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PubMed2003

Formation of stable epialleles and their paramutation-like interaction in tetraploid Arabidopsis thaliana.

Polyploidization is found frequently in plants, and species previously considered to be diploid may show remnants of earlier polyploidization events on closer inspection of their genomes. The success of polyploids may lie in increased genetic redundancy supporting subsequent genetic diversification. Although doubling the genome does not generate diversity per se, recent studies show that rapid genomic rearrangements and changes in DNA modification and gene expression patterns are associated with polyploid formation. But recessive modifications will not become phenotypically apparent in early polyploid generations. Here we show that epialleles in tetraploid plants (but not in diploids) interact in trans and lead to heritable gene silencing persisting after segregation from the inactivating allele. This mechanism, resembling paramutation, leads to the establishment of functional epigenetic homozygosity and, thus, to conversion of new recessive alleles into traits expressed in early polyploid generations. Such interactions probably contribute to rapid adaptation and evolution of polyploid plant species.

Alleles↗

PubMed2002

The genetics and evo-devo of butterfly wing patterns.

Understanding how the spectacular diversity of colour patterns on butterfly wings is shaped by natural selection, and how particular pattern elements are generated, has been the focus of both evolutionary and developmental biologists. The growing field of evolutionary developmental biology has now begun to provide a link between genetic variation and the phenotypes that are produced by developmental processes and that are sorted by natural selection. Butterfly wing patterns are set to become one of the few examples of morphological diversity to be studied successfully at many levels of biological organization, and thus to yield a more complete picture of adaptive morphological evolution.

Animals↗

PubMed2025

The chromosome-level genome assembly and annotation of the silver-lipped pearl oyster, Pinctada maxima.

The silver-lipped pearl oyster (Pinctada maxima) is a valuable tropical aquaculture species, playing a crucial economic role in the global pearl industry. However, the lack of genomic reference limits our in-depth understanding of this species in genome-based breeding, conservation, evolution and adaptation. Here, annotated chromosome-level reference genome for P. maxima was generated by integrating PacBio long-read sequencing, Illumina short-read sequencing, and Hi-C sequencing data. The total genome size is 1,264.93 Mb, with contig N50 and scaffold N50 of 649 kb and 89.19 Mb, respectively. The majority (97.94%) of the assembled genome was anchored to the 14 chromosomes by Hi-C analysis. The relatively high genome completeness was observed, with 97.38% (metazoa_odb10 database) and 95.26% (mollusca_odb10 database) in BUSCO analysis. Genome annotation revealed approximately 65.46% of the repeat sequences and 26,315 protein-coding genes. Comparative genome analysis revealed 28 expanded and 48 contracted families (p < 0.05) in P. maxima, with 3.2% of genes (894) being species-specific. This chromosome-level genome serves as an essential resource for research in evolutionary genomics, phylogenetics, and biomineralization.

Animals↗

PubMed2000

The molecular population genetics of regulatory genes.

Regulatory loci, which may encode both trans acting proteins as well as cis acting promoter regions, are crucial components of an organism's genetic architecture. Although evolution of these regulatory loci is believed to underlie the evolution of numerous adaptive traits, there is little information on natural variation of these genes. Recent molecular population genetic studies, however, have provided insights into the extent of natural variation at regulatory genes, the evolutionary forces that shape them and the phenotypic effects of molecular regulatory variants. These recent analyses suggest that it may be possible to study the molecular evolutionary ecology of regulatory diversification by examining both the extent and patterning of regulatory gene diversity, the phenotypic effects of molecular variation at these loci and their ecological consequences.

Adaptation, Physiological↗

PubMed2002

Phylogeography of endemic ermine (Mustela erminea) in southeast Alaska.

The North Pacific Coast (NPC) of North America is a region of high mammalian endemism, possibly due to its highly fragmented landscape and complex glacial history. For example, four island and one mainland subspecies of ermine, Mustela erminea, have been described as endemic to southeast Alaska alone. To better understand the role of past climatic change in generating diversity in the region, we examined DNA sequence variation in the mitochondrial cytochrome b gene of 210 ermine from across North America, with an emphasis on Alaska and British Columbia. We found three distinct (1.5-3.6% uncorrected 'p') lineages of ermine, all of which occur in southeast Alaska. One lineage includes a southeast Alaska endemic and specimens from Alaska (outside of southeast) and Eurasia. A second lineage includes two southeast Alaskan endemics and ermine from western Canada and the coterminous United States. The close relationships of these purported endemics to ermine outside of southeast Alaska suggest that they colonized the region from Beringian and southern glacial refugia, respectively, following deglaciation of the NPC. The third lineage appears restricted to the Prince of Wales Island complex in southeast Alaska (two subspecies) and Graham Island (Haida Gwaii), British Columbia. This restricted distribution suggests that these populations may be derived from relicts that persisted in a coastal refugium during the Wisconsin glaciation. Studies of nuclear genes and adaptive morphological evolution are necessary to further explore discrepancies between the geographical pattern of differentiation based on mtDNA and the existing subspecific taxonomy based on morphology.

