gymnogobius isaza is an endemic species that has adapted remarkably to the pelagic environment in Lake Biwa, Japan, a representative ancient lake in East Asia. To obtain clues that would reveal the origin and evolution of this species, we conducted phylogenetic and population genetic analyses based on partial sequences of the mitochondrial cytochrome b gene. Consistent with previous studies, our Bayesian phylogenetic analysis with a relaxed molecular clock model reconfirmed a sister relationship between G. isaza and Gymnogobius urotaenia?+?Gymnogobius petschiliensis, with a divergence time of about 2.9 million years (Myr), and provided an evolutionary rate of 3.0 %/Myr (pairwise) for their clade. Population genetic analysis revealed two distinct mtDNA groups in G. isaza, which were estimated to have diverged 0.66 million years ago (Mya) at the Lake Katata stage of Paleo-Lake Biwa, preceding the origin of the present Lake Biwa environment with its extensive deep pelagic area (0.3–0.4 Mya). A dumbbell-like haplotype network and bimodal mismatch distribution suggested that the population of G. isaza experienced secondary contact between two genetically differentiated populations. Demographic parameters from mismatch distribution analysis and Bayesian skyline plot analysis suggested that both of the mtDNA groups of G. isaza exhibited a signal of sudden population expansion at approximately the same time (80–90 thousand years ago) during the last glacial period after the development of the present Lake Biwa. These results imply the complex population history of G. isaza, including genetic isolation and secondary contact following differentiation from its relatives in the Pliocene.     

The quantitative genetic basis of adaptive divergence in the moor frog (Rana arvalis) and its implications for gene flow

Knowledge on the relative contribution of direct genetic, maternal and environmental effects to adaptive divergence is important for understanding the drivers of biological diversification. The moor frog (Rana arvalis) shows adaptive divergence in embryonic and larval fitness traits along an acidification gradient in south-western Sweden. To understand the quantitative genetic basis of this divergence, we performed reciprocal crosses between three divergent population pairs and reared embryos and larvae at acid and neutral pH in the laboratory. Divergence in embryonic acid tolerance (survival) was mainly determined by maternal effects, whereas the relative contributions of maternal, additive and nonadditive genetic effects in larval life-history traits differed between traits, population pairs and rearing environments. These results emphasize the need to investigate the quantitative genetic basis of adaptive divergence in multiple populations and traits, as well as different environments. We discuss the implications of our findings for maintenance of local adaptation in the context of migrant and hybrid fitness.     

Evidence for endothermic ancestors of crocodiles at the stem of archosaur evolution

Physiological, anatomical, and developmental features of the crocodilian heart support the paleontological evidence that the ancestors of living crocodilians were active and endothermic, but the lineage reverted to ectothermy when it invaded the aquatic, ambush predator niche. In endotherms, there is a functional nexus between high metabolic rates, high blood flow rates, and complete separation of high systemic blood pressure from low pulmonary blood pressure in a four-chambered heart. Ectotherms generally lack all of these characteristics, but crocodilians retain a four-chambered heart. However, crocodilians have a neurally controlled, pulmonary bypass shunt that is functional in diving. Shunting occurs outside of the heart and involves the left aortic arch that originates from the right ventricle, the foramen of Panizza between the left and right aortic arches, and the cog-tooth valve at the base of the pulmonary artery. Developmental studies show that all of these uniquely crocodilian features are secondarily derived, indicating a shift from the complete separation of blood flow of endotherms to the controlled shunting of ectotherms. We present other evidence for endothermy in stem archosaurs and suggest that some dinosaurs may have inherited the trait.     

Urbanization and its implications for food and farming

This paper discusses the influences on food and farming of an increasingly urbanized world and a declining ratio of food producers to food consumers. Urbanization has been underpinned by the rapid growth in the world economy and in the proportion of gross world product and of workers in industrial and service enterprises. Globally, agriculture has met the demands from this rapidly growing urban population, including food that is more energy-, land-, water- and greenhouse gas emission-intensive. But hundreds of millions of urban dwellers suffer under-nutrition. So the key issues with regard to agriculture and urbanization are whether the growing and changing demands for agricultural products from growing urban populations can be sustained while at the same time underpinning agricultural prosperity and reducing rural and urban poverty. To this are added the need to reduce greenhouse gas emissions and to build resilience in agriculture and urban development to climate change impacts. The paper gives particular attention to low- and middle-income nations since these have more than three-quarters of the world''s urban population and most of its largest cities and these include nations where issues of food security are most pressing.     

