The new problem of genetics: A response to Gifford

Recently, Fred Gifford attempted to explicate the meaning of the term genetic as applied to phenotypic traits. He takes as his primary goal the explication of how the term is used and tries to avoid conclusions about how it should be used. He proposes two independent criteria (DF and PI) which together capture much of what biologists mean when they describe traits as genetic. Although Gifford's approach is extremely insightful in many ways, I argue that his analysis is not sufficiently critical concerning the adequacy of common usage.In particular, while DF is a perfectly legitimate and useful measure of heritability in populations, it is not necessarily a genetic one and should not be labeled as such. PI on the other hand, although very intuitive, depends on an extremely problematic distinction between causes and mere conditions (e.g., genes and epigenetic factors). Both criteria will be highly relative and both, via what I term the new problem of genetics, will inspire contradictory analyses based on the same data.Fortunately, as Gifford recognizes, it is not necessary to make sense of genetic at all in order to do biology. Quantitative genetics can do the kind of (heritability) analysis that DF embodies without making questionable claims about genes. Causal-mechanical or bottom-up biology can proceed perfectly well without postulating the priveleged role for genetic causes that PI entails. In short, talk of genetic traits, under either criteria, is unnecessary and misleading.     

The rapidly growing mycobacteria: saprophytes and parasites

Rapidly growing mycobacteria are widespread saprophytes, but approximately one-third of identified species are also opportunistic pathogens in humans and animals, associated with skin, soft tissue, bone, and pulmonary infections as well as disseminated disease. Clinical and experimental evidence indicates a major role for the cell-mediated immune response in the pathogenesis of infection.     

Surrounded by mycobacteria: nontuberculous mycobacteria in the human environment

A majority of the Mycobacterium species, called the nontuberculous mycobacteria (NTM), are natural inhabitants of natural waters, engineered water systems, and soils. As a consequence of their ubiquitous distribution, humans are surrounded by these opportunistic pathogens. A cardinal feature of mycobacterial cells is the presence of a hydrophobic, lipid-rich outer membrane. The hydrophobicity of NTM is a major determinant of aerosolization, surface adherence, biofilm-formation, and disinfectant- and antibiotic resistance. The NTM are oligotrophs, able to grow at low carbon levels [>50 μg assimilable organic carbon (AOC) l⁻¹], making them effective competitors in low nutrient, and disinfected environments (drinking water). Biofilm formation and oligotrophy lead to survival, persistence, and growth in drinking water distribution systems. In addition to their role as human and animal pathogens, the widespread distribution of NTM in the environment, coupled with their ability to degrade and metabolize a variety of complex hydrocarbons including pollutants, suggests that NTM may be agents of nutrient cycling.     

Species of the genus Psoroptes (Acari: Psoroptidae): A taxonomic consideration

The biosystematic status of mite species belonging to the genus Psoroptes Gervais, 1841 is difficult to determine by phenotypic methods and has been subject to taxonomic revisions and ongoing debate. At present, the existence of five species, P. cuniculi (Delafond, 1859), P. ovis (Hering, 1838), P. equi (Hering, 1838), P. cervinus Ward, 1915 and P. natalensis Hirst, 1919, is generally accepted. This classification is based mainly on the host species, the localization of the mites on their hosts and morphological characters of male mites. However, a critical review of the literature indicates that the features used to discriminate between the five species are not unequivocal: (a) the localization of mite populations on host animals is not completely strict, (b) the lengths of the outer opisthosomal setae of male mites, which are the main morphological features used for species discrimination, overlap between the five postulated species, and (c) host specificity cannot be deduced from results of transfer experiments. Rather, conspecificity of the members of the genus Psoroptes has to be presumed which is supported by molecular genetic analyses. On these grounds and on rules of priority P. cervinus Ward, 1915, P. cuniculi (Delafond, 1859), P. natalensis Hirst, 1919 and P. ovis (Hering, 1838) are seen as synonyms of P. equi (Hering, 1838).     

Relationship between mycobacteria and amoebae: ecological and epidemiological concerns

Since the discovery that Legionella pneumophila can survive and grow within free-living amoebae, there has been an increasing number of microbial species shown to have similar relationships. These include many bacterial species, fungi, other protozoa (e.g. Cryptosporidium) and viruses. Among bacteria, mycobacteria are of particular importance because of their role in human and animal infections. This review will consider the progress made in understanding the relationships between mycobacteria and amoebae, and their consequences in terms of ecology and epidemiology.     

星果衣属(乳嘴衣科)一新种和一中国新记录种

通过形态学、解剖学、化学与分子系统学相结合的方法对中国星果衣属地衣型真菌进行研究,发现该属一新种即Astrothelium sinense和一中国新记录种A.macrocarpum.新种的主要特征为地衣体具有突起,子囊器除顶端呈黑色外边缘部分形成白色环状区域且地衣体和假子座均为UV+黄色,含有地衣黄等.分别与其相似种进...     

