Preservation of duplicate genes by complementary, degenerative mutations

The origin of organismal complexity is generally thought to be tightly coupled to the evolution of new gene functions arising subsequent to gene duplication. Under the classical model for the evolution of duplicate genes, one member of the duplicated pair usually degenerates within a few million years by accumulating deleterious mutations, while the other duplicate retains the original function. This model further predicts that on rare occasions, one duplicate may acquire a new adaptive function, resulting in the preservation of both members of the pair, one with the new function and the other retaining the old. However, empirical data suggest that a much greater proportion of gene duplicates is preserved than predicted by the classical model. Here we present a new conceptual framework for understanding the evolution of duplicate genes that may help explain this conundrum. Focusing on the regulatory complexity of eukaryotic genes, we show how complementary degenerative mutations in different regulatory elements of duplicated genes can facilitate the preservation of both duplicates, thereby increasing long-term opportunities for the evolution of new gene functions. The duplication-degeneration-complementation (DDC) model predicts that (1) degenerative mutations in regulatory elements can increase rather than reduce the probability of duplicate gene preservation and (2) the usual mechanism of duplicate gene preservation is the partitioning of ancestral functions rather than the evolution of new functions. We present several examples (including analysis of a new engrailed gene in zebrafish) that appear to be consistent with the DDC model, and we suggest several analytical and experimental approaches for determining whether the complementary loss of gene subfunctions or the acquisition of novel functions are likely to be the primary mechanisms for the preservation of gene duplicates. For a newly duplicated paralog, survival depends on the outcome of the race between entropic decay and chance acquisition of an advantageous regulatory mutation. Sidow 1996(p. 717) On one hand, it may fix an advantageous allele giving it a slightly different, and selectable, function from its original copy. This initial fixation provides substantial protection against future fixation of null mutations, allowing additional mutations to accumulate that refine functional differentiation. Alternatively, a duplicate locus can instead first fix a null allele, becoming a pseudogene. Walsh 1995 (p. 426) Duplicated genes persist only if mutations create new and essential protein functions, an event that is predicted to occur rarely. Nadeau and Sankoff 1997 (p. 1259) Thus overall, with complex metazoans, the major mechanism for retention of ancient gene duplicates would appear to have been the acquisition of novel expression sites for developmental genes, with its accompanying opportunity for new gene roles underlying the progressive extension of development itself. Cooke et al. 1997 (p. 362)

Zebrafish hox clusters and vertebrate genome evolution

HOX genes specify cell fate in the anterior-posterior axis of animal embryos. Invertebrate chordates have one HOX cluster, but mammals have four, suggesting that cluster duplication facilitated the evolution of vertebrate body plans. This report shows that zebrafish have seven hox clusters. Phylogenetic analysis and genetic mapping suggest a chromosome doubling event, probably by whole genome duplication, after the divergence of ray-finned and lobe-finned fishes but before the teleost radiation. Thus, teleosts, the most species-rich group of vertebrates, appear to have more copies of these developmental regulatory genes than do mammals, despite less complexity in the anterior-posterior axis.

Vertebrate genome evolution and the zebrafish gene map

In chordate phylogeny, changes in the nervous system, jaws, and appendages transformed meek filter feeders into fearsome predators. Gene duplication is thought to promote such innovation. Vertebrate ancestors probably had single copies of genes now found in multiple copies in vertebrates and gene maps suggest that this occurred by polyploidization. It has been suggested that one genome duplication event occurred before, and one after the divergence of ray-finned and lobe-finned fishes. Holland et al., however, have argued that because various vertebrates have several HOX clusters, two rounds of duplication occurred before the origin of jawed fishes. Such gene-number data, however, do not distinguish between tandem duplications and polyploidization events, nor whether independent duplications occurred in different lineages. To investigate these matters, we mapped 144 zebrafish genes and compared the resulting map with mammalian maps. Comparison revealed large conserved chromosome segments. Because duplicated chromosome segments in zebrafish often correspond with specific chromosome segments in mammals, it is likely that two polyploidization events occurred prior to the divergence of fish and mammal lineages. This zebrafish gene map will facilitate molecular identification of mutated zebrafish genes, which can suggest functions for human genes known only by sequence.

