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Costs of plasticity in foraging characteristics of the clonal plant Ranunculus reptans.

In clonal plants, evolution of plastic foraging by increased lengths of leaves and internodes under unfavourable conditions may be constrained by costs and limits of plasticity. We studied costs and limits of plasticity in foraging characteristics in 102 genotypes of the stoloniferous herb Ranunculus reptans. We grew three replicates of each genotype with and three without competition by the naturally co-occuring grass Agrostis stolonifera. We used regression and correlation analyses to investigate potential costs of plasticity in lengths of leaves and stolon internodes, developmental instability costs of these traits, and a developmental range limit of these traits. We used randomization procedures to control for spurious correlations between parameters calculated from the same data. Under competition the number of rosettes, rooted rosettes, and flowers was 58%, 40%, and 61% lower, respectively, than in the absence of competition. Under competition lengths of leaves and stolon internodes were 14% and 6% smaller, respectively, than in the absence of competition. We detected significant costs of plasticity in stolon internode length in the presence of competition when fitness was measured in terms of the number of rosettes and the number of flowers (selection gradients against plasticity were 0.250 and 0.214, respectively). Within-environment variation (SD) in both foraging traits was not positively correlated with the corresponding plasticity, which indicates that there were no developmental instability costs. More plastic genotypes did not have less extreme trait values than less plastic genotypes for both foraging traits, which indicates that there was no developmental range limit. We conclude that in R. reptans costs of plasticity more strongly constrain evolution of foraging in the horizontal plane (i.e., stolon internode length) than in the vertical plane (i.e., leaf length).

Adaptation, Physiological↗

Relation between changes in cellular load, evolution of viral phenotype, and the clonal composition of virus populations in the course of human immunodeficiency virus type 1 infection.

The relationship between the evolution of human immunodeficiency virus type 1 (HIV-1) biologic phenotype, changes in the proportion of infected peripheral blood mononuclear cells, and the relative contribution of non-syncytium-inducing (NSI) and syncytium-inducing (SI) HIV-1 variants to virus load was studied during the course of HIV-1 infection. In 65 HIV-1-infected subjects, the proportion of infected CD4 T cells was higher in persons who carried SI variants. Longitudinal studies revealed that the emergence of SI HIV-1 variants can occur at relatively low numbers of HIV-1-infected cells. Emergence of SI variants frequently coincided with an increase of virus load due to an expansion of both NSI and SI variants, although the contribution of SI viruses to the total virus population significantly increased with time after SI phenotype conversion. These data indicate that NSI to SI phenotype conversion, rather than resulting from high virus load, is part of the sequence of events that leads to increased virus load and CD4 cell depletion.

CD4 Lymphocyte Count↗

Evolution of tumor subclones and T-cell dynamics underlie variable ibrutinib responses in Waldenström macroglobulinemia.

To elucidate the molecular basis underlying differential responses and resistance to ibrutinib in Waldenström macroglobulinemia (WM), we conducted a prospective phase 2 trial of ibrutinib monotherapy in treatment-naïve patients. A total of 74 sequential bone marrow (BM) aspirates from 17 patients, collected from baseline through 48 treatment cycles, were profiled using single-cell multiomics. BM cells were segregated primarily into B-cell/plasma cell and T-cell compartments. Longitudinal clonal tracking of malignant B cells/plasma cells identified 3 distinct evolutionary patterns: evolution (early clone contraction with late clone expansion and increasing genomic complexity), devolution (early clone expansion with late clone contraction and genomic simplification), and no evolution (stable clonal architecture). The evolution pattern was strongly associated with disease progression, whereas devolution correlated with durable clinical response. Transcriptomic profiling of resistant clones enabled development and validation of the Waldenström ibrutinib prediction (WIP) score, which predicted treatment response at baseline. Within the WIP signature, LYN emerged as a key regulator; LYN knockdown or inhibition significantly increased WM cell sensitivity to ibrutinib, suggesting a rational combination strategy. In parallel, GZMB+ CD8+ effector-memory T cells expanded after treatment in patients with progressive disease and coexisted with tumor evolution. These cells exhibited persistently impaired cytotoxic programs (eg, GNLY), a dedifferentiated memory-like state, elevated PDCD1 expression, and reduced T-cell receptor diversity. Together, this study provides, to our knowledge, the first single-cell framework of tumor clonal evolution and T-cell dysfunction under ibrutinib in WM, introduces the WIP score as a predictive biomarker for treatment response, and identifies actionable tumor-intrinsic and immune mechanisms driving resistance. This trial was registered at www.ClinicalTrials.gov as NCT02604511.

