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PubMed2003

Fitness costs of chemical defense in Plantago lanceolata L.: effects of nutrient and competition stress.

Fitness costs of defense are often invoked to explain the maintenance of genetic variation in levels of chemical defense compounds in natural plant populations. We investigated fitness costs of iridoid glycosides (IGs), terpenoid compounds that strongly deter generalist insect herbivores, in ribwort plantain (Plantago lanceolata L.) using lines that had been artificially selected for high and low leaf IG concentrations for four generations. Twelve maternal half-sib families from each selection line were grown in four environments, consisting of two nutrient and two competition treatments. We tested whether: (1) in the absence of herbivores and pathogens, plants from lines selected for high IG levels have a lower fitness than plants selected for low IG levels; and (2) costs of chemical defense increase with environmental stress. Vegetative biomass did not differ between selection lines, but plants selected for high IG levels produced fewer inflorescences and had a significantly lower reproductive dry weight than plants selected for low IG levels, indicating a fitness cost of IG production. Line-by-nutrient and line-by-competition interactions were not significant for any of the fitness-related traits. Hence, there was no evidence that fitness costs increased with environmental stress. Two factors may have contributed to the absence of higher costs under environmental stress. First, IGs are carbon-based chemicals. Under nutrient limitation, the relative carbon excess may result in the production of IGs without imposing a further constraint on growth and reproduction. Second, correlated responses to selection on IG levels indicate the existence of a positive genetic association between IG level and cotyledon size. At low nutrient level, a path analysis based on family means revealed that in the presence of competitors, the negative direct effect of a high IG level on aboveground plant dry weight was partly offset by a positive direct effect of the associated larger cotyledon size. This indicates that fitness costs of defense may be modulated by environment-specific fitness effects of genetically associated traits.

Adaptation, Physiological↗
PubMed2002

On Richerson and Boyd's model of cultural evolution by sexual selection.

Richerson and Boyd proposed a model of sexual selection in which both the male trait and the female preference are culturally transmitted. We generalize their model by introducing sex-dependent oblique transmission rates and a fairly comprehensive female preference rule. The model differs markedly from the standard genetic models in that the male trait and the female preference are uncorrelated. Hence, there can be no "sexy son" effect to offset the assumed fertility cost to choosy females. Nevertheless, the cultural processes can support a stable polymorphic equilibrium at which the choosy females are present. Also of interest are the cyclical dynamics observed in the neighborhood of the internal equilibrium.

Cultural Evolution↗
PubMed2002

Sperm competitive ability and genetic relatedness in Drosophila melanogaster: similarity breeds contempt.

Offspring of close relatives often suffer severe fitness consequences. Previous studies have demonstrated that females, when given a choice, will choose to avoid mating with closely related males. But where opportunities for mate choice are limited or kin recognition is absent, precopulatory mechanisms may not work. In this case, either sex could reduce the risks of inbreeding through mechanisms that occur during or after copulation. During mating, males or females could commit fewer gametes when mating with a close relative. After mating, females could offset the effects of mating with a closely related male through cryptic choice. Few prior studies of sperm competition have examined the effect of genetic similarity, however, and what studies do exist have yielded equivocal results. In an effort to resolve this issue, we measured the outcome of sperm competition when female Drosophila melanogaster were mated to males of four different degrees of genetic relatedness and then to a standardized competitor. We provide the strongest evidence to date that sperm competitive ability is negatively correlated with relatedness, even after controlling for inbreeding depression.

Animals↗
PubMed2006

The biology of hernias and the abdominal wall.

The fundamental mechanism for hernia formation is loss of the mechanical integrity of abdominal wall structural tissue that results in the inability to offset and contain intra-abdominal forces during valsalva and loading of the torso. There is evidence that genetic or systemic extracellular matrix disorders may predispose patients to hernia formation. There is also evidence that acute laparotomy wound failure leads to hernia formation and increases the risk of recurrent hernia disease. It may be that hernia formation is a heterogeneous disease, not unlike cancer, where one population of patients express an extracellular matrix defect leading to primary hernia disease, while other subsets of patients acquire a defective, chronic wound phenotype following failed laparotomy and hernia repairs. It is evident that an improved understanding of structural tissue matrix biology will lead to improved results following abdominal wall reconstructions.

