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Biological Processes (biological + process)
Kinds of Biological Processes Selected AbstractsCausal mapping as a tool to mechanistically interpret phenomena in cell motility: Application to cortical oscillations in spreading cellsCYTOSKELETON, Issue 9 2006Gabriel E. Weinreb Abstract Biological processes that occur at the cellular level and consist of large numbers of interacting elements are highly nonlinear and generally involve multiple time and spatial scales. The quantitative description of these complex systems is of great importance but presents large challenges. We outline a new systems biology approach, causal mapping (CMAP), which is a coarse-grained biological network tool that permits description of causal interactions between the elements of the network and overall system dynamics. On one hand, the CMAP is an intermediate between experiments and physical modeling, describing major requisite elements, their interactions and paths of causality propagation. On the other hand, the CMAP is an independent tool to explore the hierarchical organization of cell and the role of uncertainties in the system. It appears to be a promising easy-to-use technique for cell biologists to systematically probe verbally formulated qualitative hypotheses. We apply the CMAP to study the phenomenon of contractility oscillations in spreading cells in which microtubules have been depolymerized. The precise mechanism by which these oscillations are governed by a complex mechano-chemical system is not known but the data observed in experiments can be described by a CMAP. The CMAP suggests that the source of the oscillations results from the opposing effects of Rho activation leading to a decreased level of myosin light chain phosphatase and a cyclic calcium influx caused by increased membrane tension and leading to a periodically enhanced activation of myosin light chain kinase. Cell Motil. Cytoskeleton 2006. © 2006 Wiley-Liss, Inc. [source] Manganese cell labeling of murine hepatocytes using manganese(III)-transferrin,CONTRAST MEDIA & MOLECULAR IMAGING, Issue 3 2008Christopher H. Sotak Abstract Manganese(III)-transferrin [Mn(III),Tf] was investigated as a way to accomplish manganese-labeling of murine hepatocytes for MRI contrast. It is postulated that Mn(III),Tf can exploit the same transferrin-receptor-dependent and -independent metabolic pathways used by hepatocytes to transport the iron analog Fe(III),Tf. More specifically, it was investigated whether manganese delivered by transferrin could give MRI contrast in hepatocytes. Comparison of the T1 and T2 relaxation times of Mn(III),Tf and Fe(III),Tf over the same concentration range showed that the r1 relaxivities of the two metalloproteins are the same in vitro, with little contribution from paramagnetic enhancement. The degree of manganese cell labeling following incubation for 2,7,h in 31.5,µm Mn(III),Tf was comparable to that of hepatocytes incubated in 500,µm Mn2+ for 1,h. The intrinsic manganese tissue relaxivity between Mn(III),Tf-labeled and Mn2+ -labeled cells was found to be the same, consistent with Mn(III) being released from transferrin and reduced to Mn2+. For both treatment regimens, manganese uptake by hepatocytes appeared to saturate in the first 1,2,h of the incubation period and may explain why the efficiency of hepatocyte cell labeling by the two methods appeared to be comparable in spite of the ,16-fold difference in effective manganese concentration. Hepatocytes continuously released manganese, as detected by MRI, and this was the same for both Mn2+ - and Mn(III),Tf-labeled cells. Manganese release may be the result of normal hepatocyte function, much in the same way that hepatocytes excrete manganese into the bile in vivo. This approach exploits a biological process,namely receptor binding, endocytosis and endosomal acidification,to initiate the release of an MRI contrast agent, potentially conferring more specificity to the labeling process. The ubiquitous expression of transferrin receptors by eukaryotic cells should make Mn(III),Tf particularly useful for manganese labeling of a wide variety of cells both in culture and in vivo. Published in 2008 by John Wiley & Sons, Ltd. [source] MicroRNA in the immune system, microRNA as an immune systemIMMUNOLOGY, Issue 3 2009Li-Fan Lu Summary The advent of microRNA has potentially uncovered a new level of complexity to be considered for every biological process. Through the modulation of transcription and translation, microRNA alter the basal state of cells and the outcome of stimulatory events. The exact effect of the microRNA network and individual microRNA on cellular processes is only just starting to be dissected. In the immune system, microRNA appear to have a key role in the early differentiation and effector differentiation of B cells. In T cells, microRNA have been shown to be key regulators of the lineage induction pathways, and to have a strong role in the induction, function and maintenance of the