Primate phylogeny from the perspective of molecular systematics.
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Amino Acid Sequence↗
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Results for “systematic evolution”
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[Comparison of the zymograms of isopod (Crustacea, Peracarides) digestive tubes].
The zymograms of the digestive caeca and the intestine in seven species of Isopods are established. The glucidasic activities predominate. A relative proteasic poverty is noted as well as the absence of lipases however, the esterases exist. The enzymatic pattern of the gut suggests its participation in the alimentary digestion. The enzymes distribution allows us to establish relations with the food preference of the animals. Some particularities (trypsin, alpha and beta glucosidase) favour a comparison of the marine species with the supralittoral species on one hand and with terrestrial species on the other. This fact does not exclude however the systematic interest of the zymograms.
Animals↗
Chromosomal and molecular evolution in Asiatic wild asses.
Chromosomal studies of Tibetan wild ass, Equus kiang holdereri are reported for the first time. A Robertsonian polymorphism resulting in diploid numbers of 2n = 51 and 2n = 52 was identified. This polymorphism involves the same elements that participate in the polymorphic Robertsonian rearrangement producing diploid numbers of 54-56 in E. hemionus kulan and E. hemionus onager. Comparison of mitochondrial DNA restriction fragment patterns among three unrelated kiang individuals and between kiangs and a Transcaspian kulan, E. hemionus kulan, indicates an approximately 1% nucleotide sequence divergence of mitochondrial DNAs between the two taxa. The chromosomal divergence between E. hemionus and E. kiang probably originated less than 500,000 years ago. Studies of additional Asiatic wild ass taxa are indicated in order to gain further insights into the speciation and systematics of this threatened group of mammals.
Animals↗
The rise and fall of the CR1 subfamily in the lineage leading to penguins.
The evolution of penguins has been investigated extensively, although inconclusively, by morphologists, biogeographers and molecular phylogeneticists. We investigated this issue using retroposon analysis of insertions of CR1, which is a member of the LINE (long interspersed element) family, in the genomes of penguins and penguin relatives. The retroposon method is a powerful tool for identifying monophyletic groups. Because retroposons often show different relative frequencies of retroposition during evolution, it is first necessary to identify a certain subgroup that was specifically active during the period when the species in question diverged. Hence, we systematically analyzed many CR1 members isolated from penguin and penguin-related genomes. These CR1s are divided into at least three distinct subgroups that share diagnostic nucleotide insertions and/or deletions, namely, penguin CR1 Sph I, Sph II type A and Sph II type B. The analysis of the inserted retroposons by PCR revealed that different CR1 subfamilies or types had amplified at different rates among different periods during penguin evolution. Namely, the penguin CR1 Sph I subfamily had higher rates of retroposition in a common ancestor of all orders examined in this study or at least in a common ancestor of all extant penguins, and the subfamily Sph II type A also had the same tendency. Therefore, these CR1 members can be used to elucidate the phylogenetic relationships of Sphenisciformes (penguins) among different avian orders. In contrast, the penguin CR1 Sph II type B subfamily had higher rates of retroposition just before and after the emergence of the extant genera in Spheniscidae, suggesting that they are useful for elucidating the intra-relationships among extant penguins. This is the first report for the characterization among the members of CR1 family in avian genomes excluding those of chickens. Hence, this work will be a cornerstone for elucidating the phylogenetic relationships in penguin evolution using the retroposon method.
Animals↗
Electrospun Nanofiber Dressings for Diabetic Wounds: From Single-Layer to Intelligent Composite Systems.
Diabetic chronic wounds have become a major challenge for clinical treatment due to their complex pathological microenvironment, including persistent inflammatory response, angiogenesis disorder, excessive oxidative stress, and susceptible infection. Traditional dressings as a passive barrier have difficulty meeting the above multiple treatment needs. Electrospinning technology, with its ability to mimic the fibrous network structure of the natural extracellular matrix (ECM), offers a high specific surface area, controllable porosity, and excellent drug-loading capacity, making it an ideal platform for developing a new generation of multifunctional wound dressings. This article provides a systematic review of the research progress on electrospun nanofiber dressings in the treatment of diabetic wounds, focusing on the design evolution from basic single-layer structures to advanced complex structures and elucidating the mechanisms of action and quantifiable effects of each structural type in addressing specific pathological challenges. We also compared the current status of clinical translation for electrospun dressings with that of other advanced wound care platforms and proposed a standardized preclinical evaluation framework. A large number of research data show that these advanced designs can effectively improve the quality of healing. Finally, this paper points out the challenges faced by this field, such as scalable fabrication, in vivo reliability of smart systems, and long-term biosafety, and provides theoretical basis and technical reference for the design of efficient and intelligent electrostatic spinning diabetic wound dressings.