Animals↗
PubMed2006

Genetic parameters for a heavy female turkey line: impact of simultaneous selection for body weight and total egg number.

1. The objective of this study was to investigate the strength of the genetic association between growth and reproduction traits in turkeys selected for body weight, conformation and egg production. 2. Two distinct populations but derived from the same heavy turkey female line and situated in different locations (UK and USA), were used to estimate genetic parameters using multivariate REML for the following traits: body weight at 14 (BW14), 19 (BW19) and 24 (BW24) weeks of age and total egg number (EGG). 3. A Box-Cox transformation was applied to egg production data to reduce the impact of non-normality. 4. The heritability estimates for each trait for the UK and USA populations, respectively, were: BW14 0.37 and 0.48; BW19 0.34 and 0.43; BW24 0.28 and 0.43; EGG 0.22 and 0.34. 5. The genetic correlation between the body weight at all ages and the total egg production was strongly negative, reaching a value of -0.75 for the UK and -0.55 for the USA population. 6. The comparison of our results with published estimates in turkeys suggests that the genetic correlation may get stronger in magnitude following selection for increased body weight. 7. This could arise from fixation during selection of genes favouring larger weights but with minimal effect on egg production, leaving the segregating genetic variation dominated by pleiotropic loci with antagonistic effects on the traits. 8. Thus, in order to avoid continued selection for body weight reducing egg production to a point where natural selection offsets selection gains, alternative selection strategies should be considered.

Animals↗
PubMed1997

Human thyroid-stimulating hormone (hTSH) subunit gene fusion produces hTSH with increased stability and serum half-life and compensates for mutagenesis-induced defects in subunit association.

The human thyroid-stimulating hormone (hTSH) subunits alpha and beta are transcribed from different genes and associate noncovalently to form the bioactive hTSH heterodimer. Dimerization is rate-limiting for hTSH secretion, and dissociation leads to hormone inactivation. Previous studies on human chorionic gonadotropin (hCG) and human follicle-stimulating hormone had shown that it was possible by subunit gene fusion to produce a bioactive, single chain hormone. However, neither the stability nor the clearance from the circulation of such fused glycoprotein hormones has been studied. We show here that genetic fusion of the hTSH alpha- and beta-subunits using the carboxyl-terminal peptide of the hCG beta-subunit as a linker created unimolecular hTSH whose receptor binding and bioactivity were comparable to native hTSH. Interestingly, the fused hTSH had higher thermostability and a longer plasma half-life than either native or dimeric hTSH containing the hCG beta-subunit-carboxyl-terminal peptide, suggesting that dimer dissociation may contribute to glycoprotein hormone inactivation in vivo. In addition, we show for the first time that synthesis of hTSH as a single polypeptide chain could overcome certain mutagenesis-induced defects in hTSH secretion, therefore enabling functional studies of such mutants. Thus, in addition to prolongation of plasma half-life, genetic fusion of hTSH subunits should be particularly relevant for the engineering of novel analogs where desirable features are offset by decreased dimer formation or stability. Such methods provide a general approach to expand the spectrum of novel recombinant glycoprotein hormones available for in vitro and in vivo study.

Animals↗
PubMed1996

Quantification of free plus conjugated indoleacetic acid in arabidopsis requires correction for the nonenzymatic conversion of indolic nitriles.

