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At least 1,027 records · Page 57Linked to original sources
PubMed1998

Phage display selection can differentiate insecticidal activity of soybean cystatins.

Plant cysteine proteinase inhibitors (phytocystatins) have been implicated as defensive molecules against Coleopteran and Hemipteran insect pests. Two soybean cystatins, soyacystatin N (scN) and soyacystatin L (scL), have 70% sequence identity but scN is a much more potent inhibitor of papain, vicilin peptidohydrolase and insect gut proteinases. When these cystatins were displayed on phage particles, papain-binding affinity and CPI activity of scN were substantially greater than those of scL, in direct correlation with their relative CPI activity as soluble recombinant proteins. Furthermore, scN substantially delayed cowpea weevil (Callosobruchus maculatus (F.)) growth and development in insect feeding bioassays, whereas scL was essentially inactive as an insecticide. Papain biopanning selection of phage-displayed soyacystatins resulted in a 200-1000-fold greater enrichment for scN relative to scL. These results establish that binding affinity of cystatins can be used in phage display biopanning procedures to select variants with greater insecticidal activity, illustrating the potential of phage display and biopanning selection for directed molecular evolution of biological activity of these plant defensive proteins.

Amino Acid Sequence↗
PubMed2001

Negative genetic correlation for adult fitness between sexes reveals ontogenetic conflict in Drosophila.

Because of their distinctive roles in reproduction, females and males are selected toward different optimal phenotypes. Ontogenetic conflict between the sexes arises when homologous traits are selected in different directions. The evolution of sexual dimorphism by sex-limited gene expression alleviates this problem. However, because the majority of genes are not sex-limited, the potential for substantial conflict may remain. Here we assess the degree of ontogenetic conflict in the fruit-fly, Drosophila melanogaster, by cloning 40 haploid genomes and measuring their Darwinian fitness in both sexes. The intersexual genetic correlations for juvenile viability, adult reproductive success, and total fitness were used to gauge potential conflict during development. First, as juveniles, where the fitness objectives of the two sexes appear to be similar, survival was strongly positively correlated across sexes. Second, after adult maturation, where gender roles diverge, a significant negative correlation for reproductive success was found. Finally, because of counterbalancing correlations in the juvenile and adult components, no intersexual correlation for total fitness was found. Highly significant genotype-by-gender interaction variance was measured for both adult and total fitness. These results demonstrate strong intersexual discord during development because of the expression of sexually antagonistic variation.

Adaptation, Physiological↗
PubMed2002

Hydroxylation of indole by laboratory-evolved 2-hydroxybiphenyl 3-monooxygenase.

Directed enzyme evolution of 2-hydroxybiphenyl 3-monooxygenase (HbpA; EC ) from Pseudomonas azelaica HBP1 resulted in an enzyme variant (HbpA(ind)) that hydroxylates indole and indole derivatives such as hydroxyindoles and 5-bromoindole. The wild-type protein does not catalyze these reactions. HbpA(ind) contains amino acid substitutions D222V and V368A. The activity for indole hydroxylation was increased 18-fold in this variant. Concomitantly, the K(d) value for indole decreased from 1.5 mm to 78 microm. Investigation of the major reaction products of HbpA(ind) with indole revealed hydroxylation at the carbons of the pyrrole ring of the substrate. Subsequent enzyme-independent condensation and oxidation of the reaction products led to the formation of indigo and indirubin. The activity of the HbpA(ind) mutant monooxygenase for the natural substrate 2-hydroxybiphenyl was six times lower than that of the wild-type enzyme. In HbpA(ind), there was significantly increased uncoupling of NADH oxidation from 2-hydroxybiphenyl hydroxylation, which could be attributed to the substitution D222V. The position of Asp(222) in HbpA, the chemical properties of this residue, and the effects of its substitution indicate that Asp(222) is involved in substrate activation in HbpA.

Catalysis↗
PubMed2002

Chimeric co-stimulatory molecules that selectively act through CD28 or CTLA-4 on human T cells.

