Microbiome engineering: Current applications and its future

Microbiomes exist in all ecosystems and are composed of diverse microbial communities. Perturbation to microbiomes brings about undesirable phenotypes in the hosts, resulting in diseases and disorders, and disturbs the balance of the associated ecosystems. Engineering of microbiomes can be used to modify structures of the microbiota and restore ecological balance. Consequently, microbiome engineering has been employed for improving human health and agricultural productivity. The importance and current applications of microbiome engineering, particularly in humans, animals, plants and soil is reviewed. Furthermore, we explore the challenges in engineering microbiome and the future of this field, thus providing perspectives and outlook of microbiome engineering.     

Improving soil protein extraction for metaproteome analysis and glomalin‐related soil protein detection

Soil contains low amounts of protein but high amounts of interfering substances. Current extraction methods for soil protein cannot produce high‐quality samples suitable for proteomic analysis. To resolve the problem, we devised a sequential extraction method, through sequentially extracting soil in citrate and SDS buffers, followed by phenol extraction. The method allows for obtaining applicable 1‐D and 2‐D protein profiles with various agricultural soils and detecting glomalin‐related soil protein. The method may be a valuable tool for soil proteomics.     

Swing it to the left, swing it to the right: enacting flexible spatial language using a neurodynamic framework

Research is continually expanding the empirical and theoretical picture of embodiment and dynamics in language. To date, however, a formalized neural dynamic framework for embodied linguistic processes has yet to emerge. To advance embodied theories of language, the present work develops a formalized neural dynamic framework of spatial language that explicitly integrates linguistic processes and dynamic sensory-motor systems. We then implement and test our spatial language architecture on a robotic platform continuously linked to real-time camera input. In a suite of tasks using everyday objects we demonstrate the framework’s capacity for both contextually-dependent behavioral flexibility and the seamless integration of spatial, non-spatial, and symbolic representations. To our knowledge this is the first unified, neurally-grounded architecture integrating these processes and behaviors.     

Fermentation of soybean hulls to ethanol while preserving protein value

Soybean hulls were evaluated as a resource for production of ethanol by the simultaneous saccharification and fermentation (SSF) process, and no pretreatment of the hulls was found to be needed to realize high ethanol yields with Saccharomyces cerevisiae D₅A. The impact of cellulase, β-glucosidase and pectinase dosages were determined at a 15% biomass loading, and ethanol concentrations of 25–30 g/L were routinely obtained, while under these conditions corn stover, wheat straw, and switchgrass produced 3–4 times lower ethanol yields. Removal of carbohydrates also concentrated the hull protein to over 25% w/w from the original roughly 10%. Analysis of the soybean hulls before and after fermentation showed similar amino acid profiles including an increase in the essential amino acids lysine and threonine in the residues. Thus, eliminating pretreatment should assure that the protein in the hulls is preserved, and conversion of the carbohydrates to ethanol with high yields produces a more concentrated and valuable co-product in addition to ethanol. The resulting upgraded feed product from soybean hulls would likely to be acceptable to monogastric as well as bovine livestock.     

Hedgerows as an environment for forest plants: a comparative case study of five species

Many areas in Europe are dominated by agricultural land use, and as a consequence, many typical forest plant species suffer from habitat loss and fragmentation. Hedgerows, one of the common elements of rural landscapes, have been considered as potential refuges for these species. The main objective of this study was to examine whether forests and hedgerows differ in environmental conditions, and whether important life-history attributes of the populations differ between the two habitat types. We selected five species commonly found in the region in both forests and hedgerows (Adoxa moschatellina, Anemone nemorosa, Circaea lutetiana, Polygonatum multiflorum and Stellaria holostea), and sampled data on 10 populations of each species in each habitat type, including measurements of light and various soil factors. Hedgerows had higher relative light availability and tended to have higher soil nutrient contents and lower soil water values than forests. The comparison of plant performance values between habitat types did not show consistent patterns across species. Anemone and Polygonatum performed equally well in hedgerows and forests, whereas Stellaria appeared to have a higher fitness in hedgerows. In contrast, Circaea showed a higher reproduction under forest conditions. For Adoxa, the results were somewhat contradictory: whereas the reproductive output of this species was higher in forests, population density was higher in hedgerows. The abiotic factors most closely related to the performance values were relative light and soil water availability. The majority of plant performance values did not differ between hedgerows and forests. We therefore conclude that the tested forest species are capable of growing also in hedgerows and will survive equally well in forest and its “surrogate” habitat.     