Transmission ratio distortion in intraspecific hybrids of Mimulus guttatus: implications for genomic divergence

We constructed a genetic linkage map between two divergent populations of Mimulus guttatus. We genotyped an F(2) mapping population (N = 539) at 154 AFLP, microsatellite, and gene-based markers. A framework map was constructed consisting of 112 marker loci on 14 linkage groups with a total map length of 1518 cM Kosambi. Nearly half of all markers (48%) exhibited significant transmission ratio distortion (alpha = 0.05). By using a Bayesian multipoint mapping method and visual inspection of significantly distorted markers, we detected 12 transmission ratio distorting loci (TRDL) throughout the genome. The high degree of segregation distortion detected in this intraspecific map indicates substantial genomic divergence that perhaps suggests genomic incompatibilities between these two populations. We compare the pattern of transmission ratio distortion in this map to an interspecific map constructed between M. guttatus and M. nasutus. A similar level of segregation distortion is detected in both maps. Collinear regions between maps are compared to determine if there are shared genetic patterns of non-Mendelian segregation distortion within and among Mimulus species.     

Genetic divergence and migration patterns in a North American passerine bird: implications for evolution and conservation

Like many other migratory birds, the black-throated blue warbler (Dendroica caerulescens) shows pronounced differences in migratory behaviour and other traits between populations: birds in the southern part of the breeding range have darker plumage and migrate to the eastern Caribbean during the winter, whereas those in the north have lighter plumage and migrate to the western Caribbean. We examined the phylogeography of this species, using samples collected from northern and southern populations, to determine whether differentiation between these populations dates to the Pleistocene or earlier, or whether differences in plumage and migratory behaviour have arisen more recently. We analysed variation at 369 bp of the mitochondrial control region domain I and also at seven nuclear microsatellites. Analyses revealed considerable genetic variation, but the vast majority of this variation was found within rather than between populations, and there was little differentiation between northern and southern populations. Phylogeographic analyses revealed a very shallow phylogenetic tree, a star-like haplotype network, and a unimodal mismatch distribution, all indicative of a recent range expansion from a single refugium. Coalescent modelling approaches also indicated a recent common ancestor for the entire group of birds analysed, no split between northern and southern populations, and high levels of gene flow. These results show that Pleistocene or earlier events have played little role in creating differences between northern and southern populations, suggesting that migratory and other differences between populations have arisen very recently. The implications of these results for the evolution of migration and defining taxonomic groups for conservation efforts are discussed.     

Cytoplasmic inheritance and its implications for animal biotechnology

At fertilization, the mammalian sperm transmits the haploid paternal genome. However, it also carries a variety of other factors into the oocyte that have the potential to affect embryo development. These include mRNAs left over from spermatogenesis, mitochondria with their own DNA, cytoskeletal and contractile elements, remnants of the sperm plasma membrane and, in many species, the sperm centriole. While most of these elements are eliminated, some play essential roles in early embryogenesis. In this review, I summarize the latest information on these phenomena and indicate some of the implications for animal biotechnology and, in particular, cloning.     

Cell competition and its implications for development and cancer

Cell competition is a struggle for existence between cells in heterogeneous tissues of multicellular organisms.Loser cells,which die during cell competition,are normally viable when grown only with other loser cells,but when mixed with winner cells,they are at a growth disadvantage and undergo apoptosis.Intriguingly,several recent studies have revealed that cells bearing mutant tumor-suppressor genes,which show overgrowth and tumorigenesis in a homotypic situation,are frequently eliminated,through cell competition,from tissues in which they are surrounded by wild-type cells.Here,we focus on the regulation of cellular competitiveness and the mechanism of cell competition as inferred from two different categories of mutant cells:(1) slower-growing cells and (2) structurally defective cells.We also discuss the possible role of cell competition as an intrinsic homeostasis system through which normal cells sense and remove aberrant cells,such as precancerous cells,to maintain the integrity and normal development of tissues and organs.     