The cloche and spadetail genes differentially affect hematopoiesis and vasculogenesis

In vertebrates, hematopoietic and vascular progenitors develop from ventral mesoderm. The first primitive wave of hematopoiesis yields embryonic red blood cells, whereas progenitor cells of subsequent definitive waves form all hematopoietic cell lineages. In this report we examine the development of hematopoietic and vasculogenic cells in normal zebrafish and characterize defects in cloche and spadetail mutant embryos. The zebrafish homologs of lmo2, c-myb, fli1, flk1, and flt4 have been cloned and characterized in this study. Expression of these genes identifies embryonic regions that contain hematopoietic and vascular progenitor cells. The expression of c-myb also identifies definitive hematopoietic cells in the ventral wall of the dorsal aorta. Analysis of b316 mutant embryos that carry a deletion of the c-myb gene demonstrates that c-myb is not required for primitive erythropoiesis in zebrafish even though it is expressed in these cells. Both cloche and spadetail mutant embryos have defects in primitive hematopoiesis and definitive hematopoiesis. The cloche mutants also have significant decreases in vascular gene expression, whereas spadetail mutants expressed normal levels of these genes. These studies demonstrate that the molecular mechanisms that regulate hematopoiesis and vasculogenesis have been conserved throughout vertebrate evolution and the clo and spt genes are key regulators of these programs.

The zebrafish glypican knypek controls cell polarity during gastrulation movements of convergent extension

Mutations in the zebrafish knypek locus impair gastrulation movements of convergent extension that narrow embryonic body and elongate it from head to tail. We demonstrate that knypek regulates cellular movements but not cell fate specification. Convergent extension movement defects in knypek are associated with abnormal cell polarity, as mutant cells fail to elongate and align medio-laterally. Positional cloning reveals that knypek encodes a member of the glypican family of heparan sulfate proteoglycans. Double mutant and overexpression analyses show that Knypek potentiates Wnt11 signaling, mediating convergent extension. These studies provide experimental and genetic evidence that glypican Knypek acts during vertebrate gastrulation as a positive modulator of noncanonical Wnt signaling to establish polarized cell behaviors underlying convergent extension movements.

Zebrafishsmoothenedfunctions in ventral neural tube specification and axon tract formation

Sonic hedgehog (Shh) signaling patterns many vertebrate tissues. shh mutations dramatically affect mouse ventral forebrain and floor plate but produce minor defects in zebrafish. Zebrafish have two mammalian Shh orthologs, sonic hedgehog and tiggy-winkle hedgehog, and another gene, echidna hedgehog, that could have overlapping functions. To examine the role of Hedgehog signaling in zebrafish, we have characterized slow muscle omitted (smu) mutants. We show that smu encodes a zebrafish ortholog of Smoothened that transduces Hedgehog signals. Zebrafish smoothened is expressed maternally and zygotically and supports specification of motoneurons, pituitary cells and ventral forebrain. We propose that smoothened is required for induction of lateral floor plate and a subpopulation of hypothalamic cells and for maintenance of medial floor plate and hypothalamic cells.

Molecular characterization of the zebrafish PEA3 ETS-domain transcription factor

The PEA3 subfamily of ETS-domain proteins play important roles in regulating transcriptional activation and have been implicated in several tumorigenic processes. Here we describe the identification of a further member of this family from zebrafish which most likely represents a homologue of PEA3. A high degree of sequence conservation is observed in the ETS DNA-binding domain and acidic transcriptional activation domain. The DNA binding specificity of zebrafish PEA3 is virtually identical to that exhibited by mammalian family members and is autoregulated by cisacting inhibitory domains. Transcriptional activation by zebrafish PEA3 is potentiated by the ERK MAP kinase and protein kinase A pathways. During embryogenesis, PEA3 is expressed in complex spatial and temporal patterns in both mesodermal somites and ectodermal tissues including the brain, dorsal spinal chord and neural crest. Our characterisation of zebrafish PEA3 furthers our understanding of its molecular function and its expression profile suggests a novel role in cell patterning in the early vertebrate embryo.

Chromosome complement, C-banding, Ag-NOR and replication banding in the zebrafish Danio rerio

The chromosome complement of Danio rerio was investigated by Giemsa staining and C-banding, Ag-NORs and replication banding. The diploid number of this species is 2n = 50 and the arm number (NF) = 100. Constitutive heterochromatin was located at the centromeric position of all chromosome pairs. Nucleolus organizer regions appeared in the terminal position of the long arms of chromosomes 1, 2 and 8. Replication banding pattern allowed the identification of each chromosome pair.