Mycobacteria mobility shift assay: a method for the rapid identification of Mycobacterium tuberculosis and nontuberculous mycobacteria

The identification of mycobacteria is essential because tuberculosis (TB) and mycobacteriosis are clinically indistinguishable and require different therapeutic regimens. The traditional phenotypic method is time consuming and may last up to 60 days. Indeed, rapid, affordable, specific and easy-to-perform identification methods are needed. We have previously described a polymerase chain reaction-based method called a mycobacteria mobility shift assay (MMSA) that was designed for Mycobacterium tuberculosis complex (MTC) and nontuberculous mycobacteria (NTM) species identification. The aim of this study was to assess the MMSA for the identification of MTC and NTM clinical isolates and to compare its performance with that of the PRA-hsp65 method. A total of 204 clinical isolates (102 NTM and 102 MTC) were identified by the MMSA and PRA-hsp65. For isolates for which these methods gave discordant results, definitive species identification was obtained by sequencing fragments of the 16S rRNA and hsp65 genes. Both methods correctly identified all MTC isolates. Among the NTM isolates, the MMSA alone assigned 94 (92.2%) to a complex or species, whereas the PRA-hsp65 method assigned 100% to a species. A 91.5% agreement was observed for the 94 NTM isolates identified by both methods. The MMSA provided correct identification for 96.8% of the NTM isolates compared with 94.7% for PRA-hsp65. The MMSA is a suitable auxiliary method for routine use for the rapid identification of mycobacteria.     

The new oral anticoagulants in atrial fibrillation: an update

In patients with nonvalvular atrial fibrillation, oral anticoagulation with the vitamin K antagonists acenocoumarol, phenprocoumon and warfarin reduces the risk of stroke by more than 60 %, whereas single or double antiplatelet therapy is much less effective and sometimes associated with a similar bleeding risk as vitamin K antagonists. Besides bleeding, and intracranial haemorrhage in particular, INR monitoring remains the largest drawback of vitamin K antagonists. In the last decade oral agents have been developed that directly block the activity of thrombin (factor IIa), as well as drugs that directly inhibit activated factor X (Xa), which is the first compound in the final common pathway to the activation of thrombin. These agents have been approved for stroke prevention in atrial fibrillation and are now reimbursed under a national guideline for their safe use. They have advantages in that they do not need monitoring and have a fast onset and offset of action, but lack an established specific antidote. This survey addresses the role of modern anticoagulation for stroke prevention in atrial fibrillation.     

Isolation and identification of mycobacteria from soils at an illegal dumping site and landfills in Japan

In order to study the diversity and community of genus Mycobacterium in polluted soils, we tried to isolate mycobacteria from 11 soil samples collected from an illegal dumping site and 3 landfills in Japan. Using culture methods with or without Acanthamoeba culbertsoni, a total of 19 isolates of mycobacteria were obtained from 5 soil samples and 3 of them were isolated only by the co-culture method with the amoeba. Conventional biochemical tests and sequencing of the hsp65, rpoB, and 16S rRNA genes were performed for species identification of 17 of the 19 isolates. Among the 17 isolates, there was one isolate each of Mycobacterium vanbaalenii, Mycobacterium mageritense, Mycobacterium frederiksbergense, M. vanbaalenii or Mycobacterium austroafricanum, and Mycobacterium chubuense or Mycobacterium chlorophenolicum. The remaining 12 isolates could not be precisely identified at the species level. A phylogenic tree based on the hsp65 sequences indicated that 2 of the 12 isolates were novel species. In addition, 4 isolates were phylogenically close to species that degrade polycyclic aromatic hydrocarbons, which induce some cancers in humans. These results demonstrated that there were many hitherto-unreported mycobacteria in the polluted soils, and suggested that some mycobacteria might play roles in the natural attenuation and engineered bioremediation of contaminated sites with other microorganisms.     

Fluorescence microscopy of mycobacteria in pleural effusions

The diagnostic advantage of fluorescence microscopy (FM) of Papanicolaou-stained cytological specimens obtained by bronchoscopy has been described previously. This study was designed to evaluate the method's diagnostic benefit in cytological preparations of pleural effusions in cases of active pulmonary tuberculosis. In contrast to bronchial material there is no advantage in cytological evaluation of pleural effusions by FM.     

Human disease classification in the postgenomic era: A complex systems approach to human pathobiology

Contemporary classification of human disease derives from observational correlation between pathological analysis and clinical syndromes. Characterizing disease in this way established a nosology that has served clinicians well to the current time, and depends on observational skills and simple laboratory tools to define the syndromic phenotype. Yet, this time-honored diagnostic strategy has significant shortcomings that reflect both a lack of sensitivity in identifying preclinical disease, and a lack of specificity in defining disease unequivocally. In this paper, we focus on the latter limitation, viewing it as a reflection both of the different clinical presentations of many diseases (variable phenotypic expression), and of the excessive reliance on Cartesian reductionism in establishing diagnoses. The purpose of this perspective is to provide a logical basis for a new approach to classifying human disease that uses conventional reductionism and incorporates the non-reductionist approach of systems biomedicine.     

