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Results for “systematic evolution”

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PubMed2026

Genome-wide characterization of the sugar transporter protein family identifies candidate genes for bacterial wilt resistance breeding in tobacco.

Sugar transporter proteins (STPs) play pivotal roles in hexose allocation and plant stress responses. However, systematic characterization of the STP family in tobacco (Nicotiana tabacum) and its involvement in Ralstonia solanacearum resistance remains unclear. In this study, 37 NtSTP genes were identified and classified into six groups, with Group VI being the most conserved and Group V exhibiting dicot-specific expansion. Gene structure and conserved motif analyses revealed that most NtSTP members possess the typical MFS_STP domain, although variations in exon-intron organization and motif composition suggested functional divergence. Tandem duplication (TD) served as the primary driver of NtSTP family expansion, and Ka/Ks values of all paralogous pairs were less than 1, indicative of purifying selection. Promoter cis-element analysis revealed a complex regulatory network involving hormone signaling (ABA, JA, SA, GA, ET), stress responses, and light signaling. RT-qPCR expression profiling revealed that ten NtSTP genes (NtSTP1, 5, 7, 21, 22, 24, 26, 27, 28, and 29) exhibited significant transcriptional upregulation upon R. solanacearum infection. Specifically, NtSTP5, NtSTP7, NtSTP21, NtSTP22, NtSTP24, NtSTP26, and NtSTP27 peaked at 12 h post-inoculation (hpi), whereas NtSTP1, NtSTP28, and NtSTP29 reached their highest expression levels at 24 hpi. By contrast, NtSTP6, NtSTP13, and NtSTP30 displayed reduced expression upon R. solanacearum infection. These expression patterns indicate functional diversification within the NtSTP family and imply that these members may be transcriptionally modulated during plant responses to R. solanacearum. The present work provides preliminary and valuable candidate gene resources that may facilitate future disease resistance breeding programs in tobacco.

NtSTP gene family↗

PubMed1985

[CEA and TPA in cancer of the breast. Findings and criteria of use].

In breast cancer, under rigorous and normalized conditions, the blood levels of carcinoembryonic antigen (CEA) and tissue polypeptide antigen (TPA) allow us: to differentiate with enough precision, in treated patients, the presence of tumour (EP) from illness-free situation (NED); to alert about the appearance of metastases and/or local relapse in patients put under systematic postoperative evolutional control; to evaluate the systemic palliative treatment response in patients with metastatic breast cancer and to formulate, in this case, prognostic predictions. Blood levels of CEA and TPA are, otherwise, unsuitable: to detect with accuracy the primary tumour presence; to warn about the risk of subclinical tumour existence (in treated patients in NED situation); to predict, in this last case, the chemotherapeutic treatment response, and to prevent about local relapses development. The independent but combined use of both antigens, appreciably raises the diagnostic success percentage with regard to that obtained when only one tumour marker was used.

Adult↗

PubMed1978

[Respiratory localizations of Launois-Bensaude symmetrical lipomatosis. Apropos of 3 cases].

The authors report 3 observations of cervico-facial lipomatosis with mediastinal localization. In the 3 cases the rather unusual localization of Launois and Bensaude's disease produced respiratory troubles which worsened a chronic respiratory insufficiency due to another cause. Once a tracheotomy had to be done because of tracheo-malacia. Another time there was a pharynged localization. This disease etiology always remains obscure, usually appearing in alcoholic addicts of about 50. Mediastinal localizations have been unfrequently described but must be searched for systematically. The evolution is chronic, without specific treatment. If there is already a chronic respiratory insufficiency in relation with a chronic obstructive bronchopneumopathy or a cardiac insufficiency, then the mediastinal localization becomes an aggravating factor.

Aged↗

PubMed2025

Variable rates of SARS-CoV-2 evolution in chronic infections.

