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21.
Using simulated data, we compared five methods of phylogenetic tree
estimation: parsimony, compatibility, maximum likelihood, Fitch-
Margoliash, and neighbor joining. For each combination of substitution
rates and sequence length, 100 data sets were generated for each of 50
trees, for a total of 5,000 replications per condition. Accuracy was
measured by two measures of the distance between the true tree and the
estimate of the tree, one measure sensitive to accuracy of branch lengths
and the other not. The distance-matrix methods (Fitch- Margoliash and
neighbor joining) performed best when they were constrained from estimating
negative branch lengths; all comparisons with other methods used this
constraint. Parsimony and compatibility had similar results, with
compatibility generally inferior; Fitch- Margoliash and neighbor joining
had similar results, with neighbor joining generally slightly inferior.
Maximum likelihood was the most successful method overall, although for
short sequences Fitch- Margoliash and neighbor joining were sometimes
better. Bias of the estimates was inferred by measuring whether the
independent estimates of a tree for different data sets were closer to the
true tree than to each other. Parsimony and compatibility had particular
difficulty with inaccuracy and bias when substitution rates varied among
different branches. When rates of evolution varied among different sites,
all methods showed signs of inaccuracy and bias.
相似文献
22.
Dhanashree?A?Paranjpe D?Anitha MK?Chandrashekaran Amitabh?Joshi Vijay?Kumar?SharmaEmail author 《BMC developmental biology》2005,5(1):5
Background
In insects, circadian clocks have been implicated in affecting life history traits such as pre-adult development time and adult lifespan. Studies on the period (per) mutants of Drosophila melanogaster, and laboratory-selected lines of Bactrocera cucurbitae suggested a close link between circadian clocks and development time. There is a possibility of clock genes having pleiotropic effects on clock period and pre-adult development time. In order to avoid such pleiotropic effects we have used wild type flies of same genotype under environments of different periodicities, which phenotypically either speeded up or slowed down the eclosion clock of D. melanogaster. 相似文献23.
Byrne P Huang W Wallace VM Shean MK Zhang Z Zhong Q Theodossiou C Blakesley H Kolls JK Schwarzenberger P 《BioTechniques》2002,32(2):279-80, 282-4, 286
Marine experimental stem cell transplantations require the accurate discrimination and quantification of donor cells from host cells. A Y-chromosome-specific, quantitative real-time PCR (kinetic PCR) protocol for blood-derived DNA was developed. The assay sensitivity was extremely high with accurate detection of only 10 pg (six copies of Y target DNA) in a variable background of female DNA background ranging from 2.5 to 50 ng. The dynamic range of the assay provided accurate results ranging from 2.2 x 10(-2)% to 100% of male DNA in female background. The kinetic PCR assay can be used in all mouse strains, and a sample size as low as 2.5 ng total DNA is sufficient for analysis. Therefore, kinetic PCR allows engraftment kinetic studies on repeated blood draws of individual animals with no need for sacrifice. Compared to conventional PCR, the assay is much simplified, as neither the accurate adjustment of sample DNA concentration nor a post-reaction analysis procedure is required. The procedure is simple, free of radioactivity, and permits a throughput of 500-600 reactions per day. 相似文献
24.
MK Parr F Botrè A Na? J Hengevoss P Diel G Wolber 《Biology of sport / Institute of Sport》2015,32(2):169-173
Increasing numbers of dietary supplements with ecdysteroids are marketed as “natural anabolic agents”. Results of recent studies suggested that their anabolic effect is mediated by estrogen receptor (ER) binding. Within this study the anabolic potency of ecdysterone was compared to well characterized anabolic substances. Effects on the fiber sizes of the soleus muscle in rats as well the diameter of C2C12 derived myotubes were used as biological readouts. Ecdysterone exhibited a strong hypertrophic effect on the fiber size of rat soleus muscle that was found even stronger compared to the test compounds metandienone (dianabol), estradienedione (trenbolox), and SARM S 1, all administered in the same dose (5 mg/kg body weight, for 21 days). In C2C12 myotubes ecdysterone (1 µM) induced a significant increase of the diameter comparable to dihydrotestosterone (1 µM) and IGF 1 (1.3 nM). Molecular docking experiments supported the ERβ mediated action of ecdysterone. To clarify its status in sports, ecdysterone should be considered to be included in the class “S1.2 Other Anabolic Agents” of the list of prohibited substances of the World Anti-Doping Agency. 相似文献
25.
Muhammad Nasir Nafees Ahmad Christian MK Sieber Amir Latif Salman Akbar Malik Abdul Hameed 《Journal of biomedical science》2013,20(1):70
Background
Xeroderma Pigmentosum (XP) is a rare skin disorder characterized by skin hypersensitivity to sunlight and abnormal pigmentation. The aim of this study was to investigate the genetic cause of a severe XP phenotype in a consanguineous Pakistani family and in silico characterization of any identified disease-associated mutation.Results
The XP complementation group was assigned by genotyping of family for known XP loci. Genotyping data mapped the family to complementation group A locus, involving XPA gene. Mutation analysis of the candidate XP gene by DNA sequencing revealed a novel deletion mutation (c.654del A) in exon 5 of XPA gene. The c.654del A, causes frameshift, which pre-maturely terminates protein and result into a truncated product of 222 amino acid (aa) residues instead of 273 (p.Lys218AsnfsX5). In silico tools were applied to study the likelihood of changes in structural motifs and thus interaction of mutated protein with binding partners. In silico analysis of mutant protein sequence, predicted to affect the aa residue which attains coiled coil structure. The coiled coil structure has an important role in key cellular interactions, especially with DNA damage-binding protein 2 (DDB2), which has important role in DDB-mediated nucleotide excision repair (NER) system.Conclusions
Our findings support the fact of genetic and clinical heterogeneity in XP. The study also predicts the critical role of DDB2 binding region of XPA protein in NER pathway and opens an avenue for further research to study the functional role of the mutated protein domain. 相似文献26.