regulatory T-cell lineage. MicroRNA are also important for regulating the differentiation of dendritic cells and macrophages via toll-like receptors, with responsibilities in suppressing effector function before activation and enhancing function after stimulation. In addition to regulating key processes in the immune system, microRNA may also represent an archaic immune system themselves. Small interfering RNA of viral origin has been shown to function as an intracellular mediator in the suppression of viral infection in eukaryotes as diverse as plants, insects, nematodes and fungi, and there is growing evidence that endogenous mammalian microRNA can have similar impacts. In this article we speculate that the anti-viral function of microRNA drove the expression of different subsets of microRNA in different cellular lineages, which may have, in turn, led to the myriad of roles microRNA play in lineage differentiation and stability. [source] On identifying marker genes from gene expression data in a neural framework through online feature analysisINTERNATIONAL JOURNAL OF INTELLIGENT SYSTEMS, Issue 4 2006Nikhil Ranjan Pal Many attempts have been made to analyze gene expression data. Typical goals of such analysis include discovery of subclasses, designing predictors/classifiers for diseases, identifying marker genes, and trying to get a deeper understanding of underlying biological process. Success of each of these tasks strongly depends on the features used to solve the problem. The high dimensional nature of expression profiles makes the task very difficult. Consequently, many researchers have used some feature selection criteria to reduce the dimensionality of the problem. These approaches are off-line in nature, as feature selection is done in a separate phase from the system design phase. These approaches ignore the fact that utility of features depends on both the problem that is solved and the tool that is used to solve the problem. We here propose to use a novel neural scheme that picks up the necessary features on-line when the system learns the classification task. Because it considers all the features at one go, it does not miss any subtle combination of these features. We demonstrate the effectiveness of our on-line feature selection (OFS) scheme to distinguish between acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) cancer expression data set. Our scheme could identify only five genes that can produce results as good as or even better than what is reported in the literature on this data set. It identifies an important marker gene that alone has a very good discriminating power. This analysis method is quite general in nature and can be effectively used in other areas of bioinformatics. © 2006 Wiley Periodicals, Inc. Int J Int Syst 21: 453,467, 2006. [source] Inhibition of sulfide on the simultaneous removal of nitrate and p -cresol by a denitrifying sludgeJOURNAL OF CHEMICAL TECHNOLOGY & BIOTECHNOLOGY, Issue 3 2008Edna R Meza-Escalante Abstract BACKGROUND: Many industrial discharges, such as those generated from petrochemical refineries, contain large amounts of sulfurous, nitrogenous and organic contaminants. Denitrification has emerged as a suitable technology for the simultaneous removal of these pollutants in a single reactor unit; however, more evidence is demanded to clarify the limitations of denitrification on the simultaneous removal of sulfide and phenolic contaminants and to optimize the biological process. The aim of this study was to evaluate the capacity of a denitrifying sludge to simultaneously convert sulfide and p -cresol via denitrification. RESULTS: Sulfide was the preferred electron donor over p -cresol, imposing a 5 h lag phase (required for complete sulfide removal) on organotrophic denitrification. Addition of sulfide (20 mg S2, L,1) to p -cresol-amended denitrifying cultures also decreased the reduction rate of nitrate and nitrite, as well as the production rate of nitrogen gas. Nitrite reduction rate was the most affected step by sulfide, decreasing from 35 to 21 mg N (g VSS d),1. A synergistic inhibitory effect of nitrate and sulfide was also observed on nitrite reduction. Despite the effects of sulfide on the respiratory rates monitored, complete removal of nitrate, sulfide and p -cresol could be achieved after 48 h of incubation. CONCLUSION: Our results suggest that simultaneous removal of sulfide and p -cresol could be achieved in denitrifying reactors, but a large hydraulic residence time may be required to sustain an efficient process due to inhibitory effects of sulfide. Copyright © 2008 Society of Chemical Industry [source] Bioprocesses for the removal of nitrogen oxides from polluted airJOURNAL OF CHEMICAL TECHNOLOGY & BIOTECHNOLOGY, Issue 5 2005Yaomin Jin Abstract Nitrogen oxides (NOx) of environmental concern are nitrogen monoxide (NO) and nitrogen dioxide (NO2). They are hazardous air pollutants that lead to the formation of acid rain and tropospheric ozone. Both pollutants are usually present simultaneously