Aged↗

Molecular evolution of typical enteropathogenic Escherichia coli: clonal analysis by multilocus sequence typing and virulence gene allelic profiling.

Enteropathogenic Escherichia coli (EPEC) infections are a leading cause of infantile diarrhea in developing nations. Typical EPEC isolates are differentiated from other types of pathogenic E. coli by two distinctive phenotypes, attaching effacement and localized adherence. The genes specifying these phenotypes are found on the locus of enterocyte effacement (LEE) and the EPEC adherence factor (EAF) plasmid. To describe how typical EPEC has evolved, we characterized a diverse collection of strains by multilocus sequence typing (MLST) and performed restriction fragment length polymorphism (RFLP) analysis of three virulence genes (eae, bfpA, and perA) to assess allelic variation. Among 129 strains representing 20 O-serogroups, 21 clonal genotypes were identified using MLST. RFLP analysis resolved nine eae, nine bfpA, and four perA alleles. Each bfpA allele was associated with only one perA allele class, suggesting that recombination has not played a large role in shuffling the bfpA and perA loci between separate EAF plasmids. The distribution of eae alleles among typical EPEC strains is more concordant with the clonal relationships than the distribution of the EAF plasmid types. These results provide further support for the hypothesis that the EPEC pathotype has evolved multiple times within E. coli through separate acquisitions of the LEE island and EAF plasmid.

Adhesins, Bacterial↗

Genetic classification of combined hepatocellular-cholangiocarcinoma.

Combined hepatocellular-cholangiocarcinoma (combined HCC/ CC) is a rare form of liver neoplasms showing both hepatocellular (HCC) and bile duct differentiation (CC). In an attempt to clarify the clonality and genetic/phenotypic relationships in the evolution of these neoplasms, we microdissected multiple HCC and CC foci and studied allelic status of chromosome arms 1p, 1q, 3p, 4q, 5q, 6q, 8p, 9p, 10q, 11q, 13q, 16q, 17p, 17q, 18q, and 22q. Overall, the highest frequency of loss of heterozygosity (LOH) was seen on 4q and 17p, followed by 8p and 16q. Of the 11 cases studied, 3 cases did not show any of the identical allelic losses between HCC and CC foci, indicating the biclonal nature. The remaining 8 cases showed multiple allelic losses shared between both components, strongly suggestive of a single clonal derivation. Moreover, 4 of the 8 cases showed additional or divergent allelic losses at more than 1 chromosomal locus only in HCC and/or CC foci. Thus, this heterogeneity was shown to affect the phenotypic diversity of the tumor. Summarizing the genetic patterns, combined HCC/CC could be classified into the following 3 possibilities: (1) collision tumor in which 2 independent neoplastic clones develop at close proximity; (2) single clonal tumor with homogeneous genetic background in both components--histological diversity is thus a manifestation of divergent differentiation potential of a single clone; (3) single clonal process in which genetic heterogeneity in the process of clonal evolution within the tumor parallels histologic diversity; therefore, the tumor in this category is mainly composed of mosaics of closely related subclones.

Aged↗

Multiclonality and altered RFLP patterns for immunoglobulin heavy-chain and T-cell receptor genes in relapsing lymphomas.

BACKGROUND: Alteration of morphological appearance as well as of clinical behaviour is common in relapsing non-Hodgkin's lymphomas. The aim of this study was to investigate the stability of the genes encoding the immunoglobulin heavy-chain and the T-cell receptor during the course of the disease in relapsing non-Hodgkin's lymphomas. MATERIAL AND METHODS: Nineteen patients with relapsed or progressive non-Hodgkin's lymphomas were analysed with respect to alterations of the restriction fragment length polymorphism (RFLP) pattern for Ig heavy chain (IgH) using probes for the C mu and J regions and for T-cell receptor (T-beta, T-gamma chain) genes. DNA was extracted from tumour material taken at different occasions during the course of the disease. RESULTS: All 19 cases showed clonal rearrangements of the IgH locus, and 2 cases showed simultaneous rearrangement of the genes coding for the T-cell receptors. Three or more rearranged bands, indicating more than one malignant clone, were detected in 1 case at the time of the diagnosis and in 5/19 (26%) cases in DNA from samples taken at relapse, all 6 cases showing discordant or transformed morphology. Altogether, in 11 out of 19 cases (58%), changes of the IgH rearrangement pattern could be visualized by RFLP. In all these cases except one, the new RFLP pattern included at least one rearranged band from the pattern of the first taken sample. In one case a clonal T-gamma receptor gene rearrangement was detected in a diagnostic sample but not in a sample taken at relapse. In 4 out of 6 cases with transformed lymphomas, clonal changes were observed at time of transformation. Evolution of clones with different RFLP patterns in different compartments were observed in 1 out of 6 studied cases. CONCLUSIONS: The present study illustrates that non-Hodgkin's lymphomas are unstable in their IgH genome. The observations of clonal evolution, multiclonality, and different clones in different compartments offer an explanation to the troublesome situation when treating relapsed lymphomas.

