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PubMed2003

It's time to rework the blueprints: building a science for clinical psychology.

The aims in this article are to connect the conceptual structure of clinical psychological science to what the author believes to be the omnipresent principles of evolution, use the evolutionary model to create a deductively derived clinical theory and taxonomy, link the theory and taxonomy to comprehensive and integrated approaches to assessment, and outline a framework for an integrative synergistic model of psychotherapy. These foundations also provide a framework for a systematic approach to the subject realms of personology and psychopathology. Exploring nature's deep principles, the model revives the personologic concept christened by Henry Murray some 65 years ago; it also parallels the interface between human social functioning and evolutionary biology proposed by Edward Wilson in his concept of sociobiology.

Biological Evolution↗
PubMed1994

Implications of early hominid labyrinthine morphology for evolution of human bipedal locomotion.

The upright posture and obligatory bipedalism of modern humans are unique among living primates. The evolutionary history of this behaviour has traditionally been pursued by functional analysis of the postcranial skeleton and the preserved footprint trails of fossil hominids. Here we report a systematic attempt to reconstruct the locomotor behaviour of early hominids by looking at a major component of the mechanism for the unconscious perception of movement, namely by examining the vestibular system of living primates and early hominids. High-resolution computed tomography was used to generate cross-sectional images of the bony labyrinth. Among the fossil hominids the earliest species to demonstrate the modern human morphology is Homo erectus. In contrast, the semicircular canal dimensions in crania from southern Africa attributed to Australopithecus and Paranthropus resemble those of the extant great apes. Among early Homo specimens, the canal dimensions of Stw 53 are unlike those seen in any of the hominids or great apes, whereas those of SK 847 are modern-human-like.

Animals↗
PubMed2005

Phylogeny and molecular evolution of the tribe Harpalini (Coleoptera, Carabidae) inferred from mitochondrial cytochrome-oxidase I.

The tribe Harpalini is a group of ground beetles with a world-wide distribution that comprises approximately 2000 species and about 238 genera and subgenera. Hypotheses about the phylogenetic relationships of the subtribes of Harpalini are implicit within the systematic criteria put forward by different authors. A 759 bp fragment of the mitochondrial COI was sequenced in 119 specimens (107 species) of 52 genera and subgenera that represent the main lineages of Harpalines, and 3 species of other tribes used as outgroups. A hierarchical study of sequence divergence (under uncorrected and corrected models) and ts:tv ratio pattern analyses were carried out at different taxonomic levels. A low saturation rate was detected at first and second codon positions, whereas A+T richness causes a low transitions:transversions ratio, which suggests--a priori--a high rate of saturation at the third codon position. A progressive accumulation of sequence divergence and a decreasing ts:tv ratio were found from lower to higher taxonomic levels. MP strict consensus, ML, and minimum evolution distance (under ts+tv and tv only schemes) trees showed similar major clades within the tribe. The subtribe Ditomina is a monophyletic lineage with close affinities to the subtribe Harpalina. Harpalina is a polyphyletic lineage as the genus Daptus is always related to members of the subtribe Stenolophina, and the Selenophorines resulted a polyphyletic group related to the subtribe Anisodactylina. Main lineages proposed by Noonan [Quaest. Entomol. 9 (1973) 266] within the subtribe Anisodactylina have been corroborated in this study. The Australian genus Phorticosomus is not related to Ditomina but to the Australian Notiobioids lineage. Most taxa of the subtribe Stenolophina are always included in the same clade, together with taxa of the subtribe Pelmatellina, which might be considered as a lineage of Stenolophina related to Bradycellus and Dicheirotrichus. The subtribe Amblystomina lacks a well-supported relationship to the other subtribes of Harpalini and could not be consistently related to any of them.

Animals↗
PubMed2003

"Design" in solid-state chemistry based on phase homologies. The concept of structural evolution and the new megaseries A(m)[M(1+l)Se(2+l)]2m[M(2l+n)Se(2+3l+n)].

An attractive way to advance the design and prediction of new compositions and structures of solid-state compounds is to identify large homologies that are amenable to chemical control. Homologies allow the systematization of phases under a common conceptual umbrella and have the potential to capture the vast majority of existing and possible compounds. We have demonstrated this in the broad system A/M'/M''/Se (A = K, Rb, Cs, Sr, Ba; M' = Pb, Sn; M'' = Sb, Bi) by identifying the homologous "superseries" A(m)[M(1+l)Se(2+l)]2m[M(2l+n)Se(2+3l+n)]. This series generates a large variety of compounds with predictable composition and structure. All the compounds contain fundamental building units representing different fragments of the NaCl-type lattice. The three independent integers l, m, and n determine width, height, and shape of the building units and therefore cause structural evolution of the homologous series in three different dimensions. On the basis of this general formula one can design, in a modular fashion, new compounds that fit the structural evolution of the superseries, predicting simultaneously their structure and composition. Several new phases have been discovered with this approach. Here we give an overview of the character and predictive properties of the superseries and propose the classification of phases into homologies (when possible) which could serve as devices to predict new members.