and are, therefore, called NOx. Another compound is N2O which is found in the stratosphere where it plays a role in the greenhouse effect. Concern for environmental and health issues coupled with stringent NOx emission standards generates a need for the development of efficient low-cost NOx abatement technologies. Under such circumstances, it becomes mandatory for each NOx-emitting industry or facility to opt for proper NOx control measures. Several techniques are available to control NOx emissions: selective catalytic reduction (SCR), selective non-catalytic reduction (SNCR), adsorption, scrubbing, and biological methods. Each process offers specific advantages and limitations. Since bioprocesses present many advantages over conventional technologies for flue gas cleaning, a lot of interest has recently been shown for these processes. This article reviews the major characteristics of conventional non-biological technologies and recent advances in the biological removal of NOx from flue gases based on the catalytic activity of either eucaryotes or procaryotes, ie nitrification, denitrification, the use of microalgae, and a combined physicochemical and biological process (BioDeNOx). Relatively uncomplicated design and simple operation and maintenance requirements make biological removal a good option for the control of NOx emissions in stationary sources. Copyright © 2005 Society of Chemical Industry [source] Sexual Reproduction in Higher Plants I: Fertilization and the Initiation of Zygotic ProgramJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 7 2008Yong-Feng Fan Abstract Sexual plant reproduction is a critical developmental step in the life cycle of higher plants, to allow maternal and paternal genes to be transmitted in a highly regulated manner to the next generation. During evolution, a whole set of signal transduction machinery is developed by plants to ensure an error-free recognition between male and female gametes and initiation of zygotic program. In the past few years, the molecular machineries underlying this biological process have been elucidated, particularly on the importance of synergid cells in pollen tube guidance, the Ca++ spike as the immediate response of fertilization and the epigenetic regulation of parental gene expressions in early zygotic embryogenesis. This review outlines the most recent development in this area. [source] Bayesian mixture models for complex high dimensional count data in phage display experimentsJOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES C (APPLIED STATISTICS), Issue 2 2007Yuan Ji Summary., Phage display is a biological process that is used to screen random peptide libraries for ligands that bind to a target of interest with high affinity. On the basis of a count data set from an innovative multistage phage display experiment, we propose a class of Bayesian mixture models to cluster peptide counts into three groups that exhibit different display patterns across stages. Among the three groups, the investigators are particularly interested in that with an ascending display pattern in the counts, which implies that the peptides are likely to bind to the target with strong affinity. We apply a Bayesian false discovery rate approach to identify the peptides with the strongest affinity within the group. A list of peptides is obtained, among which important ones with meaningful functions are further validated by biologists. To examine the performance of the Bayesian model, we conduct a simulation study and obtain desirable results. [source] Recent development in the design of sialyltransferase inhibitorsMEDICINAL RESEARCH REVIEWS, Issue 1 2003Xiaofang Wang Abstract Sialylation at the non-reducing end of glycoconjugates is an important biological process in cellular recognitions, tumor metastases, and immune responses, which are mediated by a family of enzymes known as sialyltransferases. Inhibition of sialyltransferases may prove useful in elucidating the biological functions of sialylation and may have therapeutic applications. This review summarizes the recent development in this field with particular focus on the strategies used for the design of carbohydrate mimetics and the structure-activity relationships of substrate-based sialyltransferase inhibitors. © 2002 Wiley Periodicals, Inc. Med Res Rev, 23, No. 1, 32,47, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/med.10030 [source] Effect of protein degradation on spot Mr distribution in 2-D gels , a case study of proteolysis during development of Streptomyces coelicolor culturesPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 12 2008Jiri Vohradsky Dr. Abstract Proteolysis, a regulated biological process, is reflected by protein spot molecular weight distribution in 2-D gel electrophoretograms. Here we report studies of Streptomyces cultures as they undergo two different developmental processes involving proteolysis. Systematic changes in protein molecular weight distribution between the control samples and those with high activity of