Cloning, Molecular↗

Coagulase gemne variants associated with distinct populations of Staphylococcus aureus.

An identifying characteristic of Staphylococcus aureus is the production of staphylocoagulase (coagulase). The aim of this study was to determine the clonal distribution of coagulase gene (coa) variants within populations of S. aureus defined by multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and protein A variation. The N-terminal region of the coa gene from 43 methicillin-susceptible (MSSA) and 252 methicillin-resistant (MRSA) S. aureus human isolates and 9 animal S. aureus isolates was amplified and digested with HinfI. Twelve types were identified amongst the MSSA isolates and the majority (93%) of MRSA isolates were assigned to 5 of the 12 types. MLST and PFGE analysis identified epidemic populations of MRSA and each epidemic population was characterized by a different coagulase type. Nine of the 12 MLST-defined clonal complex ancestral genotypes recently described each carried a different coagulase type suggesting that coagulase evolution and the evolution of the clonal complexes are intimately related.

Amino Acid Sequence↗

Clonal hematopoiesis in patients with acquired aplastic anemia.

To determine whether patients with acquired asplastic anemia (AA) exhibit clonal hematopoiesis, we used restriction fragment length polymorphisms of the X-linked genes phosphoglycerate kinase (PGK1) and hypoxanthine phosphoribosyltransferase (HPRT) and the X-linked probe M27 beta. Of the 19 female patients studied, 18 (95%) patients were informative for at least one marker. Of these, eight patients (42%) were heterozygous for PGK1, two (11%) for HPRT, and 16 (84%) for M27 beta. In 13 (72%) patients, a monoclonal pattern was found. Analysis of purified cell suspensions of four of these patients showed that both myeloid and lymphoid cells were of monoclonal origin, indicating the involvement of an early stem cell. The four patients who were studied at presentation all showed a monoclonal pattern. One of these patients showed a spontaneous recovery despite persistent clonal hematopoiesis. The presence of either clonal or polyclonal hematopoiesis did not show a correlation with the response to antithymocyte globulin (ATG) treatment. A relapse after ATG was also seen in a patient exhibiting polyclonal hematopoiesis. Conversely, a monoclonal pattern did not preclude the occurrence of a partial or complete response to ATG. Other potential markers to study clonality, including cytogenetic abnormalities or point mutations of the N-ras protooncogene, were not found in any of the patients. It is concluded that patients with AA may exhibit clonal hematopoiesis. The significance with respect to evolution to disorders with clonal hematopoiesis like paroxysmal nocturnal hemoglobinuria, myelodysplasia, and acute leukemia remains to be determined.

Adolescent↗

Molecular evolution of the Escherichia coli chromosome. III. Clonal frames.

PCR fragments, 1500-bp, from 15 previously sequenced regions in the Escherichia coli chromosome have been compared by restriction analysis in a large set of wild (ECOR) strains. Prior published observations of segmental clonality are confirmed: each of several sequence types is shared by a number of strains. The rate of recombinational replacement and the average size of the replacements are estimated in a set of closely related strains in which a clonal frame is dotted with occasional stretches of DNA belonging to other clones. A clonal hierarchy is described. Some new comparative sequencing data are presented.

Base Sequence↗

Advances in tumor subclone formation and mechanisms of growth and invasion.

Tumor subclones refer to distinct cell populations within the same tumor that possess different genetic characteristics. They play a crucial role in understanding tumor heterogeneity, evolution, and therapeutic resistance. The formation of tumor subclones is driven by several key mechanisms, including the inherent genetic instability of tumor cells, which facilitates the accumulation of novel mutations; selective pressures from the tumor microenvironment and therapeutic interventions, which promote the expansion of certain subclones; and epigenetic modifications, such as DNA methylation and histone modifications, which alter gene expression patterns. Major methodologies for studying tumor subclones include single-cell sequencing, liquid biopsy, and spatial transcriptomics, which provide insights into clonal architecture and dynamic evolution. Beyond their direct involvement in tumor growth and invasion, subclones significantly contribute to tumor heterogeneity, immune evasion, and treatment resistance. Thus, an in-depth investigation of tumor subclones not only aids in guiding personalized precision therapy, overcoming drug resistance, and identifying novel therapeutic targets, but also enhances our ability to predict recurrence and metastasis risks while elucidating the mechanisms underlying tumor heterogeneity. The integration of artificial intelligence, big data analytics, and multi-omics technologies is expected to further advance research in tumor subclones, paving the way for novel strategies in cancer diagnosis and treatment. This review aims to provide a comprehensive overview of tumor subclone formation mechanisms, evolutionary models, analytical methods, and clinical implications, offering insights into precision oncology and future translational research.