Journal Article↗
PubMed2000

Isometric scaling of maxillary sinus volume in hominoids.

Previous hypotheses of maxillary sinus size evolution have proposed one or more changes in the volume of the structure across hominoid phylogeny. These hypotheses have been used subsequently to support the phylogenetic placement of fossil taxa relative to the living Hominoidea. The null hypothesis, that no change in sinus volume independent of size has occurred in ape evolution, is evaluated here by scaling analysis. Mixed sex samples of adult dry crania for the extant ape genera were examined by computer tomography imaging and the volume of the maxillary sinus was obtained. Sinus volume was then regressed, using both least squares and reduced major axis models, against cranial size variables. The results clearly demonstrate that the null hypothesis of no change in relative sinus volume cannot be rejected; thus, there is no support for hypotheses that maxillary sinus volume, independent of cranial size, has changed in the course of hominoid evolution. This result, in turn, has implications for the phylogenetic placement of fossil taxa and highlights the need for the careful delineation of character states in studies of hominoid systematics.

Adult↗
PubMed2025

Modern biology of extrachromosomal DNA: A decade-long voyage of discovery.

Genomic instability is a hallmark of cancer and is a major driving force of tumorigenesis. A key manifestation of genomic instability is the formation of extrachromosomal DNAs (ecDNAs) - acentric, circular DNA molecules ranging from 50 kb to 5 Mb in size, distinct from chromosomes. Ontological studies have revealed that ecDNA serves as a carrier of oncogenes, immunoregulatory genes, and enhancers, capable of driving elevated transcription of its cargo genes and cancer heterogeneity, leading to rapid tumor evolution and therapy resistance. Although ecDNA was documented over half a century ago, the past decade has witnessed a surge in breakthrough discoveries about its biological functions. Here, we systematically review the modern biology of ecDNA uncovered over the last ten years, focusing on how discoveries during this pioneering stage have illuminated our understanding of ecDNA-driven transcription, heterogeneity, and cancer progression. Furthermore, we discuss ongoing efforts to target ecDNA as a novel approach to cancer therapy. This burgeoning field is entering a new phase, poised to reshape our knowledge of cancer biology and therapeutic strategies.

Humans↗
PubMedDate not supplied

Disk-covering, a fast-converging method for phylogenetic tree reconstruction.

The evolutionary history of a set of species is represented by a phylogenetic tree, which is a rooted, leaf-labeled tree, where internal nodes represent ancestral species and the leaves represent modern day species. Accurate (or even boundedly inaccurate) topology reconstructions of large and divergent trees from realistic length sequences have long been considered one of the major challenges in systematic biology. In this paper, we present a simple method, the Disk-Covering Method (DCM), which boosts the performance of base phylogenetic methods under various Markov models of evolution. We analyze the performance of DCM-boosted distance methods under the Jukes-Cantor Markov model of biomolecular sequence evolution, and prove that for almost all trees, polylogarithmic length sequences suffice for complete accuracy with high probability, while polynomial length sequences always suffice. We also provide an experimental study based upon simulating sequence evolution on model trees. This study confirms substantial reductions in error rates at realistic sequence lengths.

Algorithms↗
PubMed2005

Proteomic mass spectra classification using decision tree based ensemble methods.

MOTIVATION: Modern mass spectrometry allows the determination of proteomic fingerprints of body fluids like serum, saliva or urine. These measurements can be used in many medical applications in order to diagnose the current state or predict the evolution of a disease. Recent developments in machine learning allow one to exploit such datasets, characterized by small numbers of very high-dimensional samples. RESULTS: We propose a systematic approach based on decision tree ensemble methods, which is used to automatically determine proteomic biomarkers and predictive models. The approach is validated on two datasets of surface-enhanced laser desorption/ionization time of flight measurements, for the diagnosis of rheumatoid arthritis and inflammatory bowel diseases. The results suggest that the methodology can handle a broad class of similar problems.

Algorithms↗
PubMed1994

Structure-based systematic isolation of conditional-lethal mutations in the single yeast calmodulin gene.

