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91.
A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony 总被引:24,自引:1,他引:23
The method of evolutionary parsimony--or operator invariants--is a
technique of nucleic acid sequence analysis related to parsimony analysis
and explicitly designed for determining evolutionary relationships among
four distantly related taxa. The method is independent of substitution
rates because it is derived from consideration of the group properties of
substitution operators rather than from an analysis of the probabilities of
substitution in branches of a tree. In both parsimony and evolutionary
parsimony, three patterns of nucleotide substitution are associated
one-to-one with the three topologically linked trees for four taxa. In
evolutionary parsimony, the three quantities are operator invariants. These
invariants are the remnants of substitutions that have occurred in the
interior branch of the tree and are analogous to the substitutions assigned
to the central branch by parsimony. The two invariants associated with the
incorrect trees must equal zero (statistically), whereas only the correct
tree can have a nonzero invariant. The chi 2-test is used to ascertain the
nonzero invariant and the statistically favored tree. Examples, obtained
using data calculated with evolutionary rates and branchings designed to
camouflage the true tree, show that the method accurately predicts the
tree, even when substitution rates differ greatly in neighboring peripheral
branches (conditions under which parsimony will consistently fail). As the
number of substitutions in peripheral branches becomes fewer, the parsimony
and the evolutionary-parsimony solutions converge. The method is robust and
easy to use.
相似文献
92.
Carbamoylphosphate synthetase (CPS) catalyzes the first committed step in
pyrimidine biosynthesis, arginine biosynthesis, or the urea cycle.
Organisms may contain either one generalized or two specific CPS enzymes,
and these enzymes may be heterodimeric (encoded by linked or unlinked
genes), monomeric, or part of a multifunctional protein. In order to help
elucidate the evolution of CPS, we have performed a comprehensive
phylogenetic analysis using the 21 available complete CPS sequences,
including a sequence from Sulfolobus solfataricus P2 which we report in
this paper. This is the first report of a complete CPS gene sequence from
an archaeon, and sequence analysis suggests that it encodes an enzyme
similar to heterodimeric CPSII. We confirm that internal similarity within
the synthetase domain of CPS is the result of an ancient gene duplication
that preceded the divergence of the Bacteria, Archaea, and Eukarya, and use
this internal duplication in phylogenetic tree construction to root the
tree of life. Our analysis indicates with high confidence that this
archaeal sequence is more closely related to those of Eukarya than to those
of Bacteria. In addition to this ancient duplication which created the
synthetase domain, our phylogenetic analysis reveals a complex history of
further gene duplications, fusions, and other events which have played an
integral part in the evolution of CPS.
相似文献
93.
Yescas CP MA Segura C L Martínez C VP Álvarez R JA Montemayor T JA Orozco V JE Frías R 《Phyton》2015,84(2):272-279
The scarcity of water in arid and semiarid regions of the world is a problem that every day increases by climate change. The subsurface drip irrigation (SDI) and changes in population density of plants are alternatives that can be used to make a sustainable use of water. Therefore, the objectives of this study were to determine the combination that allows for an increased corn performance and efficient use of water without losing the quality of forage. Three different irrigation levels were applied through a system of a SDI at three different densities of forage maize plants in an arid region. The results demonstrated that by applying different levels of water, either enough or lack of soil moisture is created, which is directly reflected in crop yield, and its determining variables such as green forage and dry matter yield, and nutritional quality. The irrigation level to a 100% of potential evapotranspiration (PET), at a density of 80000 plants/ha, increased yield of green forage to 57664 kg/ha; crude protein was 8.59%, while the rest of the quality parameters decreased. This study allowed to conclude that the irrigation level was the major factor in the response of the crop. 相似文献
94.
Price DJ Campbell PG Sutton AG Grech ED Davies A Hall JA De Belder MA 《International journal of cardiovascular interventions》2001,4(1):15-20
BACKGROUND: The EPISTENT trial reported improved early outcomes with routine use of abciximab after coronary stenting. Increasing use of stents means that routine abciximab adds significantly to costs of percutaneous coronary intervention (PCI). This paper reports the results of a protocol encouraging restriction of abciximab therapy to high-risk patients only. METHODS: Data were collected prospectively over a 34-month period for patients undergoing PCI with stenting. In addition to those who fulfilled criteria for inclusion in the EPISTENT trial, patients treated in the setting of acute myocardial infarction (AMI) were studied. Demographic data, procedural details and early clinical outcomes were recorded. RESULTS: Of 808 patients studied, 601 fulfilled EPISTENT inclusion criteria and comprised 367 patients (45%) treated for stable angina and 234 (30%) treated for unstable or post-infarct angina. The additional 207 patients (25%) were treated during AMI. The 808 patients received a total of 981 stents. Abciximab was given in only 88 cases (10.9%). Major adverse clinical events occurred in 39 patients (4.8%). CONCLUSION: Selective use of abciximab for patients undergoing coronary stenting can be associated with outcomes equivalent to those reported for routine use, but with significant cost savings. 相似文献
95.