The genetic advantages to the use of Arabidopsis thaliana mutants for the study of auxin metabolism previously have been partially offset by the complexity of indolic metabolism in this plant and by the lack of proper methods. To address some of these problems, we developed isotopic labeling methods to determine amounts and examine the metabolism of indolic compounds in Arabidopsis. Isolation and indentification of endogenous indole-3-acetonitrile (IAN; a possible precursor of the auxin indole-3-acetic acid [IAA]) was carried out under mild conditions, thus proving its natural occurrence. We describe here the synthesis of 13C1-labeled IAN and its utility in the gas chromatography-mass spectrometry quantification of endogenous IAN levels. We also quantified the nonenzymatic conversion of IAN to IAA under conditions used to hydrolyze IAA conjugates. 13C1-Labeled IAN was used to assess the contribution of IAN to measured IAA following hydrolysis of IAA conjugates. We studied the stability and breakdown of the indolic glucosinolate glucobrassicin, which is known to be present in Arabidopsis. This is potentially an important concern when using Arabidopsis for studies of indolic biochemistry, since the levels of indolic auxins and auxin precursors are well below the levels of the indolic glucosinolates. We found that under conditions of extraction and base hydrolysis, formation of IAA from glucobrassicin was negligible.

Arabidopsis↗
PubMedDate not supplied

A rotational offset model for two-stranded F-actin.

We propose the following "rotational offset" model for two independent strands of F-actin to account for the observation that it is possible, at times, for the crossover repeat to either alternate between long and short periods or remain constant (Bremer et al., 1991. J. Cell Biol. 115, 689-703). Rotational offset is the manifestation of the angular component of "lateral slipping" between the two long-pitch, right-handed strands comprising the actin filament. The present model is based on the premise that the longitudinal bond connecting the subunits along a single long-pitch strand is substantially stronger than the diagonal bond that connects interstrand subunits. We pose that, over fairly long stretches, the backbones of the two right-handed strands are individually close to being ideal helices, and that it is possible for the backbone of one strand to "roll across" the other. The rotational offset angle (epsilon 0) is the amount that one helical strand is angularly displaced relative to the position that otherwise would allow the two strands to be described as an ideal single genetic helix. Such an independent movement of the two strands is shown to shift the monomers that are involved in crossover points and produce the different patterns in crossover periods which have been observed from electron micrographs analysis. We specifically demonstrate that for a constant nonzero rotational offset the length of the crossover periods alternates, whereas for a constant offset of zero the crossover period remains constant. We also show that changes in the rotational offset angle along the filament can account for variable (random) crossover periods.

Actins↗
PubMed2003

Number of ancestral human species: a molecular perspective.

Despite the remarkable developments in molecular biology over the past three decades, anthropological genetics has had only limited impact on systematics in human evolution. Genetics offers the opportunity to objectively test taxonomies based on morphology and may be used to supplement conventional approaches to hominid systematics. Our analyses, examining chromosomes and 46 estimates of genetic distance, indicate there may have been only around 4 species on the direct line to modern humans and 5 species in total. This contrasts with current taxonomies recognising up to 23 species. The genetic proximity of humans and chimpanzees has been used to suggest these species are congeneric. Our analysis of genetic distances between them is consistent with this proposal. It is time that chimpanzees, living humans and all fossil humans be classified in Homo. The creation of new genera can no longer be a solution to the complexities of fossil morphologies. Published genetic distances between common chimpanzees and bonobos, along with evidence for interbreeding, suggest they should be assigned to a single species. The short distance between humans and chimpanzees also places a strict limit on the number of possible evolutionary 'side branches' that might be recognised on the human lineage. All fossil taxa were genetically very close to each other and likely to have been below congeneric genetic distances seen for many mammals. Our estimates of genetic divergence suggest that periods of around 2 million years are required to produce sufficient genetic distance to represent speciation. Therefore, Neanderthals and so-called H. erectus were genetically so close to contemporary H. sapiens they were unlikely to have been separate species. Thus, it is likely there was only one species of human (H. sapiens) for most of the last 2 million years. We estimate the divergence time of H. sapiens from 16 genetic distances to be around 1.7 Ma which is consistent with evidence for the earliest migration out of Africa. These findings call into question the mitochondrial "African Eve" hypothesis based on a far more recent origin for H. sapiens and show that humans did not go through a bottleneck in their recent evolutionary history. Given the large offset in evolutionary rates of molecules and morphology seen in human evolution, Homo species are likely to be characterised by high levels of morphological variation and low levels of genetic variability. Thus, molecular data suggest the limits for intraspecific morphological variation used by many palaeoanthropologists have been set too low. The role of phenotypic plasticity has been greatly underestimated in human evolution. We call into question the use of mtDNA for studies of human evolution. This DNA is under strong selection, which violates the assumption of selective neutrality. This issue should be addressed by geneticists, including a reassessment of its use for molecular clocks. There is a need for greater cooperation between palaeoanthropologists and anthropological geneticists to better understand human evolution and to bring palaeoanthropology into the mainstream of evolutionary biology.