Conditional-lethal mutations of the single calmodulin gene in Saccharomyces cerevisiae have been very difficult to isolate by random and systematic methods, despite the fact that deletions cause recessive lethality. We report here the isolation of numerous conditional-lethal mutants that were recovered by systematically altering phenylalanine residues. The phenylalanine residues of calmodulin were implicated in function both by structural studies of calmodulin bound to target peptides and by their extraordinary conservation in evolution. Seven single and 26 multiple Phe-->Ala mutations were constructed. Mutant phenotypes were examined in a haploid cmd1 disrupted strain under three conditions: single copy, low copy, and overexpressed. Whereas all but one of the single mutations caused no obvious phenotype, most of the multiple mutations caused obvious growth phenotypes. Five were lethal, 6 were lethal only in synthetic medium 13 were temperature-sensitive lethal and 2 had no discernible phenotypic consequences. Overexpression of some of the mutant genes restored the phenotype to nearly wild type. Several temperature-sensitive calmodulin mutations were suppressed by elevated concentration of CaCl2 in the medium. Mutant calmodulin protein was detected at normal levels in extracts of most of the lethal mutant cells, suggesting that the deleterious phenotypes were due to loss of the calmodulin function and not protein instability. Analysis of diploid strains heterozygous for all combinations of cmd 1-ts alleles revealed four intragenic complementation groups. The contributions of individual phe-->ala changes to mutant phenotypes support the idea of internal functional redundancy in the symmetrical calmodulin protein molecule. These results suggest that the several phenylalanine residues in calmodulin are required to different extents in different combinations in order to carry out each of the several essential tasks.

Base Sequence↗
PubMed2003

From genes to proteins: in vitro expression of rickettsial proteins.

The availability of the complete genome sequences of several organisms allows the comparative analysis of genomes, a branch of bioinformatics known as genomics. With this approach, much can be learned about the biology of organisms that are difficult to culture, even when few, if any, of their proteins have been isolated and studied directly. We have focused our interest on Rickettsia conorii, an obligate intracellular bacterium responsible for Mediterranean spotted fever, a disease endemic in southern Europe. While bioinformatic annotation of the complete genome of this bacteria has allowed identification of 1,374 genes, a large number of them remain functionally uncharacterized. The final goal of many experiments in molecular biology is to use biological systems to synthesize the protein encoded by the gene being studied. Because three-dimensional structures are more resilient to evolution and change than amino acid sequences, structure determination of some open reading frames should also exhibit structural similarity to previously described protein families. We have thus initiated a systematic expression and structure determination program for the proteins encoded by rickettsial genes of interest. We have cloned different genes of R. conorii by recombinational cloning (GATEWAY), Invitrogen) a method that uses in vitro site-specific recombination to accomplish a directional cloning of PCR products and the subsequent automatic subcloning of the DNA segment into new vector backbones at high efficiency. The constructions in p-Dest17 yielded several clones able to express recombinant proteins with a C-terminal histidine tag. Expression of corresponding proteins was then performed using a cell-free protein expression system (Rapid Translation System, RTS, Roche Diagnostics). The recombinational cloning approach coupled to RTS provides an approach to rapid optimization of protein expression and is very useful to express rickettsial proteins. Moreover, this system is able to overcome some of the limitations encountered with rickettsial proteins highly toxic for E. coli or insect cells.

Bacterial Proteins↗
PubMed2025

Integrated multi-omics analyses provide new insights into genomic variation landscape and regulatory network candidate genes associated with walnut endocarp.

Persian walnut (Juglans regia) is an economically important nut oil tree; the fruit has a hard endocarp/shell to protect seeds, thus playing a key role in its evolution, and the shell thickness is an important trait for walnut breeding. However, the genomic landscape and the gene regulatory networks associated with walnut shell development remain to be systematically elucidated. Here, we report a high-quality genome assembly of the walnut cultivar 'Xiangling' and construct a graphic structure pan-genome of eight Juglans species to reveal the genetic variations at the genome level. We re-sequence 285 accessions to characterize the genomic variation landscape. Through genome-wide association studies (GWAS), we identified 19 loci associated with more than 268 loci that underwent selection during walnut domestication and improvement. Multi-omics analyses, including transcriptomics, metabolomics, DNA methylation, and spatial transcriptomics across eleven developmental stages, revealed several candidate genes related to secondary cell biosynthesis and lignin accumulation. This integrated multi-omics approach revealed several candidate genes associated with secondary cell biosynthesis and lignin accumulation, such as UGP, MYB308, MYB83, NAC043, NAC073, CCoAOMT1, CCoAOMT7, CHS2, CESA7, LAC7, COBL4, and IRX12. Overexpression of JrUGP and JrMYB308 in Arabidopsis thaliana confirmed their roles in lignin biosynthesis and cell wall thickening. Consequently, our comprehensive multi-omics findings offer novel insights into walnut genetic variation and network regulation of endocarp development and shell thickness, which enable further genome-informed breeding strategies for walnut cultivar improvement.