Alaska↗

PubMed2004

The role of viral coreceptors and enhanced macrophage tropism in human immunodeficiency virus type 1 disease progression.

Despite numerous studies on the impact of viral diversity, human immunodeficiency virus type 1 (HIV-1)-specific immune responses and host factors on disease progression, we still do not have a firm understanding of the long-term pathogenesis of HIV-1 infection. Rapid depletion of CD4+ T-lymphocytes has been associated with a switch in viral coreceptor usage from CCR5 to CXCR4 in approximately 40 to 50% of infected individuals. However, the majority of infected individuals who progress to AIDS harbour only CCR5-dependent (R5) viral strains. The progression of HIV-1 disease is associated with an enhanced tropism of R5 viral strains for monocyte/macrophage lineage cells (enhanced M-tropism). However, the underlying molecular mechanisms contributing to enhanced M-tropism by R5 HIV-1 strains, and how HIV-1 variants with enhanced M-tropism cause CD4+ T-cell depletion in vivo are unknown. This review examines the relationship between viral coreceptor usage, M-tropism, and pathogenicity of HIV-1. We highlight evidence supporting the hypothesis that enhanced M-tropism of R5 HIV-1 results from adaptive viral evolution, resulting in HIV-1 variants that have increased ability to utilise relatively low levels of CCR5 expressed on macrophages, by way of increased CCR5 affinity. The evidence also suggests that these late-emerging, R5 viral strains have reduced sensitivity to entry inhibitors, and increased ability to cause CD4+ T-lymphocyte loss. These variants are likely to impact HIV-1 disease progression, especially in patients who persistently harbour only R5 viral strains.

CD4-Positive T-Lymphocytes↗

PubMed2005

Sulfide binding is mediated by zinc ions discovered in the crystal structure of a hydrothermal vent tubeworm hemoglobin.

Key to the remarkable ability of vestimentiferan tubeworms to thrive in the harsh conditions of hydrothermal vents are hemoglobins that permit the sequestration and delivery of hydrogen sulfide and oxygen to chemoautotrophic bacteria. Here, we demonstrate that zinc ions, not free cysteine residues, bind sulfide in vestimentiferan hemoglobins. The crystal structure of the C1 hemoglobin from the hydrothermal vent tubeworm Riftia pachyptila has been determined to 3.15 A and revealed the unexpected presence of 12 tightly bound Zn(2+) ions near the threefold axes of this D(3) symmetric hollow sphere. Chelation experiments on R. pachyptila whole-coelomic fluid and purified hemoglobins reveal a role for Zn(2+) ions in sulfide binding. Free cysteine residues, previously proposed as sulfide-binding sites in vestimentiferan hemoglobins, are found buried in surprisingly hydrophobic pockets below the surface of the R. pachyptila C1 molecule, suggesting that access of these residues to environmental sulfide is restricted. Attempts to reduce the sulfide-binding capacities of R. pachyptila hemoglobins by addition of a thiol inhibitor were also unsuccessful. These findings challenge the currently accepted paradigm of annelid hemoglobin evolution and adaptation to reducing environments.

Animals↗

PubMed2026

BRCA1-A and LIG4 complexes mediate ecDNA biogenesis and cancer drug resistance.

Extrachromosomal circular DNA (ecDNA) is frequently generated within the nucleus, contributing to genome dynamics and heterogeneity, thereby promoting cancer cell evolution and adaptation. However, the mechanisms underlying ecDNA biogenesis remain poorly understood. Here, using genome-wide CRISPR screening in human cells, we identified the BRCA1-A and the LIG4 complexes as key drivers of ecDNA production. Following DNA segmentation, the upstream BRCA1-A complex protects DNA ends from excessive resection, promoting end-joining for circularization. Conversely, the MRN complex, which mediates end resection and thus antagonizes the BRCA1-A complex, suppresses ecDNA formation. Downstream, LIG4 conservatively mediates ecDNA production by joining the free ends of the DNA fragments. Furthermore, ecDNA from patient tumors harbors junction sites with a LIG4 signature. Notably, disruption of either LIG4 or the BRCA1-A complex in cancer cells impairs ecDNA-mediated adaptation, hindering the development of resistance to both chemotherapy and targeted therapies. Together, our study reveals the roles of the LIG4 and BRCA1-A complexes in ecDNA biogenesis, and uncovers therapeutic targets to block ecDNA-mediated adaptation for cancer treatment.