Distribution of an allele associated with blond hair color across northern island melanesia

Pigmentation of the skin, hair, and eyes is a complex trait controlled by multiple genetic loci. Recently a non‐synonymous mutation in the pigmentation candidate gene TYRP1 was shown to be significantly associated with a blond‐hair phenotype in populations from the Solomon Islands. The distribution of this mutation in the islands of Northern Island Melanesia, where the blondism phenotype is also prevalent, was unknown. Here, we present data describing the distribution of this allele in 550 individuals sampled from across this region, and test for associations between genotype at this locus and quantitatively measured skin and hair pigmentation phenotype. We report that the frequency of the 93C allele is notably lower than observed in the Solomons (0.12 vs. 0.26). The allele exhibits significant geographic heterogeneity across the islands sampled (χ² = 108.4, P < 0.0001). It is observed at its highest frequencies on the islands of New Ireland and New Hanover, while being almost completely absent from the large island of New Britain. Using linear regression with age, sex, and island as covariates we report that, as in the Solomons, the 93C allele is significantly associated with a decrease in hair pigmentation but not skin pigmentation. We discuss the distribution of the 93C allele across the Southwest Pacific in light of its possible place of origin and dispersal. Am J Phys Anthropol 153:653–662, 2014. © 2014 Wiley Periodicals, Inc.     

Stephanodictyon borneense (Pottiaceae,Bryophyta): new combination,typification and update of distribution

Stephanodictyon borneense was described by Dixon and later combined to Trichostomum by Zander. Until now, it had been considered endemic to Malaysia, known only from the type locality on Lobang, Kinabalu (Sabah state). Here, its taxonomic position is assessed based on morphological data. Our results suggest that the combination into the genus Chionoloma is required. Moreover, typification is performed and its distribution is increased. Stephanodictyon borneense is, therefore, newly reported for South and Central America (Colombia, Costa Rica, Haiti and Venezuela), for some Asiatic countries (India, Japan and Nepal) and for Papua New Guinea. Despite these new reports, S. borneense is a rare species with a highly scattered distribution.     

Atypical mycobacterial infection in patients with cystic fibrosis: update on clinical microbiology methods

While patients with cystic fibrosis (CF) have had dramatic improvement in their survival rates, this has been accompanied by the emergence of more virulent pathogens such as Pseudomonas aeruginosa and Burkholderia cepacia complex organisms. In addition, there has been emergence of organisms of increasing clinical significance such as the nontuberculous mycobacterial (NTM). Although TB infection in patients with CF is extremely uncommon, there is growing concern with regard to atypical Mycobacterium spp, in particular Mycobacterium abscessus. Many methods of decontamination of sputum, which have been adapted from TB methodologies, are ineffective; as shown by the overgrowth of P. aeruginosa, it is essential that decontamination methods are optimized to overcome this. Establishing optimal methods of isolation and determining accurate levels of prevalence is of importance as, although NTM may be isolated relatively infrequently in CF populations, their clinical status in pulmonary disease is now beginning to emerge.     

Uses and misinterpretations of genetics in psychology

An analysis is made of the frequently posed question in psychology of relative contribution of genotypes and environments to phenotypic variation. The illogic of the question, the inappropriateness of the methodology, the inadequacy of the data, and the misleading implications of assertions of proportionality as seen through a sampling of introductory psychology textbooks and referenced publications are outlined. To ask the question of proportionality (of the relative contribution of genotypes and environments in human populations) requires the questioner to make two major erroneous assumptions. The first error is to grant validity to heritability estimates for humans. The second is to conceptualize the genotype as having a range of potential outcomes. An examination is made of these false assumptions. This revised version was published online in August 2006 with corrections to the Cover Date.     

Environmental amoebae do not support the long‐term survival of virulent mycobacteria

Aims

To test the hypothesis that Mycobacterium bovis can persist in the environment within protozoa.

Methods and Results

In this study, we used a novel approach to detect internalized mycobacteria in environmental protozoa from badger latrines. Acid‐fast micro‐organisms were visualized in isolated amoebae, although we were unable to identify them to species level as no mycobacteria were grown from these samples nor was M. bovis detected by IS6110 PCR. Co‐incubation of Acanthamoeba castellanii with virulent M. bovis substantially reduced levels of bacilli, indicating that the amoebae have a negative effect on the persistence of M. bovis.

Conclusions

The internalization of mycobacteria in protozoa might be a rare event under environmental conditions. The results suggest that amoebae might contribute to the inactivation of M. bovis rather than representing a potential environmental reservoir.

Significance and Impact of the Study

Protozoa have been suggested to act as an environmental reservoir for M. bovis. The current study suggests that environmental amoebae play at most a minor role as potential reservoirs of M. bovis and that protozoa might inhibit persistence of M. bovis in the environment.     

The taxonomic position of Cyanidium,Cyanidioschyzon and Galdieria: an update

The ecophysiological, cytomorphological, biochemical and molecular data presently available for the acidophilic red algal species Cyanidium caldarium, Cyanidioschyzon merolae and Galdieria sulphuraria are summarised. The taxonomic position of the three genera is discussed and emendements to the generic diagnosis are presented.