Nanofibers↗
Epidemiology of inflammatory bowel disease in Spain. A systematic review.
BACKGROUND AND OBJECTIVES: Incidence and prevalence of Inflammatory Bowel Disease (IBD) differ considerably depending on the geographical region studied. In Spain, both Ulcerative Colitis (UC) and Crohn's Disease (CD) seem to have experienced an important change in terms of incidence during the past decades. Our aim was to systematically review the experience in Spain regarding the epidemiology of IBD, in particular its incidence, its geographical differences and its evolution over time. METHODS: A bibliographical search till January 2000 was conducted in Internet using the PubMed search motor and the following descriptors or key words: "Crohn's disease", "Ulcerative colitis", "Inflammatory bowel disease", "Spain" and "Spanish". Only publications providing data on IBD incidence among Spanish patients were included. References from articles that fulfilled the selection criteria were also reviewed. The endpoints considered in the review were IBD incidence rate, its geographical differences, and its evolution over time. RESULTS: UC incidence reported by different studies performed in Spain ranges from 0.6 to 8 cases/10(5)/year, with a mean value of 3.8. CD incidence rates in Spain ranges from 0.4 to 5.5 cases/105/year, with a mean value of 1.9. Some studies have shown differences in IBD incidence between regions in our country. Many studies have reported an increase in IBD incidence in Spain over time, although such increase is more evident in the case of CD. CONCLUSIONS: UC incidence in Spain ranges from 0.6 to 8 cases/105/year, with a mean value of 3.8. CD figures range from 0.4 to 5.5 cases/105/year, with an average rate of 1.9. IBD incidence seems to be relatively different depending on the geographical region studied. Finally, several authors have demonstrated an increase in IBD incidence in Spain over time, although such increase seems to be more evident in the case of CD. Consequently, IBD in Spain is no longer considered a rare disease, but a relatively frequent one.
Humans↗
Evolutionary ethics from Darwin to Moore.
Evolutionary ethics has a long history, dating all the way back to Charles Darwin. Almost immediately after the publication of the Origin, an immense interest arose in the moral implications of Darwinism and whether the truth of Darwinism would undermine traditional ethics. Though the biological thesis was certainly exciting, nobody suspected that the impact of the Origin would be confined to the scientific arena. As one historian wrote, 'whether or not ancient populations of armadillos were transformed into the species that currently inhabit the new world was certainly a topic about which zoologists could disagree. But it was in discussing the broader implications of the theory...that tempers flared and statements were made which could transform what otherwise would have been a quiet scholarly meeting into a social scandal' (Farber 1994, 22). Some resistance to the biological thesis of Darwinism sprung from the thought that it was incompatible with traditional morality and, since one of them had to go, many thought that Darwinism should be rejected. However, some people did realize that a secular ethics was possible so, even if Darwinism did undermine traditional religious beliefs, it need not have any effects on moral thought. Before I begin my discussion of evolutionary ethics from Darwin to Moore, I would like to make some more general remarks about its development. There are three key events during this history of evolutionary ethics. First, Charles Darwin published On the Origin of the Species (Darwin 1859). Since one did not have a fully developed theory of evolution until 1859, there exists little work on evolutionary ethics until then. Shortly thereafter, Herbert Spencer (1898) penned the first systematic theory of evolutionary ethics, which was promptly attacked by T.H. Huxley (Huxley 1894). Second, at about the turn of the century, moral philosophers entered the fray and attempted to demonstrate logical errors in Spencer's work; such errors were alluded to but never fully brought to the fore by Huxley. These philosophers were the well known moralists from Cambridge: Henry Sidgwick (Sidgwick 1902, 1907) and G.E. Moore (Moore 1903), though their ideas hearkened back to David Hume (Hume 1960). These criticisms were so strong that the industry of evolutionary ethics was largely abandoned (though with some exceptions) for many years. Third, E.O. Wilson, a Harvard entomologist, published Sociobiology: The New Synthesis in 1975 (Wilson E.O. 1975), which sparked renewed interest in evolutionary ethics and offered new directions of investigation. These events suggest the following stages for the history of evolutionary ethics: development, criticism and abandonment, revival. In this paper, I shall focus on the first two stages, since those are the ones on which the philosophical merits have already been largely decided. The revival stage is still in progress and we shall eventually find out whether it was a success.