CD28 and CTLA-4 (CD152) play a pivotal role in the regulation of T cell activation. Upon ligation by CD80 (B7-1) or CD86 (B7-2), CD28 induces T cell proliferation, cytokine production, and effector functions, whereas CTLA-4 signaling inhibits expansion of activated T cells and induces tolerance. Therefore, we hypothesized that co-stimulatory molecules that preferentially bind CD28 or CTLA-4 would have dramatically altered biological properties. We describe directed molecular evolution of CD80 genes derived from human, orangutan, rhesus monkey, baboon, cat, cow, and rabbit by DNA shuffling and screening. In contrast to wild-type CD80, the evolved co-stimulatory molecules, termed CD28-binding protein (CD28BP) and CTLA-4-binding protein (CTLA-4BP), selectively bind to CD28 or CTLA-4, respectively. Furthermore, CD28BP has improved capacity to induce human T cell proliferation and interferon-gamma production compared with wild-type CD80. In contrast, CTLA-4BP inhibited human mixed leukocyte reaction (MLR) and enhanced interleukin 10 production in MLR, supporting a role for CTLA-4BP in inducing T cell anergy and tolerance. In addition, co-stimulation of purified human T cells was significantly suppressed when CTLA-4BP was cotransfected with either CD80 or CD28BP. The amino acid sequences of CD28BP and CTLA-4BP were 61 and 96% identical with that of human CD80 and provide insight into the residues that are critical in the ligand binding. These molecules provide a new approach to characterization of CD28 and CTLA-4 signals and to manipulation of the T cell response.

Abatacept↗
PubMedDate not supplied

Biomechanics and energetics in aquatic and semiaquatic mammals: platypus to whale.

A variety of mammalian lineages have secondarily invaded the water. To locomote and thermoregulate in the aqueous medium, mammals developed a range of morphological, physiological, and behavioral adaptations. A distinct difference in the suite of adaptations, which affects energetics, is apparent between semiaquatic and fully aquatic mammals. Semiaquatic mammals swim by paddling, which is inefficient compared to the use of oscillating hydrofoils of aquatic mammals. Semiaquatic mammals swim at the water surface and experience a greater resistive force augmented by wave drag than submerged aquatic mammals. A dense, nonwettable fur insulates semiaquatic mammals, whereas aquatic mammals use a layer of blubber. The fur, while providing insulation and positive buoyancy, incurs a high energy demand for maintenance and limits diving depth. Blubber contours the body to reduce drag, is an energy reserve, and suffers no loss in buoyancy with depth. Despite the high energetic costs of a semiaquatic existence, these animals represent modern analogs of evolutionary intermediates between ancestral terrestrial mammals and their fully aquatic descendants. It is these intermediate animals that indicate which potential selection factors and mechanical constraints may have directed the evolution of more derived aquatic forms.

Animals↗
PubMed2005

Hybridization in the recent past.

The question we address in this article is how hybridization in the recent past can be detected in recently evolved species. Such species may not have evolved genetic incompatibilities and may hybridize with little or no fitness loss. Hybridization can be recognized by relatively small genetic differences between sympatric populations because sympatric populations have the opportunity to interbreed whereas allopatric populations do not. Using microsatellite DNA data from Darwin's finches in the Galapagos archipelago, we compare sympatric and allopatric genetic distances in pairs of Geospiza and Camarhynchus species. In agreement with the hybridization hypothesis, we found a statistically strong tendency for a species to be more similar genetically to a sympatric relative than to allopatric populations of that relative. Hybridization has been studied directly on two islands, but it is evidently more widespread in the archipelago. We argue that introgressive hybridization may have been a persistent feature of the adaptive radiation through most of its history, facilitating evolutionary diversification and occasionally affecting both the speed and direction of evolution.

Animals↗
PubMed2026

Diploids derived from polyploids: genetic characteristics of four novel interspecific Sorghum populations.

Polyploidy has repeatedly shaped grass evolution, yet direct observations of how polyploid-derived chromosomes behave when returned to diploidy remain rare. Interspecific crosses between diploid Sorghum bicolor and tetraploid hybrids derived from Sorghum halepense generate mixed-ploidy progeny, providing an opportunity to examine chromosome transmission during the early stages of diploidization. Using genome-wide SNP markers, we characterized chromosomal inheritance patterns in 2 diploid and 2 tetraploid families derived from these crosses. Genotype-dosage profiles alone distinguished diploids from tetraploids with complete accuracy, reflecting strong ploidy-dependent differences in dosage-class distributions. Although diploid progeny retained much of the halepense-derived genomic background, several genomic intervals exhibited extended, nonrandom runs of S. bicolor homozygosity that remained polymorphic in corresponding tetraploid populations. These patterns, together with recurrent segregation distortion across independent families, suggest that the transition from tetraploidy to diploidy can expose allelic combinations that differ in transmission or viability. Analyses of flowering time further indicated that diploid and tetraploid derivatives possess distinct genomic architectures, with major association peaks occurring in different chromosomal regions across ploidy levels. Collectively, these results indicate that early diploidization involves nonrandom retention and loss of parental haplotypes shaped by both selective and structural constraints. The diploid extractions characterized here provide a rare empirical system for investigating the early stages of diploidization and a practical framework for studying and eventually mobilizing polyploid-derived variation for sorghum germplasm development. However, broader integration into elite breeding programs will require additional evaluation of cross-fertility, meiotic behavior, and chromosomal stability across diverse breeding backgrounds.