Humans↗

General procedure to construct highly specific kDNA probes for clones of Trypanosoma cruzi for sensitive detection by polymerase chain reaction.

Our strategy of probes designing for major clones of Trypanosoma cruzi was performed taking into account the: (i) clear identification of the major clones under multilocus study; (ii) hypothesis of a parallel evolution between the extranuclear and nuclear markers; (iii) structure of kDNA which allowed to amplify high variable regions of the minicircle (HVRm) by PCR. The large production of HVRm was very useful to test their ability to be used as probes for detection of DNA from a diversified genetic panel of T. cruzi. Our success in designing such probes has important implications on: the enhancement of 2 evolutive hypothesis about the clonal structure of T. cruzi and the parallel evolution of their extranuclear and nuclear genetics markers; direct diagnosis in patients and vectors. Studies on bio-clinical significance of major clones are discussed. This procedure could be used as a general strategy to generate DNA probes for Kinetoplastida.

Animals↗

Molecular evolution of the Escherichia coli chromosome. II. Clonal segments.

Remarkable sequence similarities in the trp region among Escherichia coli strains of diverse natural origins imply the existence of worldwide clones of very recent origin. This in turn implies a low rate of fixation of new universally favorable alleles, which carry adjacent stretches of chromosome to high frequency. These clonal segments begin as entire chromosomes; recombination shortens them progressively by substituting less closely related homologous DNA. The rate of this recombination, comprising the introduction of a homologous chromosomal fragment to a cell and the replacement of part of the original chromosome, is estimated from observations.

Biological Evolution↗

Molecular evolution of Mycobacterium tuberculosis: phylogenetic reconstruction of clonal expansion.

SETTING: M. tuberculosis isolates were collected from patients attending health clinics in a high incidence urban community and in a low incidence rural setting in South Africa. OBJECTIVE: To reconstruct the evolutionary history of a group of closely related M. tuberculosis isolates using IS6110, DRr and MTB484(1) restriction fragment length polymorphism (RFLP) data. DESIGN: Mycobacterium tuberculosis isolates containing an average of ten IS6110 elements, with a similarity index of > or = 65% were genotypically classified by DNA fingerprinting using the IS6110 derived probes IS-3' and IS-5', as well as the DRr and MTB484(1) probes, in combination with PvuII or Hinfl endonuclease digestion. These RFLP data were subjected to phylogenetic analysis using both genetic distance and parsimony algorithms. RESULTS: Phylogenetic analysis predicted the existence of two independently evolving lineages, possibly evolving from a common ancestral strain. The topology of the phylogenetic tree was supported by comprehensive bootstrapping and the specific partitioning of DNA methylation phenotypes. The observed difference in the branch lengths of the two lineages may suggest differential evolutionary rates. Isolates collected from different geographical regions demonstrate independent evolution, suggesting that it is highly unlikely that strains have been recently transmitted between the two regions. The number of evolutionary events identified in this strain family differs significantly from that of previously characterized strain families, implying that evolutionary rate may be strain family dependent. CONCLUSION: Based on this analysis we propose that the algorithm used to calculate recent epidemiological events should be revised to incorporate the evolutionary characteristics of individual strain families, thereby enhancing the accuracy of molecular epidemiological calculations.

Algorithms↗

Karyotypic evolution in B-cell chronic lymphocytic leukaemia.

Sequential cytogenetic studies were performed on a minimum of two and a maximum of nine occasions (mean 3.6) on the peripheral blood leucocytes of 112 patients with B-CLL. On initial cytogenetic analysis, 58 had a normal karyotype and 64 had a clonal abnormality. Karyotypic evolution occurred in 18 patients (16%). There was no significant difference in the incidence of disease progression between patients with a stable karyotype and those who underwent karyotypic evolution. In only one patient was there a clear association between disease progression, a change in cell morphology and karyotypic evolution.

Clone Cells↗

Origins and evolution of methicillin-resistant Staphylococcus aureus clonal lineages.