Biological Evolution↗
Evolution of genes, evolution of species: the case of aminoacyl-tRNA synthetases.
All of the aminoacyl-tRNA synthetase (aaRS) sequences currently available in the data banks have been subjected to a systematic analysis aimed at finding gene duplications, genetic recombinations, and horizontal transfers. Evidence is provided for the occurrence (or probable occurrence) of such phenomena within this class of enzymes. In particular, it is suggested that the monomeric PheRS from the yeast mitochondrion is a chimera of the alpha and beta chains of the standard tetrameric protein. In addition, it is proposed that the dimeric and tetrameric forms of GlyRS are the result of a double and independent acquisition of the same specificity within two different subclasses of aaRS. The phylogenetic reconstructions of the evolutionary histories of the genes encoding aaRS are shown to be extremely diverse. While large segments of the population are consistent with the broad grouping into the three Woesian domains, some phylogenetic reconstructions do not place the Archae and the Eucarya as sister groups but, rather, show a gram-negative bacteria/eukaryote clustering. In addition, many individual genes pose difficulties that preclude any simple evolutionary scheme. Thus, aaRS's are clearly a paradigm of F. Jacob's "odd jobs of evolution" but, on the whole, do not call into question the evolutionary scenario originally proposed by Woese and subsequently refined by others.
Amino Acid Sequence↗
[Genomic evolution and epidemiological patterns of respiratory syncytial virus and their implications for surveillance and early warning].
Respiratory syncytial virus (RSV) is an important respiratory pathogen in infants, young children and older adults. Based on global RSV genomic surveillance data, this review systematically summarizes the geographic distribution, seasonal epidemic patterns, and long-term evolutionary trends of RSV, with particular emphasis on the sustained circulation and evolutionary mechanisms of dominant genotypes such as ON1 in RSV-A and BA9 in RSV-B. Current evidence indicates that RSV transmission dynamics are tightly coupled with viral evolution. The G gene evolves relatively rapidly and contains multiple positively selected sites, suggesting an important role in immune escape and population adaptation. In recent years, changes in social behavior patterns and population immunity have further disrupted the seasonal rhythm of RSV and may have influenced the spread of dominant genotypes. Under routine respiratory infectious disease surveillance, strengthened genomic monitoring and integration of multi-source data are needed to improve early warning of abnormal RSV epidemics and variant-associated risks, thereby providing prospective evidence for protecting high-risk populations and informing public health decision-making.
Humans↗
Systematic genome-wide annotation of spliceosomal proteins reveals differential gene family expansion.
Although more than 200 human spliceosomal and splicing-associated proteins are known, the evolution of the splicing machinery has not been studied extensively. The recent near-complete sequencing and annotation of distant vertebrate and chordate genomes provides the opportunity for an exhaustive comparative analysis of splicing factors across eukaryotes. We describe here our semiautomated computational pipeline to identify and annotate splicing factors in representative species of eukaryotes. We focused on protein families whose role in splicing is confirmed by experimental evidence. We visually inspected 1894 proteins and manually curated 224 of them. Our analysis shows a general conservation of the core spliceosomal proteins across the eukaryotic lineage, contrasting with selective expansions of protein families known to play a role in the regulation of splicing, most notably of SR proteins in metazoans and of heterogeneous nuclear ribonucleoproteins (hnRNP) in vertebrates. We also observed vertebrate-specific expansion of the CLK and SRPK kinases (which phosphorylate SR proteins), and the CUG-BP/CELF family of splicing regulators. Furthermore, we report several intronless genes amongst splicing proteins in mammals, suggesting that retrotransposition contributed to the complexity of the mammalian splicing apparatus.
Animals↗
Paraaortic lymphadenectomy is not necessary in the treatment of localized paratesticular rhabdomyosarcoma.