Juglans↗
PubMed1980

The interpretation of variation in the classification of nerve cells.

Within any biological population there is considerable variation in the physical characteristics of individual members, and the understanding and classification of such populations always depends on the interpretation of this variation. A major point of this paper is that groups of neurones can also be regarded as biological populations, and that at least three distinct types of variation can be found within any neural population:role-indicating variation, which enables different cells or groups of cells to perform different functions; systematic variation, which allows different cells (or sometimes the same cell) to perform a particular function under varying conditions; and residual variation, which is principally related to mechanisms of evolution and provides the population with its biological adaptability. Examples of these three types of variation are suggested for a number of properties of retinal ganglion cell populations. A second major point is that any functional classification of nerve cells should contain multiple taxonomic levels, corresponding to different levels of complexity and interaction within the nervous system. Thus, individual cells can belong to more than one group, each at a different taxonomic level, and these groups of cells can be viewed as interacting with each other rather than as operating in isolation. A multiple-level classification of cat retinal ganglion cells is presented with two broad groups, each subdivided into two lower-level groups, and an attempt is made to identify the categories of visual function to which these groups are related.

Animals↗
PubMed1997

A second generation of terminological systems is coming.

Diverse achievements by recent computer-based terminological systems are outlining a new generation of systems (i.e. a "second generation"). We collected the relevant features of various advanced terminological systems and we systematized these features into four components of a unique framework. We review a set of systems according to our framework, and we discuss how standardization activities can support the evolution of computer-based terminological systems towards a complete set of new performances.

Humans↗
PubMed2004

[Molecular anthropology and the origin of modern human].

Since Watson & Crick put forward the double-helix model of DNA structure and hereditary mechanism in 1953, it is generally accepted that this event marks the birth of modern molecular biology. This new field of biology has experienced a flourishing development in the past 50 years. On one hand, the development of molecular biology has been deeply influencing many relative fields; on the other hand, its own proceeding pace has been accelerated by the reaction from the other fields. Anthropology is one of the fields most deeply impacted by the theory and method of molecular biology. Most importantly, molecular anthropology was born as a result of combination of molecular biology, anthropology as well as paleoanthropology. This new branch provides reliable method and vital direction for paleoanthropology. This paper systematically reviews the history, principle and method of molecular anthropology. Two hypotheses on the origin of modern human, which include "out-of-African theory" and "theory of multiregional evolution" are also discussed for the purpose of showing how molecular anthropology is applied in paleoanthropology.

Animals↗
PubMed1989

[Systematic study of various tumoral markers in prevalent bone metastasis].

In the presence of prevalent bone metastases, the precise histo-pathological diagnosis of the primary tumor is often difficult. The authors study the diagnostic value of systematic serum assay of a series of tumoral tracers (ACE, AFP, PAP and PSA, SCC, CA 19:9, CA 15:3, CA 125) which until now were used in evolutive and therapeutic monitoring. 34 patients were selected for this preliminary retrospective study (including 20 with a demonstrated histopathological diagnosis). 70 p. cent of prevalent bone metastases express a target tracer corresponding to the initial location. In some cases, an elevated tracer, because of its specificity, may bring about a diagnostic or therapeutic decision (always according to the context). No conclusion may currently be drawn in case of discordance between the anatomo-clinical context and the "profile" of the markers (1 case in our series).

Biomarkers, Tumor↗
PubMed1987

[Streptobacillus moniliformis endocarditis. Apropos of 2 cases].

The authors report two cases of endocarditis secondary to Streptobacillus moniliformis. A 41 year-old man, bitten by a rat, is hospitalized 5 weeks later for an endocarditis demonstrated by echocardiography, with massive aortic escape and hemodynamic failure requiring emergency valve replacement: after a favorable course, the patient dies suddenly 4 months later. A 63 year-old woman is admitted for a septicemic syndrome with sterno-clavicular arthritis which occurred 10 days after a rat bite; followed by a transient ischemic cerebral vascular accident; echocardiogram shows a clubshaped bulge of the distal end of the large mitral valve; the course is uneventful under antibiotherapy. In both cases, blood cultures isolate a Streptobacillus moniliformis. Infections secondary to Streptobacillus moniliformis are rare; this Gram negative bacillus, saprophyte of the rat's rhinopharynx, is transmitted to man, most of the time, by bite, and this causes a septicemia, the evolution of which is usually favorable. Complications, especially endocarditis, are exceptionally rare: only 12 cases are found in the world's literature. The evolution is always fatal in the absence of treatment which must include the association penicillin-aminoside. Prophylaxis of this disease is provided by penicillin antibiotherapy which should be systematic after a rodent's bite.

Adult↗