234 research outputs found
Of fingers, toes and penises
Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62765/1/390029a0.pd
Intra-Organ Variation in Age-Related Mutation Accumulation in the Mouse
Using a transgenic mouse model harboring chromosomally integrated lacZ mutational target genes, we previously demonstrated that mutations accumulate with age much more rapidly in the small intestine than in the brain. Here it is shown that in the small intestine point mutations preferentially accumulate in epithelial cells of the mucosa scraped off the underlying serosa. The mucosal cells are the differentiated villus cells that have undergone multiple cell divisions. A smaller age-related increase, also involving genome rearrangements, was observed in the serosa, which consists mainly of the remaining crypts and non-dividing smooth muscle cells. In the brain we observed an accumulation of only point mutations in no other areas than hypothalamus and hippocampus. To directly test for cell division as the determining factor in the generation of point mutations we compared mutation induction between mitotically active and quiescent embryonic fibroblasts from the same lacZ mice, treated with either UV (a point mutagen) or hydrogen peroxide (a clastogen). The results indicate that while point mutations are highly replication-dependent, genome rearrangements are as easily induced in non-dividing cells as in mitotically active ones. This strongly suggests that the point mutations found to have accumulated in the mucosal part of the small intestine are the consequence of replication errors. The same is likely true for point mutations accumulating in hippocampus and hypothalamus of the brain since neurogenesis in these two areas continues throughout life. The observed intra-organ variation in mutation susceptibility as well as the variation in replication dependency of different types of mutations indicates the need to not only extend observations made on whole organs to their sub-structures but also take the type of mutations and mitotic activity of the cells into consideration. This should help elucidating the impact of genome instability and its consequences on aging and disease
Mice with targeted disruptions in the paralogous genes hoxa-3 and hoxd-3 reveal synergistic interactions.
Journal ArticleThe Hox genes encode transcription factors which mediate the formation of the mammalian body plan along the anteroposterior and appendicular axes. Paralogous Hox genes within the separate linkage groups are closely related with respect to DNA sequence and expression, suggesting that they could have at least partially redundant functions. We showed previously that mice homozygous for independent targeted disruptions in the paralogous genes hoxa-3 and hoxd-3 had no defects in common. But our current analysis of double mutants has revealed strong, dosage-dependent interactions between these genes. We report here that in hoxd-3- homozygotes the first cervical vertebra, the atlas, is homeotically transformed to the adjacent anterior structure. Unexpectedly, in double mutants, rather than observing a more extensive homeotic transformation, the entire atlas is deleted. These observations are interpreted in terms of a model in which these Hox genes differentially regulate the proliferation rates of the appropriate sets of precursor cells
Age- and Temperature-Dependent Somatic Mutation Accumulation in Drosophila melanogaster
Using a transgenic mouse model harboring a mutation reporter gene that can be efficiently recovered from genomic DNA, we previously demonstrated that mutations accumulate in aging mice in a tissue-specific manner. Applying a recently developed, similar reporter-based assay in Drosophila melanogaster, we now show that the mutation frequency at the lacZ locus in somatic tissue of flies is about three times as high as in mouse tissues, with a much higher fraction of large genome rearrangements. Similar to mice, somatic mutations in the fly also accumulate as a function of age, but they do so much more quickly at higher temperature, a condition which in invertebrates is associated with decreased life span. Most mutations were found to accumulate in the thorax and less in abdomen, suggesting the highly oxidative flight muscles as a possible source of genotoxic stress. These results show that somatic mutation loads in short-lived flies are much more severe than in the much longer-lived mice, with the mutation rate in flies proportional to biological rather than chronological aging
Molecular evolution of HoxA13 and the multiple origins of limbless morphologies in amphibians and reptiles
