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Results for “systematic evolution”

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At least 433 records · Page 24Linked to original sources

PubMed1998

Primordial nucleosynthesis.

With the advent of the new extragalactic deuterium observations, Big Bang nucleosynthesis (BBN) is on the verge of undergoing a transformation. In the past, the emphasis has been on demonstrating the concordance of the BBN model with the abundances of the light isotopes extrapolated back to their primordial values by using stellar and galactic evolution theories. As a direct measure of primordial deuterium is converged upon, the nature of the field will shift to using the much more precise primordial D/H to constrain the more flexible stellar and galactic evolution models (although the question of potential systematic error in 4He abundance determinations remains open). The remarkable success of the theory to date in establishing the concordance has led to the very robust conclusion of BBN regarding the baryon density. This robustness remains even through major model variations such as an assumed first-order quark-hadron phase transition. The BBN constraints on the cosmological baryon density are reviewed and demonstrate that the bulk of the baryons are dark and also that the bulk of the matter in the universe is nonbaryonic. Comparison of baryonic density arguments from Lyman-alpha clouds, x-ray gas in clusters, and the microwave anisotropy are made.

Astronomical Phenomena↗

PubMed2000

Evolution of interfaces and expansion in width

Interfaces in a model with a single, real nonconserved order parameter and purely dissipative evolution equation are considered. We show that a systematic perturbative approach, called the expansion in width and developed for curved domain walls, can be generalized to the interfaces. A procedure for calculating curvature corrections is described. We also derive formulas for local velocity and local surface tension of the interface. As an example, evolution of spherical interfaces is discussed, including an estimate of the critical size of small droplets.

Journal Article↗

PubMed2006

The evolution of unisexuality in Calligrapha leaf beetles: molecular and ecological insights on multiple origins via interspecific hybridization.

Interspecific hybridization is a well-established cause of unisexual origins in vertebrates. This mechanism is also suspected in other apomictic taxa, but compelling evidence is rare. Here, we evaluate this mechanism and other hypotheses for the evolutionary origins of unisexuality through an investigation of Calligrapha leaf beetles. This group provides an intriguing subject for studies of unisexual evolution because it presents a rare insect example of multiple apomictic thelytokous species within a primarily bisexual genus. To investigate unisexual evolution, this study conducts the first molecular systematic analysis of Calligrapha. This involved the collection and analysis of about 3000 bp of DNA sequences--representing RNA and protein-coding loci from mitochondrial and nuclear genomes--from 54 specimens of 25 Calligrapha species, including four unisexual tetraploid taxa. Phylogenetic and molecular clock analyses indicated independent and single evolutionary origins of each of these unisexual species during the Pleistocene. Significant phylogenetic incongruence was detected between mitochondrial and nuclear datasets and found to be especially associated with the asexual taxa. This pattern is expected when unisexual lineages arise via interspecific hybridization and thus represent genetic mosaics that possess certain nuclear alleles from the paternal species lineage and mitochondrial DNA (mtDNA) alleles from the maternal parent. Analyzing the mtDNA and nuclear relatedness of unisexuals with corresponding haplotypes of bisexual Calligrapha species allowed the putative identification of these maternal and paternal species lineages for each unisexual species. Strong phenotypic similarities between unisexual taxa and their paternal parent species supported a model that involves both backcrosses of interspecific hybrids with a paternal parent and unreduced gametes. This model accounts for the origins of apomixis, polyploidy, and an overrepresentation of paternal nuclear alleles (and associated phenotypes) in unisexuals. This model is also consistent with the tetraploid karyotypes of unisexual Calligrapha, in which three sets of chromosomes (of presumed paternal ancestry) are quite morphologically homogeneous compared to the fourth. Especially intriguing was a consistent association of unisexual species with the host plant of the paternal parent but never with the maternal host. The statistical implausibility of these patterns occurring by chance further supports our inference of parental species. Moreover, it points to a potentially critical role for host-association in the formation and preservation of unisexual lineages. These findings suggest that ecological factors are critical for the diversification of unisexual as well as bisexual taxa and thus point out new research directions in the area of ecological speciation.

Animals↗

PubMed1991

Ribosomal DNA: molecular evolution and phylogenetic inference.