Assignment of zebrafish genetic linkage groups to chromosomes

In this report the zebrafish genetic linkage groups are assigned to specific chromosomes using fluorescence in situ hybridization (FISH) with BAC probes containing genes mapped to each linkage group (LG). Chromosomes were identified using a combination of relative size and arm ratios. The largest genetic maps generally corresponded to the largest chromosomes, but genetic recombination tended to be elevated in the smaller chromosomes and near telomeres. Large insert clones containing genes near telomeres often hybridized to telomeres of multiple chromosome pairs, suggesting the presence of shared subtelomeric repetitive DNAs near telomeres. Evidence from comparative gene mapping in medaka, zebrafish, pufferfish, and humans suggests that the linkage groups of these species have the content of duplicate proto-chromosomes. However, these duplicate linkage groups are not associated with chromosomes of similar size or morphology. This suggests that considerable chromosome restructuring occurred subsequent to the genome duplication in teleosts.

Effects of short read quality and quantity on a de novo vertebrate transcriptome assembly

For many researchers, next generation sequencing data holds the key to answering a category of questions previously unassailable. One of the important and challenging steps in achieving these goals is accurately assembling the massive quantity of short sequencing reads into full nucleic acid sequences. For research groups working with non-model or wild systems, short read assembly can pose a significant challenge due to the lack of pre-existing EST or genome reference libraries. While many publications describe the overall process of sequencing and assembly, few address the topic of how many and what types of reads are best for assembly. The goal of this project was use real world data to explore the effects of read quantity and short read quality scores on the resulting de novo assemblies. Using several samples of short reads of various sizes and qualities we produced many assemblies in an automated manner. We observe how the properties of read length, read quality, and read quantity affect the resulting assemblies and provide some general recommendations based on our real-world data set.

Cell-mediated immune response and cytokine production in idiopathic senile anorexia

Some aspects of humoral and cell-mediated immunity and the capacity of peripheral blood mononuclear cells (PBMCs) of fourteen elderly persons with idiopathic anorexia to produce several cytokines, such as tumor necrosis factor alpha (TNF alpha), interleukin-1 beta (IL-1 beta), interleukin-6 and interferon-gamma (IFN gamma), were studied and the results were compared with those obtained in a control group of ten age-matched, normal weight healthy subjects. In addition, spontaneous and induced production of these cytokines was also measured in cultures of PBMCs of fourteen healthy young individuals as a control group of age. A significant decrease in CD2 (pan T-cells) and CD4 (T-helper) lymphocyte subpopulations, but unchanged CD8 (T-suppressor) subset, and a reduced response in delayed cutaneous hypersensitivity tests were observed in senile underweight anorectic patients. Monocyte counts did not show significant differences between patients and control subjects. The spontaneous release by PBMCs of all the cytokines measured did not differ between the anorectic and either the elderly or young control group. A significant increase in IL-6 production after mitogen stimulation with tetradecanoylphorbol acetate (TPA) and phytohemagglutinin (PHA) after 24 and 48 h of culture, as well as a greater induced TNF alpha production after 48 h of incubation with the same mitogens, was found in the anorectic patients as compared with the elderly controls. However, stimulated production of both IL-1 beta with TPA and of IFN gamma with PHA did not differ significantly between anorectics and aged controls.(ABSTRACT TRUNCATED AT 250 WORDS)

Karyotype, C-banding, and Ag-NOR analysis in Diplodus bellottii (Sparidae, Perciforms). Intra-individual polymorphism involving heterochromatic regions

A karyotype analysis was carried out in nine specimens of the Sparid species Diplodus bellottii using conventional staining, as well as C-banding and Ag-NOR banding techniques, showing, respectively, 2n = 46 and fundamental number (FN) = 54, and scarce heterochromatic areas irregularly distributed and up to four NOR active regions that were C positive. When compared with the karyotypes of other related species, one centric fusion giving rise to a large metacentric pair and several pericentric inversions seem to have been involved in the karyotype evolution. An intra-individual polymorphism was detected in one specimen, resulting in two karyotypic forms in roughly identical proportion, owing to a larger C-band by the NOR regions, appearing either in a terminal position of the short arms of pair 2 or in telomeric position of pair 3. These findings suggest that the extra heterochromatic segment responsible for the heteromorphism apparently only involves associated heterochromatin and not the NORs themselves. This C-positive block seems to have eventually been transferred between heterologous NOR chromosomes by a somatic event, facilitated by the physical proximity of NOR pairs in the nucleolus.Key words: Sparidae, karyotype, heterochromatin, nucleolus organizers, chromosome polymorphism.