Developmental processes and their results, morphological characters, are inherited through transmission of genes regulating development. While there is ample evidence that cis-regulatory elements tend to be modular, with sequence segments dedicated to different roles, the situation for proteins is less clear, being particularly complex for transcription factors with multiple functions. Some motifs mediating protein-protein interactions may be exclusive to particular developmental roles, but it is also possible that motifs are mostly shared among different processes. Here we focus on HoxA13, a protein essential for limb development. We asked whether the HoxA13 amino acid sequence evolved similarly in three limbless clades: Gymnophiona, Amphisbaenia and Serpentes. We explored variation in ω (dN/dS) using a maximum-likelihood framework and HoxA13sequences from 47 species. Comparisons of evolutionary models provided low ω global values and no evidence that HoxA13 experienced relaxed selection in limbless clades. Branch-site models failed to detect evidence for positive selection acting on any site along branches of Amphisbaena and Gymnophiona, while three sites were identified in Serpentes. Examination of alignments did not reveal consistent sequence differences between limbed and limbless species. We conclude that HoxA13 has no modules exclusive to limb development, which may be explained by its involvement in multiple developmental processes
Effect of Ku80 Deficiency on Mutation Frequencies and Spectra at a LacZ Reporter Locus in Mouse Tissues and Cells
Non-homologous end joining (NHEJ) is thought to be an important mechanism for preventing the adverse effects of DNA double strand breaks (DSBs) and its absence has been associated with premature aging. To investigate the effect of inactivated NHEJ on spontaneous mutation frequencies and spectra in vivo and in cultured cells, we crossed a Ku80-deficient mouse with mice harboring a lacZ-plasmid-based mutation reporter. We analyzed various organs and tissues, as well as cultured embryonic fibroblasts, for mutations at the lacZ locus. When comparing mutant with wild-type mice, we observed a significantly higher number of genome rearrangements in liver and spleen and a significantly lower number of point mutations in liver and brain. The reduced point mutation frequency was not due to a decrease in small deletion mutations thought to be a hallmark of NHEJ, but could be a consequence of increased cellular responses to unrepaired DSBs. Indeed, we found a substantial increase in persistent 53BP1 and γH2AX DNA damage foci in Ku80−/− as compared to wild-type liver. Treatment of cultured Ku80-deficient or wild-type embryonic fibroblasts, either proliferating or quiescent, with hydrogen peroxide or bleomycin showed no differences in the number or type of induced genome rearrangements. However, after such treatment, Ku80-deficient cells did show an increased number of persistent DNA damage foci. These results indicate that Ku80-dependent repair of DNA damage is predominantly error-free with the effect of alternative more error-prone pathways creating genome rearrangements only detectable after extended periods of time, i.e., in young adult animals. The observed premature aging likely results from a combination of increased cellular senescence and an increased load of stable, genome rearrangements
LIFE BEEF CARBON: a common framework for quantifying grass and corn based beef farms’ carbon footprints
peer-reviewedEurope’s roadmap to a low-carbon economy aims to cut greenhouse gas (GHG) emissions 80% below 1990 levels by 2050. Beef
production is an important source of GHG emissions and is expected to increase as the world population grows. LIFE BEEF CARBON
is a voluntary European initiative that aims to reduce GHG emissions per unit of beef (carbon footprint) by 15% over a 10-year
period on 2172 farms in four large beef-producing countries. Changes in farms beef carbon footprint are normally estimated via
simulation modelling, but the methods current models apply differ. Thus, our initial goal was to develop a common modelling
framework to estimate beef farms carbon footprint. The framework was developed for a diverse set of Western Europe farms
located in Ireland, Spain, Italy and France. Whole farm and life cycle assessment (LCA) models were selected to quantify emissions
for the different production contexts and harmonized. Carbon Audit was chosen for Ireland, Bovid-CO2 for Spain and CAP’2ER for
France and Italy. All models were tested using 20 case study farms, that is, 5 per country and quantified GHG emissions associated
with on-farm live weight gain. The comparison showed the ranking of beef systems gross carbon footprint was consistent across the
three models. Suckler to weaning or store systems generally had the highest carbon footprint followed by suckler to beef systems
and fattening beef systems. When applied to the same farm, Carbon Audit’s footprint estimates were slightly lower than CAP’2ER,
but marginally higher than Bovid-CO2. These differences occurred because the models were adapted to a specific region’s production
circumstances, which meant their emission factors for key sources; that is, methane from enteric fermentation and GHG emissions
from concentrates were less accurate when used outside their target region. Thus, for the common modelling framework, regionspecific
LCA models were chosen to estimate beef carbon footprints instead of a single generic model. Additionally, the Carbon
Audit and Bovid-CO2 models were updated to include carbon removal by soil and other environmental metrics included in CAP’2ER,
for example, acidification. This allows all models to assess the effect carbon mitigation strategies have on other potential pollutants.