proteases were demonstrated. The observations were supported by a numerical model of degradation and its influence on the Mr distribution. Simple statistics could be used to distinguish between normal and degradative 2-D gel electrophoretic patterns. [source] Strong and weak lifespan extension: what is most feasible and likely?AUSTRALASIAN JOURNAL ON AGEING, Issue 2 2006Jayne C Lucke Abstract Recent advances in biomedical science indicate that it may eventually be possible to intervene in the biological process of human ageing. This paper overviews the current state of the science of lifespan extension and promising future directions. It is uncertain whether ,strong' lifespan extension , the extension of human life beyond the maximum 122 years so far observed , will become a reality. It is more likely that cumulative effects of numerous scientific and biomedical advances in the treatment of common disease will produce ,weak' lifespan extension , the extension of average life expectancy. The practical application of molecular, genetic and nanomaterials research may also lead to advances in life expectancy. It is not too early to begin to consider the policy implications of either form of lifespan extension. [source] Expression, purification, and analysis of unknown translation factors from Escherichia coli: A synthesis approachBIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, Issue 1 2010Justin D. Walter Abstract New approaches are currently being developed to expose biochemistry and molecular biology undergraduates to a more interactive learning environment. Here, we propose a unique project-based laboratory module, which incorporates exposure to biophysical chemistry approaches to address problems in protein chemistry. Each of the experiments described herein contributes to the stepwise process of isolating, identifying, and analyzing a protein involved in a central biological process, prokaryotic translation. Students are provided with expression plasmids that harbor an unknown translation factor, and it is their charge to complete a series of experiments that will allow them to develop hypotheses for discovering the identity of their unknown (from a list of potential candidates). Subsequent to the identification of their unknown translation factor, a series of protein unfolding exercises are performed employing circular dichroism and fluorescence spectroscopies, allowing students to directly calculate thermodynamic parameters centered around determining the equilibrium constant for unfolding as a function of denaturant (temperature or chemical). The conclusion of this multi-part laboratory exercise consists of both oral and written presentations, emphasizing synthesis of the roles of each translation factor during the stepwise process of translation. [source] Comparative analysis of efficiency, environmental impact, and process economics for mature biomass refining scenariosBIOFUELS, BIOPRODUCTS AND BIOREFINING, Issue 2 2009Mark Laser Abstract Fourteen mature technology biomass refining scenarios , involving both biological and thermochemical processing with production of fuels, power, and/or animal feed protein , are compared with respect to process efficiency, environmental impact , including petroleum use, greenhouse gas (GHG) emissions, and water use,and economic profitability. The emissions analysis does not account for carbon sinks (e.g., soil carbon sequestration) or sources (e.g., forest conversion) resulting from land-use considerations. Sensitivity of the scenarios to fuel and electricity price, feedstock cost, and capital structure is also evaluated. The thermochemical scenario producing only power achieves a process efficiency of 49% (energy out as power as a percentage of feedstock energy in), 1359 kg CO2 equivalent avoided GHG emissions per Mg feedstock (current power mix basis) and a cost of $0.0575/kWh ($16/GJ), at a scale of 4535 dry Mg feedstock/day, 12% internal rate of return, 35% debt fraction, and 7% loan rate. Thermochemical scenarios producing fuels and power realize efficiencies between 55 and 64%, avoided GHG emissions between 1000 and 1179 kg/dry Mg, and costs between $0.36 and $0.57 per liter gasoline equivalent ($1.37 , $2.16 per gallon) at the same scale and financial structure. Scenarios involving biological production of ethanol with thermochemical production of fuels and/or power result in efficiencies ranging from 61 to 80%, avoided GHG emissions from 965 to 1,258 kg/dry Mg, and costs from $0.25 to $0.33 per liter gasoline equivalent ($0.96 to $1.24/gallon). Most of the biofuel scenarios offer comparable, if not lower, costs and much reduced GHG emissions (>90%) compared to petroleum-derived fuels. Scenarios producing biofuels result in GHG displacements that are comparable to those dedicated to power production (e.g., >825 kg CO2 equivalent/dry Mg biomass), especially when a future power mix less dependent upon fossil fuel is assumed. Scenarios integrating biological and thermochemical processing enable waste heat from