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At least 1,297 records · Page 72Linked to original sources
PubMed2000

Bacteriorhodopsin: mutating a biomaterial into an optoelectronic material.

Bacteriorhodopsin (BR) is the key protein for the halobacterial photosynthetic capabilities and is one of the very rare molecules which occur in crystalline form in nature. Since its discovery, which was reported in 1971, many efforts have been made to exploit the obvious technical potential of this molecule. Successful application of gene technology methods for the modification of the physical function of a biomolecule was first demonstrated with BR. This approach points the way to a new class of materials derived from evolutionary optimized biomaterials by genetic re-engineering. Mutated BRs proved to have significant advantages over the wild type in optical applications. The current status of potential technical applications of BR is reviewed. BR is employed as a photoelectric, photochromic or energy-converting element. First systems now exist which demonstrate the successful integration of this new material into existing technologies. Analyzing the patents filed, which claim the processing or application of BR, gives an indication to areas where further technical uses are to be expected in the near future.

Bacteriorhodopsins↗
PubMed2005

A new Web site compiling forensic chromosome X research is now online.

We would like to announce the opening of a new Web site ( http://www.chrx-str.org ), which contains a database surveying current research on chromosome X markers used for forensic purposes, evolutionary anthropology and other genetic research. Currently, we summarise short tandem repeat data with regard to the physical and genetic localisation, repeat structure, allele nomenclature, mutation rates and population genetics. In the future, we may include diallelic markers. The results contained in this database come from published journal articles. The authors of published articles are invited to complement their own papers by submitting data obtained from follow-up studies here. Furthermore, population data which are not able to find space in journals may be published at this Web site. The growing field of ChrX haplotyping is producing an extensive amount of data, which requires a place that can complement journal publications.

Chromosomes, Human, X↗
PubMed2006

Resolving the genetic basis of invasiveness and predicting invasions.

Considerable effort has been invested in determining traits underlying invasiveness. Yet, identifying a set of traits that commonly confers invasiveness in a range of species has proven elusive, and almost nothing is known about genetic loci affecting invasive success. Incorporating genetic model organisms into ecologically relevant studies is one promising avenue to begin dissecting the genetic underpinnings of invasiveness. Molecular biologists are rapidly characterizing genes mediating developmental responses to diverse environmental cues, i.e., genes for plasticity, as well as to environmental factors likely to impose strong selection on invading species, e.g., resistance to herbivores and competitors, coordination of life-history events with seasonal changes, and physiological tolerance of heat, drought, or cold. Here, we give an overview of molecular genetic tools increasingly used to characterize the genetic basis of adaptation and that may be used to begin identifying genetic mechanisms of invasiveness. Given the divergent traits that affect invasiveness, "invasiveness genes" common to many clades are unlikely, but the combination of developmental genetic advances with further evolutionary studies and modeling may provide a framework for identifying genes that account for invasiveness in related species.

Arabidopsis↗
PubMed2006

Molecular evolution of toxin genes in Elapidae snakes.

The venom of the sea krait, Laticauda semifasciata, consists primarily of two toxic proteins, phospholipase A(2) (PLA(2)) and a three-finger-structure toxin. We have cloned both toxic protein genes, including the upstream region. PLA(2) genes contain three types of inserted sequences: an AG-rich region, a chicken repeat 1-like long interspersed nucleotide element sequence and an intron II 3' side repeat sequence. The molecular divergence of L. semifasciata PLA(2) genes was defined on the basis of the inserted sequences and their sequence homology. The length of intron I in the three-finger-structure toxin genes differs from species to species. The alignment analysis of intron I of the three-finger-structure toxin genes revealed that the intron I sequence of the ancestral gene comprised ten genetic regions. A hypothetical evolutionary process for the three-finger-structure toxin genes has also been developed.

Animals↗
PubMed2004

SNPs, SSRs and inferences on cassava's origin.

Despite its importance as a staple food throughout the tropics, the root crop cassava (it Manihot esculenta ssp. esculenta) has traditionally not been a major focus of research. One basic question about cassava that remained unresolved until recently concerns the crop's origin. This paper describes analyses of SNPs (single nucleotide polymorphisms) and SSR (simple sequence repeat) variation as a means of tracing cassava's evolutionary and geographical origins. Genetic diversity was examined in a sample of 20 cassava varieties that are representative of germplasm diversity within the crop, and in 212 individuals collected from wild populations of two closely related Manihot species. SNP and indel variation was examined in portions of two low copy nuclear genes, BglA and Hnl. Inferences from these genes were compared to those from previously examined loci, including the low copy nuclear gene G3pdh and 5 SSR loci. For all genes examined, SNPs and SSR alleles are shared between domesticated cassava and a specific geographical subset of wild Manihot populations, which suggests the following: (1) Cassava was likely domesticated from a single wild Manihot species, M. esculenta ssp. flabellifolia, rather than from multiple hybridizing species, as traditionally believed; and (2) the crop most likely originated in the southern Amazon basin.

