Principal methods for isolation and identification of soil microbial communities

Soil microbial populations play crucial role in soil properties and influence below-ground ecosystem processes. Microbial composition and functioning changes the soil quality through decomposition of organic matter, recycling of nutrients, and biological control of parasites of plants. Moreover, the discovery that soil microbes may translate into benefits for biotechnology, management of agricultural, forest, and natural ecosystems, biodegradation of pollutants, and waste treatment systems maximized the need of scientists for the isolation and their characterization. Operations such as the production of antibiotics and enzymic activities from microorganisms of soil constitute objectives of industry in her effort to cope with the increase of population of earth and disturbance of environment and may ameliorate the effects of global climate change. In the past decades, new biochemical and molecular techniques have been developed in our effort to identify and classify soil bacteria. The goal of measuring the soil microbial diversity is difficult because of the limited knowledge about bacteria species and classification through families and orders. Molecular techniques extend our knowledge about microbial diversity and help the taxonomy of species. Measuring and monitoring soil microbial communities can lead us to better understanding of their composition and function in many ecosystem processes.     

Stress amplification during development of the tendon-to-bone attachment

Mechanical stress is necessary to sustain the mineral content of bone in adults. However, in a developing neonatal mouse, the mineralization of soft tissues progresses despite greatly reduced average mechanical stresses. In adults, these reduced loads would likely lead to bone loss. Although biochemical factors may partly explain these different responses, it is unclear how mineralization is initiated in low load environments. We present here the effect of morphometric data and initial modeling supporting a hypothesis that mechanical factors across several length scales amplify stresses, and we suggest that these stresses are of a level adequate to contribute to mechanical signaling for initiation of mineralization at the developing tendon-to-bone enthesis. A mineral gradient is evident across the insertion from the onset of mineralization. This grading maintains a constant size from early postnatal time points to adulthood. At the tissue level, this grading contributes to reduced stresses in an adult animal and to a minor elevation of stresses in a neonatal animal. At the cellular level, stress concentrations around mineralizing chondrocytes are enhanced in neonatal animals compared with adult animals. The enhancement of stresses around cells at early time points may serve to amplify and transduce low loads in order to initiate mineralization.     

The developing shoulder has a limited capacity to recover after a short duration of neonatal paralysis

Mechanical stimuli are required for the proper development of the musculoskeletal system. Removal of muscle forces during fetal or early post-natal timepoints impairs the formation of bone, tendon, and their attachment (the enthesis). The goal of the current study was to examine the capacity of the shoulder to recover after a short duration of neonatal rotator cuff paralysis, a condition mimicking the clinical condition neonatal brachial plexus palsy. We asked if reapplication of muscle load to a transiently paralyzed muscle would allow for full recovery of tissue properties. CD-1 mice were injected with botulinum toxin A to paralyze the supraspinatus muscle from birth through 2 weeks and subsequently allowed to recover. The biomechanics of the enthesis was determined using tensile testing and the morphology of the shoulder joint was determined using microcomputed tomography and histology. A recovery period of at least 10 weeks was required to achieve control properties, demonstrating a limited capacity of the shoulder to recover after only two weeks of muscle paralysis. Although care must be taken when extrapolating results from an animal model to the human condition, the results of the current study imply that treatment of neonatal brachial plexus palsy should be aggressive, as even short periods of paralysis could lead to long-term deficiencies in enthesis biomechanics and shoulder morphology.     

Research experience modifies how participants profit from journal clubs in academia

Because Journal Clubs (JClubs) represent valued educational tools, we often assume optimality of Journal Club practices. We analyze here JClubs records from a research group to identify factors that modify how much attendants benefit from discussing a paper. We demonstrate that attendants benefit most from papers focusing on systems similar to those they work on and that their ability to profit from different contribution types changes with research experience. Common JClubs practices such as the assignment of the paper selection to a single individual could thus compromise participant experience. Our conclusions may also be generalizable to situations outside academia.     