An important feature of the evolution of the SARS-CoV-2 virus has been the emergence of highly mutated novel variants, which are characterised by the gain of multiple mutations relative to viruses circulating in the general global population. Cases of chronic viral infection have been suggested as an explanation for this phenomenon, whereby an extended period of infection, with an increased rate of evolution, creates viruses with substantial genetic novelty. However, measuring a rate of evolution during chronic infection is made more difficult by the potential existence of compartmentalisation in the viral population, whereby the viruses in a host form distinct subpopulations. We here describe and apply a novel statistical method to study within-host virus evolution, identifying the minimum number of subpopulations required to explain sequence data observed from cases of chronic infection, and inferring rates for within-host viral evolution. Across nine cases of chronic SARS-CoV-2 infection in hospitalised patients we find that non-trivial population structure is relatively common, with five cases showing evidence of more than one viral population evolving independently within the host. The detection of non-trivial population structure was more common in severely immunocompromised individuals (p = 0.04, Fisher's Exact Test). We find cases of within-host evolution proceeding significantly faster, and significantly slower, than that of the global SARS-CoV-2 population, and of cases in which viral subpopulations in the same host have statistically distinguishable rates of evolution. Non-trivial population structure was associated with high rates of within-host evolution that were systematically underestimated by a more standard inference method.

Humans↗

PubMed1992

An rbcL sequence from a Miocene Taxodium (bald cypress).

During the past decade, ancient DNAs from both animals and plants have been successfully extracted and analyzed. Recently, the age of DNA that can be recovered and sequenced was increased manyfold by the amplification and sequencing of a DNA fragment from a Magnolia fossil obtained from the Miocene Clarkia deposit (17-20 million yr old). However, the validity of this report has been questioned based on models predicting that DNA should be completely degraded after 4 million yr. We report here the successful amplification, sequencing, and analysis of a 1320-base-pair portion of the chloroplast gene rbcL from a Miocene Taxodium specimen, also from the Clarkia site. These data not only validate the earlier report of sequence data for a Magnolia species from the same site but also suggest that it may be possible to isolate and sequence DNAs routinely from the Clarkia deposit. The ability to recover and sequence DNAs of such age offers enormous research possibilities in the areas of molecular evolution, biogeography, and systematics.

Base Sequence↗

PubMed1991

An improved photochemical model of embolic cerebral infarction in rats.

To provide further evidence that the multiple cerebral infarcts found in rats following photochemical damage to the carotid artery are caused by emboli and to eliminate the systemic hypotension and heating of the blood reported with the previous photochemical embolic stroke model (rose bengal and a green laser), I have modified the photochemical technique. Brain pathology was studied in 18 Wistar rats following carotid artery irradiation with a red laser (632 nm) at powers ranging from 100 to 800 mW/cm2 for 10 or 20 minutes following the injection of the photosensitizing dye Photofrin II. Multiple cerebral arterioles were occluded by platelet aggregates containing frequent erythrocytes and leukocytes, identical to the thrombotic material in the carotid artery but different from the platelet aggregates seen in the carotid artery and the brain in the rose bengal model. Eighty infarcts were distributed randomly throughout the brain ipsilateral to the nonocclusive carotid thrombus. Significant heating (0.5 degree C or more) of the blood occurred only with laser powers higher (1,600 mW/cm2) or laser irradiations longer (25 minutes) than those used in the improved model of embolic stroke. This model mimics one mechanism of stroke in humans and provides a means to study systematically the morphological evolution of small cerebral infarcts.

Animals↗

PubMed1992

Evolution of the common cetacean highly repetitive DNA component and the systematic position of Orcaella brevirostris.

The common cetacean highly repetitive DNA component was analyzed with respect to its evolution and value for establishing phylogenetic relationships. The repeat length of the component, which is tandemly organized, is approximately 1750 bp in all cetaceans except the delphinids, in which the repeat length is approximately 1580 bp. The evolution of the component was studied after sequencing the component in different odontocetes representing the Delphinidae (delphinids), Monodontidae (narwhals), and Ziphiidae (beaked whales). The evolution of this component is very slow, and comparisons showed that sequence divergence among species corresponds closely to their generally accepted phylogenetic relationships and that the component evolves in a concerted manner. The phylogenetic information obtained in this study identified the Irrawaddy dolphin (Orcaella brevirostris) as a delphinid and did not support a close relationship of this species with the Monodontidae.

Animals↗

PubMed1991

Molecular evolutionary history of ancient aquatic angiosperms.