Aldehyde-Lyases↗
PubMed1987

Dynamics and stability in coevolutionary ecological systems. I. Community stability and coevolutionarily stable states.

An extension of J. Roughgarden's [1979, Theor. Pop. Biol. 9, 388; 1979, "An Introduction to Evolutionary Ecology and Population Genetic Theory," Macmillan, New York] formalism for investigating the effects of coevolution on community structure is presented. The extension assumes the result that a coevolved community is asymptotically stable when coevolution takes place at a genetically noninvasible boundary. This is proved for the general case of n interacting species. From this a community persistence function, phi (P), is defined that allows measuring the domain of attraction for the community as well as the resilience time, that is, the time taken for a perturbation to decay to 1-1/e (63%) of its initial value.

Animals↗
PubMed1982

Duplication and deletion in the human immunoglobulin epsilon genes.

The human IgE gene encodes a polypeptide chain that is involved in allergic reactions and in the immune response to parasitic disease in man. We have cloned three chromosomal regions corresponding to this sequence and find that two of them derive from curiously duplicated gene segments that also encode IgA constant-region genes. One of the IgE sequences corresponds to the active gene, and its structure defines a complete amino acid sequence of the human IgE constant region. The other cloned segment is a pseudogene from which the first two IgE coding domains have been deleted and replaced by a switch-like sequence that also occurs close to the normal IgE gene. The third IgE segment remains unlinked to the other heavy-chain genes. Evidently, the epsilon-alpha locus has been the site of several complicated genetic rearrangements during recent evolutionary time.

Amino Acid Sequence↗
PubMed1991

Organisation and expression of small subunit ribosomal RNA genes encoded by a 35-kilobase circular DNA in Plasmodium falciparum.

A restriction map of the 35-kb circular DNA molecule of Plasmodium falciparum showed that a region of about 6 kb, encoding both a large and a small subunit ribosomal RNA gene, has been duplicated in inverted orientation. The complete sequence of one small subunit rRNA gene is presented as well as an analysis of transcripts from erythrocytic stage parasites. Comparative sequence analysis of the rRNA gene and the proposed secondary structure of the rRNA suggest that it is of organellar origin. Intriguingly, while some characteristics of the small subunit rRNA gene are similar to mitochondrial sequences, others are more like those of plastids. The origin of the circular DNA molecule and evolutionary implications of its genetic content are discussed.

Animals↗
PubMed2006

Evolutionary aspects of diet, the omega-6/omega-3 ratio and genetic variation: nutritional implications for chronic diseases.

Anthropological and epidemiological studies and studies at the molecular level indicate that human beings evolved on a diet with a ratio of omega-6 to omega-3 essential fatty acids (EFA) of approximately 1 whereas in Western diets the ratio is 15/1 to 16.7/1. A high omega-6/omega-3 ratio, as is found in today's Western diets, promotes the pathogenesis of many diseases, including cardiovascular disease, cancer, osteoporosis, and inflammatory and autoimmune diseases, whereas increased levels of omega-3 polyunsaturated fatty acids (PUFA) (a lower omega-6/omega-3 ratio), exert suppressive effects. Increased dietary intake of linoleic acid (LA) leads to oxidation of low-density lipoprotein (LDL), platelet aggregation, and interferes with the incorporation of EFA in cell membrane phospholipids. Both omega-6 and omega-3 fatty acids influence gene expression. Omega-3 fatty acids have anti-inflammatory effects, suppress interleukin 1beta (IL-1beta), tumor necrosis factor-alpha (TNFalpha) and interleukin-6 (IL-6), whereas omega-6 fatty acids do not. Because inflammation is at the base of many chronic diseases, dietary intake of omega-3 fatty acids plays an important role in the manifestation of disease, particularly in persons with genetic variation, as for example in individuals with genetic variants at the 5-lipoxygenase (5-LO). Carotid intima media thickness (IMT) taken as a marker of the atherosclerotic burden is significantly increased, by 80%, in the variant group compared to carriers with the common allele, suggesting increased 5-LO promoter activity associated with the (variant) allele. Dietary arachidonic acid (AA) and LA increase the risk for cardiovascular disease in those with the variants, whereas dietary intake of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) decrease the risk. A lower ratio of omega-6/omega-3 fatty acids is needed for the prevention and management of chronic diseases. Because of genetic variation, the optimal omega-6/omega-3 fatty acid ratio would vary with the disease under consideration.

Biological Evolution↗
PubMed2026

Transgenerational continuity: Persistence as a dimension of inheritance and evolution.

