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PubMed1997

In search of a bacterial species definition.

The bacterial species concept was examined within the framework of plant and animal associated alpha-2 proteobacteria, taking into consideration the phylogenetic, taxonomic and biological approaches as well as the microbiologists' perception. The virtue of the phylogenetic approach is that it gives an evolutionary perspective of the bacterial lineage; however the methods used possess low resolution for defining species located at the terminal branches of the phylogenetic trees. The merit of the taxonomic approach is that species are defined on the basis of multiple characteristics allowing high resolution at the terminal branches of dendograms; its disadvantage is the inaccuracy in the earlier nodes. On an individual level, the qualitative biological characteristics used for the definition of species frequently reveal shortcomings because many of these properties are the result of coevolution, parallel evolution or the horizontal transfer of genes. Nevertheless, when considered together with the phylogenetic and taxonomic approaches, important uncertainties are discovered: these must be weighed if a practical definition of bacterial species is conceived. The microbiologists' perception is the criterion expressed by a group of sponsors who, based on scientific and practical grounds, propose a new bacterial species. The success of this new proposal is measured by its widespread acceptance and its permanence. A difficult problem concerned with defining bacterial species is how to distinguish if they are independent evolutionary units or if they are reticulate evolutionary units. In the first case the inherence is vertically transmitted as a result of binary fission and clonal expansion. This may be the case of some animal cell associated bacteria in which recombination appears to be precluded or exceptional. In the second case adaptive changes occurring within an individual can be horizontally transferred to many or all group members. This seems to be the condition of many intestinal and plant associated bacteria. Genetic drift and speciation in clonal bacteria will depend almost exclusively on mutation and internal genetic rearrangement processes, whereas speciation in reticulate bacteria will depend not only on these processes but in their genetic interactions with other bacterial strains. This uncertainty, which corresponds to the evolutionary process, is at the same time one of the key factors in defining a bacterial species.

Bartonella↗
PubMed1998

[Prevalence of uro-nephrologic complications of urinary bilharziasis in hyperendemic focus in Madagascar].

This prospective study was designed to look for and describe urologic and nephrologic consequences of urinary bilharziosis due to schistosoma haematobium in a hyperendemic hotbed in the middle west of Madagascar. Methodology included clinical examination, kidney and bladder ultrasonography, urine dipsticks and creatininemia. Amongst a population of 574 persons aged 5 years ore more, 436 (76%) had bilharziosis ova in the urine (filtration method). From the clinical point of view, 257 patients (58.9%) had microscopic hematuria, 178 (40.8%) had presently an hematuria; 111 patients (25.5%) suffered from dysuria; 18 patients (4.1%) had limb oedema when 3 patients had present oedema (0.7%). Among 436 checked people, 267 (61.2%) had an ultrasonography abnormality. In 252, it was bladder wall abnormalities (57.8%). They were wall irregularities in 182 cases (41.7%); vesico-ureteral reflux in 22 cases (5.3%); ureteral dilatations in 22 cases (5.3%) and pyelocalyceal dilatations in 61 cases (13.9%). Prevalence of proteinuria 75.2% (316 amongst 420 checked people) of whom 5.7% (24 cases) had 5 g/l or more. Hematuria was found in 352 patients (83.8%) of whom 238 (56.7%) had more than 250 erythrocytes per microliter. Prevalence of leucocyturia was 56.7% (238 cases). Creatininemia was measured in 140 people with positive filtration; it was normal in all except two patients. This study highlights the parallel evolution between parasitic infection and uronephrological manifestations of the disease.

Adolescent↗
PubMed2026

The Spatial and Temporal Repeatability of Genomic Responses to Natural Selection as Demonstrated in Stickleback Populations Experiencing Highly Dynamic Environments.