Aquatic plants are notoriously difficult to study systematically due to convergent evolution and reductionary processes that result in confusing arrays of morphological features. Plant systematists have frequently focused their attention on the "water lilies," putative descendants of the most archaic angiosperms. Classification of these 10 plant genera varies from recognition of one to three orders containing three to six families. We have used DNA sequence analysis as a means of overcoming many problems inherent in morphologically based studies of the group. Phylogenetic analyses of sequence data obtained from a 1.2-kilobase portion of the chloroplast gene rbcL provide compelling evidence for the recognition of three distinct lineages of "water lily" plants. Molecular phylogenies including woody Magnoliidae sequences and sequences of these aquatic plants depict Ceratophyllum as an early diverging genus. Our results support hypotheses that most taxonomic concepts of the order Nymphaeales reflect polyphyletic groups and that the unusual genus Ceratophyllum represents descendants of some of the earliest angiosperms.

Base Sequence↗

PubMed1985

Lipid composition of the nervous system of earthworms (Lumbricus terrestris).

As part of a systematic study of the evolution of the nervous system, the lipid composition of the ventral nerves of earthworms was examined. The nerve axons are wrapped in copious layers of loosely bound membrane, superficially resembling the myelin sheath of vertebrates. However, neither galactocerebroside nor sulfatide, both of which are considered to be markers for myelin, was present, and only traces of glucocerebroside, which is abundant in shrimp nerve, were detected. The lipids were rich in cholesterol (15.3 mumol/g of fresh tissue) and phospholipids (21.7 mumol/g of fresh tissue). The phospholipids were composed of phosphatidylethanolamine, -choline, -serine, and -inositol in the ratio of 41:44:8:7. Most of the ethanolamine-containing phospholipids were in the form of plasmalogens. The fatty acid moieties of these phospholipids were predominantly 18:1, 18:0, and 20:1, whereas the aldehyde moieties of plasmalogen were mostly 18:0. Sphingomyelin, which is considered a ubiquitous component of animal membranes, was not detected. How the unique structure of the membranes of earthworm nerves may be related to the function of the nervous system in this organism is discussed.

Animals↗

PubMed2026

Genome-wide identification and cold-stress-responsive expression analysis of the NOX gene family in Cucumis melo.

NADPH oxidases (NOXs) are crucial enzymes for reactive oxygen species (ROS) generation in plants and play vital roles in growth, development, and stress responses. To elucidate the sequence characteristics of the NOX gene family and its low-temperature response patterns in melon (Cucumis melo L.), this study conducted genome-wide identification and expression profiling of NOX family members using bioinformatics analysis, RNA-seq transcriptome sequencing, and real-time quantitative PCR (RT-qPCR). The results revealed that eight NOX members were identified in the melon genome, distributed across six chromosomes. All members harbored conserved domains including Ferric_reductase, FAD_binding_8, NAD_binding_6, and NADPH_Ox, and the encoded proteins were generally basic and hydrophilic. Phylogenetic analysis classified the NOX proteins into five subgroups. Synteny analysis indicated the presence of only one pair of intraspecific duplicated genes in melon, which was under purifying selection. The promoter regions contained multiple hormone- and stress-responsive cis-acting elements, with CmNOX2 and CmNOX4 harboring low-temperature responsive elements. Following treatment at 4℃ for 24 h and 48 h, leaf relative electrolyte leakage (REL) increased from 28.33% to 42.67% and 52.67%, respectively; transcriptome analysis identified 5,633 and 6,882 differentially expressed genes (DEGs), respectively. Cold-responsive genes exhibited significant differential expression, with SLAC1 and CPK19 showing sustained upregulation. RT-qPCR results demonstrated that the expression of CmNOX2, CmNOX5, CmNOX6, and CmNOX7 was significantly downregulated after low-temperature treatment, whereas CmNOX4 expression was significantly upregulated at 48 h. Integrating promoter elements and expression characteristics, CmNOX4 may represent an important candidate gene involved in melon low-temperature response. This study systematically characterized the structure, evolution, and expression patterns of the melon NOX gene family, identified candidate genes responsive to low temperature, and provides a reference for further investigation into the mechanisms underlying melon cold adaptation.

