Multiplex strand displacement amplification (SDA) and detection of DNA sequences from Mycobacterium tuberculosis and other mycobacteria.

Strand Displacement Amplification (SDA) is an isothermal, in vitro method of amplifying a DNA target sequence prior to detection [Walker et al (1992) Nucleic Acids Res., 20, 1691-1693]. Here we describe a multiplex form of SDA that allows two target sequences and an internal amplification control to be co-amplified by a single pair of primers after common priming sequences are spontaneously appended to the ends of target fragments. Multiplex SDA operates at a single temperature, under the same simple protocol previously developed for single-target SDA. We applied multiplex SDA to co-amplification of a target sequence (IS6110) that is specific to members of the Mycobacterium tuberculosis-complex and a target (16S ribosomal gene) that is common to most clinically relevant species of mycobacteria. Both targets are amplified 10(8)-fold during a 2 hour, single temperature incubation. The relative sensitivity of the system was evaluated across a number of clinically relevant mycobacteria and checked for crossreactivity against organisms that are closely related to mycobacteria.     

Northern Ontario MDs seek solution to region's huge accidental-death toll.

A recently published study discussed the trauma-related death toll that plagues northeastern Ontario, which has a much higher death rate from nonintentional trauma than the rest of the province Dr. Gary Bota, one of the study authors hates calling these tragedies accidents because that implies a random, act-of-God nature that he does not accept. "They''re not accidents," he maintains. "They''re patterns, just like infectious diseases."     

Rock geochemistry induces stress and starvation responses in the bacterial proteome

Interactions between microorganisms and rocks play an important role in Earth system processes. However, little is known about the molecular capabilities microorganisms require to live in rocky environments. Using a quantitative label‐free proteomics approach, we show that a model bacterium (Cupriavidus metallidurans CH34) can use volcanic rock to satisfy some elemental requirements, resulting in increased rates of cell division in both magnesium‐ and iron‐limited media. However, the rocks also introduced multiple new stresses via chemical changes associated with pH, elemental leaching and surface adsorption of nutrients that were reflected in the proteome. For example, the loss of bioavailable phosphorus was observed and resulted in the upregulation of diverse phosphate limitation proteins, which facilitate increase phosphate uptake and scavenging within the cell. Our results revealed that despite the provision of essential elements, rock chemistry drives complex metabolic reorganization within rock‐dwelling organisms, requiring tight regulation of cellular processes at the protein level. This study advances our ability to identify key microbial responses that enable life to persist in rock environments.     

The potential influence of the heel counter on internal stress during static standing: a combined finite element and positional MRI investigation

Confinement of the heel due to the counter of the shoe is believed to influence heel pad biomechanics. Using a two-dimensional finite element model of the heel pad and shoe during a simulation of static standing, the aim of this study was to quantify the potential effect of confinement on internal heel pad stress. Non-weightbearing MRI and weightbearing MRI with plantar pressure and ground reaction force data were recorded for a single subject. The non-weightbearing MRI was used to create two FE models of the heel pad, using either homogeneous or composite material properties. The composite model included a distinction in material properties between fat pad and skin. Vertical and medial-lateral forces, as measured on the subject's heel, were applied to the models and vertical compressive strains for both models were comparable with those observed by weightbearing MRI. However, only for the composite model was the predicted plantar pressure distribution comparable with measured data. The composite model was therefore used in further analyses. In this composite model, the internal stresses were located mainly in the skin and were predominantly tensile in nature, whereas the stress state in the fat pad approached hydrostatic conditions. A representation of a running shoe, including an insole, midsole and heel counter was then added to the composite heel pad to form the shod model. In order to investigate the counter effect, the load was applied to the shod model with and without the heel counter. The effect of the counter on peak stress was to elevate compression (0-50%), reduce tension (22-34%) and reduce shear (22-28%) in the skin. In addition, the counter reduced both compressive (20-40%) and shear (58-80%) stress in the fat pad and tension in the fat pad remained negligible. Taken together the results indicate that a well-fitted counter works in sympathy with the internal structure of the heel pad and could be an effective reducer of heel pad stress. However, further research needs to be undertaken to assess the long-term effects on the soft-tissues, practicalities of achieving good fit and behavior under dynamic events.     