The evolution of genotypic parallelism under shared environmental conditions provides strong evidence for the role of natural selection. However, analyses typically examine genomic signatures of selection long after the putative selection event and only assess the repeatability of responses across spatial population replicates. This impedes our ability to attribute a particular response to a given selection pressure and to distinguish non-parallel responses caused by stochastic processes from those caused by local selection. As such, the consistency of natural selection over space and time is unknown, and the role of persistent local selection pressures is unclear. Here, we leveraged the natural bar-built estuary system of Santa Cruz, California, to examine the repeatability of seasonal genomic change in threespine stickleback (Gasterosteus aculeatus) over space and time. By comparing allele-frequency shifts that are shared across locations (spatial repeatability) with those that are shared across years within locations (temporal repeatability), we identified both spatially shared and local components of putative selection. We found that repeated seasonal outlier responses occurred more often than expected under a neutral null model. Although repeatability declined as the number of estuaries sharing an outlier increased, enrichment above neutral expectations increased with broader spatial sharing, particularly for outliers repeated across both years. While the precise outlier SNPs varied across years, estuary-specific patterns of responses were broadly consistent, suggesting an important role for local conditions. Together, our findings show that temporal sampling can reveal components of putative selection that would be missed from spatial comparisons alone. More broadly, they highlight the importance of examining repeatability over both space and time to understand the parallel and non-parallel components of adaptive genomic change.

Animals↗
PubMed1995

Evolution of safety in anesthesia.

The evolution of anesthesia safety has paralleled the evolution of anesthesia over the last several hundred years. This article describes the introduction of safer practices of anesthesia and the impetus for these changes in practice that improved patient safety. It discusses both the role of technology in the advancement of safety and the policies developed by professional organizations of anesthesia care providers.

Anesthesia↗
PubMed1995

Hepatic granulomatosis in a patient with Graves' disease.

We report a case of granulomatous hepatitis in a patient with hyperthyroidism resulting from Graves' disease. A 30-year-old man presented with massive weight loss, jaundice, tachyarrhythmia and goitre. Liver function tests showed mild cytolysis and cholestasis and massive hyperbilirubinaemia. The echogram of liver and bile ducts was normal and no infection was found. A liver biopsy revealed a mixed cytolytic and cholestatic hepatitis with intralobular epithelioid granulomas. No specific cause was identified, and sarcoidosis and primary biliary cirrhosis were ruled out. The outcome was favourable with antithyroid therapy and short-term glucocorticoid therapy, and the patient was totally free of symptoms after 2 years. To our knowledge, this is the first case of granulomatous hepatitis to be reported in association with Graves' disease. The clinical evolution of the liver disease paralleled the evolution of hyperthyroidism.

Adult↗
PubMed1998

Parallel and divergent genotypic evolution in experimental populations of Ralstonia sp.

Genetic rearrangements within a population of bacteria were analyzed to understand the degree of divergence occurring after experimental evolution. We used 18 replicate populations founded from Ralstonia sp. strain TFD41 that had been propagated for 1,000 generations with 2,4-dichlorophenoxyacetic acid (2,4-D) as the carbon source. Genetic divergence was examined by restriction fragment length polymorphism analysis of the incumbent plasmid that carries the 2,4-D catabolic genes and by amplification of random regions of the genome via PCR. In 18 evolved clones examined, we observed duplication within the plasmid, including the tfdA gene, which encodes a 2,4-D dioxygenase that catalyzes the first step in the 2,4-D catabolic pathway. In 71 of 72 evolved clones, a common 2.4-kb PCR product was lost when genomic fingerprints produced by PCR amplification using degenerate primers based on repetitive extragenic palindromic (REP) sequences (REP-PCR) were compared. The nucleotide sequence of the 2.4-kb PCR product has homology to the TRAP (tripartite ATP-independent periplasmic) solute transporter gene family. Hybridization of the 2. 4-kb REP-PCR product from the ancestor to genomic DNA from the evolved populations showed that the loss of the PCR product resulted from deletions in the genome. Deletions in the plasmid and presence and/or absence of other REP-PCR products were also found in these clones but at much lower frequencies. The common and uncommon genetic changes observed show that both parallel and divergent genotypic evolution occurred in replicate populations of this bacterium.

Chlorophenols↗
PubMed1987

The evolution of antibiotic production and public health problems.

