An overview of evolution, systematics, population biology, cytogenetics, molecular biology and speciation in Ctenomys.
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Animals↗
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Results for “systematic evolution”
Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.
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SELEXION. Systematic evolution of ligands by exponential enrichment with integrated optimization by non-linear analysis.
Recently, novel technologies for isolation of nucleic acid molecules with specific biological activities have been reported. In each case, the enrichment process involves repeated rounds of selection from complex mixtures of nucleic acid sequences, followed by polymerase chain reaction (PCR) amplification of ligand sequences that function in the desired manner. Particular variations in experimental conditions can dramatically alter the outcome of these processes. In this study, we use mathematical analysis and computer simulation to predict which variations have the greatest impact and to develop strategies and guidelines for enhanced effectiveness. First, we perform reconstruction tests to demonstrate that a mathematical description based on equilibrium binding is sufficient to explain the high levels of enrichment attained in the laboratory after just a few rounds. Then, we show the expected enrichment for an extensive range of conditions; and, finally, we determine the optimum protein and nucleic acid concentrations to use for maximum enrichment, while also ensuring a high likelihood of recovering even the rare molecule that binds well. The strategies and guidelines for enhanced effectiveness are generally applicable to processes for systematic enrichment of DNA, RNA or peptide ligands and have been implemented in an interactive simulation program for integrated non-linear optimization of enrichment using any target of interest.
Biological Evolution↗
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.
High-affinity nucleic acid ligands for a protein were isolated by a procedure that depends on alternate cycles of ligand selection from pools of variant sequences and amplification of the bound species. Multiple rounds exponentially enrich the population for the highest affinity species that can be clonally isolated and characterized. In particular one eight-base region of an RNA that interacts with the T4 DNA polymerase was chosen and randomized. Two different sequences were selected by this procedure from the calculated pool of 65,536 species. One is the wild-type sequence found in the bacteriophage mRNA; one is varied from wild type at four positions. The binding constants of these two RNA's to T4 DNA polymerase are equivalent. These protocols with minimal modification can yield high-affinity ligands for any protein that binds nucleic acids as part of its function; high-affinity ligands could conceivably be developed for any target molecule.
Base Sequence↗
Tarsius delta- and beta-globin genes: conversions, evolution, and systematic implications.
Comparisons between duplicated genes have shown that gene conversions play an important role in the evolution of multigene families. Previous comparisons have documented in the recently duplicated gamma-fetal globin genes of catarrhine primates, over 15 separate conversions affecting extensive stretches of coding and noncoding sequences. In the present study, delta- and beta- globin genes from a lower primate Tarsius syrichta, and the delta-globin gene of the Asian great ape, Pongo pygmaeus, have been isolated and sequenced. Comparisons of these sequences with other primate delta and beta sequences confirmed a previously reported conversion in an anthropoid ancestor and revealed additional conversions in basal primate, stem haplorhine, tarsier, and early lemur lineages. Conversions found between primate delta- and beta-globin genes contrast with those found in the gamma-genes in that delta-beta conversions appear much less frequently and are more restricted to regions conserved by selection (i.e. coding and 5'-regulatory sequences). These differences indicate that soon after a duplication occurs, conversions can be quite frequent and encompass extensive portions of the duplicated region. With time, sequence differences accumulate, particularly in noncoding regions, and limit both the frequency and size of the conversions. Sequences conserved by selection accumulate differences more slowly and are therefore subject to gene conversions for a longer period of time. Both unconverted and converted sequences were consistent in supporting the placement of tarsier with anthropoids.
Animals↗
Questions in digenean systematics and evolution.
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Animals↗
A systematic capsid evolution approach performed in vivo for the design of AAV vectors with tailored properties and tropism.
