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Results for “systematic evolution”

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PubMed2026

Spatial proteomics reveals four-stage molecular evolution in cancer immunotherapy-related gastritis.

BACKGROUND: Immune checkpoint inhibitors (ICIs) have transformed cancer treatment, yet immune-related adverse events (irAEs) including immunotherapy-related gastritis (IRAEG) pose significant clinical challenges-often necessitating treatment interruption that may compromise antitumor efficacy. IRAEG presents with atypical symptoms, lacks specific biomarkers, and shows histopathological overlap with other forms of gastritis, complicating diagnosis and management. Despite increasing clinical recognition, a systematic understanding of spatial molecular alterations across the full disease course remains limited. Here, we used spatial proteomics to map the molecular landscape of IRAEG during disease progression and to define stage-specific patterns of molecular evolution relevant to cancer immunotherapy management. METHODS: We analyzed tissue samples from seven patients, including four non-immunotherapy-related gastritis controls and three cancer patients who developed IRAEG following ICI therapy for solid tumors, sampled longitudinally across four disease stages: baseline (G1), acute severe inflammation (G2), early recovery (G3), and complete recovery (G4). Using laser capture microdissection coupled with data-independent acquisition mass spectrometry, we profiled 177 spatially resolved gastric tissue regions. Multiplex immunohistochemistry and immunofluorescence characterized features of the immune microenvironment, while Gene Ontology, KEGG pathway analysis, Gene Set Variation Analysis, and xCell inference enabled functional, metabolic, and immune profiling. Key immune and NET-related findings were further validated by multiplex immunofluorescence in an independent, expanded cohort of IRAEG and non-immunotherapy-related gastritis samples. RESULTS: IRAEG was characterized by widespread HLA molecule activation and enhanced antigen processing, resembling the immune phenotype observed in organ transplant rejection. The acute G2 stage exhibited excessive neutrophil extracellular trap formation, profound metabolic suppression, and collapse of immune homeostasis-features that may inform early intervention strategies to preserve ICI treatment continuity. During early recovery (G3), inflammatory injury transitioned toward repair, marked by activation of fatty acid metabolism and PPAR signaling. Notably, even at complete clinical recovery (G4), more than 1,000 proteins remained differentially expressed, reflecting sustained enhancement of metabolic and immune functions and establishing a distinct molecular "memory" state with implications for ICI rechallenge decisions. CONCLUSIONS: These findings define four molecularly distinct stages of IRAEG progression and recovery. The stage-specific signatures identified here serve as candidate biomarkers for diagnosis, disease staging, and therapeutic response assessment, and may guide clinical decisions regarding irAE management, treatment modification, and safe ICI rechallenge to support continued antitumor therapy.

Humans↗

PubMed2004

"Active" refuges can inhibit the evolution of resistance in insects towards transgenic insect-resistant plants.

Negative cross-resistance (NCR) toxins that hitherto have not been thought to have practical uses may indeed be useful in the management of resistance alleles. Practical applications of NCR for pest management have been limited (i) by the scarcity of high toxicity NCR toxins among pesticides, (ii) by the lack of systematic methodologies to discover and develop such toxins, as well as (iii) by the lack of deployment tactics that would make NCR attractive. Here we present the concept that NCR toxins can improve the effectiveness of refuges in delaying the evolution of resistance by herbivorous insect pests to transgenic host plants containing insecticidal toxins. In our concept, NCR toxins are deployed in the refuge, and thus are physically separated from the transgenic plants containing the primary plant-protectant gene (PPPG) encoding an insecticidal toxin. Our models show: (i) that use of NCR toxins in the refuge dramatically delays the increase in the frequency of resistance alleles in the insect population; and (ii) that NCR toxins that are only moderately effective in killing insects resistant to the PPPG can greatly improve the durability of transgenic insecticidal toxins. Moderately toxic NCR toxins are more effective in minimizing resistance development in the field when they are deployed in the refuge than when they are pyramided with the PPPG. We explore the potential strengths and weaknesses of deploying NCR toxins in refuges.

Animals↗

PubMed1986

Cytogenetic studies on human breast carcinomas.