Animals↗
PubMed2026

Climate-Driven Niche Tracking and Genomic Resilience Shape Future Distribution of a Widespread Agricultural Weed.

Understanding how agriculturally important species respond to environmental change is critical for maintaining productivity, mitigating agroecosystem threats and sustaining resilience. While crops have traditionally been the focus in agroecosystems, agricultural weeds are integral components that often face even stronger selective pressures, making them powerful models for investigating ecological and evolutionary responses to climatic and human-mediated challenges. Insights from how weeds adapt rapidly under these pressures can inform strategies to improve agricultural outcomes, since both pests and crops evolve under the same multivariate selective pressures. Here, we integrate two centuries of distribution records with whole-genome sequencing from natural populations of the most damaging weed in Europe-Alopecurus myosuroides (blackgrass) - to examine its ecological and evolutionary responses in agroecosystems. Blackgrass largely maintained its historical climatic niche, expanding its range primarily by tracking environments analogous to those it historically occupied. Genome-wide analyses revealed a polygenic basis of environmental responses, with most loci linked to single environmental variables and a subset showing limited environmental pleiotropy, indicating modular adaptation to the complex selective pressures of managed agricultural landscapes. Coupling these genomic-environment relationships with projected climate change and genomic offset analyses indicated that most blackgrass populations will remain well aligned with future conditions. Our findings show that ecological niche tracking and polygenic adaptation allow agricultural weeds like blackgrass to persist under rapid environmental change, offering insights relevant not only for weed management but also for designing resilient cropping systems under future climates.

Plant Weeds↗
PubMed2005

Family size in white gay and heterosexual men.

There is some evidence for a genetic influence on sexual orientation. However, gay men have fewer children than heterosexual men. Increased fecundity in the biological relatives of gay men could offset this selection pressure. We measured family size in gay (n = 301) and heterosexual (n = 404) men, attending clinics for sexually transmitted infections. The main outcome measure was the number of each man's uncles and aunts, first cousins, siblings, nephews and nieces, and his own children. With the exception of the participants' own offspring, mean family size of each category of relatives was significantly larger for gay men (paternal and maternal total OR = 1.02, CI = 1.01-1.03). This remained the case after adjustment for other predictors of family size (paternal and maternal total OR = 1.02, CI = 1.00-1.03). We found increased fecundity in the relatives of gay men and this is one explanation of how a genetic influence might persist in spite of reduced reproductive fitness in the gay phenotype. There are, however, a number of alternative explanations for our finding, including unknown psychological and social factors, which might mediate the association between family size and sexual orientation.

Adult↗
PubMed1999

DNA technology in the clinical laboratory.