Antibiotic evolution is closely paralleled by the evolution of bacterial resistance. Prior to wide usage of penicillin G, resistance to beta-lactam antibiotics as a consequence of beta-lactamase production had been recognized, and has been an increasing clinical problem ever since. Discovery of antibiotics other than beta-lactams, such as macrolides, tetracyclines and aminoglycosides, has also resulted in the eventual selection of bacteria resistant to these agents. Synthesis of novel beta-lactam derivatives from 6-APA, such as methicillin and isoxazolyl penicillins, resistant to staphylococcal beta-lactamase, overcame the clinical problem of penicillin-resistant S. aureus. Likewise, the isolation of cephamycins and monobactams, and further exploitation of the cephalosporin nucleus, led to the development of derivatives which display a high degree of stability to a wide range of gram-positive and gram-negative bacterial beta-lactamases, thus rendering organisms producing these enzymes susceptible to these agents. Analogous modification of the penicillin nucleus, to give 6 alpha-substituted penicillins, also resulted in derivatives with exceptional stability to beta-lactamases. An alternative approach to the problem of beta-lactamase was the isolation or synthesis of substances able to inhibit the activity of enzymes, thus protecting the unstable beta-lactams from inactivation by beta-lactamase. In this way the activity of beta-lactamase-labile agents was effectively restored against a wide range of beta-lactamase-producing bacterial pathogens. The wide diversity of new antibacterial agents, together with an increasing knowledge and understanding of mechanisms of resistance, indicates that further advances against resistant bacterial pathogens is ensured.

Anti-Bacterial Agents↗
PubMed2025

Genome-wide Parallelism Underlies Rapid Freshwater Adaptation Fueled by Standing Genetic Variation in a Wild Fish.

A fundamental focus of ecological and evolutionary biology is determining how natural populations adapt to environmental changes. Rapid parallel phenotypic evolution can be leveraged to uncover the genetics of adaptation. Using population genomic approaches, we investigated the genetic architecture underlying rapid parallel freshwater adaptation of Neosalanx brevirostris by comparing four freshwater-resident populations with their common ancestral anadromous population. We demonstrated that the rapid parallel adaptation to freshwater followed a complex polygenic architecture and was characterized by genomic-level parallelism, which proceeded predominantly through repeated selection on the preexisting standing genetic variations. Frequencies of the genome-wide adaptive standing variations were moderate in the ancestral anadromous population, which had pre-adapted to fluctuating salinities. Relatively large allele frequency shifts were observed at some adaptive single-nucleotide polymorphisms (SNPs) during parallel adaptation to freshwater environments, with a large fraction of freshwater-favored alleles being fixed or nearly fixed. These adaptive SNPs were involved in multiple biological functions associated with osmoregulation, immunoregulation, locomotion, metabolism, etc., which were highly consistent with the polygenic architecture of adaptive divergence between the two ecotypes involving multiple complex physiological and behavioral traits. This work provides insight into the mechanisms by which natural populations rapidly evolve to changes in the environment and highlights the importance of standing genetic variation for the evolutionary potential of populations facing global environmental changes.

Animals↗
PubMed1994

A parallel between development and evolution: germ cell recruitment by the gonads.

In gonad-bearing animals gametogenesis can be divided into three main phases. During embryonic development the primordial germ cells move towards the gonadal primordia. A long, intra-gonadal phase follows during which the germ cells grow and differentiate. Mature germ cells are finally released from the gonads and brought to the exterior. Thus, germ cells are successively motile, non-motile and motile again. This complex life history is given here a simple evolutionary interpretation. The basic assumption is that primitive Metazoa already had germ cells, but no gonads to harbour them. Higher animals acquired gonads, which sequestered the germ cells, thus creating the temporary confinement experienced by germ cells in most present-day Metazoa. This evolutionary scheme may explain why several steps of germ cell differentiation are totally or partially independent of the gonads. These steps presumably existed in primitive, gonad-free Metazoa, and conserved their autonomy in higher animals.

Animals↗
PubMed1984

Human alcohol dehydrogenase: structural differences between the beta and gamma subunits suggest parallel duplications in isoenzyme evolution and predominant expression of separate gene descendants in livers of different mammals.