Ribosomal DNA (rDNA) sequences have been aligned and compared in a number of living organisms, and this approach has provided a wealth of information about phylogenetic relationships. Studies of rDNA sequences have been used to infer phylogenetic history across a very broad spectrum, from studies among the basal lineages of life to relationships among closely related species and populations. The reasons for the systematic versatility of rDNA include the numerous rates of evolution among different regions of rDNA (both among and within genes), the presence of many copies of most rDNA sequences per genome, and the pattern of concerted evolution that occurs among repeated copies. These features facilitate the analysis of rDNA by direct RNA sequencing, DNA sequencing (either by cloning or amplification), and restriction enzyme methodologies. Constraints imposed by secondary structure of rRNA and concerted evolution need to be considered in phylogenetic analyses, but these constraints do not appear to impede seriously the usefulness of rDNA. An analysis of aligned sequences of the four nuclear and two mitochondrial rRNA genes identified regions of these genes that are likely to be useful to address phylogenetic problems over a wide range of levels of divergence. In general, the small subunit nuclear sequences appear to be best for elucidating Precambrian divergences, the large subunit nuclear sequences for Paleozoic and Mesozoic divergences, and the organellar sequences of both subunits for Cenozoic divergences. Primer sequences were designed for use in amplifying the entire nuclear rDNA array in 15 sections by use of the polymerase chain reaction; these "universal" primers complement previously described primers for the mitochondrial rRNA genes. Pairs of primers can be selected in conjunction with the analysis of divergence of the rRNA genes to address systematic problems throughout the hierarchy of life.

Animals↗

PubMed2004

Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP).

MOTIVATION: Interacting pairs of proteins should co-evolve to maintain functional and structural complementarity. Consequently, such a pair of protein families shows similarity between their phylogenetic trees. Although the tendency of co-evolution has been known for various ligand-receptor pairs, it has not been studied systematically in the widest possible scope. We investigated the degree of co-evolution for more than 900 family pairs in a global protein structural interactome map (PSIMAP--a map of all the structural domain-domain interactions in the PDB). RESULTS: There was significant correlation in 45% of the total SCOPs Family level pairs, rising to 78% in 454 reliable family interactions. Expectedly, the intra-molecular interactions between protein families showed stronger co-evolution than inter-molecular interactions. However, both types of interaction have a fundamentally similar pattern of co-evolution except for cases where different interfaces are involved. These results validate the use of co-evolution analysis with predictive methods such as PSIMAP to improve the accuracy of prediction based on "homologous interaction". The tendency of co-evolution enabled a nearly 5-fold enrichment in the identification of true interactions among the potential interlogues in PSIMAP. The estimated sensitivity was 79.2%, and the specificity was 78.6%. AVAILABILITY: The results of co-evolution analysis are available online at http://www.biointeraction.org

Amino Acid Sequence↗

PubMed1993

Mapping the stability determinants of bacterial tyrosyl transfer RNA synthetases by an experimental evolutionary approach.

The tyrosyl-tRNA synthetases from Bacillus stearothermophilus (Bst-TyrTS) and Escherichia coli (Eco-TyrTS) are 56% identical in amino acid sequence. To map and characterize the set of interactions that makes Bst-TyrTS more stable than Eco-TyrTS, a family of nine hybrid proteins was constructed between the two enzymes. The N-terminal part of each hybrid came from Eco-TyrTS and the C-terminal part from Bst-TyrTS. The stability and activity of these hybrids were estimated by experiments of thermal inactivation and tRNA charging. For all the hybrids, the temperature of half-inactivation in 30 minutes was above 44 degrees C and the rate of charging was at least 40% that of Bst-TyrTS. In general, the temperature of half-inactivation increased and the rate of charging decreased monotonically when the number of residues coming from the more stable and less active Bst-TyrTS increased. As a result, the rate of charging decreased when the temperature of half-inactivation increased. These results show that the sequences and structures of the two enzymes can replace each other locally and still give a stable and active TyrTS, and that the greater stability of Bst-TyrTS is due to cumulative changes of residues scattered along the sequence. They suggest that Bst-TyrTS is more rigid than Eco-TyrTS at low temperature. The existence of a few exceptional hybrids, having stabilities or activities lower than those of the neighbouring hybrids, shows that compensatory changes of residues have occurred between the two sequences during evolution. These exceptions could be explained by the systematic identification of the couples of residues that are in contact in the Bst-TyrTS structure and become heterologous in some hybrids.