OBJECTIVES: To review the advances in clinically useful molecular biological techniques and to identify their applications in clinical practice, as presented at the Eighth Annual William Beaumont Hospital Symposium. DATA SOURCES: The 10 manuscripts submitted were reviewed, and their major findings were compared with literature on the same topic. STUDY SELECTION: Two manuscripts addressed specimen (nucleic acid) stability, 2 described novel analytic approaches, 3 discussed detection of B- or T-cell clonality in lymphoproliferative disorders, and 3 reported the frequency of a variety of genetic polymorphisms found in cardiac disorders. DATA SYNTHESIS: DNA from dried blood spots is stable and may be purified rapidly for amplification and mutation analysis. RNA is much less stable, and a variety of methods may be used to reduce ribonuclease degradation of enteroviral RNA. False-negative reactions may be reduced by genomic amplification of ligated padlock probes by cascade rolling circle or polymerase chain reaction. A multiplex polymerase chain method using fluorescence-labeled products that separate both the wild-type and mutant hemochromatosis gene alleles by capillary gel electrophoresis represents another approach for detecting the 2 major missense mutations (C282Y and H63D) in hemochromatosis. Southern blotting and polymerase chain reaction have been used to detect B- and T-cell clonality in lymphoproliferative diseases, including mantle cell lymphoma and lymphoma of the breast. Genetic polymorphisms in a variety of coagulation factors and platelet glycoprotein IIIa are associated with ischemic heart disease. CONCLUSIONS: As the Human Genome Project continues to define disease-associated mutations, the number of clinically useful molecular pathologic techniques and assays will expand. Clinical outcome analysis is still required to document a decrease in the patient's length of stay to offset the cost of introducing molecular biological assays in the routine clinical pathology laboratory.

Clinical Laboratory Techniques↗
PubMed2025

Dosage sensitivity of the loop extrusion rate confers tunability to genome folding while creating vulnerability to genetic disruption.

Genome folding is not static, but emerges from dynamic processes that control transcription, replication, recombination, and repair. DNA loop extrusion by cohesin is central to genome organization, yet it remains unclear how cells can tune extrusion kinetics to achieve precise and functional chromosome folding patterns. Here we discover extrusion rate acts as a tunable biophysical parameter in cells, quantitatively dialed by the respective dosage of the cohesin cofactors NIPBL and PDS5. Modulation of extrusion rate can offset changes in cohesin lifetime to buffer steady-state chromosome structure and transcriptional states, even in the face of abnormal extrusion dynamics. These findings provide a long-sought mechanistic basis for the genetic interactions between cohesin cofactors and the molecular origin of haploinsufficiency in cohesinopathies, such as Cornelia de Lange syndrome.

Journal Article↗
PubMed2003

Explaining trends in child support: economic, demographic, and policy effects.

We use data from the Panel Study of Income Dynamics to examine trends in the receipt of child support (and the determinants of trends) between 1968 and 1997. The findings suggest that political, demographic, and economic forces all exerted downward pressure on child-support payments during this 30-year period, with inflation, the shift to unilateral divorce, and declines in fertility and men's earnings being more important during the earlier years and decreases in men's earnings being more important during the later years. These negative forces were offset by the passage of new child-support legislation in the 1980s and 1990s, including numeric guidelines, universal withholding, and genetic testing.

Adolescent↗
PubMed2006

Migration, isolation, and speciation of hydrothermal vent limpets (Gastropoda; Lepetodrilidae) across the Blanco Transform Fault.

The Sovanco Fracture Zone and Blanco Transform Fault separate the Explorer, Juan de Fuca, and Gorda ridge systems of the northeastern Pacific Ocean. To test whether such offsets in the ridge axis create barriers to along-axis dispersal of the endemic hydrothermal vent animals, we examined the genetic structure of limpet populations previously identified as Lepetodrilus fucensis McLean, 1988 (Gastropoda, Lepetodrilidae). Mitochondrial DNA sequences and patterns of allozyme variation revealed no evidence that the 150-km-long Sovanco Fracture Zone impeded gene flow between the Explorer and Juan de Fuca populations. In contrast, the 450-km-long Blanco Transform Fault separates the limpets into highly divergent northern and southern lineages that we recognize as distinct species. We describe southern populations from the Gorda Ridge (Seacliff) and Escanaba Trough as Lepetodrilus gordensis new species and refer northern populations from the Explorer and Juan de Fuca ridge systems to L. fucensis sensu stricto. The species are similar morphologically, but L. gordensis lacks a sensory neck papilla and has a more tightly coiled teleconch. To assess the degree of isolation between these closely related species, we used the Isolation with Migration method to estimate the time of population splitting, effective sizes of the ancestral and derived populations, and rates of migration across the Blanco Transform Fault.