Human alcohol dehydrogenase (ADH; alcohol:NAD+ oxidoreductase, EC 1.1.1.1) occurs in multiple forms, which exhibit distinct electrophoretic mobilities and enzymatic properties. The homogeneous isoenzymes beta 1 beta 1 and gamma 1 gamma 1 were isolated from livers of Caucasians with "typical" ADH phenotype by double ternary complex affinity chromatography and ion exchange chromatography. The differences between the beta 1 and gamma 1 subunits were determined by structural analysis of all tryptic peptides from the carboxymethylated proteins. The human beta 1 and gamma 1 chains differ at 21 of the 373 positions (5.6%). Ten tryptic peptides account for the differences. All residue substitutions are compatible with one-base mutations and result in largely unaltered properties, but five lead to charge differences. Sixteen substitutions are at positions corresponding to the catalytic domain of the well-known horse enzyme; five correspond to the coenzyme-binding domain. Substitutions adjacent to important regions may correlate with differences in coenzyme binding, substrate specificities, and active-site relationships. The residue replacements between the beta 1 and gamma 1 subunits of human ADH are not identical to the known substitutions between ethanol-active (E) and steroid-active (S) subunits of horse ADH. Thus, the duplication leading to human beta 1 and gamma 1 subunits is separate and different from that leading to equine E and S subunits. Both duplications are likely to have occurred after the ancestral separation of human and equine ADH. Of the 21 residues that are different between beta 1/gamma 1, 13 in gamma 1 but only 6 in beta 1 are identical to those of the horse E chain. This suggests a closer relationship between gamma 1 and E, although beta 1 in man and E in the horse are the subunits recovered in highest yield from liver ADH preparations. Consequently, in these two mammalian species, relative activities of genes for an isoenzyme family appear to be different.

Alcohol Dehydrogenase↗
PubMedDate not supplied

Michigan's fisheater cohorts: a prospective history of exposure.

Interest in environmental contaminants and their effect on human health emerged as a primary focus in the 1970s following the discovery of significant levels of mercury, dichloro diphenyl trichloroethane (DDT), and polychlorinated bihpenyls (PCBs) in recreationally caught Great Lakes fish. In response to these findings, the Michigan Department of Public Health, in 1971, initiated a series of "fisheater" cohort studies. These studies continue to be conducted today. The evolution of human exposure assessment by serum PCB determination parallels the evolution of more precise and sensitive analytical laboratory procedures over the past 25 years. Early work quantitated PCB with Aroclor 1254 standards. By 1980, the Webb and McCall packed-column method (Webb and McCall, 1972, 1973), which quantitates total PCB with Aroclor 1016 and 1260 standards, had gained the Association of Official Analytical Chemists (AOAC) approval and became the accepted method. This method was used in the 1978-1980 Michigan Great Lakes Fisheater Study, the first sizable study of this kind in the nation. The study confirmed that fisheaters had significantly more exposure (median 21.4 ppb vs 6.6 ppb) than controls. Toxicology studies have indicated the need to quantitate individual PCB congeners, in order to correlate exposure with possible toxicological and health outcomes. Today, capillary column gas chromatography and gas chromatography/mass spectrometry are used to search for trace components of the total PCB dose (Mullen et al., 1984). Because of the legacy of the earlier analytical data, Michigan also continues to conduct packed-column analysis for longitudinal comparisons. The Michigan fisheater study database and registry provide a significantly exposed and historic foundation for research testing health outcome hypotheses.

Cohort Studies↗
PubMed1994

Perspectives on interactions with QA--the regulatory perspective.

It has been my experience that the quality assurance unit (QAU) normally serves as the facility point-of-contact with the agency on matters relating to a Good Laboratory Practice (GLP) compliance inspection. The QAU usually receives the notification letter, does most of the coordinating for the GLP inspection, and often bears the criticism for deficiencies found during the inspection. In general, as inspectors, we have found it difficult to get management to show any interest in the inspection and, in many facilities, have been forced to communicate almost entirely with the QAU. The evolution of the relationship between regulators and the QA community, which parallels the evolution of the image of quality assurance personnel from inexperienced technicians to recognized professionals, is discussed. Also discussed are both typical and atypical examples of interaction between government inspectors and quality assurance units.