Binding Sites↗

PubMed1995

Graphical user interface for the analysis of noise induced hearing loss.

We have developed a Windows-based computer program which will help the user to collect data needed for calculation models of noise induced hearing loss (NIHL). The program has a graphical user interface and it includes several methods to calculate NIHL. We have tried to make our system to cover all the factors concerning NIHL and also to take into account other possible reasons of hearing loss. The system is used not only for estimating noise induced hearing loss, but also as a systematic way to collect data for future evolution of new models and for other research purposes. For this sake the program asks some questions that are not currently included to these models, but which have been shown to have some impact on noise induced hearing loss.

Computer Graphics↗

PubMed2000

In the arms of Morpheus the development of morphine for postoperative pain relief.

PURPOSE: To analyse the historical development of morphine for postoperative analgesia and how this development was shaped by the evolution of anesthetic techniques. METHODS: After a systematic review of the literature, information was gathered from primary sources. PRINCIPAL FINDINGS: In ancient medicine, some plant derivatives were used to alleviate pain including: alcohol, cannabis, mandrake, and opium. Over the past two centuries, opium and its derivatives have become the most widely used analgesics for severe pain. Before the development of general anesthesia, surgery was only performed out of extreme necessity. It is probable that an analgesic such as opium would have been given following surgery although its use may not have been recorded. The first description of postoperative opium was by James Moore in 1784. Morphine was isolated from opium by Friedrich Serturner in 1805. However, it was not until the development of the hypodermic needle and syringe nearly 50 yr later that the use of morphine became widespread. Over the last century, various delivery systems for morphine have been developed including subarachanoid and epidural injection, and more recently patient-controlled intravenous, epidural and intranasal analgesia. In addition, many new opioids have been synthesized. CONCLUSION: Since its isolation from opium almost 200 yr ago, morphine remains the most widely used analgesic and the standard against which all new opioids for postoperative pain relief are compared.

Analgesics, Opioid↗

PubMed2006

Promoting environmental health policy through community based participatory research: a case study from Harlem, New York.

Community-academic partnerships have demonstrated potential for studying and improving community and environmental health, but only recently have their policy impacts been systematically studied. This case study highlights the evolution, research, and policy processes and outcomes of a community based participatory research (CBPR) partnership that has had multilevel impacts on health policy concerning diesel bus emissions and related environmental justice issues. The partnership between West Harlem Environmental ACTion, Inc. (WE ACT) and the Columbia University Center for Children's Environmental Health was explored using a multimethod case study approach. The conversion of New York City's bus fleet to clean diesel and the installation by the EPA of permanent air monitors in Harlem and other "hot spots" were among the outcomes for which the partnership's research and policy work was given substantial credit. Lessons for other urban community-academic partnerships interested in using CBPR to promote healthy public policy are discussed.

Community Participation↗

PubMed2004

Phylogenetic relationships within the fish family Goodeidae based on cytochrome b sequence data.

A phylogeny of the species in the family Goodeidae was constructed based on the complete mitochondrial cytochrome b gene (1140 bp). Molecular phylogeny was used to revise current systematic of this group, to characterize the evolution of reproductive characters, and to infer a biogeographical model for the Mesa Central of Mexico during the Cenozoic period. We confirmed the monophyly of the subfamily Goodeinae and defined five different lineages within Goodeinae: Chapalichthyini, Girardinichthyini, Goodiini, Ilyodontini, and Charachontini. The morphology of trophotaeniae widely used to infer phylogenetic relationships within goodeids appears to be homoplasious. In a primitive condition, trophotaeniae seem to be very simple structure as occurs in the Charachontini lineage. There is an evolutionary trend to increase trophotaeniae surface via an increase in the number of branches (ribbon type) or branch widening (rosette type). Goodeidae originated in the middle Miocene and it was in the Pliocene when they radied their highest diversity during a dry period that caused basin splitting in the Mesa Central of Mexico.