Brdu replication bands in the anguilliform fish Echelus myrus

High-resolution replication banding patterns have been obtained in prometaphase and metaphase chromosomes of the anguilliform fish species Echelus myrus by treating kidney cell cultures with 5-bromodeoxyuridine during the mid-late synthesis phase. The results show the superiority of the in vitro technique in obtaining a higher number of bands which permit an accurate identification of all chromosome pairs. Different replication patterns were compared with C-bands and silver-stained nucleolus organizer regions, providing information on the replication order of different chromatin regions.

A tandem fusion in the fish Gobius paganellus (Gobiidae, Perciformes), a karyotypically polymorphic species

In 1 of 384 cytologically analyzed specimens of the polymorphic fish Gobius paganellus a new type of chromosome was observed. On the basis of the conventional and C-banding analysis, centromeric–telomeric fusion, involving the heterochromatin, of two different acrocentrics is suggested to be responsible for the observation.Key words: Gobiidae, tandem fusion, heterochromatin.

Generation of a P1 artificial chromosome library of the Southern pufferfish

We describe the generation of a P1 artificial chromosome genomic library from the Southern pufferfish, Spheroides nephelus. The arrayed library consists of approximately 30,000 clones and has an average insert size of 125-150 kb. The coverage is estimated to encompass seven to eight genome equivalents. The library has been used for isolating numerous genomic clones and for establishing contigs of several multigene families. Analysis of several of the clones from this library suggests a preponderance of CA repeat tracts relative to their abundance in humans. The library and high-density filters have been made available to the scientific public through genomics distribution companies.

GH gene expression in the submaxillary gland in normal and Ames dwarf mice

High local GH-releasing hormone (GHRH) levels are capable of inducing transdifferentiation in salivary cells to synthesize GH. However, the factors implicated in this process remain unknown. To study this subject, normal and Ames dwarf mice were implanted in the submaxillary gland with a slow release pellet releasing 21 microgram GHRH (1-29)-NH(2)/day for 2 months. Control animals received placebo pellets at the same site. After 60 days, heart blood was collected and submaxillary glands were removed. Circulating levels of GH and IGF-I were significantly decreased (P<0.05) in dwarf mice in comparison with controls, and GHRH treatment did not modify either of these two parameters. Controls carrying GHRH pellets showed a significantly higher GH content (P<0.05) in the submaxillary gland than the placebo-treated normal mice. There were no differences between the IGF-I concentrations of placebo- and GHRH-treated salivary tissue from normal mice. Analysis of GH mRNA by RT-PCR followed by Southern blot revealed that GH transcripts were present in the salivary gland samples carrying the placebo pellets in both normal and dwarf mice. The expression of GH was significantly (P<0.05) increased by the GHRH pellets in salivary tissue from normal mice, but not in submaxillary glands from dwarf mice. Pit-1 mRNA was not detected in the GHRH-treated glands of normal and dwarf mice by RT-PCR or by Southern blot. Using these highly sensitive methods, we have been able to detect the transcription of both GH and Pit-1 in pituitaries from Pit-1-deficient Ames dwarf mice. The present experiment demonstrates that salivary tissue synthesizes GH when it is exposed to the influence of GHRH. Both basal and GHRH-induced salivary GH expression appear to be independent of Pit-1.