Paraaortic lymphadenectomy is routinely recommended to treat paratesticular rhabdomyosarcoma (RMS) because of the high incidence of lymph node involvement. Taking into account the effectiveness of chemotherapy to sterilize micrometastases and aiming to reduce short-term and long-term side effects due to lymph node dissection, the RMS Group of the SIOP decided to avoid lymphadenectomy in Stage I paratesticular RMS defined by (1) complete tumor removal with negative cord section and (2) negative pedal lymphangiography. A series of 19 children (mean age 5 years, 6 months), treated between 1971 and 1981, were analyzed. Eighteen of 19 patients received adjuvant chemotherapy, using vincristine, actinomycin, cyclophosphamide, singly or alternately with vincristine, Adriamycin (doxorubicin) every 3 weeks. Duration was either 18 months (7 cases) or 8 months (11 cases). Fourteen patients are in first remission with a follow-up of more than 3 years (median 5 years); three are disease-free 35, 23, and 20 months since diagnosis; two patients are alive without evolutive disease, 32 and 56 months after an abdominal relapse. Results obtained in this series demonstrate the ineffectiveness of systematic paraaortic lymphadenectomy in Stage I paratesticular RMS and the effectiveness of chemotherapy to eradicate occult micrometastases, which obviously may exist in paraaortic lymph nodes in spite of apparently normal lymphographic findings.
Antineoplastic Combined Chemotherapy Protocols↗
Binding of amino acid side-chains to S1 cavities of serine proteinases.
The P1 or primary specificity residue of standard mechanism canonical protein inhibitors of serine proteinases, inserts into the S1 primary specificity cavity of the cognate enzyme upon enzyme-inhibitor complex formation. Both natural evolution and protein engineering often change the P1 residue to greatly alter the specificity and the binding strength. To systematize such results we have obtained all 20 coded P1 variants of one such inhibitor, turkey ovomucoid third domain, by recombinant DNA technology. The variants were extensively characterized. The association equilibrium constants were measured at pH 8.30, 21 (+/-2) degrees C, for interaction of these variants with six well characterized serine proteinases with hydrophobic S1, cavities. The enzyme names are followed by the best, worst and most specific coded residue for each. Bovine chymotrypsin A alpha (Tyr, Pro, Trp), porcine pancreatic elastase (Leu/Ala, Arg, Ala), subtilisin Carlsberg (Cys, Pro, Glu), Streptomyces griseus proteinase A (Cys, Pro, Leu) and B (Cys, Pro, Lys) and human leukocyte elastase (Ile, Asp, Ile). The data set was merged with Ka values for five non-coded variants at P1 of turkey ovomucoid third domain obtained in our laboratory by enzymatic semisynthesis. The ratios of the highest to the lowest Ka for each of the six enzymes range from 10(6) to 10(8). The dominant force for binding to these pockets is the hydrophobic interaction. Excess steric bulk (too large for the pocket), awkward shape (Pro, Val and Ile), polarity (Ser) oppose interaction. Ionic charges, especially negative charges on Glu- and Asp- are strongly unfavorable. The Pearson pro duct moment correlations for all the 15 enzyme pairs were calculated. We suggest that these may serve as a quantitative description of the specificity of the enzymes at P1. The sets of Streptomyces griseus proteinases A and B and of the two elastases are strongly positively correlated. Strikingly, chymotrypsin and pancreatic elastase are negatively correlated (-0.10). Such correlations can be usefully extended to many other enzymes and to many other binding pockets to provide a general measure of pocket binding specificity.
Amino Acid Sequence↗
Bridging sulfur substitutions in the analysis of pre-mRNA splicing.
Accurate excision of intervening sequences (introns) from messenger RNA precursors is accomplished by a very large and complicated ribonucleoprotein complex called the spliceosome. Elucidating the mechanisms of the two phosphotransesterification reactions that result in intron removal is important for our understanding of the molecular evolution of early genetic systems, as well as our knowledge of contemporary eukaryotic gene expression. The functional consequences of systematic alterations in the reactive groups can be invaluable for understanding catalytic mechanisms, especially for enzymes, such as the spliceosome, whose size and complexity place them beyond the reach of crystallographic and spectroscopic analysis. One type of modification that can be incorporated into a scissile phosphate linkage is the phosphorothiolate, in which a bridging phosphate oxygen is substituted with sulfur. Phosphorothiolate substitutions can be used to detect metal ion-ligand interactions by a "metal specificity switch" strategy. I review recent advances in the synthesis, incorporation, and manipulation of nucleoside phosphorothiolates (with an emphasis on 3'-S-phosphorothiolates), and describe their utility in the study of pre-mRNA splicing.