Transgenerational continuity (TC) describes the persistence of inherited molecular architectures across generations. Progress in identity-by-descent (IBD) detection, recombination dynamics, and epigenetic research highlights the growing need for a more comprehensive model of inheritance. This theoretical framework synthesizes evidence from genomics, population studies, and epigenetics to outline how inherited molecular architectures, which are transmitted through IBD, together with heritable epigenetic modifications, can preserve ancestral information across generations. IBD captures genomic continuity across three nested scales, where recent familial segments link close relatives, population-level haplotypes are shared across cohorts, and archaic fragments from Neanderthal and Denisovan admixture persist as molecular fossils of ancient lineages. Although recombination and selection reshape these regions, their persistence across time scales highlights the evolutionary durability of genomic continuity. Epigenetic memory reflects regulatory persistence, whereby molecular modifications can preserve functional states across cell divisions and sometimes across generations. Together with familial and population-level IBD persistence and the long-term retention of introgressed haplotypes, these findings demonstrate that inherited molecular architectures can persist across multiple timescales. Evolutionary processes shape this persistence. Purifying selection preferentially removes deleterious inherited variants, whereas positive selection can favor the persistence of functionally relevant genomic architectures. From this perspective, evolutionary dynamics arise not only from the generation of variation, but also from the differential persistence of inherited molecular architectures through selection. Transgenerational continuity therefore provides a conceptual framework in which persistence serves as an explanatory dimension of inheritance and evolution that complements variation and explains the persistence of biological identity across generations and evolutionary time.

Biological identity↗
PubMed2006

State of the knowledge of bacterial resistance.

Bacteria have adapted a variety of different ways to acquire antibiotic resistance, fostering the rapid development of resistance within a short evolutionary time. The general genetic basis of events leading to and promoting antibiotic resistance formation in bacteria are presented and exemplified by showing the evolution of methicillin, glycopeptide, linezolid, and ketolide resistance in Staphylococcus aureus.

Acetamides↗
PubMed2004

Mirror writing ability is genetic and probably transmitted as a sex-linked dominant trait: it is hypothesised that mirror writers have bilateral language centres with a callosal interconnection.

Mirror writing is the ability to write from right to left, reversing each letter so that when held to a mirror the script appears normal. There is no information on the prevalence of this trait but a suggestion was received that it may be hereditary. A newspaper survey was carried out to discover the approximate prevalence and whether a hereditary factor is involved. The results indicated a prevalence of 1 in 6500. There is strong evidence that the trait is hereditary and is associated with non-right-handedness'. It is hypothesised that mirror writers may comprise a very small group of people who not only have bilateral language centres but also have an interconnecting pathway between these centres via the corpus callosum. The surprising genetic nature of a trait with no obvious evolutionary consequences is discussed. The data can best be explained on the basis of the trait being the phenotypic expression of an X-linked dominant gene, which does have evolutionary consequences. Similarities are noted between the proposed genetics of mirror writing and those of synaesthesia and of a few pathological X-linked dominant syndromes such as Rett syndrome. Other similarities and contrasts between mirror writing and synaesthesia are noted.

Adult↗
PubMed2026

Evolutionary history of Aotearoa New Zealand's extinct mātuhituhi | bush wren.

The reconstruction of ecosystem responses to past climate change has historically focused on large vertebrates. In contrast, small vertebrates with potentially stricter habitat preferences have been neglected in ancient DNA studies despite their potential utility as proxies for inferring geographic and temporal changes in habitat. Aotearoa New Zealand's acanthisittid wrens are a speciose group of tiny perching birds, including the mātuhituhi | bush wren (Xenicus longipes ssp.). Despite its relatively recent extinction in the 1970s, very little is known about this enigmatic bird. Here we sequence mitochondrial genomes and nuclear ultra conserved genomic elements from 32 historical bush wren specimens to reconstruct their evolutionary history. We also genetically sex specimens and reanalyse their plumage to reconstruct aspects of bush wren plumage variation. Our analyses suggest North and South Island bush wren populations diverged 2.6 million years ago when narrowing and closure of Plio-Pleistocene seaways allowed colonisation of new habitats, followed by rapid glaciation-driven diversification of South Island populations 470,000-94,000 years ago. Genetic sexing allowed an accurate reconstruction of ontogenetic, sexual, and geographic variation in plumage. Our multidisciplinary data supports recognition of North and South Island populations as separate species, and the description of a new subspecies X. longipes perditus subsp. nov. This research shows how ecosystems can buffer against the impacts of climate change up to an ecological tipping point, which has important lessons for conservation management in a fast-changing world.

Acanthisittidae↗
PubMed2000

The expression of nonchordate deuterostome Brachyury genes in the ascidian Ciona embryo can promote the differentiation of extra notochord cells.