Cytogenetic studies were performed on cell material obtained from surgical specimens of 50 human breast carcinomas and from 61 cancerous effusions of 46 patients. Classical cytogenetic analyses of numerical chromosome changes and marker chromosomes revealed the non-random involvement of chromosomes #X and #22 as monosomics, of chromosomes #3, #7, and #19 as trisomics, and chromosome #1 (particularly p 13 to q 12) in marker formation. Karyotypic evolution was followed in vitro and in vivo and showed a highly individualistic pattern of stability and variability. In addition, a systematic screening for the presence of cytogenetic equivalents of gene amplification (double minutes 'DM', homogeneously staining regions 'HSR') was carried out. A high incidence of DM-positive cases was detected in primary tumors (48%) as well as in metastatic cells from effusions (40%), with the frequency of DM-containing metaphases ranging from 1 to 100% in the positive cases. This finding supports the assumption of the fundamental biological importance of gene amplification in human solid tumors. Furthermore, chromosome breakage and micronuclei were observed in breast carcinoma cells as an apparent consequence of therapy-independent mutability.

Breast Neoplasms↗

PubMed2004

Evidence-based public health: an evolving concept.

Evidence-based public health (EBPH) has been proposed as a practice model that builds upon the success of evidence-based medicine (EBM). EBM has been described as a more scientific and systematic approach to the practice of medicine. It has enhanced medical training and practice in many settings. Both EBM and EBPH systematically use data, information, and scientific principles to enhance clinical care and population health, respectively. In this paper, we review the evolution of EBPH, propose a new definition for EBPH, and discuss developments that may support its further advancement.

Evidence-Based Medicine↗

PubMed2004

The iProClass integrated database for protein functional analysis.

Increasingly, scientists have begun to tackle gene functions and other complex regulatory processes by studying organisms at the global scales for various levels of biological organization, ranging from genomes to metabolomes and physiomes. Meanwhile, new bioinformatics methods have been developed for inferring protein function using associative analysis of functional properties to complement the traditional sequence homology-based methods. To fully exploit the value of the high-throughput system biology data and to facilitate protein functional studies requires bioinformatics infrastructures that support both data integration and associative analysis. The iProClass database, designed to serve as a framework for data integration in a distributed networking environment, provides comprehensive descriptions of all proteins, with rich links to over 50 databases of protein family, function, pathway, interaction, modification, structure, genome, ontology, literature, and taxonomy. In particular, the database is organized with PIRSF family classification and maps to other family, function, and structure classification schemes. Coupled with the underlying taxonomic information for complete genomes, the iProClass system (http://pir.georgetown.edu/iproclass/) supports associative studies of protein family, domain, function, and structure. A case study of the phosphoglycerate mutases illustrates a systematic approach for protein family and phylogenetic analysis. Such studies may serve as a basis for further analysis of protein functional evolution, and its relationship to the co-evolution of metabolic pathways, cellular networks, and organisms.

Amino Acid Sequence↗

PubMed2004

The evolution of supertrees.

Supertrees result from combining many smaller, overlapping phylogenetic trees into a single, more comprehensive tree. As such, supertree construction is probably as old as the field of systematics itself, and remains our only way of visualizing the Tree of Life as a whole. Over the past decade, supertree construction has gained a more formal, objective footing, and has become an area of active theoretical and practical research. Here, I review the history of the supertree approach, focusing mainly on its current implementation. The supertrees of today represent some of the largest, complete phylogenies available for many groups, but are not without their critics. I conclude by arguing that the ever-growing molecular revolution will result in supertree construction taking on a new role and implementation in the future for analyzing large DNA sequence matrices as part of a divide-and-conquer phylogenetic approach.

Journal Article↗

PubMed2025

Oncogenic roles of young human de novo genes and their potential as neoantigens in cancer immunotherapy.

