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21.
Phylogenetic inference under the pure drift model 总被引:1,自引:1,他引:0
When pairwise genetic distances are used for phylogenetic reconstruction,
it is usually assumed that the genetic distance between two taxa contains
information about the time after the two taxa diverged. As a result, upon
an appropriate transformation if necessary, the distance usually can be
fitted to a linear model such that it is expressed as the sum of lengths of
all branches that connect the two taxa in a given phylogeny. This kind of
distance is referred to as "additive distance." For a phylogenetic tree
exclusively driven by random genetic drift, genetic distances related to
coancestry coefficients (theta XY) between any two taxa are more suitable.
However, these distances are fundamentally different from the additive
distance in that coancestry does not contain any information about the time
after two taxa split from a common ancestral population; instead, it
reflects the time before the two taxa diverged. In other words, the
magnitude of theta XY provides information about how long the two taxa
share the same evolutionary pathways. The fundamental difference between
the two kinds of distances has led to a different algorithm of evaluating
phylogenetic trees when theta XY and related distance measures are used.
Here we present the new algorithm using the ordinary- least-squares
approach but fitting to a different linear model. This treatment allows
genetic variation within a taxon to be included in the model. Monte Carlo
simulation for a rooted phylogeny of four taxa has verified the efficacy
and consistency of the new method. Application of the method to human
population was demonstrated.
相似文献
22.
Background
Genetic disruption of an important phenotype should favor compensatory mutations that restore the phenotype. If the genetic basis of the phenotype is modular, with a network of interacting genes whose functions are specific to that phenotype, compensatory mutations are expected among the genes of the affected network. This perspective was tested in the bacteriophage T3 using a genome deleted of its DNA ligase gene, disrupting DNA metabolism. 相似文献23.
Filippini M Buesing N Bettarel Y Sime-Ngando T Gessner MO 《Applied and environmental microbiology》2006,72(7):4893-4898
The discovery of an abundant and diverse virus community in oceans and lakes has profoundly reshaped ideas about global carbon and nutrient fluxes, food web dynamics, and maintenance of microbial biodiversity. These roles are exerted through massive viral impact on the population dynamics of heterotrophic bacterioplankton and primary producers. We took advantage of a shallow wetland system with contrasting microhabitats in close proximity to demonstrate that in marked contrast to pelagic systems, viral infection, determined directly by transmission electron microscopy, and consequently mortality of prokaryotes were surprisingly low in benthic habitats in all seasons. This was true even though free viruses were abundant throughout the year and bacterial infection and mortality rates were high in surrounding water. The habitats in which we found this pattern include sediment, decomposing plant litter, and biofilms on aquatic vegetation. Overall, we detected viruses in only 4 of a total of approximately 15,000 bacterial cells inspected in these three habitats; for comparison, nearly 300 of approximately 5,000 cells suspended in the water column were infected. The strikingly low incidence of impact of phages in the benthos may have important implications, since a major portion of microbial biodiversity and global carbon and nutrient turnover are associated with surfaces. Therefore, if failure to infect benthic bacteria is a widespread phenomenon, then the global role of viruses in controlling microbial diversity, food web dynamics, and biogeochemical cycles would be greatly diminished compared to predictions based on data from planktonic environments. 相似文献
24.