Animal Migration↗
PubMed2026

Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption.

Genome folding is not static but emerges from dynamic processes that control transcription, replication, recombination, and repair. DNA loop extrusion by cohesin is central to genome organization, yet it remains unclear how cells can tune extrusion kinetics to achieve precise and functional chromosome folding patterns. Here, we show that extrusion rate acts as a tunable biophysical parameter in cells, quantitatively dialed by the respective dosage of the cohesin cofactors NIPBL and PDS5. Modulation of extrusion rate can offset changes in cohesin lifetime to buffer steady-state chromosome structure and transcriptional states, even in the face of abnormal extrusion dynamics. These findings provide a long-sought mechanistic basis for the genetic interactions between cohesin cofactors and for the molecular origin of haploinsufficiency in cohesinopathies, such as Cornelia de Lange syndrome.

Cell Cycle Proteins↗
PubMed2025

Genomic Insights Into Local Adaptation Across Heterogeneous Understory Habitats and Climate Change Vulnerability.

Understanding adaptive evolution and survival risks in understory herbs is crucial for the effective conservation of biodiversity. How environmental gradients shape species local adaptation patterns is not well understood, nor is how populations of understory herbs respond to a changing climate. In this study, we conducted population genomic analyses of Adenocaulon himalaicum (Asteraceae) with a pan-East Asian distribution, representing a good model for dominant understory herbs to elucidate adaptation mechanisms in heterogeneous forest ecosystems. Based on 34,398 putatively neutral single nucleotide polymorphisms (SNPs) across 27 populations, we identified three genetic lineages accompanied by high levels of genetic differentiation between populations. Our isolation by environment results (IBE) indicated a significant effect of environmental gradients on genomic variation of A. himalaicum (r = 0.18, p = 0.03). To decompose the relative contributions of climate, geography and population structure in explaining genetic variance, our partial RDA found that the prominent contribution of environmental effects (climatic and soil variables) explained 29% and 36% of the neutral and adaptive genetic variation, respectively. Using two genotype-environment association (GEA) methods, we identified 13 SNPs as candidates for core climate-related adaptation loci, with two of these loci further validated by qRT-PCR experiments. Projections of spatiotemporal genomic vulnerability under different future climate scenarios revealed that populations in the southeastern edge of the Himalayas, near the Sichuan Basin, the southernmost region of Northeast China and the northern Korean Peninsula, as well as northern Japan, were identified as the most vulnerable and should be prioritised for conservation. Therefore, our current study provides the genomic foundations for conservation and management strategies to elucidate how these understory herbs cope with future climate changes.

Climate Change↗
PubMed2005

Physiological basis for novel drug therapies used to treat the inflammatory bowel diseases I. Pathophysiological basis and prospects for probiotic therapy in inflammatory bowel disease.

Mechanisms underlying the conditioning influence of the intestinal flora on mucosal homeostasis, including development and function of immune responses, are attracting increasing scientific scrutiny. The intestinal flora is a positive asset to host defense, but some of its components may, in genetically susceptible hosts, become a risk factor for development of inflammatory bowel disease (IBD). It follows that strategies to enhance assets or offset microbial liabilities represent a therapeutic option; therein lies the rationale for manipulation of the flora in IBD. In addition, the diversity of regulatory signalling among the flora and host epithelum, lymphoid tissue, and neuromuscular apparatus is an untapped reservoir from which novel therapeutics may be mined. Moreover, the capacity to engineer food-grade or commensal bacteria to deliver therapeutic molecules to the intestinal mucosa promises to extend the scope of microbial manipulation for the benefit of mankind.

Animals↗