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1.
A comparative description of mitochondrial DNA differentiation in selected avian and other vertebrate genera 总被引:14,自引:1,他引:13
Levels of mitochondrial DNA (mtDNA) sequence divergence between species
within each of several avian (Anas, Aythya, Dendroica, Melospiza, and
Zonotrichia) and nonavian (Lepomis and Hyla) vertebrate genera were
compared. An analysis of digestion profiles generated by 13-18 restriction
endonucleases indicates little overlap in magnitude of mtDNA divergence for
the avian versus nonavian taxa examined. In 55 interspecific comparisons
among the avian congeners, the fraction of identical fragment lengths (F)
ranged from 0.26 to 0.96 (F = 0.46), and, given certain assumptions, these
translate into estimates of nucleotide sequence divergence (p) ranging from
0.007 to 0.088; in 46 comparisons among the fish and amphibian congeners, F
values ranged from 0.00 to 0.36 (F = 0.09), yielding estimates of P greater
than 0.070. The small mtDNA distances among avian congeners are associated
with protein-electrophoretic distances (D values) less than approximately
0.2, while the mtDNA distances among assayed fish and amphibian congeners
are associated with D values usually greater than 0.4. Since the
conservative pattern of protein differentiation previously reported for
many avian versus nonavian taxa now appears to be paralleled by a
conservative pattern of mtDNA divergence, it seems increasingly likely that
many avian species have shared more recent common ancestors than have their
nonavian taxonomic counterparts. However, estimates of avian divergence
times derived from mtDNA- and protein-calibrated clocks cannot readily be
reconciled with some published dates based on limited fossil remains. If
the earlier paleontological interpretations are valid, then protein and
mtDNA evolution must be somewhat decelerated in birds. The empirical and
conceptual issues raised by these findings are highly analogous to those in
the long-standing debate about rates of molecular evolution and times of
separation of ancestral hominids from African apes.
相似文献
2.
Nyquist OL McLeod A Brede DA Snipen L Aakra Å Nes IF 《Molecular genetics and genomics : MGG》2011,285(4):297-311
Lactobacillus sakei is a lactic acid bacterium important in food microbiology mainly due to its ability to ferment and preserve meat. The genome
sequence of L. sakei strain 23K has revealed specialized metabolic capacities that reflect the bacterium’s adaption to meat products, and that
differentiate it from other LAB. An extensive genomic diversity analysis was conducted to elucidate the core features of the
species, and to provide a better comprehension of niche adaptation of the organism. Here, we describe the genomic comparison
of 18 strains of L. sakei originating mainly from processed meat against the 23K strain by comparative genome hybridization. Pulsed field gel electrophoresis
was used to estimate the genome sizes of the strains, which varied from 1.880 to 2.175 Mb, and the 23K genome was among the
smallest. Consequently, a large part of the genome of this strain belongs to a common gene pool invariant in this species.
The majority of genes important in adaption to meat products, the ability to flexibly use meat components, and robustness
during meat processing and storage were conserved, such as genes involved in nucleoside scavenging, catabolism of arginine,
and the ability to cope with changing redox and oxygen levels, which is indicative of the role these genes play in niche specialization
within the L. sakei species. Moreover, an additional set of sequenced L. sakei genes beyond the 23K genome was present on the microarray used, and it was demonstrated that all the strains carry remnants
of or complete bacteriocin operons. The genomic divergence corresponded mainly to five regions in the 23K genome, which showed
features consistent with horizontal gene transfer. Carbohydrate-fermentation profiles of the strains were evaluated in light
of the CGH data, and for most substrates, the genotypes were consistent with the phenotypes. We have demonstrated a highly
conserved organization of the L. sakei genomes investigated, and the 23K strain is a suitable model organism to study core features of the L. sakei species. 相似文献
3.
Tahir Mehmood Harald Martens Solve Sæbø Jonas Warringer Lars Snipen 《Algorithms for molecular biology : AMB》2011,6(1):1-12
Background
We consider the following problem: Given an undirected network and a set of sender-receiver pairs, direct all edges such that the maximum number of "signal flows" defined by the pairs can be routed respecting edge directions. This problem has applications in understanding protein interaction based cell regulation mechanisms. Since this problem is NP-hard, research so far concentrated on polynomial-time approximation algorithms and tractable special cases.Results
We take the viewpoint of parameterized algorithmics and examine several parameters related to the maximum signal flow over vertices or edges. We provide several fixed-parameter tractability results, and in one case a sharp complexity dichotomy between a linear-time solvable case and a slightly more general NP-hard case. We examine the value of these parameters for several real-world network instances.Conclusions
Several biologically relevant special cases of the NP-hard problem can be solved to optimality. In this way, parameterized analysis yields both deeper insight into the computational complexity and practical solving strategies. 相似文献4.
5.