Physical activity and recreational screen time change among adolescents in Canada: Examining the impact of COVID-19 in worsening inequity

The purpose of this study was to assess if sub-populations of adolescents in Canada (i.e., race/ethnicity, sex/gender, and socioeconomic status [SES]) experienced a larger change in physical activity and screen time between the 2019-2020 (pre-pandemic) and the 2020-2021 (mid-pandemic) school years. Longitudinally linked data from pre-pandemic and mid-pandemic school years of a prospective cohort study of secondary school students in Canada (n = 8209) were used for these analyses. Multivariable regression modelling tested the main effects of race/ethnicity, sex/gender, and SES on changes in moderate-to-vigorous physical activity (MVPA) and screen time duration as well as adherence to Canada's 24-h Movement Guidelines. Overall between groups difference were assessed using type II analysis of deviance tests. Interactions between variables of interest were subsequently tested with a series of regression models compared to the main effects model using likelihood-ratio test. Post-hoc comparisons found Male participants' MVPA time decreased less compared to their female counterparts (M [95% CI] = -16.3 [-13.5, -19.2] min/day), but also reported greater increases in screen time compared to females (23.7 [14.7, 32.8] min/day) during the same period. MVPA in White participants decreased less than Asian participants (-10.7 [-19.5, -1.9] min/day) with a similar non-significant pattern observed in Black and Latin participants. Adolescents in higher SES categories fared better on adherence to MVPA (highest vs. lowest OR = 1.41 [0.97, 2.06]) and screen time recommendations(highest vs. lowest AOR = 3.13 [0.91, 11.11]). Results support the hypothesis that existing inequitable sociodemographic differences in MVPA participation and screen time have worsened throughout the pandemic.

Changes in breakfast and water consumption among adolescents in Canada: examining the impact of COVID-19 in worsening inequity

BACKGROUND

To assess whether changes in breakfast and water consumption during the first full school year after the emergence of the COVID-19 pandemic varied based on sex/gender, race/ethnicity, and socioeconomic status among Canadian adolescents.

METHODS

Prospective annual survey data collected pre- (October 2019-March 2020) and post-COVID-19 onset (November 2020-June 2021) the Cannabis, Obesity, Mental health, Physical activity, Alcohol, Smoking, and Sedentary behaviour (COMPASS) study. The sample consisted of 8,128 students; mean (SD) age = 14.2 (1.3) years from a convenience sample of 41 Canadian secondary schools. At both timepoints self-reported breakfast and water consumption were dichotomized as daily or not. Multivariable logistic generalized estimating equations with school clustering were used to estimate differences in maintenance/adoption of daily consumption post-COVID-19 based on demographic factors, while controlling for pre-COVID-19 behaviour.

RESULTS

Adjusted odds ratios (AOR) with 95% confidence intervals are reported. Females (AOR = 0.71 [0.63, 0.79]) and lower socioeconomic status individuals (AORLowest:Highest=0.41 [0.16, 1.00]) were less likely to maintain/adopt daily breakfast consumption than male and higher socioeconomic status peers in the 2020-2021 school year. Black identifying individuals were less likely than all other racial/ethnic identities to maintain/adopt plain water consumption every day of the week (AOR = 0.33 [0.15, 0.75], p < 0.001). No significant interaction effects were detected.

CONCLUSIONS

Results support the hypothesis that changes in nutritional behaviours were not equal across demographic groups. Female, lower socioeconomic status, and Black adolescents reported greater declines in healthy nutritional behaviours. Public health interventions to improve adherence to daily breakfast and water consumption should target these segments of the population.

TRIAL REGISTRATION

Not a trial.

Inequities in dietary intake and eating behaviours among adolescents in Canada

OBJECTIVE

To provide contemporary evidence of how dietary intake and eating behaviours vary by social positions among adolescents.

METHODS

We used survey data collected during the 2020-2021 school year from 52,138 students attending 133 secondary schools in Alberta, British Columbia, Ontario, and Quebec, Canada. Multiple regression models tested whether self-reported indicators of dietary intake and eating behaviours differed by gender, race/ethnicity, and socioeconomic status (SES).

RESULTS

Females were more likely than males to skip breakfast, restrict eating, and consume fruit, vegetables, and fast food on more days. Gender-diverse/"prefer not to say" students were more likely to restrict eating than males and the least likely to consume breakfast and drink water daily, and fruits and vegetables regularly. Black and Latin American students were more likely to restrict eating and consume purchased snacks and fast food, and less likely to drink water daily than white and Asian adolescents. Daily breakfast consumption was most likely among Latin American students. Black students were the least likely to report eating breakfast daily and fruits and vegetables regularly. Lower SES was associated with lower odds of eating breakfast and drinking water daily and regular fruit and vegetable consumption, and higher odds of restrictive eating and purchased snack consumption. Fast food consumption had a u-shaped association with SES.