Facility Regulation and Control↗
PubMed1999

Evolution of the carabid ground beetles.

The phylogenetic relationships of the carabid ground beetles have been estimated by analysing a large part of the ND5 gene sequences of more than 1,000 specimens consisting of the representative species and geographic races covering most of the genera and subgenera known in the world. From the phylogenetic analyses in conjunction with the mtDNA-based dating, a scenario of the establishment of the present habitats of the respective Japanese carabids has been constructed. The carabid diversification took place ca. 40 MYA as an explosive radiation of the major genera. During evolution, occasional small or single bangs also took place, sometimes accompanied by parallel morphological evolution in phylogenetically remote as well as close lineages. The existence of silent periods, in which few morphological changes took place, has been recognized during evolution. Thus, the carabid evolution is discontinuous, alternatively having a phase of rapid morphological change and a silent phase.

Animals↗
PubMed2000

Progress in understanding hominoid dental development.

Teeth preserve a record of the way they grow in the form of incremental markings in enamel, dentine and cementum. These make it possible to reconstruct cellular activity and the timing of dental development in living and fossil primates, including hominids. They also provide a way of exploring the mechanisms that underlie morphological change during evolution and the nature of the relationship between ontogeny and phylogeny. All living great apes are dentally mature by about 11 y, irrespective of their body mass. While the early period of root formation in living great apes is shorter than in modern humans, enamel takes approximately the same time to form, irrespective of how thick it is. In general, differences in the total time taken to form enamel seem not to be due to differences in the rate at which enamel and dentine are secreted, but rather to faster or slower rates of differentiation of ameloblasts and odontoblasts and therefore to the number of secretory cells active at any one time during tooth formation. Tooth size, especially height, may influence the sequence of appearance of tooth mineralisation stages. The space available in the jaws may also have an influence on both the timing of tooth bud/crypt appearance and the sequence of gingival emergence. When each of these potential influences on dental development are carefully considered, and incremental markings used to calibrate key events, the developing dentition can provide an estimate of the period of dental maturation in fossil hominoids. However, the influence of body mass on the period of dental development among primates remains unclear. The earliest hominoids, dated at around 18 Mya, may still have had modern monkey-like maturational profiles, and the earliest hominids, dated between 1.8 and 3.7 Mya, modern great ape-like maturational profiles. Exactly when the extended or prolonged modern human-like maturational profile first appeared remains debatable, but the most secure suggestion might be at the time of the appearance of the earliest archaic Homo sapiens, when brain size and body mass were finally both within the ranges known for modern humans. But at present we should not reject the hypothesis that an extended, modern human-like, maturational profile arose more than once during human evolution in parallel with an increase in brain size.

Animals↗
PubMed2024

Repeated evolution on oceanic islands: comparative genomics reveals species-specific processes in birds.

Understanding the interplay between genetic drift, natural selection, gene flow, and demographic history in driving phenotypic and genomic differentiation of insular populations can help us gain insight into the speciation process. Comparing patterns across different insular taxa subjected to similar selective pressures upon colonizing oceanic islands provides the opportunity to study repeated evolution and identify shared patterns in their genomic landscapes of differentiation. We selected four species of passerine birds (Common Chaffinch Fringilla coelebs/canariensis, Red-billed Chough Pyrrhocorax pyrrhocorax, House Finch  Haemorhous mexicanus and Dark-eyed/island Junco Junco hyemalis/insularis) that have both mainland and insular populations. Changes in body size between island and mainland populations were consistent with the island rule. For each species, we sequenced whole genomes from mainland and insular individuals to infer their demographic history, characterize their genomic differentiation, and identify the factors shaping them. We estimated the relative (Fst) and absolute (dxy) differentiation, nucleotide diversity (π), Tajima's D, gene density and recombination rate. We also searched for selective sweeps and chromosomal inversions along the genome. All species shared a marked reduction in effective population size (Ne) upon island colonization. We found diverse patterns of differentiated genomic regions relative to the genome average in all four species, suggesting the role of selection in island-mainland differentiation, yet the lack of congruence in the location of these regions indicates that each species evolved differently in insular environments. Our results suggest that the genomic mechanisms involved in the divergence upon island colonization-such as chromosomal inversions, and historical factors like recurrent selection-differ in each species, despite the highly conserved structure of avian genomes and the similar selective factors involved. These differences are likely influenced by factors such as genetic drift, the polygenic nature of fitness traits and the action of case-specific selective pressures.