Humans↗

PubMed2026

Pregnancy diet based on ancestral patterns increases growth in subcortical fetal brain regions.

Evidence on the biological basis for maternal nutrition effects on fetal and newborn neurodevelopment remains limited. This randomized controlled trial in Ecuador tested a maternal dietary pattern-derived from empirical studies of nutrition in human evolution and adapted locally-on offspring growth and brain development. Pregnant women (n = 215) in their first trimester were randomized to: 1) control (n = 104); or 2) Mikhuna ("nourish" in Kichwa) intervention (n = 111). The intervention, from 12 wk gestation to birth, consisted of a weekly food delivery (8 eggs, 500 g fish, and a variety of sustainably sourced fruits and vegetables) and a behavior change communication strategy encouraging diet diversity and limiting highly processed foods. Longitudinal data collection occurred at 12 wk, 21 wk, 35 wk gestation, and 2 wk postpartum, and included ultrasound imaging of fetal bone and brain parameters, maternal dietary intakes, anthropometry, socioeconomic and demographic variables, and other biomarkers. At close of intervention, a significantly higher percentage of women met the minimum dietary diversity threshold in Mikhuna (74.5%) vs. control groups (55.8%) (P = 0.004). Generalized linear regression models showed significant differences in Mikhuna compared to control for: corpus callosum length 0.19 cm (95% CI [0.02, 0.35]), gangliothalamic ovoid height 0.15 cm (95% CI [0.03 to 0.26]), and femur length -0.10 cm (95% CI [-0.19, -0.02]) from 21 wk to 35 wk; and corpus callosum Z 0.56 (95% CI [0.03, 1.09]) and femur length Z -0.21 (95% CI [-0.42, 0.00]) at 35 wk. The Mikhuna intervention increased the growth of subcortical fetal brain structures, which have established roles in motor control, cognition, and signal transmission.

Female↗

PubMed1997

The rational design and construction of a cuboidal iron-sulfur protein.

Rational protein design is an emerging approach for testing general theories of protein chemistry through the creation of new structures and functions. Here we present the first successful introduction by rational design of a [Fe4S4] cuboidal cluster into the hydrophobic core of Escherichia coli thioredoxin, a protein normally devoid of metal centers. Cuboidal [Fe4S4] is one of the stable forms of self-assembled iron-sulfur clusters that are thought to represent some of the earliest evolved biological redox centers. [Fe4S4] clusters have been recruited for use in a variety of proteins whose functions are central to many of the major biochemical processes ranging from simple soluble electron-transfer agents, to membrane-bound components of electron-transfer chains, to electron reservoirs in complex metalloenzymes such as nitrogenase. By situating an [Fe4S4] cluster into a protein environment not previously adapted by evolution we can explore the factors by which their activity is modulated by the protein matrix.

Algorithms↗

PubMed2001

Calcium needs of the elderly to reduce fracture risk.

Contemporary calcium intakes in the industrialized nations are substantially lower than those to which human physiology is adapted by evolution. As a result, compensatory adjustment is required lifelong. This adjustment consists of high levels of parathyroid activity, leading to parathyroid hyperplasia, high circulating levels of 1,25(OH)2D and high bone turnover. The capacity of these compensatory mechanisms to provide sufficient calcium to offset daily losses from the body declines with age; hence, increasingly the body tears down bone to access its calcium. As a result, the calcium requirement for skeletal maintenance is said to rise with age. Supplemented intakes to a total in the range of 32.5-42.5 mmol (1300-1700 mg)/day have been shown to arrest age-related bone loss and to reduce fracture risk in individuals 65 and older and intakes of 60 mmol (2400 mg), to restore the setting of the parathyroid glands to young adult values. Intakes at such levels also minimize the expression of other disorders such as colon cancer, hypertension and obesity, all of which, while multifactorial, have a calcium deficiency component. Milk, mainly because of constructive interactions among its several key nutrients, is probably the most nutritionally and cost effective way of meeting the calcium requirement in the elderly.

Aged↗

PubMed2026

Yeast Strain Development and Process Intensification in High-Gravity Fermentation.