Analysis of dihydroethidium fluorescence for the detection of intracellular and extracellular superoxide produced by NADPH oxidase

All methods used for quantitation of superoxide have limitations when it comes to differentiating between extracellular and intracellular sites of superoxide production. In the present study, we monitored dihydroethidium (DHE)-derived fluorescence at 570 nm, which indicates hydroxyethidium derived from reaction with superoxide produced by human leukemia cells (HL-60) and microvascular endothelial cells (HMEC-1). Phorbol-12-myristate 13-acetate (PMA; 100 ng/ml) caused an increase in fluorescence and lucigenin chemiluminescence in HL-60, which was abolished by superoxide dismutase (SOD; 600 U/ml) indicating that DHE detects extracellular superoxide. Furthermore, both HL-60 cells and HMEC-1 generated a fluorescence signal in the presence of DHE under resting conditions, which was unaffected by SOD, but abolished by polyethylene glycosylated-SOD (PEG-SOD) (100 U/ml) and MnTmPyP (25 μM), indicating that DHE also detects superoxide produced intracellularly. In HMEC-1, silencing of either Nox2 or Nox4 components of NADPH oxidase with small interference RNA (siRNA) resulted in a significant reduction in superoxide detected by both DHE fluorescence (Nox2 siRNA; 71 ± 6% and Nox4 siRNA 83 ± 7% of control) and lucigenin chemiluminescence (Nox2; 54 ± 6% and Nox4 74 ± 4% of control). In conclusion, DHE-derived fluorescence at 570 nm is a convenient method for detection of intracellular and extracellular superoxide produced by phagocytic and vascular NADPH oxidase.     

IL-6 is not required for parathyroid hormone stimulation of RANKL expression, osteoclast formation, and bone loss in mice

Continuous elevation of parathyroid hormone (PTH) increases osteoclast precursors, the number of osteoclasts on cancellous bone, and bone turnover. The essential molecular mediators of these effects are controversial, however, and both increased receptor activator of NF-kappaB ligand (RANKL) and IL-6 have been implicated. The goal of these studies was to determine whether continuous elevation of endogenous PTH alters IL-6 gene expression in vivo and whether IL-6 is required for PTH-induced bone loss. To accomplish this, we generated transgenic mice harboring a luciferase reporter gene under the control of IL-6 gene regulatory regions to allow accurate quantification of IL-6 gene activity in vivo. In these mice, induction of secondary hyperparathyroidism using a calcium-deficient diet did not alter IL-6-luciferase transgene expression, whereas RANKL mRNA expression was elevated in bone tissue. Moreover, secondary hyperparathyroidism induced an equivalent amount of bone loss in wild-type and IL-6-deficient mice, and PTH elevated RANKL mRNA and osteoclast formation to the same extent in bone marrow cultures derived from wild-type and IL-6-deficient mice. These results demonstrate that IL-6 is not required for the osteoclast formation and bone loss that accompanies continuous elevation of PTH.     

Cell Cycle-dependent Subcellular Translocation of the Human DNA Licensing Inhibitor Geminin

Once per cell cycle replication is crucial for maintaining genome integrity. Geminin interacts with the licensing factor Cdt1 to prevent untimely replication and is controlled by APC/C-dependent cell cycle specific proteolysis during mitosis and in G₁. We show here that human geminin, when expressed in human cells in culture under a constitutive promoter, is excluded from the nucleus during part of the G₁ phase and at the transition from G₀ to G₁. The N-terminal 30 amino acids of geminin, which contain its destruction box, are essential for nuclear exclusion. In addition, 30 amino acids within the central domain of geminin are required for both nuclear exclusion and nuclear accumulation. Cdt1 overexpression targets geminin to the nucleus, while reducing Cdt1 levels by RNAi leads to the appearance of endogenous geminin in the cytoplasm. Our data propose a novel means of regulating the balance of Cdt1/geminin in human cells, at the level of the subcellular localization of geminin.     

Interaction of spatial diffusion and delays in models of genetic control by repression

A class of models based on the Jacob and Monod theory of genetic repression for control of biosynthetic pathways in cells is considered. Both spatial diffusion and time delays are taken into account. A method is developed for representing the effects of spatial diffusion as distributed delay terms. This method is applied to two specific models and the interaction between the diffusion and the delays is treated in detail. The destabilization of the steadystate and the bifurcation of oscillatory solutions are studied as functions of the diffusivities and the delays. The limits of very small and very large diffusivities are analyzed and comparisons with well-mixed compartment models are made.On leave from North Carolina State University