Animals↗
PubMed2000

The evolution of sex differences in language, sexuality, and visual-spatial skills.

The evolutionary neurological and physical foundations for human sex differences in language, sexuality, and visual spatial skills are detailed and primate and human studies are reviewed. Trends in the division of labor were established early in evolution and became amplified with the emergence of the "big brained" Homo erectus. A bigger brain necessitated a size increase in the birth canal and female pelvis. These and other physical changes, e.g., the swelling of the breasts and buttocks, may have paralleled the evolution of full-time sexual receptivity, the establishment of the home base, and exaggerated sex differences in the division of labor (hunting vs. gathering), which in turn promoted innate sex differences in visual spatial vs. language skills. For example, female primates produce more social and emotional vocalizations and engage in more tool use and gathering activities, whereas males tend to hunt and kill. Similar labor divisions are evident over the course of human evolution. "Woman's work" such as child rearing, gathering, and domestic tool construction and manipulation contributed to the functional evolution of Broca's speech area and the angular gyrus--which injects temporal sequences and complex concepts into the stream of language and thought. These activities gave rise, therefore, to a female superiority in grammatical (temporal sequential) vocabulary-rich language. Hunting as a way of life does not require speech but requires excellent visual-spatial skills and, thus, contributed to a male visual-spatial superiority and sex difference in the brain. Over the course of evolution males acquired modern human speech through genetic inheritance and because they had mothers who taught them language.

Affect↗
PubMed1994

Bioenergetics: the evolution of molecular mechanisms and the development of bioenergetic concepts.

Possible routes for the evolution of cell energetics are considered. It is assumed that u.v. light was the primary energy source for the precursors of the primordial living cell and that primitive energetics might have been based on the use of the adenine moiety of ADP as the u.v. chromophore. It is proposed that the excitation of the adenine residue facilitated phosphorylation of its amino group with subsequent transfer of a phosphoryl group to the terminal phosphate of ADP to form ATP. ATP-driven carbohydrate synthesis is considered as a mechanism for storing u.v.-derived energy, which was then used in the dark. Glycolysis presumably produced compounds like ethanol and CO2, which easily penetrate the membrane and therefore were lost by the cell. Later lactate-producing glycolysis appeared, the end product being non-penetrant and, hence, retained inside the cell to be utilized to regenerate carbohydrates when light energy became available. Production of lactate was accompanied by accumulation of equimolar H+. To avoid acidification of the cell interior, an F0-type H+ channel was employed. Later it was supplemented with F1. This allowed the ATP energy to be used for 'uphill' H+ pumping to the medium, which was acidified due to glycolytic activity of the cells. In the subsequent course of evolution, u.v. light was replaced by visible light, which has lower energy but is less dangerous for the cell. It is assumed that bacteriorhodopsin, a simple and very stable light-driven H+ pump which still exists in halophilic and thermophilic Archaea, was the primary system utilizing visible light. The delta mu-H+ formed was used to reverse the H(+)-ATPase, which began to function as H(+)-ATP-synthase. Later, bacteriorhodopsin photosynthesis was substituted by a more efficient chlorophyll photosynthesis, producing not only ATP, but also carbohydrates. O2, a side product of this process, was consumed by the H(+)-motive respiratory chain to form delta mu-H+ in the dark. At the next stage of evolution, a parallel energy-transducing mechanism appeared which employed Na+ instead of H+ as the coupling ion (the Na+ cycle).(ABSTRACT TRUNCATED AT 400 WORDS)

Adenine↗