JA Kiernan 《Biotechnic & histochemistry》2018,93(2):133-148
Previous investigators have disagreed about whether hemalum stains DNA or its associated nucleoproteins. I review here the literature and describe new experiments in an attempt to resolve the controversy. Hemalum solutions, which contain aluminum ions and hematein, are routinely used to stain nuclei. A solution containing 16 Al3+ ions for each hematein molecule, at pH 2.0–2.5, provides selective progressive staining of chromatin without cytoplasmic or extracellular “background color.” Such solutions contain a red cationic dye-metal complex and an excess of Al3+ ions. The red complex is converted to an insoluble blue compound, assumed to be polymeric, but of undetermined composition, when stained sections are blued in water at pH 5.5–8.5. Staining experiments with DNA, histone and DNA + histone mixtures support the theory that DNA, not histone, is progressively colored by hemalum. Extraction of nucleic acids, by either a strong acid or nucleases at near neutral pH, prevented chromatin staining by a simple cationic dye, thionine, pH 4, and by hemalum, with pH adjustments in the range, 2.0–3.5. Staining by hemalum at pH 2.0–3.5 was not inhibited by methylation, which completely prevented staining by thionine at pH 4. Staining by hemalum and other dye-metal complexes at pH ≤ 2 may be due to the high acidity of DNA-phosphodiester (pKa ~ 1). This argument does not explain the requirement for a much higher pH to stain DNA with those dyes and fluorochromes not used as dye-metal complexes. Sequential treatment of sections with Al2(SO4)3 followed by hematein provides nuclear staining that is weaker than that attainable with hemalum. Stronger staining is seen if the pH is raised to 3.0–3.5, but there is also coloration of cytoplasm and other materials. These observations do not support the theory that Al3+ forms bridges between chromatin and hematein. When staining with hematein is followed by an Al2(SO4)3 solution, there is no significant staining. Taken together, the results of my study indicate that the red hemalum cation is electrostatically attracted to the phosphate anion of DNA. The bulky complex cation is too large to intercalate between base pairs of DNA and is unlikely to fit into the minor groove. The short range van der Waals forces that bind planar dye cations to DNA probably do not contribute to the stability of progressive hemalum staining. The red cation is precipitated in situ as a blue compound, insoluble in water, ethanol and water-ethanol mixtures, when a stained preparation is blued at pH > 5.5. 相似文献
96.
Kathryn E Wheatley Corey JA Bradshaw Robert G Harcourt Lloyd S Davis Mark A Hindell 《BMC veterinary research》2006,2(1):1-8
Background
Postweaning diarrhoea (PWD) in pigs is usually the main infectious problem of large-scale farms and is responsible for significant losses worldwide. The disease is caused mainly by enterotoxigenic E. coli (ETEC) and Shiga-toxin producing E. coli (STEC). In this study a total of 101 E. coli isolated from pigs with PWD in Slovakia were characterized using phenotypic and genotypic methods.Results
These 101 isolates belonged to 40 O:H serotypes. However, 57% of the isolates belonged to only six serotypes (O9:H51, O147:H-, O149:H10, O163:H-, ONT:H-, and ONT:H4), including two new serotypes (O163:H- and ONT:H4) not previously found among porcine ETEC and STEC isolated in other countries. Genes for EAST1, STb, STa, LT and Stx2e toxins were identified in 64%, 46%, 26%, 20%, and 5% of isolates, respectively. PCR showed that 35% of isolates carried genes for F18 colonization factor, and further analyzed by restriction endonuclease revealed that all of them were F18ac. Genes for F4 (K88), F6 (P987), F17, F5 (K99), F41, and intimin (eae gene) adhesins were detected in 19 %, 5%, 3%, 0.9%, 0.9%, and 0.9% of the isolates, respectively. The study of genetic diversity, carried out by PFGE of 46 representative ETEC and STEC isolates, revealed 36 distinct restriction profiles clustered in eight groups. Isolates of the same serotype were placed together in the dendrogram, but high degree of polymorphism among certain serotypes was detected.Conclusion
Seropathotype O149:H10 LT/STb/EAST1/F4 (14 isolates) was the most commonly detected followed by O163:H- EAST1/F18 (six isolates), and ONT:H4 STa/STb/Stx2e/F18 (five isolates). Interestingly, this study shows that two new serotypes (O163:H- and ONT:H4) have emerged as pig pathogens in Slovakia. Furthermore, our results show that there is a high genetic variation mainly among ETEC of O149:H10 serotype. 相似文献97.