Cucumis melo↗

PubMed2025

The plastid genome of the critically endangered Valeriana trinervis (= Centranthus trinervis) and insights from comparison with other Valeriana plastomes (Caprifoliaceae).

The first complete plastid genome of the critically endangered species Valeriana trinervis was sequenced, assembled and compared with other published Valeriana plastomes. In this study, we assembled the plastid genome of the critically endangered, endemic species Valeriana trinervis (= Centranthus trinervis) and compare it with all published plastomes of Valeriana. We found not only differences in the inverted repeats boundaries, in the type and abundance of repeats, but also similarities in codon usage and microsatellite numbers. We detected non-canonical start codons in several genes and identified variation in several regions that could be useful for phylogenetic and phylogeographic studies. The phylogenetic tree inference based on both full plastomes and coding sequence data indicated that V. trinervis is sister to all Eurasian Valeriana accessions confirming the phylogenetic position recently investigated. This is the first plastome available for a species of the Mediterranean clade of Valeriana previously known as Centranthus, and it adds further data to understand the evolution and diversification of this systematically debated genus.

Genome, Plastid↗

PubMed1987

Phylogenetic comparison of the photoaffinity-labeled benzodiazepine receptor subunits.

The late evolutionary appearance of the benzodiazepine receptor (BZR) allows an experimental approach for evaluation of the qualitative development of its subunits. Photoaffinity labeling of brain membranes with [3H]flunitrazepam followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and fluorography offers a suitable method for tracing the qualitative evolution of the BZR. A systematic comparison of the subunit patterns in fishes, amphibians, reptiles, birds, and mammals revealed that the subunit of 53K is phylogenetically the oldest photoaffinity labeled subunit; whereas it is the only band present in the lungfish and most amphibians, additional bands are apparent in higher tetrapods. In fishes, the evolution of the BZR subunits leads to the loss of the 53K subunit. KD values are discussed in relation to specific subunit patterns. Possible explanations for the observed variation of the subunits are discussed, with special emphasis placed on the possible evolution by gene duplication and subsequent divergence.

Amphibians↗

PubMed2026

Global epidemiology, genomic evolution, and clinical implications of dual- and multiple-carbapenemase-producing Klebsiella pneumoniae: A systematic qualitative review.

BACKGROUND: The global emergence of dual- and multiple-carbapenemase-producing Klebsiella pneumoniae, particularly isolates co-harbouring blaNDM and blaOXA-48/OXA-48-like determinants, represents a critical threat to global health because of limited therapeutic options and expanding genomic complexity. METHODS: This systematic qualitative review synthesized evidence from 44 English-language peer-reviewed studies published between 2017 and 2026 and indexed in Scopus, with a focus on genomic evolution and spatiotemporal distribution. RESULTS: High-risk clones ST147, ST101, and ST11 were identified as major drivers of dissemination. Genomic analysis revealed key adaptive mechanisms, including stable IncL 96-kb fusion plasmids and IS10-mediated truncation of blaNDM-1, potentially reducing fitness costs while preserving resistance. Convergence events were also documented in which dual-carbapenemase-producing isolates acquired additional colistin resistance determinants (mcr-1 or mgrB alterations) and virulence-associated markers such as iuc1. Importantly, related resistance determinants were identified beyond hospital settings, including community, environmental, and food-associated reservoirs. CONCLUSION: The shift from single to dual and multiple carbapenemase production in K. pneumoniae underscores the need for integrated genomic surveillance, improved antimicrobial stewardship, and broader reservoir monitoring to address this evolving public health threat.

Klebsiella pneumoniae↗

PubMed2026

Paralogous evolution of the ITS2 region in Xiphophorus.