The objective is to predict future plant growth using data from greenhouse grown poinsettias. A population‐mean growth trajectory can be predicted from growth conditions using previously published results. Four different predictors are used to identify the local group‐effects that come in addition to the population‐mean response to growth conditions, in order to improve the predictions of the final plant height for specific plant groups. A search for optimal model complexity and use of growth history during calibration is conducted using cross‐validation. 相似文献
6.
We studied different genetic models and evaluation systems to select against a genetic disease with additive, recessive or polygenic inheritance in genetic conservation schemes. When using optimum contribution selection with a restriction on the rate of inbreeding (ΔF) to select against a disease allele, selection directly on DNA-genotypes is, as expected, the most efficient strategy. Selection for BLUP or segregation analysis breeding value estimates both need 1–2 generations more to halve the frequency of the disease allele, while these methods do not require knowledge of the disease mutation at the DNA level. BLUP and segregation analysis methods were equally efficient when selecting against a disease with single gene or complex polygene inheritance, i.e. knowledge about the mode of inheritance of the disease was not needed for efficient selection against the disease. Smaller schemes or schemes with a more stringent restriction on ΔF needed more generations to halve the frequency of the disease alleles or the fraction of diseased animals. Optimum contribution selection maintained ΔF at its predefined level, even when selection of females was at random. It is argued that in the investigated small conservation schemes with selection against a genetic defect, control of ΔF is very important. 相似文献
7.
Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae) 总被引:2,自引:1,他引:1
We examine rate heterogeneity among evolutionary lineages of the grass
family at two plasmid loci, ndhF and rbcL, and we introduce a method to
determine whether patterns of rate heterogeneity are correlated between
loci. We show both that rates of synonymous evolution are heterogeneous
among grass lineages and that are heterogeneity is correlated between loci
at synonymous sites. At nonsynonymous sites, the pattern of rate
heterogeneity is not correlated between loci, primarily due to an aberrant
pattern of rate heterogeneity at nonsynonymous sites of rbcL. We compare
patterns of synonymous rate heterogeneity to predictors based on the
generation time effect and the speciation rate hypotheses. Although there
is some evidence for generation time effects, neither generation time
effects nor speciation rates appear to be sufficient to explain patterns of
rate heterogeneity in the grass plastid sequences.
相似文献
8.
Job B Bernheim A Beau-Faller M Camilleri-Broët S Girard P Hofman P Mazières J Toujani S Lacroix L Laffaire J Dessen P Fouret P;LG Investigators 《PloS one》2010,5(12):e15145
Background
Lung cancer in never smokers would rank as the seventh most common cause of cancer death worldwide.Methods and Findings
We performed high-resolution array comparative genomic hybridization analysis of lung adenocarcinoma in sixty never smokers and identified fourteen new minimal common regions (MCR) of gain or loss, of which five contained a single gene (MOCS2, NSUN3, KHDRBS2, SNTG1 and ST18). One larger MCR of gain contained NSD1. One focal amplification and nine gains contained FUS. NSD1 and FUS are oncogenes hitherto not known to be associated with lung cancer. FISH showed that the amplicon containing FUS was joined to the next telomeric amplicon at 16p11.2. FUS was over-expressed in 10 tumors with gain of 16p11.2 compared to 30 tumors without that gain. Other cancer genes present in aberrations included ARNT, BCL9, CDK4, CDKN2B, EGFR, ERBB2, MDM2, MDM4, MET, MYC and KRAS. Unsupervised hierarchical clustering with adjustment for false-discovery rate revealed clusters differing by the level and pattern of aberrations and displaying particular tumor characteristics. One cluster was strongly associated with gain of MYC. Another cluster was characterized by extensive losses containing tumor suppressor genes of which RB1 and WRN. Tumors in that cluster frequently harbored a central scar-like fibrosis. A third cluster was associated with gains on 7p and 7q, containing ETV1 and BRAF, and displayed the highest rate of EGFR mutations. SNP array analysis validated copy-number aberrations and revealed that RB1 and WRN were altered by recurrent copy-neutral loss of heterozygosity.Conclusions
The present study has uncovered new aberrations containing cancer genes. The oncogene FUS is a candidate gene in the 16p region that is frequently gained in never smokers. Multiple genetic pathways defined by gains of MYC, deletions of RB1 and WRN or gains on 7p and 7q are involved in lung adenocarcinoma in never smokers. 相似文献9.
Morten Nilsen Asima Lokmic Inga Leena Angell Karin C. Ldrup Carlsen Kai-Hkon Carlsen Guttorm Haugen Gunilla Hedlin Christine Monceyron Jonassen Benjamin J. Marsland Bjrn Nordlund Eva Maria Rehbinder Carina Madelen Saunders Hvard O. Skjerven Lars Snipen Anne Cathrine Staff Cilla Sderhll Riyas Vettukattil Knut Rudi 《Applied and environmental microbiology》2021,87(6)
10.
Margrete Solheim Mari C Brekke Lars G Snipen Rob JL Willems Ingolf F Nes Dag A Brede 《BMC microbiology》2011,11(1):3