Animals↗

PubMed2005

Analytical methods for detecting paralogy in molecular datasets.

Paralogy (common ancestry through gene duplication rather than speciation) is widely recognized as an important problem for molecular systematists. This chapter introduces the concepts of paralogy and orthology and explains why paralogy can complicate both systematic work and other studies of molecular evolution. The definition of paralogy is explicitly phylogenetic, and phylogenetic methods are crucial in elucidating the pattern of paralogy. In particular, knowledge of the species phylogeny is key. I introduce the theory behind methods for detecting paralogy and briefly discuss two particular software implementations of phylogenetic methods to detect paralogy from molecular data. I also introduce a statistical method for detecting paralogy and some future directions for work on paralogy detection.

Animals↗

PubMed2003

Application of optimal control theory to the design of broadband excitation pulses for high-resolution NMR.

Optimal control theory is considered as a methodology for pulse sequence design in NMR. It provides the flexibility for systematically imposing desirable constraints on spin system evolution and therefore has a wealth of applications. We have chosen an elementary example to illustrate the capabilities of the optimal control formalism: broadband, constant phase excitation which tolerates miscalibration of RF power and variations in RF homogeneity relevant for standard high-resolution probes. The chosen design criteria were transformation of I(z)-->I(x) over resonance offsets of +/- 20 kHz and RF variability of +/-5%, with a pulse length of 2 ms. Simulations of the resulting pulse transform I(z)-->0.995I(x) over the target ranges in resonance offset and RF variability. Acceptably uniform excitation is obtained over a much larger range of RF variability (approximately 45%) than the strict design limits. The pulse performs well in simulations that include homonuclear and heteronuclear J-couplings. Experimental spectra obtained from 100% 13C-labeled lysine show only minimal coupling effects, in excellent agreement with the simulations. By increasing pulse power and reducing pulse length, we demonstrate experimental excitation of 1H over +/-32 kHz, with phase variations in the spectra <8 degrees and peak amplitudes >93% of maximum. Further improvements in broadband excitation by optimized pulses (BEBOP) may be possible by applying more sophisticated implementations of the optimal control formalism.

Algorithms↗

PubMed2000

Molecular cloning and structural analysis of 3-hydroxy-3-methylglutaryl coenzyme A reductase of the moth Agrotis ipsilon.

The enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase, which plays a key role in isoprenoid biosynthesis, catalyses the synthesis of mevalonate from HMG-CoA. Insects do not synthesize cholesterol de novo, rather mevalonate derivatives lead to non-sterol isoprenoids which are essential for development and reproduction. In this paper, we describe an HMG-CoA reductase of the moth Agrotis ipsilon and we report its expression in fat body, ovary, muscle, brain and corpora allata tissues of adult specimens. The analysis of the cDNA reveals that it encodes a polypeptide of 833 amino acids (Mr = 89785). Alignments of this HMG-CoA reductase from A. ipsilon with the homologous sequences of other eukaryotes shows a high degree of conservation in all species studied. Parsimony analysis based on these alignments produced dendrograms congruent with the current systematic schemes. This suggests that, during eukaryote evolution, HMG-CoA reductase diversified in parallel with taxonomic splitting.

Amino Acid Sequence↗

PubMed1987

Interpretation of DNA vibration modes. II--The adenosine and thymidine residues involved in oligonucleotides and polynucleotides.

Normal coordinate analysis of the adenosine and thymidine residues involved in the right- and left-handed conformations of oligonucleotides and polynucleotides has been performed. The valence force field, employed in this work, allowed recently to reproduce the vibrational spectra of 2'-deoxythymidine and 2'-deoxyadenosine. The calculated wavenumbers based on a non-redundant set of internal coordinates have been compared to the Raman and infrared peak positions arising from A, B, C, D and Z conformations, in the 1550-1250 cm-1 and 800-600 cm-1 spectral regions: i.e. characteristic of adenosine and thymidine residues. Moreover, a systematic study has been performed on the evolution of the vibrational wavenumbers as a function of the glycosidic angle (chi) and the sugar pucker conformation.