High- and very-high-gravity (HG/VHG) fermentation increases substrate loading and product titers, thereby improving fermenter utilisation and potentially reducing water use and downstream processing requirements. Initially developed for brewing and fuel ethanol production, these approaches are now applied more broadly in food, beverage, and bioproduct manufacturing. This MiniReview summarises operational definitions and industrial drivers of HG/VHG fermentation and examines the associated constraints in rheology, mass and heat transfer, osmotic and ethanol stress, nutrient availability, and oxidative damage. Yeast improvement strategies are reviewed, including adaptive laboratory evolution, mutagenesis, genome shuffling, multiplex genome editing, non-conventional yeasts, and multi-omics-guided selection. Process developments such as no-cook simultaneous liquefaction, saccharification and fermentation (SLSF), enzyme formulation, nutrient management, and in situ product recovery are considered together with applications in alcoholic beverages, organic acids, microbial lipids, and other value-added products. The review also discusses coproduct valorisation and the need to integrate strain development with process design. Current evidence supports HG/VHG fermentation as a useful process-intensification platform, although performance and sustainability depend strongly on feedstock, operating conditions, product requirements, and the basis used to report fermentation outcomes.

circular bioeconomy↗

PubMed2003

Sequence variation of alcohol dehydrogenase (Adh) paralogs in cactophilic Drosophila.

This study focuses on the population genetics of alcohol dehydrogenase (Adh) in cactophilic Drosophila. Drosophila mojavensis and D. arizonae utilize cactus hosts, and each host contains a characteristic mixture of alcohol compounds. In these Drosophila species there are two functional Adh loci, an adult form (Adh-2) and a larval and ovarian form (Adh-1). Overall, the greater level of variation segregating in D. arizonae than in D. mojavensis suggests a larger population size for D. arizonae. There are markedly different patterns of variation between the paralogs across both species. A 16-bp intron haplotype segregates in both species at Adh-2, apparently the product of an ancient gene conversion event between the paralogs, which suggests that there is selection for the maintenance of the intron structure possibly for the maintenance of pre-mRNA structure. We observe a pattern of variation consistent with adaptive protein evolution in the D. mojavensis lineage at Adh-1, suggesting that the cactus host shift that occurred in the divergence of D. mojavensis from D. arizonae had an effect on the evolution of the larval expressed paralog. Contrary to previous work we estimate a recent time for both the divergence of D. mojavensis and D. arizonae (2.4 +/- 0.7 MY) and the age of the gene duplication (3.95 +/- 0.45 MY).

Alcohol Dehydrogenase↗

PubMed1973

Gene conversion and transfer of genetic information within the inverted region of inversion heterozygotes.

Prior studies of recombination which monitor exchange events in exceedingly short intervals (i.e., separable sites within a cistron) reveal that the basic event in recombination involves a non-reciprocal transfer of information, termed conversion. As a logical consequence of the model suggested by the work in Drosophila, the present investigation examined recombination between rosy mutant alleles (ry:3-52.0) in Drosophila melanogaster in a paracentric inversion (In(3R)P(18)) heterozygote, which placed the rosy region approximately at the center of the inverted region. Comparison of the results of this study with experiments carried out in standard chromosome homozygotes reveals a dramatic suppression of classical crossovers between the rosy mutant alleles in the inversion heterozygote. However, conversions continue to occur for all rosy mutant alleles in all heterozygous combinations in the inversion heterozygote. Moreover, the order of magnitude of conversion frequencies seen in the inversion heterozygote does not change from that seen in the standard chromosome homozygote study. The significance of these observations with reference to the role of rearrangements as barriers of information transfer is discussed. Particular attention is directed to the elaborate inversion polymorphisms seen in natural populations, and to notions concerning their role in the evolution of adaptive gene complexes.

Animals↗

PubMed2006

Cause and effect considerations in diagnostic pathology and pathology phenotyping of genetically engineered mice (GEM).

Over the next several decades, biology is embarking on its most ambitious project yet: to annotate the human genome functionally, prioritizing and focusing on those genes relevant to development and disease. Model systems are fundamental prerequisites for this task, and genetically engineered mice (GEM) are by far the most accessible mammalian system because of their anatomical, physiological, and genetic similarity to humans. The scientific utility of GEM has become commonplace since the technology to produce them was established in the early 1980s. Conceptually, however, an efficiently coordinated high-throughput approach that permits correlation between newly discovered genes, functional properties of their protein products, and biological relevance of these products as drug targets has yet to be established. The discipline of veterinary anatomical pathology (hereafter referred to as pathology) is not immune to this requirement for evolution and adaptation, and to address relationships and tissue consequences between tens of thousands of genes and their cognate proteins, novel interdisciplinary technologies and approaches must emerge. Although many of the techniques of pathology are well established, in the context of pathology's contribution to functional annotation of the genome, several conceptually important and unresolved issues remain to be addressed. While an ever-increasing arsenal of genetic and molecular tool-sets are available to evaluate and understand the function of genes and their pathophysiological mechanisms, pathology will continue to play an essential role in confirming cause and effect relationships of gene function in development and disease. This role will continue to be dependent on keen observation, a systematic but disciplined approach, expert knowledge of strain-dependent anatomical differences and incidental lesions, and relevant tissue-based evidence. Miniaturization and high-throughput adaptation of these methods must also continue so that they can complement parallel phenotyping efforts, provide pathology-based data in pace with concurrent phenotyping efforts, and continue to find new utility in the collective effort of functional annotation.