CONCLUSION

Results emphasize gender, racial/ethnic, and socioeconomic inequities in the diets and eating behaviours of adolescents. There is a critical need to address the structural factors contributing to inequities and prevent the consequences of dietary disparities.

The impact of 12 modifiable lifestyle behaviours on depressive and anxiety symptoms in middle adolescence: prospective analyses of the Canadian longitudinal COMPASS study

BACKGROUND

Unhealthy lifestyle behaviours are becoming increasingly common and might contribute to the growing burden of mental disorders in adolescence. We examined the associations between a comprehensive set of lifestyle behaviours and depression and anxiety in middle adolescents.

METHODS

School-based survey responses were collected from 24,274 Canadian high school students at baseline and 1-year follow-up (average age 14.8 and 15.8 years, respectively). Using linear mixed-effects models, we examined prospective associations of adherence to recommendations for vegetables and fruit, grains, milk and alternatives, meat and alternatives, sugar-sweetened beverages [SSB], physical activity, screen time, sleep, and no use of tobacco, e-cigarettes, cannabis, and binge drinking at baseline with the depressive and anxiety symptoms (measured by CESD-R-10 and GAD-7 scales, respectively) at follow-up.

RESULTS

Adherence to recommendations was low overall, particularly for vegetables and fruit (3.9%), grains (4.5%), and screen time (4.9%). Students adhering to individual recommendations, particularly for meat and alternatives, SSB, screen time, sleep, and no cannabis use, at baseline had lower CESD-R-10 and GAD-7 scores at follow-up. Adhering to every additional recommendation was associated with lower CESD-R-10 (β=-0.15, 95% CI -0.18, -0.11) and GAD-7 scores (β=-0.10, 95% CI -0.14, -0.07) at follow-up. Assuming cumulative impact, this might translate into 7.2- and 4.8-point lower CESD-R-10 and GAD-7 scores, respectively, among students adhering to 12 vs. 0 recommendations over four years of high school.

CONCLUSIONS

The results highlight the preventive potential of population-based approaches promoting healthy lifestyle behaviours, particularly those with the lowest prevalence, as a strategy to improve mental health in adolescence.

[Dysphagia as a symptom of diffuse idiopathic skeletal hyperostosis (Forestier-Rotes disease). A case report and literature review]

Swallowing disorders can be caused by cervical spine diseases, such as diffuse skeletal hyperostosis (DISH). This entity is diagnosed as a cause of dysphagia only after excluding all other possible causes. We report a case in which dysphagia was the initial symptom of DISH. The most important clinical and diagnostic aspects of the disease are discussed.

Youth perception of difficulty accessing cannabis following cannabis legalization and during the early and ongoing stages of the COVID-19 pandemic: repeat cross-sectional and longitudinal data from the COMPASS study

BACKGROUND

Very little research has examined how perceptions of cannabis access among underage youth in Canada have changed since cannabis was legalized and since the onset of the COVID-19 pandemic. As such, this paper examines the effect of the early and ongoing stages of the COVID-19 pandemic period on youth perceptions of cannabis access over time since the onset of the Cannabis Act in 2018 in a large sample of Canadian youth.

METHODS

Using data from the COMPASS study (T1:2018/19, T2:2019/20, T3:2020/21), we used both repeat cross-sectional data [T1 (n = 38,890), T2 (n = 24,109), and T3 (n = 22,795)] to examine overall trends in perceptions of cannabis access, and sequential cohort longitudinal data [n = 4,677 students linked from T1 to T3] to examine the differential changes in perceptions of cannabis access among students over time.

RESULTS

In the cross-sectional sample, the frequency of students reporting that cannabis was easy to access decreased by 26.7% from T1 (51.0%) to T3 (37.4%), although respondents who have used cannabis were more likely to report access was easy. In the longitudinal sample, perceptions of cannabis access being easy increased over time, especially among cannabis users. Perceived ease of access appears to have been slightly impeded during the initial pandemic period but rebounded during the ongoing pandemic period.

CONCLUSIONS

While the prevalence of youth reporting that cannabis is easy to access has declined since legalization and throughout the early and ongoing pandemic periods, a substantial number of underage youth continue to report that cannabis is easy to access. This suggest that there is an ongoing need for continued cannabis control efforts to address this issue.