Adeno-associated virus (AAV) capsid modification enables the generation of recombinant vectors with tailored properties and tropism. Most approaches to date depend on random screening, enrichment, and serendipity. The approach explored here, called BRAVE (barcoded rational AAV vector evolution), enables efficient selection of engineered capsid structures on a large scale using only a single screening round in vivo. The approach stands in contrast to previous methods that require multiple generations of enrichment. With the BRAVE approach, each virus particle displays a peptide, derived from a protein, of known function on the AAV capsid surface, and a unique molecular barcode in the packaged genome. The sequencing of RNA-expressed barcodes from a single-generation in vivo screen allows the mapping of putative binding sequences from hundreds of proteins simultaneously. Using the BRAVE approach and hidden Markov model-based clustering, we present 25 synthetic capsid variants with refined properties, such as retrograde axonal transport in specific subtypes of neurons, as shown for both rodent and human dopaminergic neurons.
barcoding↗
DNA systematics and evolution of the artiodactyl family Bovidae.
Nine additional sequences from representatives of different tribes of the family Bovidae were combined with six published artiodactyl sequences to provide orthologous mtDNA for investigation of bovid phylogeny and evolution. Each species was represented by a homologous 2.7-kilobase-pair stretch of mtDNA for the complete 12S and 16S rRNA genes and three adjacent tRNA genes. These data, when compared to other results, provided evidence for a monophyletic Bovidae and for two clades within the family: one including the tribes Boselaphini, Bovini, and Tragelaphini and another for an Antilopini/Neotragini grouping. All other intrafamilial relationships were only weakly supported. These sequence comparisons suggest that most bovid tribes originated early in the Miocene with all extant lineages present by approximately 16-17 million years ago. Thus, bovid tribes provide an example of rapid cladogenesis, following the origin of families in the infraorder Pecora.
Animals↗
Systematics and evolution of the genus Paraceroglyphus and related taxa (Acari: Acaridae) associated with fleas (Insecta: Siphonaptera).
Collections of fleas from terrestrial Sciuridae from New Mexico and Montana yielded 2 species of acarid mites: Acarus monopsyllus from Ceratophyllus ciliatus and Paraceroglyphus cynomydis n. sp. from 4 species of Oropsylla. The genera Acarus, Paraceroglyphus, and Trichopsyllopus form a clade distinct from other genera of flea-associated mites, with Paraceroglyphus the sister group of the other 2 genera. Paraceroglyphus cynomydis is the sister group of a clade comprising P. xenopsylla and possibly P. californicus, with P. meles as the nearest outgroup.
Animals↗
The evolution of Ca2+-ATPases across plants with profiles in Rhododendron and the function of key members in alleviating high calcium stress.
Ca2+-ATPase (CAP) is a key Ca2+ efflux protein in plants. Our previous research suggests that CAPs may play a crucial role in the adaptation of rhododendrons to high calcium environments. However, the evolution, variation, characteristic expression, and subfunctionalization of this gene family in Rhododendron remain unknown. Through the analysis of pan-genomes and pan-transcriptomes, we elucidated the systematic evolution of CAPs in plants, as well as their characteristic expression patterns in Rhododendron. During the evolutionary process from lower to higher plants, CAPs can be divided into six clades and exhibit structural conservation. CAPs have emerged and differentiated in lower plants such as algae, and they have undergone significant amplification in Eudicots plants like rhododendrons. Three Rhododendron species (Rhododendron bailiense, R. delavayi, and R. irroratum) located in the karst province of Guizhou in Southwest China exhibit the highest copies of CAPs, suggesting a strong association between CAP copy number variation and habitat, particularly in high calcium environments. Through multiple transcriptome analyses, we revealed that CAPs are induced under various environmental/developmental conditions (e.g. karst environments, high altitude, early flower development, hormones, etc.). Co-expression network analysis highlighted key members of calcineurin B-like protein (CBL) and CBL-interacting protein kinases (CIPK) that are associated with the high expression of CAPs. Experimental validation demonstrated that CAPb1 and CAPd1 significantly alleviate high calcium stress, and the CAPb1-CIPK1-CBL1 and CAPd1-CIPK2-CBL1 modules can further enhance the alleviation. These findings provide new insights into the evolution, characteristic expression, and function of CAPs, as well as new perspectives on the high calcium adaptability of rhododendrons.
Journal Article↗
RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase.