The notochord is a structure present in all chordates and its development requires the transcription of Brachyury. While previous studies have shown that Brachyury is essential for notochord formation in vertebrate embryos, this gene is also expressed during the embryogenesis of nonchordate deuterostomes, hemichordates and echinoderms. Here we report that nonchordate deuterostome Brachyury genes can trigger the differentiation of extra notochord cells when these genes are ectopically expressed in ascidian embryos. The 2.6 kb upstream region of fork head gene (Ci-fkh) of Ciona intestinalis promotes the tissue-specific expression of a reporter gene in endoderm, notochord and nerve cord. By taking advantage of this promoter, we misexpressed the Brachyury gene of ascidian (Ci-Bra), cephalochordate amphioxus (Am(Bb)Bra2), hemichordate acorn worm (PfBra), and echinoderm sea urchin (SpBra), in Ciona embryos. The misexpression of not only the chordate Brachyury, but also the nonchordate deuterostome Brachyury, resulted in the transformation of presumptive endodermal cells into notochord cells. This was confirmed by in situ hybridization experiments using four different notochord-specific probes from Ciona that have different temporal expression patterns. RT-PCR analyses indicated that Ci-Bra was not upregulated by the product of Am(Bb)Bra2, PfBra or SpBra. In situ hybridization showed no ectopic expression of Ci-Bra in the manipulated embryos. These results suggest that the introduction of nonchordate deuterostome Brachyury genes into ascidian embryos can trigger the differentiation of notochord cells in ascidian embryos. Evolutionary alteration in the genetic circuitry, especially downstream of this transcription factor, seems critical for the evolution of notochord and chordate body plan.

Amino Acid Sequence↗
PubMed1998

Developmental phenotypic plasticity: where internal programming meets the external environment.

Developmental plasticity has long been the focus of research in both evolutionary ecology and molecular genetics. Recently, the concept of ontogenetic contingency has been proposed to indicate the dependence of plastic responses on the timing and sequence of developmental events. Also, the idea of the developmental reaction norm has been put forward to indicate the complex interactions among development, phenotypic plasticity, and allometry of different structures. Finally, for the first time, studies ranging from the ecological to the molecular aspects of the same plastic response are available on insect and flowering plant model systems.

Biological Evolution↗
PubMed2001

An integrative evolutionary perspective on ethnicity.

This paper integrates several different but mutually consistent evolutionary approaches to ethnicity: genetic similarity theory, social identity theory, individualism/collectivism, an evolved racial/ethnic human kinds module, and rational choice mechanisms relying on domain general cognitive mechanisms. These theories are consistent with each other, and together they illustrate the interplay of evolved cognitive and motivational systems with mechanisms of rational choice that are able to choose adaptive strategies in uncertain, novel environments.

Journal Article↗
PubMedDate not supplied

VSMP: a novel variable selection and modeling method based on the prediction.

The use of numerous descriptors that are indicative of molecular structure and topology is becoming more common in quantitative structure-activity relationship (QSAR). How to choose the adequate descriptors for QSAR studies is important but difficult because there are no absolute rules to govern this choice. A variety of variable selection techniques including stepwise, partial least squares/principal component analysis (PLS/PCA), neural network, and evolutionary algorithm such as genetic algorithm have been applied to this common problem. All-subsets regression (ASR) is capable of finding out the best variable subset from among a large pool. In this paper, a novel variable selection and modeling method based on the prediction, for short VSMP, has been developed. Here two controllable parameters, the interrelation coefficient between the pairs of the independent variables (r(int)) and the correlation coefficient (q(2)) obtained using the leave-one-out (LOO) cross-validation technique, are introduced into the ASR to improve its performances. This technique differs from the other variable selection procedures related to the ASR by two main features: (1) The search of various optimal subset search is controlled by the statistic q(2) or root-mean-square error (RMSEP) in the LOO cross-validation step rather than the correlation coefficient obtained in the modeling step (r(2)). (2) The searching speed of all optimal subsets is expedited by the statistic r(int) together with q(2). A comparison of the results of the VSMP applied to the Selwood data set (n = 31 compounds, m = 53 descriptors) with those obtained from alternative algorithms shows the good performance of the technique.

Journal Article↗
PubMed1997

Endosymbiotic interactions in anaerobic protozoa.

Several aspects of the endosymbiosis of methanogenic archaea with anaerobic protozoa are reviewed. Special attention is played to the role of hydrogenosomes and plastid-like organelles that seem to provide the substrates for the methanogenic endosymbionts. Evidence is presented that hydrogenosomes evolved several times in the various protoctistan taxa. Hydrogenosomes are seemingly different, and their common denominator is the production of hydrogen. The absence of nucleic acids and a protein-synthesizing machinery hampers the analysis of their divergent evolutionary history, and molecular genetic data argue not only for different but even a chimeric origin of the hydrogenosomes.

Anaerobiosis↗