Animals↗

PubMed2003

The foldback-like transposon Galileo is involved in the generation of two different natural chromosomal inversions of Drosophila buzzatii.

Chromosomal inversions are the most common type of genome rearrangement in the genus Drosophila. Although the potential of transposable elements (TEs) for generating inversions has been repeatedly demonstrated in the laboratory, little is known on their role in the generation of natural inversions, which are those effectively contributing to the adaptation and/or evolution of species. We have cloned and sequenced the two breakpoints of the polymorphic inversion 2q7 of D. buzzatii. The sequence analysis of the breakpoint regions revealed the presence in the inverted chromosomes of large insertions, formed by complex assemblies of transposons, that are absent from the chromosomes without the inversion. Among the transposons inserted, the Foldback-like element Galileo, that was previously found responsible of the generation of the widespread inversion 2j of D. buzzatii, is present at both 2q7 breakpoints and is the most likely inducer of the inversion. A detailed study of the nucleotide and structural variation in the breakpoint regions of six chromosomal lines with the 2q7 inversion detected no nucleotide differences between them, which suggests a monophyletic and recent origin. In contrast, a remarkable degree of structural variation was observed in the same six chromosomal lines. It thus appears that the two breakpoints of the inverted chromosomes have become genetically unstable hotspots, as was previously found for the 2j inversion breakpoints. The possibility that this instability is caused by structural properties of Foldback elements is discussed.

Animals↗

PubMed2005

Positive and negative selection on mammalian Y chromosomes.

Y chromosomes are genetically degenerate in most organisms studied. The loss of genes from Y chromosomes is thought to be due to the inefficiency of purifying selection in nonrecombining regions, which leads to the accumulation of deleterious mutations via the processes of hitchhiking, background selection, and Muller's ratchet. As the severity of these processes depends on the number of functional genes linked together on the nonrecombining Y, it is not clear whether these processes are still at work on the old, gene-poor mammalian Y chromosomes. If purifying selection is indeed less efficient in the Y-linked, compared to the X-linked genes, deleterious nonsynonymous substitutions are expected to accumulate faster on the Y chromosome. However, positive selection on Y-linked genes could also increase the rate of amino acid-changing substitutions. Thus, the previous reports of an elevated nonsynonymous substitution rate in Y-linked genes are still open to interpretation. Here, we report evidence for positive selection in two out of three studied mammalian Y-linked genes, suggesting that adaptive Darwinian evolution may be common on mammalian Y chromosomes. Taking positive selection into account, we demonstrate that purifying selection is less efficient in mammalian Y-linked genes compared to their X-linked homologues, suggesting that these genes continue to degenerate.

Animals↗

PubMed1997

Deletion endpoint allele-specificity in the developmentally regulated elimination of an internal sequence (IES) in Paramecium.

Ciliated protozoa undergo thousands of site-specific DNA deletion events during the programmed development of micronuclear genomes to macronuclear genomes. Two deletion elements, W1 and W2, were identified in the Paramecium primaurelia wild-type 156 strain. Here, we report the characterization of both elements in wild-type strain 168 and show that they display variant deletion patterns when compared with those of strain 156. The W1 ( 168 ) element is defective for deletion. The W2 ( 168 ) element is excised utilizing two alternative boundaries on one side, both are different from the boundary utilized to excise the W2156 element. By crossing the 156 and 168 strains, we demonstrate that the definition of all deletion endpoints are each controlled by cis -acting determinant(s) rather than by strain-specific trans-acting factor(s). Sequence comparison of all deleted DNA segments indicates that the 5'-TA-3'terminal sequence is strictly required at their ends. Furthermore the identity of the first eight base pairs of these ends to a previously established consensus sequence correlates with the frequency of the corresponding deletion events. Our data implies the existence of an adaptive convergent evolution of these Paramecium deleted DNA segment end sequences.

Alleles↗