Ribosomal ITS2 is widely used in phylogenetic studies, yet its multigene organization and potential paralogy can obscure true species relationships. This proof-of-concept study investigates whether ITS2 sequences derived from long-read genomic data in multiple Xiphophorus species primarily reflect orthologous history or are shaped by ancient and local duplications. Phylogenetic analyses reveal two major, reciprocally mirroring ITS2 clades that represent long-standing paralogous rDNA lineages rather than simple allelic variants. The two paralogons show strong asymmetry in copy retention and loss for the majority of the species analyzed in this study. Exceptionally some other species are confined to one paralogon group and exhibit alternating ITS2 variants consistent with persistent ancestral polymorphism. A striking copy number imbalance in X. variatus, combined with its phylogenetic incongruence relative to the established species tree, is best explained by historical rDNA introgression followed by biased concerted evolution that nearly erased one paralogous copy. Despite incomplete homogenization, heterogeneous evolutionary rates, and occasional long-branch artifacts, the recovered paralog-specific topologies largely recapitulate the accepted Xiphophorus species phylogeny, indicating that ITS2 retains a robust organismal signal while also recording episodes of introgression and differential paralog evolution. These results demonstrate that explicit recognition of ITS2 paralogs can both improve phylogenetic interpretation and open avenues for future sequence-structure-based analyses of rDNA evolution and genus-level systematics in Xiphophorus.

Gene duplication↗

PubMed1992

[Gene pool and gene geography of the USSR population].

Gene pool and gene geography are discussed from the point of view of their conceptual history beginning from the original concept of A.S. Serebrovskiĭ (1928). Difference between the present-day gene geography and gene geography of gene pool is accentuated: the former only represents a portion of the latter. Historical and territorial integrity of the USSR population gene pool, in conjunction with its huge diversity, is the main problem being analysed by various means of computerized genetic cartography. Coupled with the gene frequency mapping, following methods were also used: mapping of average heterozygosity, of interpopulation differentiation, of principal component scores and mapping of geographical trend for each mapped genetic parameter. The work is based on 100 allelic genes and haplotypes from 30 independent loci studied on the average in 225 local populations. Statistical analysis of gene geographical maps is based on 3975 nodes of regular cartographic net for the USSR territory. The wind rose of systematic changes in the USSR gene pool has three main geographic orientations: W-E, SW-NE and S-N. At the same time, there are only two main systematic forces of gene pool evolution: the force of social history with predominant W-E orientation and the force of natural history with predominant S-N orientation of their actions. The heterozygosity level of gene pool declines strictly in accordance with the resultant in the SW-NE direction.

Alleles↗

PubMedDate not supplied

[Role of oxygen in the vital activity of aerobic organisms].

New experimental data that underlie construction of an adaptive-metabolic conception as to curative effect of hyperbaric oxygenation are systematized in the aspect of evolution. Oxygen under high pressure (300 kPa, 60 min) exerts a specific effect on functions of redox and antiredox systems and nonspecific effect determining adaptation mechanisms of functional (regulatory, effector), metabolic (bioenergy, detoxication, biosynthetic) and morphogenetic (cellular and intracellular regeneration) types at different (hyper-, normo- and hypobiotic) levels of vital activity as dependent on the metabolic activity of the functional structures under pathology conditions.

Adaptation, Physiological↗

PubMed1976

[Historical origin and evolution of the agents of infectious diseases].

Data on the establishment and further evolution of the causative agents of human infectious diseases were systematized. Saprophytes proved to be the initial stage of this evolution for all the parasitic species. It was demonstrated by concrete examples that evolution of parasitism was the result of an interaction of many factors (the mechanism of transmission of the causative agents, the immunity formation in the population, hereditary resistance, etc.) and not only the sequence of a unilateral action of the transmission mechanism. The author considers that some properties of the causative agents of the infecticus diseases of man (spore formation, the capacity to reproduction on the objects of the external environment) were not newly acquired in the process of the parasitic species formation, but atavistic signs which persisted from saprophytic ancestors. The dialectics of progressive and regressive processes in the acqisition of the parasitic properties by saprophytes is considered.

Biological Evolution↗

PubMed1991

Taxonomy, evolution and life cycles.

Three lectures were given, the first on haplodiploidy in the Oxyurida (Nematoda), the second on rodent Oxyurida and the third on the life cycle of Leishmania (Kinetoplastida, Trypanosomatidae). The oral communications and posters were divided into five subsections, covering systematics at supraspecific, specific and subspecific levels, evolution, and life cycles of parasites with hosts in both aquatic and terrestrial environments. A wide range of topics was discussed, including recent developments in the fields of genetics and cellular and molecular biology, and computer-assisted numerical taxonomy.

Animals↗