Several options were identified to reduce beef farms carbon footprint, for example, improving genetic merit. These options were
assessed for beef systems, and a mitigation plan was created by each nation. The cumulative mitigation effect of the LIFE BEEF
CARBON plan was estimated to exceed the projects reduction target (−15%)
Nutritional Factors Modulating Alu Methylation inan Italian Sample from The Mark-Age StudyIncluding Offspring of Healthy Nonagenarians
Alu hypomethylation promotes genomic instability and is associated with aging and
age-related diseases. Dietary factors affect global DNA methylation, leading to
changes in genomic stability and gene expression with an impact on longevity and
the risk of disease. This preliminary study aims to investigate the relationship
between nutritional factors, such as circulating trace elements, lipids and
antioxidants, and Alu methylation in elderly subjects and offspring of healthy
nonagenarians. Alu DNA methylation was analyzed in sixty RASIG (randomly
recruited age-stratified individuals from the general population) and thirty-two
GO (GeHA offspring) enrolled in Italy in the framework of the MARK-AGE project.
Factor analysis revealed a different clustering between Alu CpG1 and the other
CpG sites. RASIG over 65 years showed lower Alu CpG1 methylation than those of GO
subjects in the same age class. Moreover, Alu CpG1 methylation was associated
with fruit and whole-grain bread consumption, LDL2-Cholesterol and plasma copper.
The preserved Alu methylation status in GO, suggests Alu epigenetic changes as a
potential marker of aging. Our preliminary investigation shows that Alu
methylation may be affected by food rich in fibers and antioxidants, or
circulating LDL subfractions and plasma copper
Expression of Distal-less, dachshund, and optomotor blind in Neanthes arenaceodentata (Annelida, Nereididae) does not support homology of appendage-forming mechanisms across the Bilateria
The similarity in the genetic regulation of
arthropod and vertebrate appendage formation has been
interpreted as the product of a plesiomorphic gene
network that was primitively involved in bilaterian
appendage development and co-opted to build appendages
(in modern phyla) that are not historically related
as structures. Data from lophotrochozoans are needed to
clarify the pervasiveness of plesiomorphic appendage forming
mechanisms. We assayed the expression of three
arthropod and vertebrate limb gene orthologs, Distal-less
(Dll), dachshund (dac), and optomotor blind (omb), in
direct-developing juveniles of the polychaete Neanthes
arenaceodentata. Parapodial Dll expression marks premorphogenetic
notopodia and neuropodia, becoming restricted
to the bases of notopodial cirri and to ventral
portions of neuropodia. In outgrowing cephalic appendages,
Dll activity is primarily restricted to proximal
domains. Dll expression is also prominent in the brain. dac
expression occurs in the brain, nerve cord ganglia, a pair
of pharyngeal ganglia, presumed interneurons linking a
pair of segmental nerves, and in newly differentiating
mesoderm. Domains of omb expression include the brain,
nerve cord ganglia, one pair of anterior cirri, presumed
precursors of dorsal musculature, and the same pharyngeal
ganglia and presumed interneurons that express dac.
Contrary to their roles in outgrowing arthropod and
vertebrate appendages, Dll, dac, and omb lack comparable
expression in Neanthes appendages, implying independent
evolution of annelid appendage development. We infer
that parapodia and arthropodia are not structurally or
mechanistically homologous (but their primordia might
be), that Dll’s ancestral bilaterian function was in sensory
and central nervous system differentiation, and that
locomotory appendages possibly evolved from sensory
outgrowths
- …