Phylogenetic evidence for role-reversals of gender-associated mitochondrial DNA in Mytilus (Bivalvia: Mytilidae) 总被引:1,自引:0,他引:1
Hoeh WR; Stewart DT; Saavedra C; Sutherland BW; Zouros E 《Molecular biology and evolution》1997,14(9):959-967
Distinct gender-associated mitochondrial DNA (mtDNA) lineages (i.e.,
lineages which are transmitted either through males or through females)
have been demonstrated in two families of bivalves, the Mytilidae (marine
mussels) and the Unionidae (freshwater mussels), which have been separated
for more than 400 Myr. The mode of transmission of these M (for
male-transmitted) and F (for female-transmitted) molecules has been
referred to as doubly uniparental inheritance (DUI), in contrast to
standard maternal inheritance (SMI), which is the norm in animals. A
previous study suggested that at least three origins of DUI are required to
explain the phylogenetic pattern of M and F lineages in freshwater and
marine mussels. Here we present phylogenetic evidence based on partial
sequences of the cytochrome c oxidase subunit I gene and the 16S RNA gene
that indicates the DUI is a dynamic phenomenon. Specifically, we
demonstrate that F lineages in three species of Mytilus mussels, M. edulis,
M. trossulus, and M. californianus, have spawned separate lineages which
are now associated only with males. This process is referred to as
"masculinization" of F mtDNA. By extension, we propose that DUI may be a
primitive bivalve character and that periodic masculinization events
combined with extinction of previously existing M types effectively reset
the time of divergence between conspecific gender-associated mtDNA
lineages.
相似文献
25.
While the potential for intermittent hydrostatic pressure to promote cartilaginous matrix synthesis is well established, its potential to influence chondroinduction remains poorly understood. This study examined the effects of relatively short- and long-duration cyclic hydrostatic compression on the chondroinduction of C3H/10T1/2 murine embryonic fibroblasts by recombinant human bone morphogenetic protein-2 (rhBMP-2). Cells were seeded at high density into round bottom wells of a 96-well plate and supplemented with 25 ng/ml rhBMP-2. Experimental cultures were subjected to either 1,800 cycles/day or 7,200 cycles/day of 1 Hz sinusoidal hydrostatic compression to 5 MPa (applied 10 min on/10 min off) for 3 days. Non-pressurized control and experimental cultures were maintained in static culture for an additional 5 days. Cultures were then analyzed for alcian blue staining intensity, DNA and sulfated glycosaminoglycan (sGAG) content, and for the rate of collagen synthesis. Whereas cultures subjected to 1,800 pressure cycles exhibited no significant differences (statistical or qualitative) compared to controls, those subjected to 7,200 cycles stained more intensely with alcian blue, contained nearly twice as much sGAG, and displayed twice the rate of collagen synthesis as non-pressurized controls. This study demonstrates the potential for cyclic hydrostatic compression to stimulate chondrogenic differentiation of the C3H/10T1/2 cell line in a duration-dependent manner. 相似文献
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27.
John WR Kincaid Nathan A Berger 《Experimental biology and medicine (Maywood, N.J.)》2020,245(17):1594
NAD+ and its derivatives NADH, NADP+, and NADPH are essential cofactors in redox reactions and electron transport pathways. NAD serves also as substrate for an extensive series of regulatory enzymes including cyclic ADP-ribose hydrolases, mono(ADP-ribosyl)transferases, poly(ADP-ribose) polymerases, and sirtuin deacetylases which are O-acetyl-ADP-ribosyltransferases. As a result of the numerous and diverse enzymes that utilize NAD as well as depend on its synthesis and concentration, significant interest has developed in its role in a variety of physiologic and pathologic processes, and therapeutic initiatives have focused both on augmenting its levels as well as inhibiting some of its pathways. In this article, we examine the biosynthesis of NAD, metabolic processes in which it is involved, and its role in aging, cancer, and other age-associated comorbidities including neurodegenerative, cardiovascular, and metabolic disorders. Therapeutic interventions to augment and/or inhibit these processes are also discussed.Impact statementNAD is a central metabolite connecting energy balance and organismal growth with genomic integrity and function. It is involved in the development of malignancy and has a regulatory role in the aging process. These processes are mediated by a diverse series of enzymes whose common focus is either NAD’s biosynthesis or its utilization as a redox cofactor or enzyme substrate. These enzymes include dehydrogenases, cyclic ADP-ribose hydrolases, mono(ADP-ribosyl)transferases, poly(ADP-ribose) polymerases, and sirtuin deacetylases. This article describes the manifold pathways that comprise NAD metabolism and promotes an increased awareness of how perturbations in these systems may be important in disease prevention and/or progression. 相似文献
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