Most methicillin-resistant Staphylococcus aureus (MRSA) isolates identified among blood isolates collected in Denmark between 1957 and 1970 belonged to either phage group III or the closely related 83A complex and had a PSTM antibiotype (resistance to penicillin [P], streptomycin [S], tetracycline [T], and methicillin [M]). Recently, some of these isolates were shown to have the same genetic backgrounds as contemporary epidemic MRSA isolates, and Danish methicillin-susceptible S. aureus (MSSA) isolates from the 1960s with a PST antibiotype were proposed to have been the recipients of the mecA gene in those lineages. In this study, we investigated the genetic backgrounds of isolates from the 83A complex that were fully susceptible or resistant to penicillin only in order to try to trace the evolutionary trajectory of contemporary MRSA lineages. We also studied MSSA and MRSA isolates from other phage groups in order to investigate if they had the potential to develop into contemporary MRSA clones. Most susceptible or penicillin-resistant isolates from phage group III or the 83A complex belonged to sequence type 8 (ST8) or ST5, while four isolates were ST254. STs 30, 45 and 25 were represented by MSSA isolates from other phage groups, which also included several singletons. Representatives of most of the current major epidemic MRSA lineages were identified among fully susceptible isolates collected in the 1960s, suggesting that these were MSSA lineages which carried genetic traits important for superior epidemicity before the acquisition of methicillin resistance.

Anti-Bacterial Agents↗

Evolution of high mutation rates in experimental populations of E. coli.

Most mutations are likely to be deleterious, and so the spontaneous mutation rate is generally held at a very low value. Nonetheless, evolutionary theory predicts that high mutation rates can evolve under certain circumstances. Empirical observations have previously been limited to short-term studies of the fates of mutator strains deliberately introduced into laboratory populations of Escherichia coli, and to the effects of intense selective events on mutator frequencies in E. coli. Here we report the rise of spontaneously originated mutators in populations of E. coli undergoing long-term adaptation to a new environment. Our results corroborate computer simulations of mutator evolution in adapting clonal populations, and may help to explain observations that associate high mutation rates with emerging pathogens and with certain cancers.

Adaptation, Physiological↗

Molecular epidemiology of diphtheria.

Molecular subtyping of Corynebacterium diphtheriae identified significant genetic diversity within the species and led to the identification of a unique clonal group that emerged in Russia in 1990 at the beginning of the current epidemic. Strains of this group belong to a distinct electrophoretic type complex and are of ribotypes D1 and D4. Identification of the group allowed for precise monitoring of the epidemic's progression and for rapid detection of cases imported to other countries. The evolution of this clonal group was monitored, and changes were identified. Molecular analysis revealed that no amino acid substitutions have occurred in the diphtheria toxin gene of the epidemic clone strains, reaffirming the use of the current vaccine as the single most effective preventive measure. Application of molecular subtyping methods and continuous monitoring of the spread of these clones has made it possible to distinguish rapidly between epidemic, endemic, and imported cases, allowing for implementation of timely and adequate preventive measures and providing reassurance that no secondary spread resulted from importations.

Bacterial Typing Techniques↗

Limited genetic diversity of Candida albicans in fecal flora of healthy volunteers and inpatients: a proposed basis for strain homogeneity in clinical isolates.

Molecular analysis of Candida albicans isolates from individual patients often yields a single strain at multiple sites. Whether this strain-limitation is due to virulence factors favoring the invasive strain or to lack of genetic diversity in the gastrointestinal reservoir is uncertain. We elected to study C. albicans genotypes in the fecal flora among healthy volunteers and inpatients. Self-obtained stool swabs or stool samples were cultured on inhibitory mold agar. From each subject with C. albicans, nine colonies were randomly selected, individually propagated, and typed utilizing random amplified polymorphic DNA. Colonies were considered identical (all bands matched), related variants (one to three unique bands), or distinct strains (more than three unique bands). Analysis showed a single clone in 33/43 (76.7%) volunteers and 6/18 (33.3%) inpatients (P = 0.018), two to four related variants in eight (18.6%) volunteers and 10 (55.6%) inpatients, and two distinct strains in two volunteers (4.6%) and two inpatients (11.1%). Strain variation was more common in females (33.5 versus 5.6%; P = 0.04) and tended to increase with age (r = 0.245, P = 0.06). These findings illustrate that most healthy subjects harbor a single strain of C. albicans in the fecal flora. This strain may undergo genetic evolution leading to minor clonal variations. The mechanisms for strain selection, maintenance and possible evolution remain to be delineated.

Candida albicans↗