High-affinity ligands of the reverse transcriptase of human immunodeficiency virus type 1 (HIV-1) were isolated by the SELEX procedure (systematic evolution of ligands by exponential enrichment) from RNA populations randomized at 32 positions. Analysis of these ligands revealed a pseudoknot consensus with primary sequence bias at some positions. We demonstrated that at least one of the ligands inhibits cDNA synthesis by HIV reverse transcriptase but fails to inhibit other reverse transcriptases. These experiments highlight the power of SELEX to yield highly specific ligands that reduce the activity of target proteins. Such ligands may provide therapeutic reagents for viral and other diseases.
Antiviral Agents↗
Rectosigmoidoscopic findings during isolated rectal bleeding in the neonate.
This study describes a group of 34 infants under 1 1/2 months of age presenting with isolated rectal bleeding not related to hemorrhagic disease of the newborn or to campylobacter infection and with spontaneously favorable evolution. Systematic rectosigmoidoscopy showed the presence of mucosal alterations in the form of either longitudinally stretched ecchymoses lying on a normal mucosa or diffuse ecchymotic patches dispersed on a congestive and friable mucosa, rarely associated to visible micro-ulcerations. Biopsies showed mucosal hemorrhage, capillary vessel congestion, and epithelial erosions, as well as various grades of inflammation. Clinical data indicate that this hemorrhagic colitis is a heterogeneous group where dietary protein intolerance may account for some cases.
Enterocolitis, Pseudomembranous↗
[Oniscoidea hemocyanins. Effect of pH on dissociation and structural data].
The pH has an influence on the molecular dissociation of the Oniscoidea hemocyanins. The dissociation electrophoretic patterns are characteristic for the species investigated. This method allows to confirm the systematic evolution and the adaptative possibilities of terrestrial Isopods. The hemocyanins of Oniscoidea are similar to those of Decapoda having a structure of comparable molecular weight protomers.
Animals↗
Childhood leukemia near nuclear plants in the United Kingdom: the evolution of a systematic approach to studying rare disease in small geographic areas.
A cluster of childhood leukemia in a village near a nuclear plant in northern England prompted further studies of cancer in the vicinity of other nuclear plants in the United Kingdom. These studies demonstrated that the risk of childhood leukemia was increased near certain other nuclear plants. Although the reasons for the increase are still unclear, the scientific debate stimulated by these findings has clarified some of the special methodological problems encountered when studying rare diseases in small areas. Firstly, unless a specific hypothesis is defined in advance, the relevance of a single geographic cluster of disease can rarely be interpreted. Even when a prior hypothesis exists, the small number of cases which generally occur in a small area make the findings highly sensitive to reporting, diagnostic, or classification errors. The statistical power of such investigations is also usually low and only marked increases in risk can be detected. Furthermore, conventional statistical tests may be inappropriate if the underlying spatial distribution of the disease is not random; and little is known about the background distribution of disease in small areas. Investigations of specific hypotheses about defined sources of environmental contamination, especially if they can be replicated, are more likely to result in conclusive findings that are in-depth studies of individual clusters.
Adolescent↗
Phylogenetic comparison of lens crystallins from the vertebrate and invertebrate--convergent or divergent evolution?
A systematic biochemical comparison has been made of the crystallins isolated from the lenses of five different species belonging to the five major classes of vertebrates. Gel-permeation chromatography of the lens homogenates on Fractogel TSK HW-55(S) revealed well-defined elution patterns with a characteristic distribution of different classes of crystallins from each species. SDS gel electrophoresis and statistical comparison of the amino acid contents indicated that all crystallin groups from different classes share some common subunits and similarity in their amino acid compositions. The results coupled with the relatedness shown in the amino acid compositions of fish gamma-crystallin with those of mammalian gamma-crystallin and the squid crystallin from the invertebrate pointed to the possibility of the existence of a common ancestral protein for all crystallins. This is in favor of the divergent rather than convergent evolution of lens crystallins as commonly assumed in the literature.
Amino Acid Sequence↗
There is gold in the graveyard: a new lineage of zombie-ant fungi in the genus Ophiocordyceps (Ophiocordycipitaceae: Hypocreales) from Minas Gerais, Brazil.