Sorghum↗
PubMed1996

Duplication of a gene-rich cluster between 16p11.1 and Xq28: a novel pericentromeric-directed mechanism for paralogous genome evolution.

We have identified a 26.5 kb gene-rich duplication shared by human Xq28 and 16p11.1. Complete comparative sequence analysis of cosmids from both loci has revealed identical Xq28 and 16p11.1 genomic structures for both the human creatine transporter gene (SLC6A8) and five exons of the CDM gene (DXS1357E). Overall nucleotide similarity within the duplication was found to be 94.6%, suggesting that this interchromosomal duplication occurred within recent evolutionary time (7-10 mya). Based on comparisons between genomic and cDNA sequence, both the Xq28 creatine transporter and DXS1357E genes are transcriptionally active. Predicted translation of exons and RT-PCR analysis reveal that chromosome 16 paralogs likely represent pseudogenes. Comparative fluorescent in situ hybridization (FISH) analyses of chromosomes from various primates indicate that this gene-rich segment has undergone several duplications. In gorilla and chimpanzee, multiple pericentromeric localizations on a variety of chromosomes were found using probes from the duplicated region. In other species, such as the orangutan and gibbon, FISH signals were only identified at the distal end of the X chromosome, suggesting that the Xq28 locus represents the ancestral copy. Sequencing of the 16p 11.1/Xq28 duplication breakpoints has revealed the presence of repetitive immunoglobulin-like CAGGG pentamer sequences at or near the paralogy boundaries. The mobilization and dispersal of this gene-rich 27 kb element to the pericentromeric regions of primate chromosomes defines an unprecedented form of recent genome evolution and a novel mechanism for the generation of genetic diversity among closely related species.

Animals↗
PubMed2025

Newly Developed Structure-Based Methods Do Not Outperform Standard Sequence-Based Methods for Large-Scale Phylogenomics.

Recent developments in protein structure prediction have allowed the use of this previously limited source of information at genome-wide scales. It has been proposed that the use of structural information may offer advantages over sequences in phylogenetic reconstruction, due to their slower rate of evolution and direct correlation to function. Here, we examined how recently developed methods for structure-based homology search and tree reconstruction compare with current state-of-the-art sequence-based methods in reconstructing genome-wide collections of gene phylogenies (i.e. phylomes). While structure-based methods can be useful in specific scenarios, we found that their current performance does not justify using the newly developed structure-based methods as a default choice in large-scale phylogenetic studies. On the one hand, the best performing sequence-based tree reconstruction methods still outperform structure-based methods for this task. On the other hand, structure-based homology detection methods provide larger lists of candidate homologs, as previously reported. However, this comes at the expense of missing hits identified by sequence-based methods, as well as providing sets of homolog candidates with higher fractions of false positives. These insights help to guide the use of structural data in comparative genomics and highlight the need to continue improving structure-based approaches. Our pipeline is fully reproducible and has been implemented in a Snakemake workflow. This will facilitate a continuous assessment of future improvements of structure-based tools in the AlphaFold era.

Phylogeny↗
PubMed2000

Evolution of technique of the direct transblepharoplasty approach for the correction of lower lid and midfacial aging: maximizing results and minimizing complications in a 5-year experience.

During the past 5 years, the authors have used a direct trans-lower lid blepharoplasty subperiosteal approach to the lower lid and midface for the purpose of correction of midfacial aging in 757 patients. In a smaller but significant group, this approach has proven valuable in difficult reconstructive situations. The purpose of this article is twofold: (1) to provide a comprehensive retrospective evaluation of the value and promise of the technique and (2) to provide a comprehensive discussion of the pitfalls and complications that have been associated with use of this technique. In addition, technical modifications that may lower the rate of morbidity associated with the use of the procedure are described.