Land use legacies in post-agricultural forests in the Doupovské Mountains,Czech Republic

Questions: Do differences in previous land use cause long-lasting changes in soil chemistry? Is vegetation composition affected by the previous land use after 50 years of secondary succession? Is the effect of previous land use caused by pre-existing differences in environmental conditions or mediated through changes in soil chemistry? How important is the effect of previous land use in relation to other factors? Location: Doupovské Mountains, Czech Republic. Methods: A stratified random sampling design was used to collect 91 vegetation relevés with accompanying soil samples. The effects of previous land use (arable field, meadow, pasture) on soil pH, organic carbon (C), total nitrogen (N), C:N ratio and available phosphorus were tested by an analysis of covariance. A canonical correspondence analysis and variation partitioning procedure were used to reveal relationships among previous land use, environmental factors and species composition. Results: Organic C, total N and C:N ratio were significantly influenced by previous land use, while available phosphorus and soil pH were not. Previous land use explained a significant part of the variation in species composition and its effects only partly overlapped with the effects of soil chemistry and terrain attributes. However, the species composition of post-agricultural forests was mostly determined by environmental factors not modified by previous land use. Conclusions: Forest communities that originate on abandoned agricultural land are primarily determined by natural environmental conditions. Nevertheless, the type of previous land use also modifies the species assemblages of these forests and needs to be considered as an important determinant of their composition.     

The influence of pulsed magnetic fields (PMFs) on nonsynaptic potentials recorded from the central and peripheral nervous systems in vitro

The influence of pulsed magnetic fields (PMFs) on nonsynaptic potentials recorded from the central and peripheral nervous system in vitro has been investigated. The population spikes (PSs) recorded from hippocampal slices during antidromic stimulation and compound action potentials (CAPs) recorded from the segments of the sciatic nerve were used as indicators of neuronal activity. The potentials recorded from both preparations were significantly and permanently enhanced following PMF (0.16 Hz, 15 mT) exposure. The increase in the antidromic PS occurred even in the presence of potassium channel blocker tetraethylammonium (TEA) and was accompanied by multiple spiking. Among all frequencies of PMF tested (0.5, 0.16, 0.07, 0.03, 0.0 Hz), the frequency of 0.5 Hz was the most effective in enhancement of potential amplitude. The influence of PMF on the amplitude of two CAPs evoked by the pair of electrical stimuli applied in rapid succession has also been evaluated. In control conditions the potential triggered by the second stimuli was slightly smaller expressing the phenomenon of short‐term depression (STD). Although PMF exposure amplified the amplitude of both potentials, the increase in the size of the first potential was significantly greater increasing further the magnitude of STD. The blocking of potassium channels reversed STD into facilitation. One of the possible mechanisms involved in PMF action could be the modification of the axonal threshold, which was significantly reduced following exposure to PMF. Bioelectromagnetics 30:621–630, 2009. © 2009 Wiley‐Liss, Inc.     

Exposure to a MRI‐type high‐strength static magnetic field stimulates megakaryocytic/erythroid hematopoiesis in CD34+ cells from human placental and umbilical cord blood

The biological response after exposure to a high‐strength static magnetic field (SMF) has recently been widely discussed from the perspective of possible health benefits as well as potential adverse effects. To clarify this issue, CD34⁺ cells from human placental and umbilical cord blood were exposed under conditions of high‐strength SMF in vitro. The high‐strength SMF exposure system was comprised of a magnetic field generator with a helium‐free superconducting magnet with built‐in CO₂ incubator. Freshly prepared CD34⁺ cells were exposed to a 5 tesla (T) SMF with the strongest magnetic field gradient (41.7 T/m) or a 10 T SMF without magnetic field gradient for 4 or 16 h. In the harvested cells after exposure to 10 T SMF for 16 h, a significant increase of hematopoietic progenitors in the total burst‐forming unit erythroid‐ and megakaryocytic progenitor cells‐derived colony formation was observed, thus producing 1.72‐ and 1.77‐fold higher than the control, respectively. Furthermore, early hematopoiesis‐related and cell cycle‐related genes were found to be significantly up‐regulated by exposure to SMF. These results suggest that the 10 T SMF exposure may change gene expressions and result in the specific enhancement of megakaryocytic/erythroid progenitor (MEP) differentiation from pluripotent hematopoietic stem cells and/or the proliferation of bipotent MEP. Bioelectromagnetics 30:280–285, 2009. © 2009 Wiley‐Liss, Inc.     

A nonlinear model of ionic wave propagation along microtubules

Microtubules (MTs) are important cytoskeletal polymers engaged in a number of specific cellular activities including the traffic of organelles using motor proteins, cellular architecture and motility, cell division and a possible participation in information processing within neuronal functioning. How MTs operate and process electrical information is still largely unknown. In this paper we investigate the conditions enabling MTs to act as electrical transmission lines for ion flows along their lengths. We introduce a model in which each tubulin dimer is viewed as an electric element with a capacitive, inductive and resistive characteristics arising due to polyelectrolyte nature of MTs. Based on Kirchhoff’s laws taken in the continuum limit, a nonlinear partial differential equation is derived and analyzed. We demonstrate that it can be used to describe the electrostatic potential coupled to the propagating localized ionic waves. An erratum to this article can be found at