The mechanical significance of the occlusal geometry of great ape molars in food breakdown

Analyses of dental function are an essential component of the study of human evolution. However, with few exceptions, they have utilized the traditional analogizing method of comparative anatomy, and have assumed rather than demonstrated that proposed adaptive characters confer a performance benefit. Since food reduction is a mechanical process, it is appropriate to measure performance using mechanical parameters, specifically the ability of a given morphology to induce failure in food particle by either of the two major regimes: crush and shear, corresponding to simple stresses (tensile and compressive) and shear stress, respectively. We apply finite elements stress analysis to model the relationship between the angulation of the intercuspal occlusal surfaces in a “puncture crushing” mode of mastication. On the basis of morphological data acquired from sectioned great ape molars, we have predicted the nature, magnitude and distribution of stress in a standard food particle by models representing each morphotype. Results indicate that the blunt-cusped molars ofHomo, the gradually-sloping supporting (buccal) cusps but high-angled guiding (lingual) cusps of the lower molars ofPan, and the high angled occlusal surfaces ofGorillaare all more likely to fracture small food particles by shear, while the gradually sloping occlusal surfaces ofPongomolars are more likely to break them down by “crush”. Mechanisms of food failure induced by molars ofPanandHomowill vary according to the orientation of the tooth–food contacting surfaces, which in turn will vary according to the size of the food particle. These genera may be able to break food down either by shear or by “crush”.     

The mitochondrial genomes of Amphiascoides atopus and Schizopera knabeni (Harpacticoida: Miraciidae) reveal similarities between the copepod orders Harpacticoida and Poecilostomatoida

Members of subclass Copepoda are abundant, diverse, and—as a result of their variety of ecological roles in marine and freshwater environments—important, but their phylogenetic interrelationships are unclear. Recent studies of arthropods have used gene arrangements in the mitochondrial (mt) genome to infer phylogenies, but for copepods, only seven complete mt genomes have been published. These data revealed several within-order and few among-order similarities. To increase the data available for comparisons, we sequenced the complete mt genome (13,831 base pairs) of Amphiascoides atopus and 10,649 base pairs of the mt genome of Schizopera knabeni (both in the family Miraciidae of the order Harpacticoida). Comparison of our data to those for Tigriopus japonicus (family Harpacticidae, order Harpacticoida) revealed similarities in gene arrangement among these three species that were consistent with those found within and among families of other copepod orders. Comparison of the mt genomes of our species with those known from other copepod orders revealed the arrangement of mt genes of our Harpacticoida species to be more similar to that of Sinergasilus polycolpus (order Poecilostomatoida) than to that of T. japonicus. The similarities between S. polycolpus and our species are the first to be noted across the boundaries of copepod orders and support the possibility that mt-gene arrangement might be used to infer copepod phylogenies. We also found that our two species had extremely truncated transfer RNAs and that gene overlaps occurred much more frequently than has been reported for other copepod mt genomes.     

Collagen concentrations in dissected tissue compartments of rat uterus on days 6, 7 and 8 of pregnancy.

Implantation and non-implantation sites were dissected into myometrial and stromal components; a decidual/embryonic region was obtained on Days 7 and 8 of pregnancy. The concentration of collagen (as a percentage of the dry weight of tissue), measured by hydroxyproline analysis, was significantly lower in the implantation regions than in the non-implant regions in all areas studied. The concentrations in the antimesometrial myometrium and stroma of the implantation region remained the same over the days studied. In contrast, the mesometrial collagen concentration in the implantation region declined from Day 6 to Day 8 of pregnancy. Collagen concentration was low within the decidual/embryonic tissue on Days 7 and 8 of pregnancy. Remodelling of collagen within the embryonic area appears to be an important feature of the uterine response to implantation in rats.     

Effect of prism orientation and loading direction on contact stresses in prismatic enamel of primates: implications for interpreting wear patterns

The ability of prisms to effectively dissipate contact stress at the surface will influence wear rates in teeth. The aim of this investigation was to begin to quantify the effect of prism orientation on surface stresses. Seven finite element models of enamel microstructure were created, each model differing in the angulation of prism orientation with regard to the wear surface. For validation purposes, the mechanical behavior of the model was compared with published experimental data. In order to test the enamel under lateral loads, a compressed food particle was dragged across the surface from the dentino-enamel junction (DEJ) towards the outer enamel surface (OES). Under these conditions, tensile stresses in the enamel model increased with increases in the coefficient of friction. More importantly, stresses were found to be lowest in models in which the prisms approach the surface at lower angles (i.e., more obliquely cut prisms), and highest when the prisms approached the surface at 60 degrees (i.e., less obliquely cut). Finally, the direction of travel of the simulated food particle was reversed, allowing comparison of the difference in behavior between trailing and leading edge enamels (i.e., when the food particle was dragged either towards or away from the DEJ). Stresses at the trailing edge were usually lower than stresses at the leading edge. Taken together with what is known about prism orientation in primate teeth, such findings imply greater wear resistance at the intercuspal region and less wear resistance at the lateral enamel at midcrown. Such findings appear to be supported by archeological evidence.     

Psychologic scars remain 50 years after Dieppe raid,study of Canadian veterans finds.

A Toronto psychologist has conducted a 50-year follow-up study of the psychologic problems faced by Canadian troops who landed on the beaches of Dieppe, France, in 1942. Lynne Beal says many of the men have suffered in silence, never realizing that they were experiencing the widespread condition known as post-traumatic stress disorder. The veterans hope her work will help them win greater official recognition of their condition.