Late divergence of survival curves in cancer immunotherapy trials: interpretation and implications

Late divergence of survival curves of treated patients and controls is commonly seen in successful cancer immunotherapy trials. Although late survival curve divergence may be caused by a delayed action of therapy, it may also be related to early effects of the treatment. We suggest that late survival divergence most often reflects a specific benefit of therapy for patients who suffer from a comparatively slow progression of disease. The occurrence of delayed survival curve divergence has important implications for the statistical analysis of immunotherapy trials. Thus, it leads to non-proportional hazard ratios that make commonly used statistical tests, e.g., the logrank test, suboptimal. It is therefore suggested that the statistical analysis of immunotherapy trials primarily should be based on a test that compares the survival curves at or after a prespecified, fixed, late time point.     

Cell competition and its implications for development and cancer

Cell competition is a struggle for existence between cells in heterogeneous tissues of multicellular organisms.Loser cells,which die during cell competition,are normally viable when grown only with other loser cells,but when mixed with winner cells,they are at a growth disadvantage and undergo apoptosis.Intriguingly,several recent studies have revealed that cells bearing mutant tumor-suppressor genes,which show overgrowth and tumorigenesis in a homotypic situation,are frequently eliminated,through cell competition,from tissues in which they are surrounded by wild-type cells.Here,we focus on the regulation of cellular competitiveness and the mechanism of cell competition as inferred from two different categories of mutant cells:(1) slower-growing cells and (2) structurally defective cells.We also discuss the possible role of cell competition as an intrinsic homeostasis system through which normal cells sense and remove aberrant cells,such as precancerous cells,to maintain the integrity and normal development of tissues and organs.     

Phytoferritin and its implications for human health and nutrition

Background

Plant and animal ferritins stem from a common ancestor, but plant ferritins exhibit various features that are different from those of animal ferritins. Phytoferritin is observed in plastids (e.g., chloroplasts in leaves, amyloplasts in tubers and seeds), whereas animal ferritin is largely found in the cytoplasm. The main difference in structure between plant and animal ferritins is the two specific domains (TP and EP) at the N-terminal sequence of phytoferritin, which endow phytoferritin with specific iron chemistry. As a member of the nonheme iron group of dietary iron sources, phytoferritin consists of 24 subunits that assemble into a spherical shell storing up to ∼ 2000 Fe^3 + in the form of an iron oxyhydroxide-phosphate mineral. This feature is distinct from small molecule nonheme iron existing in cereals, which has poor bioavailability.

Scope of review

This review focuses on the relationship between structure and function of phytoferritin and the recent progress in the use of phytoferritin as iron supplement.

Major conclusions

Phytoferritin, especially from legume seeds, represents a novel alternative dietary iron source.

General significance

An understanding of the chemistry and biology of phytoferritin, its interaction with iron, and its stability against gastric digestion is beneficial to design diets that will be used for treatment of global iron deficiency.     

Aberrant auditory system and its developmental implications for autism

Most infants who are later diagnosed with autism show delayed speech and language and/or atypical language profile. There is a large body of research on abnormal speech and language in children with autism. However, auditory development has been relatively under-investigated in autism research, despite its inextricable relationship with language development and despite researchers' ability to detect abnormalities in brain development and behavior in early infancy. In this review, we synthesize research on auditory processing in the prenatal period through infancy and childhood in typically developing children, children at high risk for autism, and children diagnosed with autism. We conclude that there are clear neurobiological and behavioral links between abnormal auditory development and the deficits in social communication seen in autism. We then offer perspectives on the need for a systematic characterization of early auditory development in autism, and identified questions to be addressed in future research on the development of autism.     

Dimerization of TCTP and its clinical implications for allergy

Following the detection of histamine-releasing activity (HRA) in the supernatants of peripheral blood mononuclear cell cultures, research efforts were directed at characterizing the source of this activity, mostly focusing, on IgE-dependent histamine-releasing factors (HRFs). HRF is now variously called translationally controlled tumor protein (TCTP), p21, p23, and fortilin. TCTP exhibits cytokine-like functions including release of histamine, induction of TH₂ cytokines and chemoattractants, augmentation of B cell proliferation, and immunoglobulin production during late phase allergic inflammation. Because of its association with the allergic status of patients, TCTP emerged as a potential key agent in the modulation of allergic diseases. Several lines of evidence suggest that TCTP exhibits its cytokine-like functions only after it is modified by the proteases, altered oxidant–antioxidant balance and immunoglobulin E, present in the inflamed sites. This review will try to show that dimerization is the critical modification of TCTP if not the only modification, responsible for its cytokine-like activity causing allergic diseases.