GC fractionation enhances microbial community diversity assessment and detection of minority populations of bacteria by denaturing gradient gel electrophoresis

Effectively and accurately assessing total microbial community diversity is one of the primary challenges in modern microbial ecology. This is particularly true with regard to the detection and characterization of unculturable populations and those present only in low abundance. We report a novel strategy, GC fractionation combined with denaturing gradient gel electrophoresis (GC-DGGE), which combines mechanistically different community analysis approaches to enhance assessment of microbial community diversity and detection of minority populations of microbes. This approach employs GC fractionation as an initial step to reduce the complexity of the community in each fraction. This reduced complexity facilitates subsequent detection of diversity in individual fractions. DGGE analysis of individual fractions revealed bands that were undetected or only poorly represented when total bacterial community DNA was analyzed. Also, directed cloning and sequencing of individual bands from DGGE lanes corresponding to individual G+C fractions allowed detection of numerous phylotypes that were not recovered using a traditional random cloning and sequencing approach.     

The effect of low temperature (5–29 °C) and adaptation on the methanogenic activity of biomass

The influence of low temperature (5–29 °C) on the methanogenic activity of non-adapted digested sewage sludge and on temperature/leachate-adapted biomass was assayed by using municipal landfill leachate, intermediates of anaerobic degradation (propionate) and methane precursors (acetate, H₂/CO₂) as substrates. The temperature dependence of methanogenic activity could be described by Arrhenius-derived models. However, both substrate and adaptation affected the temperature dependence. The adaptation of biomass in a leachate-fed upflow anaerobic sludge-blanket reactor at approximately 20 °C for 4 months resulted in a sevenfold and fivefold increase of methanogenic activity at 11 °C and 22 °C respectively. Both acetate and H₂/CO₂ were methanized even at 5 °C. At 22 °C, methanogenic activities (acetate 4.8–84 mM) were 1.6–5.2 times higher than those at 11 °C. The half-velocity constant (K _s) of acetate utilization at 11 °C was one-third of that at 22 °C while a similar K _i was obtained at both temperatures. With propionate (1.1–5.5 mM) as substrate, meth‐anogenic activities at 11 °C were half those at 22 °C. Furthermore, the residual concentration of the substrates was not dependent on temperature. The results suggest that the adaptation of biomass enables the achievement of a high treatment capacity in the anaerobic process even under psychrophilic conditions. Received: 23 December 1996 / Received last revision: 18 June 1997 / Accepted: 23 June 1997     

Factors relevant to the production of (R)-(+)-glycidol (2,3-epoxy-1-propanol) from racemic glycidol by enantioselective oxidation with Acetobacter pasteurianus ATCC 12874

Acetobacter pasteurianus oxidizes glycidol with high activity, comparable to the oxidation of ethanol. The organism has a preference for the S-enantiomer, and the kinetic resolution process obeys a simple relationship, indicating an enantiomeric ratio (E) of 19. The compound is converted into glycidic acid, although a transient accumulation of glycidaldehyde occurs initially. Determination of other parameters revealed a temperature optimum of 50°C, long-term stability (cells in the resting state), and a pH optimum compatible with the chemical stability of glycidol. However, it was also noted that respiration rates decrease at concentrations of glycidol above 1 . This is most likely caused by substrate inhibition of the glycidol-oxidizing enzyme, the quinohemoprotein ethanol dehydrogenase. Comparison with existing methods for enantiomerically pure glycidol production indicated a number of attractive points for the method described here, although definitive evaluation must await further studies on the long-term stability under process conditions, reusability of the cells, and the mechanism of glycidol inhibition.     