Young human de novo genes, recently emerging from non-coding regions, are expected to contribute to human-specific traits and diseases. However, systematic explorations of this connection have been lacking. Here, we report 37 recently originated de novo genes in humans, with their evolution and characteristics defined within an updated genomic context. The expression of these genes is significantly upregulated and temporospatially expanded in tumors, partially associated with extrachromosomal DNA amplification. Depletion of 57.1% of these genes suppresses tumor cell proliferation, underscoring their roles in tumorigenesis. As a proof of concept, we developed mRNA vaccines expressing ELFN1-AS1 and TYMSOS-young genes specifically expressed during early development but reactivated exclusively in tumors. In humanized mice, these vaccines triggered specific T cell activation and inhibited tumor growth. The antigens derived from these genes are immunogenic and capable of eliciting antigen-specific T cell activation in colorectal cancer patients. These findings underscore young human de novo genes as neoantigens in cancer immunotherapy.

Humans↗

PubMed2005

Infrared spectra of V(n)Bz(n+1) sandwich clusters: a theoretical study of size evolution.

Results of density functional theory computations of infrared (IR) spectra of linear sandwich V(n)Bz(n+1), n = 1-6, complexes are presented. It is shown that the systematic changes in the spectra as a function of the complex size can be categorized and understood in terms of responses of the "parent" modes of the Bz molecule and the VBz complex. The analysis presented should be applicable to a broad class of linear sandwich systems.

Letter↗

PubMed2000

Mutational spectrum of the EPM2A gene in progressive myoclonus epilepsy of Lafora: high degree of allelic heterogeneity and prevalence of deletions.

Progressive myoclonus epilepsy of the Lafora type (Lafora disease) is an autosomal recessive disease characterised by epilepsy, myoclonus, progressive neurological deterioration and the presence of glycogen-like intracellular inclusion bodies (Lafora bodies). We recently cloned the major gene for Lafora disease (EPM2A) and characterised the corresponding product, a putative protein tyrosine phosphatase (LAFPTPase). Here we report the complete coding sequence of the EPM2A gene and the analysis of this gene in 68 Lafora disease chromosomes. We describe 11 novel mutations: three missense (F84L, G240S and P301L), one nonsense (Y86stop), three < 40 bp microdeletions (K90fs, Ex1-32bpdel, Ex1-33bpdel), and two deletions affecting the entire exon 1 (Ex1-del1 and Ex1-del2). In addition, we have identified three patients with a null allele in non-exonic microsatellites EPM2A-3 or EPM2A-4, suggesting the presence of two distinct > 3 kb deletions affecting exon 2 (Ex2-del1 and Ex2-del2). Considering these mutations, a total of 25 mutations, 60% of them generating truncations, have been described thus far in the EPM2A gene. In spite of this remarkable allelic heterogeneity, the R241stop EPM2A mutation was found in approximately 40% of the Lafora disease patients. We also report the characterisation of five new microsatellite markers and one SNP in the EPM2A gene and describe the haplotypic associations of alleles at these sites in normal and EPM2A chromosomes. This analysis suggests that both founder effect and recurrence have contributed to the relatively high prevalence of R241stop mutation in Spain. The data reported here represent the first systematic analysis of the mutational events in the EPM2A gene in Lafora disease patients and provide insight into the origin and evolution of the different EPM2A alleles.

Adolescent↗

PubMed2001

The quality assurance programme for the national radioactivity surveillance network in Italy.

The quality assurance programme (QAP) carried out by the ENEA and ANPA for the laboratories belonging to the radioactivity surveillance network in Italy is outlined. The organisation of the QAP and the measurement campaigns performed from 1983 to 2000 are reviewed under different aspects such as network evolution, measurement types, standard sources needed for the calibration and intercomparison campaigns. network homogeneity and accuracy level, and main sources of systematic errors. The results show the effectiveness of the programme in obtaining a uniform accuracy level among the participating laboratories. Nevertheless a few sources of systematic errors are still present.

Calibration↗

PubMed2002

A genus-level supertree of the Dinosauria.

One of the ultimate aims of systematics is the reconstruction of the tree of life. This is a huge undertaking that is inhibited by the existence of a computational limit to the inclusiveness of phylogenetic analyses. Supertree methods have been developed to overcome, or at least to go around this problem by combining smaller, partially overlapping cladograms. Here, we present a very inclusive generic-level supertree of Dinosauria (covering a total of 277 genera), which is remarkably well resolved and provides some clarity in many contentious areas of dinosaur systematics.