Anthony A Fryer Richard D Emes Khaled MK Ismail Kim E Haworth Charles Mein William D Carroll William E Farrell 《Epigenetics》2011,6(1):86-94
Supplementation with folic acid during pregnancy is known to reduce the risk of neural tube defects and low birth weight. It is thought that folate and other one-carbon intermediates might secure these clinical effects via DNA methylation. We examined the effects of folate on the human methylome using quantitative interrogation of 27,578 CpG loci associated with 14,496 genes at single-nucleotide resolution across 12 fetal cord blood samples. Consistent with previous studies, the majority of CpG dinucleotides located within CpG islands exhibited hypomethylation while those outside CpG islands showed mid-high methylation. However, for the first time in human samples, unbiased analysis of methylation across samples revealed a significant correlation of methylation patterns with plasma homocysteine, LINE-1 methylation and birth weight centile. Additionally, CpG methylation significantly correlated with either birth weight or LINE-1 methylation were predominantly located in CpG islands. These data indicate that levels of folate-associated intermediates in cord blood reflect their influence and consequences for the fetal epigenome and potentially on pregnancy outcome. In these cases, their influence might be exerted during late gestation or reflect those present during the peri-conceptual period.Key words: cord blood, birth weight, folic acid, homocysteine, BeadArray, hierarchical clustering, Illumina 相似文献
27.
Entomopathogenic fungi have been used for biocontrol of insect pests for many decades. However, the efficacy of such fungi in field trials is often inconsistent, mainly due to environmental stresses, such as UV radiation, temperature extremes, and desiccation. To circumvent these hurdles, metabolic engineering of dihydroxynaphthalene (DHN) melanin biosynthetic genes (polyketide synthase, scytalone dehydratase, and 1,3,8-trihydroxynaphthalene reductase genes) cloned from Alternaria alternata were transformed into the amelanotic entomopathogenic fungus Metarhizium anisopliae via Agrobacterium-mediated transformation. Melanin expression in the transformant of M. anisopliae was verified by spectrophotometric methods, liquid chromatography/mass spectrometry (LC/MS), and confocal microscopy. The transformant, especially under stresses, showed notably enhanced antistress capacity and virulence, in terms of germination and survival rate, infectivity, and reduced median time to death (LT50) in killing diamondback moth (Plutella xylostella) larvae compared with the wild type. The possible mechanisms in enhancing the stress tolerance and virulence, and the significance and potential for engineering melanin biosynthesis genes in other biocontrol agents and crops to improve antistress fitness are discussed. 相似文献
28.
29.
M Küüsmaa-Schildt J Liukkonen MK Vuong K Nyman K Häkkinen A Häkkinen 《Chronobiology international》2019,36(6):811-825
The aim of the present study was to examine how combined strength and endurance training in the morning and evening influences the adaptations in strength and endurance performance, perception of time management, psychological well-being and sleep. The combined training period lasted for 24 weeks and the participants were divided into the morning training (MG, n = 18), evening training (EG, n = 24) and control groups (CG, n = 10). Isometric leg press force (iLP), maximal oxygen consumption (VO2max), sleep behavior, fatigue, time management, motivation, self-esteem and health-related quality of life (HRQoL) were assessed. Morning to evening difference in iLP was observed in both MG and EG at Pre and Post, with higher force values in the evening, but not for VO2max. iLP force increased significantly in EG in the morning (p < 0.001) and evening (p = 0.010). VO2max increased in MG and EG both in the morning (both p < 0.001) and in the evening (MG: p < 0.001; EG: p = 0.003). Participants of the present study slept 7–8 h per night and the self-reported sleep duration, get-up time and the average time to go to bed were similar between the groups and did not change from Pre to Post. From HRQoL dimensions, the score for bodily pain decreased in MG (p = 0.029) and significant between-group differences were observed for Pre-Post changes in MG and EG (p = 0.001) as well as between MG and CG (p < 0.001). In vitality, a significant between-group difference was observed for Pre to Post changes in MG and EG (p = 0.014). Perception of time management decreased in EG (p = 0.042) but stayed unchanged for MG and CG. For the intrinsic motivation to participate, significant between-group differences were observed for MG and EG (p = 0.033) and between MG and CG (p = 0.032) for Pre to Post changes. Self-esteem improved in MG (p = 0.029) and EG (p = 0.024). The present combined strength and endurance training program performed in the morning and in the evening led to similar improvements in strength and endurance performance. Training in the morning or in the evening did not disrupt the already good sleep behavior and it was able to further increase the self-esteem. Although training in the morning hours may leave more time for free time activities or social life (i.e. family and friends) compared to the evening training, it might be more challenging to stay motivated to participate in prolonged training programs in the morning hours. 相似文献
30.