Adult↗
PubMedDate not supplied

Regulatory approval of peripheral endovascular revascularization devices in the United States: is the horse still in the barn?

The regulatory processes by which industry obtains approval for marketing and sales of medical devices from the United States Food and Drug Administration is distinct from the drug approval pathways, poorly understood by clinicians, and widely criticized by clinical investigators and industrial sponsors of new technology. This paper reviews the most common pathways for obtaining such approval for endovascular devices used in the treatment of peripheral arterial disease. Unique issues pertinent to clinical trials carried out in this area are highlighted. Future directions for evolution of the regulatory process consonant with the mandated requirements for demonstration of safety and efficacy are discussed.

Angioplasty, Balloon↗
PubMed2005

Angiographic considerations in patients undergoing liver-directed therapy.

The rapid evolution and increasing complexity of liver-directed therapies has forced the medical community to further advance its understanding of hepatic arterial anatomy. The anatomy of the mesenteric system, and particularly the hepatic arterial bed, has been demonstrated to have a high degree of variation. This is important when considering presurgical planning, catheterization, and transarterial hepatic therapies. Although anatomic variants have been well described, the characterization and understanding of regional hepatic perfusion is also required to optimize endovascular therapy and intervention. Although this is true for patients undergoing bland embolization or chemoembolization, drug delivery, and hepatic infusional pump therapy, it is particularly true for intraarterial brachytherapy. The purpose of this review is to provide historical perspective in angiographic aspects of liver-directed therapy, as well as a discussion of normal vascular anatomy, commonly encountered variants, and factors involved in changes to regional perfusion in the presence of liver tumors. Methods of optimizing the safety and efficacy of liver-directed therapies with use of percutaneous techniques will be discussed. This review is based on the experience gained in treating more than 500 patients with transarterial liver-directed therapies. Although the principles described in this article apply to all liver-directed therapies such as chemoembolization and administration of drug-coated microspheres, they apply particularly to intraarterial brachytherapy.

Angiography↗
PubMed2002

Quality and irreversibility: constraints on ecosystem development.

We discuss one of the most general mathematical tools for analysing dynamical systems: the master equation (ME). The ME is used to derive models for entropy production in closed and open systems. Due to dissipation in open systems, the direction of evolution of important characteristics can be opposite to those imposed on closed systems. When applying these models to soil organic matter it can be shown that the principle of minimum entropy production necessitates that more and more recalcitrant organic matter is produced the further the decomposition proceeds. The necessity to dissipate entropy can also impose a limit on the degree to which litters can decompose, but interaction between litters of differing ages can remove this constraint. This is an example of the 'priming' effect.

Ecosystem↗
PubMed2005

Pathogen adaptation under imperfect vaccination: implications for pertussis.

Mass vaccination campaigns have drastically reduced the burden of infectious diseases. Unfortunately, in recent years several infectious diseases have re-emerged. Pertussis poses a well-known example. Inspired by pertussis, we study, by means of an epidemic model, the population and evolutionary dynamics of a pathogen population under the pressure of vaccination. A distinction is made between infection in immunologically naive individuals (primary infection) and infection in individuals whose immune system has been primed by vaccination or infection (secondary infection). The results show that (i) vaccination with an imperfect vaccine may not succeed in reducing the infection pressure if the transmissibility of secondary infections is higher than that of primary infections; (ii) pathogen strains that are able to evade the immunity induced by vaccination can only spread if escape mutants incur no or only a modest fitness cost and (iii) the direction of evolution depends crucially on the distribution of the different types of susceptibles in the population. We discuss the implications of these results for the design and use of vaccines that provide temporary immunity.

Adaptation, Biological↗
PubMed2006

Solitons in two-dimensional lattices possessing defects, dislocations, and quasicrystal structures.

Localized nonlinear modes, or solitons, are obtained for the two-dimensional nonlinear Schrödinger equation with various external potentials that possess large variations from periodicity, i.e., vacancy defects, edge dislocations, and quasicrystal structure. The solitons are obtained by employing a spectral fixed-point computational scheme. Investigation of soliton evolution by direct numerical simulations shows that irregular-lattice solitons can be stable, unstable, or undergo collapse.

Journal Article↗