Electrophoresis↗
Spontaneous resolution of arachnoid cysts: review and features of an unusual case.
Most intra-cranial arachnoid cysts are quiescent and remain asymptomatic throughout life. Within the natural course of arachnoid cyst evolution, spontaneous resolution has been known to occur rarely, but its frequency is probably underestimated due to lack of systematic detection and long-term observation. We illustrate the spontaneous regression of arachnoid cysts with a patient which was conjointly diagnosed with an arachnoid cyst and a post-traumatic epidural haematoma. Cyst regression was observed 16 months later, upon examination following a second benign cranial trauma. Mechanisms underlying the resolution of the arachnoid cyst are discussed.
Adult↗
Anatomical and descriptive study of the radial extensor muscle (M. extensor carpi radialis).
The M. extensores carpi radiales have been studied in detail in humans. The aim of this study was to carry out a comparative anatomical study of these muscles using four species--rabbit, cat, dog and sheep--and to propose a 'systematization' in a few standard models according to the morphological variations seen. In these species, there is marked morphological evolution, with two muscles in humans, one in sheep and a more or less distinct division of the muscle in the rabbit, cat and dog. Examination of the vascularization and nerve supply enables us to determine degrees of division in species with similar muscle morphology. Thus we were able to distinguish three morphological types which allow us to infer the morphological evolution of the M. extensores carpi radiales and to estimate the point at which one muscle became two. However, there is a strong chance that some process of convergence may have occurred, and in pentadactyl species many elements represent the plesiomorphis and are therefore of little use in constructing a classification on the basis of evolution.
Animals↗
Interstitial hybridization sites of the (TTAGGG)n telomeric sequence on the chromosomes of some North American hylid frogs.
Interstitial hybridization sites for the (TTAGGG)n telomeric repeat sequence were present in all seven species of hylid frogs examined and in a triploid hybrid between two of the species. Intra- and interspecific differences and similarities in hybridization sites agreed with what is known about the systematics of these species. Chromosome fusions, fissions, and inversions do not appear to have played a role in the evolution of the interstitial sites for the telomeric repeat in the species examined.
Animals↗
Multiple-scattering-based lidar retrieval: method and results of cloud probings.
Recent developments in the search for a practical method of exploiting the multiple-scattering contributions to lidar returns are consolidated in a robust retrieval algorithm. The theoretical basis is the small-angle diffusion approximation. This implies that the algorithm is limited to media of sufficient optical thickness to generate measurable multiple scattering and to geometries for which the receiver's footprint diameter is less than the scattering mean free path. The primary retrieval products are the range-resolved extinction coefficient and the effective particle diameter from which secondary products such as the particle volume mixing ratio and the extinction at other wavelengths can be calculated. We recall briefly earlier validation tests and present new data and analysis that demonstrate and quantify the solutions' accuracy. The results show that systematic lidar probings with the proposed multiple-scattering technique can provide valuable physical information on cloud formation and evolution.
Journal Article↗
Heritable endosymbionts of Drosophila.
Although heritable microorganisms are increasingly recognized as widespread in insects, no systematic screens for such symbionts have been conducted in Drosophila species (the primary insect genetic models for studies of evolution, development, and innate immunity). Previous efforts screened relatively few Drosophila lineages, mainly for Wolbachia. We conducted an extensive survey of potentially heritable endosymbionts from any bacterial lineage via PCR screens of mature ovaries in 181 recently collected fly strains representing 35 species from 11 species groups. Due to our fly sampling methods, however, we are likely to have missed fly strains infected with sex ratio-distorting endosymbionts. Only Wolbachia and Spiroplasma, both widespread in insects, were confirmed as symbionts. These findings indicate that in contrast to some other insect groups, other heritable symbionts are uncommon in Drosophila species, possibly reflecting a robust innate immune response that eliminates many bacteria. A more extensive survey targeted these two symbiont types through diagnostic PCR in 1225 strains representing 225 species from 32 species groups. Of these, 19 species were infected by Wolbachia while only 3 species had Spiroplasma. Several new strains of Wolbachia and Spiroplasma were discovered, including ones divergent from any reported to date. The phylogenetic distribution of Wolbachia and Spiroplasma in Drosophila is discussed.
Animals↗