98.
López-Valenzuela BE Armenta-Bojórquez AD Hernández-Verdugo S Apodaca- Sánchez MA Samaniego-Gaxiola JA Valdez-Ortiz A 《Phyton》2019,88(1):37-46
Microbes that are beneficial to plants are used to
enhance the crop growth, yield and are alternatives to chemical
fertilizers. Trichoderma and Bacillus are the predominant plant
growth-promoting fungi and bacteria. The objective of this study
was select, characterize, and evaluate isolates of Trichoderma
spp. and Bacillus spp. native from the northern region of Sinaloa,
Mexico, and assess their effect on growth promotion in maize (Zea
mays L.). In greenhouse conditions, four Trichoderma isolates and
twenty Bacillus isolates, as well as two controls, were tested in a
completely randomized design with three replicates. We selected
the two best strains of Trichoderma and Bacillus: TB = Trichoderma
asperellum, TF = Trichoderma virens, B14 = Bacillus cereus sensu
lato and B17 = Bacillus cereus, which were evaluated in the field in
a completely randomized blocks in factorial arrangement design
with three replicates applying different rates of nitrogen fertilizer
(0, 150 kg N/ha, and 300 kg N/ha). Treatments 5 (B17 = B. cereus)
and 11 (TF = T. virens) both fertilized with 150 kg N/ha showed
similar yields and they did not reveal significant differences from
the treatments fertilized with 300 kg N/ha. This indicated that
treatment 5 (B17= B. cereus with 150 kg N/ha) and treatment
11 (TF= T. virens with 150 kg N/ha) were efficient as growth
promoters, by not showing significant differences in root volume
and dry weight of foliage. The results indicated a reduction of 50%
in the rate of nitrogen to fertilizer required for maize (Zea mays
L.) crops. These microorganisms Trichoderma and Bacillus could
be an alternative to reduce the use of chemical fertilizers in maize. 相似文献
99.
The segregation of laboratory maintained male and larval Myrmecia gulosa from workers resulted in increased levels of culturable microbiota. After 29 days, microbial levels recovered from segregated males and larvae were 27 and 126 times greater than from males and larvae not segregated from workers. These findings are consistent with the hypothesis that metapleural gland secretions, absent in larvae and males, are transferred from workers to larvae, and males contribute to the inhibition of cuticular microbiota. 相似文献
100.
Alves-Gomes JA; Orti G; Haygood M; Heiligenberg W; Meyer A 《Molecular biology and evolution》1995,12(2):298-318
The order Gymnotiformes (South American electric fishes) is a fascinating
assemblage of freshwater fishes that share the unusual ability to produce
and sense electric fields used for electrolocation and social
communication. In the last few decades, the electrogenic and electrosensory
systems (EES) of these fish have served as an excellent model to study
motor and sensory physiology in vertebrates. In an attempt to the evolution
of characters associated with the EES in the group, we applied
maximum-parsimony (MP), minimum-evolution (ME), and maximum-likelihood (ML)
methods to analyze 302 aligned bases of the mitochondrial 12S rRNA and 416
bases of the mitochondrial 16S rRNA of 19 gymnotiform genera representing
all six recognized families. Six catfish genera (order Siluriformes) were
also sequenced and used as outgroups. The phylogenetic hypothesis resultant
from molecular data analysis differs in some respects from previous
hypotheses based on morphological studies. Our results were most
informative within the family level, as we were unable to elucidate the
relationships among deeper branches in this order with sufficient
confidence by using molecular data alone. The phylogenetic information of
both mitochondrial DNA segments appears to be affected by functional
constraints, and the resultant topologies were sensitive to different
weighting schemes and the algorithm used. Nonetheless, we found unanimous
support for the following phylogenetic relationships: (1) the family
Sternopygidae is an unnatural group, and Sternopygus is the sole
representative of a unique lineage within the order; (2) the family
Hypopomidae is not monophyletic; and (3) the order Gymnotiformes is
composed of at least six natural clades: Sternopygus, family Apteronotidae,
a new clade consisting of the remaining sternopygids, families Hypopomidae
+ Rhamphicthyidae, family Electrophoridae, and family Gymnotidae. By
combining molecular, morphological, and physiological information, we
propose a new hypothesis for the phylogeny of this group and suggest a new
family Eigenmanniidae n. (order Gymnotiformes).
相似文献