Sema3A chemorepellant regulates the timing and patterning of dental nerves during development of incisor tooth germ

Semaphorin 3A (Sema3A) axon repellant serves multiple developmental functions. Sema3A mRNAs are expressed in epithelial and mesenchymal components of the developing incisor in a dynamic manner. Here, we investigate the functions of Sema3A during development of incisors using Sema3A-deficient mice. We analyze histomorphogenesis and innervation of mandibular incisors using immunohistochemistry as well as computed tomography and thick tissue confocal imaging. Whereas no apparent disturbances in histomorphogenesis or hard tissue formation of Sema3A ^?/? incisors were observed, nerve fibers were prematurely seen in the presumptive dental mesenchyme of the bud stage Sema3A ^?/? tooth germ. Later, nerves were ectopically present in the Sema3A ^?/? dental papilla mesenchyme during the cap and bell stages, whereas in the Sema3A ^+/+ mice the first nerve fibers were seen in the pulp after the onset of dental hard tissue formation. However, no apparent topographic differences in innervation pattern or nerve fasciculation were seen inside the pulp between postnatal and adult Sema3A ^+/+ or Sema3A ^?/? incisors. In contrast, an abnormally large number of nerves and arborizations were observed in the Sema3A ^?/? developing dental follicle target field and periodontium and, unlike in the wild-type mice, nerve fibers were abundant in the labial periodontium. Of note, the observed defects appeared to be mostly corrected in the adult incisors. The expressions of Ngf and Gdnf neurotrophins and their receptors were not altered in the Sema3A ^?/? postnatal incisor or trigeminal ganglion, respectively. Thus, Sema3A is an essential, locally produced chemorepellant, which by creating mesenchymal exclusion areas, regulates the timing and patterning of the dental nerves during the development of incisor tooth germ.     

Neolithic dairy farming at the extreme of agriculture in northern Europe

The conventional ‘Neolithic package’ comprised animals and plants originally domesticated in the Near East. As farming spread on a generally northwest trajectory across Europe, early pastoralists would have been faced with the challenge of making farming viable in regions in which the organisms were poorly adapted to providing optimal yields or even surviving. Hence, it has long been debated whether Neolithic economies were ever established at the modern limits of agriculture. Here, we examine food residues in pottery, testing a hypothesis that Neolithic farming was practiced beyond the 60th parallel north. Our findings, based on diagnostic biomarker lipids and δ¹³C values of preserved fatty acids, reveal a transition at ca 2500 BC from the exploitation of aquatic organisms to processing of ruminant products, specifically milk, confirming farming was practiced at high latitudes. Combining this with genetic, environmental and archaeological information, we demonstrate the origins of dairying probably accompanied an incoming, genetically distinct, population successfully establishing this new subsistence ‘package’.     

The zebrafish amyloid precursor protein-b is required for motor neuron guidance and synapse formation

The amyloid precursor protein (APP) is a transmembrane protein mostly recognized for its association with Alzheimer's disease. The physiological function of APP is still not completely understood much because of the redundancy between genes in the APP family. In this study we have used zebrafish to study the physiological function of the zebrafish APP homologue, appb, during development. We show that appb is expressed in post-mitotic neurons in the spinal cord. Knockdown of appb by 50–60% results in a behavioral phenotype with increased spontaneous coiling and prolonged touch-induced activity. The spinal cord motor neurons in these embryos show defective formation and axonal outgrowth patterning. Reduction in Appb also results in patterning defects and changed density of pre- and post-synapses in the neuromuscular junctions. Together, our data show that development of functional locomotion in zebrafish depends on a critical role of Appb in the patterning of motor neurons and neuromuscular junctions.     

Primary thyroid angiosarcoma: an unusual localization

ABSTRACT: The finding of thyroid nodules is a very common occurrence in routine clinical practice. Approximately 5% to 7% of the entire population have thyroid nodules. Vascular lesions are one of the most controversial issues in thyroid pathology. These include benign lesions such as hemangiomas and, rarely, malignant tumors such as angiosarcomas or undifferentiated angiosarcomatoid carcinomas. In particular, angiosarcoma of the thyroid gland is a rare, highly aggressive malignant vascular tumor and in Italy the greatest geographical incidence of this lesion is witnessed near the Alps. Here, a case of thyroid angiosarcoma in a 71-year-old man with a history of goiter for about 20 years is described. The unusual localization of this lesion, the difficulties in reaching a definitive diagnosis for this particular histological type of primary tumor and a history of long-standing multinodular goiter in thyroid of an older man from outside the Alpine region prompted us to report this case of thyroid angiosarcoma mainly to discuss surgical, histopathological and immunohistochemical features.