Ophiocordyceps serves as a key model for studying cryptic fungal diversity and behavioural manipulation of hymenopterous insects. Here, we describe Ophiocordyceps acanthoponerae, a newly discovered species infecting Acanthoponera mucronata (Heteroponerini: Formicidae) in a Brazilian Atlantic rainforest-Cerrado ecotone. Morphological analyses revealed mixed traits characteristic of Ophiocordyceps lineages associated with ants and wasps, including leaf biting behaviour manipulation, dark brown ascostromata covering 360º of the stalk, ascospores producing capilliconidia and hirsutelloid asexual morphs. Phylogenetic analyses based on four genomic regions (SSU, LSU, TEF and RPB1) placed this species outside the traditional myrmecophilous hirsutelloid clades O. unilateralis and O. kniphofioides, and within a novel clade closely related to the wasp pathogen O. humbertii. This discovery represents the first record of Ophiocordyceps infecting Heteroponerini and highlights an unexplored lineage of manipulative fungi. Our findings expand the known host range for myrmecophilous Ophiocordyceps and underscore the importance of studying fungal diversity in under-sampled ecological niches. Citation: Lima-Santos SJ, Araújo JPM, Feitosa RM, Mendes-Pereira T, Elliot SL, Evans HC (2025). There is gold in the graveyard: a new lineage of zombie-ant fungi in the genus Ophiocordyceps (Ophiocordycipitaceae: Hypocreales) from Minas Gerais, Brazil. Fungal Systematics and Evolution 16: 243-264. doi: 10.3114/fuse.2025.16.14.
Acanthoponera↗
Molecular approach in spider mites (Acari: Tetranychidae): preliminary data on ribosomal DNA sequences.
DNA sequence data were used to examine phylogenetic relationships between six species of economically important Tetranychidae mites: Eotetranychus carpini (Oudemans), E. pruni (Reck), Tetranychus pacificus McGregor, T. mcdanieli McGregor, T. turkestani Ugarov & Nikolski and T. urticae Koch. With primers directed toward conserved elements flanking the target region, the Polymerase Chain Reaction was used to amplify the ITS2 spacer of the ribosomal DNA molecule. The nucleotide sequence of a 300-bp fragment of the ITS2 was determined by direct sequencing and nucleotide divergence used for intra-generic comparison in mites. The resulting phylogenetic tree expressing interspecific relationships in genus Tetranychus agrees with morphological data. The study demonstrates the usefulness of the approach in the assessment of the systematics and evolution of the group.
Acari↗
Hidden diversity of coronaviruses in high-altitude plateau mammals.
• Pikas and marmots from plateaus host divergent α- and β-CoVs, including the candidate subgenera Pibecovirus and Mabecovirus. • The plateau CoVs show distinctive genomic features (relocated HE gene, variable ORFs), indicating lineage-specific evolution. • High-altitude plateau ecosystems are a key yet understudied frontier of CoV evolution, warranting systematic surveillance.
Journal Article↗
A molecular view of primate phylogeny and important systematic and evolutionary questions.
Phylogenetic analysis of extensive nucleotide sequence data from primate beta-globin gene clusters elucidates the systematics and evolution of the order Primates and reveals that rates of accumulation of mutations vary by as much as a factor of seven among different primate lineages. The picture of primate phylogeny from DNA sequences clarifies many ambiguities of the morphological picture. In the molecular picture, dwarf and brown lemurs group together into superfamily Lemuroidea, Lemuroidea and Lorisoidea into suborder Strepsirhini, and Tarsius and Anthropoidea into suborder Haplorhini. The molecular picture also provides both significant evidence for a human-chimpanzee clade that narrowly excludes gorilla and overwhelming evidence for the gorilla-chimpanzee-human clade within Hominoidea. Rates of DNA sequence evolution appear to have been fastest in the early primates ancestral to Anthropoidea and next fastest on the lorisoid branch. Rates were slowest over the past 25 Myr of hominoid descent, suggesting that mechanisms lowering the mutation rate evolved in correlation with lengthened life spans.
Animals↗