Adenosine↗

PubMed2000

Variation in mandible shape in Thrichomys apereoides (Mammalia: Rodentia): geometric analysis of a complex morphological structure.

The model of development and evolution of complex morphological structures conceived by Atchley and Hall in 1991 (Biol. Rev. 66:101-157), which establishes that changes at the macroscopic, morphogenetic level can be statistically detected as variation in skeletal units at distinct scales, was applied in combination with the formalism of geometric morphometrics to study variation in mandible shape among populations of the rodent species Thrichomys apereoides. The thin-plate spline technique produced geometric descriptors of shape derived from anatomical landmarks in the mandible, which we used with graphical and inferential approaches to partition the contribution of global and localized components to the observed differentiation in mandible shape. A major pattern of morphological differentiation in T. apereoides is attributable to localized components of shape at smaller geometric scales associated with specific morphogenetic units of the mandible. On the other hand, a clinical trend of variation is associated primarily with localized components of shape at larger geometric scales. Morphogenetic mechanisms assumed to be operating to produce the observed differentiation in the specific units of the mandible include mesenchymal condensation differentiation, muscle hypertrophy, and tooth growth. Perspectives for the application of models of morphological evolution and geometric morphometrics to morphologically based systematic biology are considered.

Animals↗

PubMed1995

Observations on the pathological spectrum and clinical course of microsporidiosis in men infected with the human immunodeficiency virus: follow-up study.

The purposes of this research were to determine whether microsporidian infection is accompanied by structural alterations of the duodenal mucosa and to characterize the clinical and morphological evolution of intestinal microsporidiosis. In a previous systematic electron microscopic evaluation of mucosal biopsy specimens from patients with human immunodeficiency virus infection, we detected Enterocytozoon bieneusi in the duodenal tissue of 31 men. This report concerns a follow-up study of these 31 men, who underwent repeated clinical and laboratory evaluations, including repeated duodenal biopsies. Eighteen men had chronic diarrhea at enrollment and 13 had no diarrhea. The CD4+ cell counts (per mm3) ranged from 10 to 660 and were normal for three men. E. bieneusi infection was accompanied by a wide spectrum of histopathology of duodenal tissue; over a mean follow-up of 15 months, no consistent change in duodenal mucosal morphology was observed, and diarrhea did not invariably develop. These observations indicate that diarrhea and severe villus injury do not invariably accompany infection. Further studies are needed to determine the relationship between E. bieneusi infection and clinical illness.

AIDS-Related Opportunistic Infections↗

PubMed2026

Reference genomes of Japanese raccoon dog (Nyctereutes viverrinus) and a Japanese red fox (Vulpes vulpes japonica).

We established primary fibroblast cultures from a Japanese raccoon dog (Nyctereutes viverrinus) and a Japanese red fox (Vulpes vulpes japonica) and generated highly contiguous reference genome assemblies using Oxford Nanopore Technologies PromethION long-read sequencing. The Japanese raccoon dog assembly spanned 2.69 Gb in 813 scaffolds, with a scaffold N50 of 52 Mb and a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score of 98.2%. The Japanese red fox assembly spanned 2.47 Gb in 903 scaffolds, with a scaffold N50 of 139 Mb and a BUSCO completeness score of 97.5%. Phylogenomic analysis placed the Japanese raccoon dog in a lineage distinct from the continental raccoon dog, supporting its evolutionary differentiation within Nyctereutes. The Japanese red fox formed a distinct lineage within the red fox clade, consistent with its recognized regional differentiation. These genome assemblies and associated fibroblast cultures provide resources for studies of canid systematics, population history, local adaptation, comparative genome evolution, and conservation genetics.

Canidae↗

PubMed1999

Flow of a vortex-pair street and the evolution of salt fingers.

We considered the geometry of a double row of vortex pairs in an ideal fluid, and studied the evolution of salt fingers from the geometry systematically. This study illustrates the mechanism of the generation of large-scale convective cells at the final stage of the fingering instability. We discuss why in the growth of double-diffusive salt fingers the emergence of such large convection cells has been implicated phenomenologically as an onset to turbulence, terminating the finger growth.

Journal Article↗