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.     

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.     

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).     

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.     

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.     

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.     

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.     

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.     

Shifting paradigms of nontuberculous mycobacteria in cystic fibrosis

Important paradigms of pulmonary disease with nontuberculous mycobacteria (NTM) are currently shifting based on an increasing attention within the field of cystic fibrosis (CF). These shifts are likely to benefit the management of all patients with pulmonary NTM, regardless of underlying pathology. Currently several key areas are being revised: The first outbreak of human NTM transmission has been proven and new evidence of biofilm growth in vivo has been demonstrated. A better understanding of the clinical impact of NTM infection has led to increased diagnostic vigilance and new recommendations for lung transplantation are under way. While recent changes have reinvigorated the interest in NTM disease, the challenge remains, whether such advances can be successfully translated into improved management and care.     

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.     

Meloidogyne haplanaria n. sp. (Nematoda: Meloidogynidae), a Root-knot Nematode Parasitizing Peanut in Texas

Meloidogyne haplanaria n. sp. is described and illustrated from specimens parasitizing peanut in Texas. The perineal pattern of the female is rounded to oval with a dorsal arch that is high and rounded except for striae near the vulva, which are low with rounded shoulders. The striae are distinctly forked in the lateral field, and punctations often occur as a small group near the tail tip and singly within the whole perineal pattern. The female stylet is 13-16 µm long and has broad, distinctly set-off knobs. The excretory pore opens 40-118 µm from the head, approximately halfway between the anterior end and the metacorpus. Males are 1.2-2.4 µm in length and have a high, wide head cap that slopes posteriorly. The labial disc and medial lips are partially fused to form an elongated lip structure. In some specimens the labial disk is distinctly separated from the lips by a groove. The stylet is 17-22 µm long and has wide knobs that are rounded and distinctly set off from the shaft. Mean second-stage juvenile length is 419 µm. The head region is not annulated, and the large labial disc and crescent-shaped medial lips are fused to form a dumbbell-shaped head cap. The stylet is 9-12 µm long and has rounded, posteriorly sloping knobs. The slender tail, 58-74 µm long, has a distinct, inflated rectum and a slightly rounded tip. The hyaline tail terminus is 11-16 µm long. The isozyme phenotypes for esterase and malic dehydrogenase do not correspond to any other recognized Meloidogyne species. Tomato and peanut are good hosts; corn and wheat are very poor hosts; and cotton, tobacco, pepper, and watermelon are nonhosts.     

Catecholates and mixed catecholate hydroxamates as artificial siderophores for mycobacteria

Different mono-, bis- or triscatecholates and mixed mono- or biscatecholate hydroxamates were synthesized as potential siderophores for mycobacteria. Siderophore activity was tested by growth promotion assays using wild type strains and iron transport mutants of mycobacteria as well as Gram-negative bacteria. Some triscatecholates and biscatecholate hydroxamates were active in mutants of Mycobacterium smegmatis deficient in mycobactin and exochelin biosynthesis or exochelin permease, respectively, indicating an uptake route independent of the exochelin/mycobactin pathway. Structure activity relationships were studied. Ampicillin conjugates of some of these compounds were inactive against mycobacteria but active against Gram-negative bacteria.     

The intracrine hypothesis: an update

The intracellular actions of peptide hormones, growth factors, as well as of extracellular-signaling enzymes and DNA-binding proteins, either within target cells or within their cells of synthesis has been called intracrine action. Although these intracrine moieties are structurally diverse, they share certain characteristics of synthesis and function. This has given rise to the development of a theory of intracrine action which permits testable predictions to be made regarding the functioning of these peptides/proteins. Here the intracrine hypothesis is briefly described and then recent experimental findings which bear on predictions made earlier on the basis of the theory are discussed. These findings provide new support for the intracrine hypothesis.     

The freemartin syndrome: an update

The freemartin condition represents the most frequent form of intersexuality found in cattle, and occasionally other species. This review considers the current state of knowledge of freemartin biology, incidence, experimental models, diagnosis, uses for freemartins in cattle herds, occurrence in non-bovine species, effects on the male, and highlights potential new research areas. Freemartins arise when vascular connections form between the placentae of developing heterosexual twin foeti, XX/XY chimerism develops, and ultimately there is masculinisation of the female tubular reproductive tract to varying degrees. With twinning rates in Holstein cows increasing, there will be greater economic importance to establish early diagnosis of the freemartin and the detection of the less common single born freemartin. New diagnostic methods based on the detection of Y-chromosome DNA segments by polymerase chain reaction (PCR) show improved assay sensitivity and efficiency over karyotyping and clinical examination. The implications for the chimeric male animal born co-twin to the freemartin are contentious as to whether fertility is affected; if germ cell chimerism does indeed occur; and, if there are any real effects on the sex ratio of offspring produced. In beef cattle, the freemartin carcass has similar characteristics to normal herdmates. Hormonal treatment of freemartins for use as oestrous detectors has been used to obtain salvage value. The biology of freemartin sheep has recently been studied in detail, and the condition may be increasing in prevalence with the introduction of high fecundity genes into flocks. Potential new research areas are discussed, such as detection of foetal DNA in maternal circulation for prenatal diagnosis and investigation of the anti-tumour properties of Mullerian inhibiting substance (MIS). The freemartin syndrome will always be a limiting factor in cattle and to a lesser extent in sheep production systems that have the goal to produce multiple reproductively normal female offspring from a single dam without using sex predetermination.     

Cryptosporidium hominis n. sp. (Apicomplexa: Cryptosporidiidae) from Homo sapiens

The structure and infectivity of the oocysts of a new species of Cryptosporidium from the feces of humans are described. Oocysts are structurally indistinguishable from those of Cryptosporidium parvum. Oocysts of the new species are passed fully sporulated, lack sporocysts. and measure 4.4-5.4 microm (mean = 4.86) x 4.4-5.9 microm (mean = 5.2 microm) with a length to width ratio 1.0-1.09 (mean 1.07) (n = 100). Oocysts were not infectious for ARC Swiss mice, nude mice. Wistar rat pups, puppies, kittens or calves, but were infectious to neonatal gnotobiotic pigs. Pathogenicity studies in the gnotobiotic pig model revealed significant differences in parasite-associated lesion distribution (P = 0.005 to P = 0.02) and intensity of infection (P = 0.04) between C. parvum and this newly described species from humans. In vitro cultivation studies have also revealed growth differences between the two species. Multi-locus analysis of numerous unlinked loci, including a preliminary sequence scan of the entire genome demonstrated this species to be distinct from C. parvum and also demonstrated a lack of recombination, providing further support for its species status. Based on biological and molecular data, this Cryptosporidium infecting the intestine of humans is proposed to be a new species Cryptosporidium hominis n. sp.