Animals↗

PubMed2005

Phylogenetics of modern birds in the era of genomics.

In the 14 years since the first higher-level bird phylogenies based on DNA sequence data, avian phylogenetics has witnessed the advent and maturation of the genomics era, the completion of the chicken genome and a suite of technologies that promise to add considerably to the agenda of avian phylogenetics. In this review, we summarize current approaches and data characteristics of recent higher-level bird studies and suggest a number of as yet untested molecular and analytical approaches for the unfolding tree of life for birds. A variety of comparative genomics strategies, including adoption of objective quality scores for sequence data, analysis of contiguous DNA sequences provided by large-insert genomic libraries, and the systematic use of retroposon insertions and other rare genomic changes all promise an integrated phylogenetics that is solidly grounded in genome evolution. The avian genome is an excellent testing ground for such approaches because of the more balanced representation of single-copy and repetitive DNA regions than in mammals. Although comparative genomics has a number of obvious uses in avian phylogenetics, its application to large numbers of taxa poses a number of methodological and infrastructural challenges, and can be greatly facilitated by a 'community genomics' approach in which the modest sequencing throughputs of single PI laboratories are pooled to produce larger, complementary datasets. Although the polymerase chain reaction era of avian phylogenetics is far from complete, the comparative genomics era-with its ability to vastly increase the number and type of molecular characters and to provide a genomic context for these characters-will usher in a host of new perspectives and opportunities for integrating genome evolution and avian phylogenetics.

Animals↗

PubMed2005

Structure of positive decompositions of exponential operators.

The solution of many physical evolution equations can be expressed as an exponential of two or more operators acting on initial data. Accurate solutions can be systematically derived by decomposing the exponential in a product form. For time-reversible equations, such as the Hamilton or the Schrödinger equation, it is immaterial whether or not the decomposition coefficients are positive. In fact, most symplectic algorithms for solving classical dynamics contain some negative coefficients. For time-irreversible systems, such as the Fokker-Planck equation or the quantum statistical propagator, only positive-coefficient decompositions, which respect the time-irreversibility of the diffusion kernel, can yield practical algorithms. These positive time steps only, forward decompositions, are a highly effective class of factorization algorithms. This work presents a framework for understanding the structure of these algorithms. By a suitable representation of the factorization coefficients, we show that specific error terms and order conditions can be solved analytically. Using this framework, we can go beyond the Sheng-Suzuki theorem and derive a lower bound for the error coefficient e(VTV). By generalizing the framework perturbatively, we can further prove that it is not possible to have a sixth-order forward algorithm by including only the commutator [VTV] tripple bond [V, [T,V]]. The pattern of these higher-order forward algorithms is that in going from the (2n)th to the (2n+2)th order, one must include a different commutator [V T(2n-1)V] in the decomposition process.

Journal Article↗

PubMed2003

Transposable elements in filamentous fungi.

The past 10 years have been productive in the characterization of fungal transposable elements (TEs). All eukaryotic TEs described are found including an extraordinary prevalence of active members of the pogo family. The role of TEs in mutation and genome organization is well documented, leading to significant advances in our perception of the mechanisms underlying genetic changes in these organisms. TE-mediated changes, associated with transposition and recombination, provide a broad range of genetic variation, which is useful for natural populations in their adaptation to environmental constraints, especially for those lacking the sexual stage. Interestingly, some fungal species have evolved distinct silencing mechanisms that are regarded as host defense systems against TEs. The examination of forces acting on the evolutionary dynamics of TEs should provide important insights into the interactions between TEs and the fungal genome. Another issue of major significance is the practical applications of TEs in gene tagging and population analysis, which will undoubtedly facilitate research in systematic biology and functional genomics.

DNA Transposable Elements↗

PubMed1999

Differentiation of vascular dementia from AD on neuropsychological tests.

BACKGROUND: The concept of vascular dementia (VaD) is currently in a state of evolution. Memory impairment is emphasized as a primary criterion, reflecting the influence of AD on the concept of dementia. We have systematically reviewed whether the nature of neuropsychological dysfunction is distinct in AD and VaD, and whether similar defining criteria for the concept of dementia in both disorders can be supported. METHODS: We searched five bibliographic databases (Medline, Biological Abstracts, EMBASE, PsychINFO, PsychLIT) for research articles in which VaD and AD had been compared using neuropsychological tests and that met criteria for scientific merit. RESULTS: Of the 45 studies, 18 were excluded because of inadequacies, and the remaining 27 were analyzed. There were a number of similarities of dysfunction between VaD and AD. However, when matched for age, education, and severity of dementia, VaD patients had relatively superior function in verbal long-term memory and more impairment in frontal executive functioning compared with AD patients. Interpretation of the results is limited by uncertainty in diagnostic criteria for VaD, possible inclusion bias due to use of clinical diagnosis alone, possible overlap of AD and VaD, and the methodologic shortcomings of some studies. CONCLUSIONS: The neuropsychological differentiation of VaD from AD was consistent with the different neuroimaging findings in the two disorders, and argues for differential criteria for the definition of the syndromes. The simple application of Alzheimer's dementia criteria to VaD, with the inclusion of cerebrovascular disease etiology, may not be sufficient to capture the uniqueness of VaD.

Alzheimer Disease↗

PubMed2004

Retroposon mapping in molecular systematics.

Advances in genome sciences are demonstrating the dynamic nature of noncoding DNA regions, which are comprised largely of repetitive elements with no apparent function. Retroposons are one class of mobile genetic elements that amplify and move about the genome via a copy-and-paste mechanism that employs an RNA intermediate. Short and long interspersed elements (SINEs and LINEs, respectively) are types of retroposons of particular interest because of their active role in shaping the architecture of genomes and their diagnostic value as evolutionary markers for studies of phylogeny and population biology. Although the use of SINEs and LINEs for molecular systematic studies is proliferating, a comprehensive laboratory protocol that explicitly outlines how to isolate and characterize retroposons for systematic studies in a detailed, step-by-step fashion has been lacking. The present chapter addresses this gap in the literature by focusing on the strategy for isolating new SINEs from a genomic library, the screening process, the sequencing and characterization of clones into subfamilies, quantification of copy number in host taxa, and the critical diagnosis of phylogenetically informative SINE and LINE insertion patterns. Practical limits to the method are discussed in relation to sampling design, systematic character theory, and the empirical distribution of elements observed in eukaryotic lineages. Major steps in the experimental process are illustrated with case examples from a diversity of taxonomic groups and by published results in the molecular biology and systematics literature.

Animals↗

PubMed2001

[The advancement of G protein and coupled signal transduction pathways].

G protein coupled signal transduction system is one major transmembrane signaling pathways in cell. Research of biochemistry and pharmacology in medicine showed that a lot of medicines play their role through G protein coupled signaling pathways. Thus, systematic study on G protein structure and functions had very important effects on new medicine producing. In the process of creature evolution, there are highly conserved amino-acid sequences in G protein. Study on G protein and coupled signal components in plants and insects signaling processes may benefit to determine the mechanism of crop resistance to disease and pest insect and resistant chemicals effect on insect behavior and physiology. This paper reviews the research progress and prospect of practical use in recent studies of G protein and coupled components in animal, insect and plant signaling pathways.

Animals↗

PubMed1981

[Social mobility in France, 1953-1970: a new look].

The authors attempt to extend Thelot's analysis of social mobility in France between 1953 and 1970. In particular, they examine "whether observed changes in mobility rates are entirely attributable to 'structural' influences. [They conclude] that while (as Thelot has suggested) the evolution of the occupational structure has been of major importance in altering the amount and pattern of mobility, changes of a systematic kind are none the less still evident when mobility is assessed independently of all structural effects." Data are from two surveys conducted by the National Institute of Statistics and Economic Studies (SUMMARY IN ENG, GER, RUS,)

Developed Countries↗