the thermochemical process to power the biological process, resulting in higher overall process efficiencies than would otherwise be realized , efficiencies on par with petroleum-based fuels in several cases. © 2009 Society of Chemical Industry and John Wiley & Sons, Ltd [source] Cell-free synthesis of functional proteins using transcription/translation machinery entrapped in silica sol,gel matrixBIOTECHNOLOGY & BIOENGINEERING, Issue 1 2009Kyeong-Ohn Kim Abstract Herewith we report the encapsulation of functional protein synthesis machinery in a silica sol,gel matrix. When the sol,gel reaction using alkoxysilane monomers was carried out in the presence of Escherichia coli cell extract, macromolecular protein synthesis machinery in the cell extract was successfully immobilized within a silica gel matrix, catalyzing the translation of co-immobilized DNA when supplied with small-molecular-weight substrates for protein synthesis. The efficiency of protein synthesis was affected by the pore size of the gel structure, which was controlled through the use of appropriate additives during the sol,gel reactions. To the best of our knowledge, this is the first report describing the reproduction of the entire set of complicated biological process within an inorganic gel matrix, and we expect that the developed technology will find many applications in numerous fields such as high-throughput gene expression and the development of multifunctional biosensors. Biotechnol. Bioeng. 2009;102: 303,307. © 2008 Wiley Periodicals, Inc. [source] Techno-economic evaluation of a two-step biological process for hydrogen productionBIOTECHNOLOGY PROGRESS, Issue 2 2010Mattias Ljunggren Abstract An integrated biological process for the production of hydrogen based on thermophilic and photo-heterotrophic fermentation was evaluated from a technical and economic standpoint. Besides the two fermentation steps the process also includes pretreatment of the raw material (potato steam peels) and purification of hydrogen using amine absorption. The study aimed neither at determining the absolute cost of biohydrogen nor at an economic optimization of the production process, but rather at studying the effects of different parameters on the production costs of biohydrogen as a guideline for future improvements. The effect of the key parameters, hydrogen productivity and yield and substrate concentration in the two fermentations on the cost of the hydrogen produced was studied. The selection of the process conditions was based mainly on laboratory data. The process was simulated by use of the software Aspen Plus and the capital costs were estimated using the program Aspen Icarus Process Evaluator. The study shows that the photo-fermentation is the main contributor to the hydrogen production cost mainly because of the cost of plastic tubing, for the photo-fermentors, which represents 40.5% of the hydrogen production cost. The costs of the capital investment and chemicals were also notable contributors to the hydrogen production cost. Major economic improvements could be achieved by increasing the productivity of the two fermentation steps on a medium-term to long-term scale. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010 [source] Actin on DNA,An ancient and dynamic relationship,CYTOSKELETON, Issue 8 2010Kari-Pekka Skarp Abstract In the cytoplasm of eukaryotic cells the coordinated assembly of actin filaments drives essential cell biological processes, such as cell migration. The discovery of prokaryotic actin homologues, as well as the appreciation of the existence of nuclear actin, have expanded the scope by which the actin family is utilized in different cell types. In bacteria, actin has been implicated in DNA movement tasks, while the connection with the RNA polymerase machinery appears to exist in both prokaryotes and eukaryotes. Within the nucleus, actin has further been shown to play a role in chromatin remodeling and RNA processing, possibly acting to link these to transcription, thereby facilitating the gene expression process. The molecular mechanism by which actin exerts these newly discovered functions is still unclear, because while polymer formation seems to be required in bacteria, these species lack conventional actin-binding proteins to regulate the process. Furthermore, although the nucleus contains a plethora of actin-regulating factors, the polymerization status of actin within this compartment still remains unclear. General theme, however, seems to be actin's ability to interact with numerous binding partners. A common feature to the novel modes of actin utilization is the connection between actin and DNA, and here we aim to review the recent literature to explore how this connection is exploited in different contexts. [source] Fibroblast elongation and dendritic extensions in constrained versus unconstrained microtissuesCYTOSKELETON, Issue 3 2009Dylan M. Dean Abstract Cytoskeletal tension is fundamental to many biological processes, including germ layer sorting during embryogenesis [Krieg et al., 2008]. In vitro, such tension influences cell sorting in self-assembled, 3D microtissues and can be of sufficient magnitude to cause complex-shaped microtissue failure [Dean et al., 2007]. To examine the process of failure under cell-derived tension, we subjected normal human fibroblasts (NHFs) to directed self-assembly [Dean et al., 2007] in micro-molds designed to yield self-constraining microtissues. As cells contracted in this assay, the constrained microtissues narrowed, thinned and ultimately failed at their midpoints. By adding small numbers of GFP+ cells, changes in cell movement and morphology were assessed and compared to those of unconstrained microtissues. We found that cells formed numerous dendritic extensions within an hour of self-assembly and retracted these extensions as they elongated up to 30 times their initial diameter (,600 ,m) just prior to failure. Surprisingly, significant coordination in cell motility was observed over large distances within microtissues. Pharmacologic interventions showed that failure was myosin II and Rho kinase dependent and inhibition of failure resulted in shorter cells with greater numbers of extensions. These findings further our understanding of cellular self-assembly and introduce the use of GFP+ cells with directed self-assembly as a scaffold-free analogue to fibroblast-populated collagen gels (FPCGs). Cell Motil. Cytoskeleton 2009. © 2009 Wiley-Liss, Inc. [source] Development of micropost force sensor array with culture experiments for determination of cell traction forcesCYTOSKELETON, Issue 7 2007Bin Li Abstract Cell traction forces (CTFs) are critical for cell motility and cell shape maintenance. As such, they play a fundamental role in many biological processes such as angiogenesis, embryogenesis, inflammation, and wound healing. To determine CTFs at the sub-cellular level with high sensitivity, we have developed high density micropost force sensor array (MFSA), which consists of an array of vertically standing poly(dimethylsiloxane) (PDMS) microposts, 2 ,m in diameter and 6 ,m in height, with a center-to-center distance of 4 ,m. In combination with new image analysis algorithms, the MFSA can achieve a spatial resolution of 40 nm and a force sensitivity of 0.5 nN. Culture experiments with various types of cells showed that this MFSA technology can effectively determine CTFs of cells with different sizes and traction force magnitudes. Cell Motil. Cytoskeleton 2007. © 2007 Wiley-Liss, Inc. [source] Probing events with single molecule sensitivity in zebrafish and Drosophila embryos by fluorescence correlation spectroscopyDEVELOPMENTAL DYNAMICS, Issue 12 2009Xianke Shi Abstract Zebrafish and Drosophila are animal models widely used in developmental biology. High-resolution microscopy and live imaging techniques have allowed the investigation of biological processes down to the cellular level in these models. Here, using fluorescence correlation spectroscopy (FCS), we show that even processes on a molecular level can be studied in these embryos. The two animal models provide different advantages and challenges. We first characterize their autofluorescence pattern and determine usable penetration depth for FCS especially in the case of zebrafish, where tissue thickness is an issue. Next, the applicability of FCS to study molecular processes is shown by the determination of blood flow velocities with high spatial resolution and the determination of diffusion coefficients of cytosolic and membrane-bound enhanced green fluorescent protein,labeled proteins in different cell types. This work provides an approach to study molecular processes in vivo and opens up the possibility to relate these molecular processes to developmental biology questions. Developmental Dynamics 238:3156,3167, 2009. © 2009 Wiley-Liss, Inc. [source] Pleiotropic function of FGF-4: Its role in development and stem cellsDEVELOPMENTAL DYNAMICS, Issue 2 2009Nobuyoshi Kosaka Abstract Fibroblast growth factors (FGFs) were initially recognized as fibroblast-specific growth factor, and it is now apparent that these growth factors regulate multiple biological functions. The diversity of FGFs function is paralleled by the emerging diversity of interactions between FGF ligands and their receptors. FGF-4 is a member of the FGF superfamily and is a mitogen exhibiting strong action on numerous different cell types. It plays a role in various stages of development and morphogenesis, as well as in a variety of biological processes. Recent studies reveal the molecular mechanisms of FGF-4 gene regulation in mammalian cells, which is involved in the developmental process. Furthermore, FGF-4 also acts on the regulation of proliferation and differentiation in embryonic stem cells and tissue stem cells. In this review, we focus on the diverse biological functions of FGF-4 in the developmental process and also discuss its putative roles in stem cell biology. Developmental Dynamics 238:265,276, 2009. © 2008 Wiley-Liss, Inc. [source] Id2, Id3, and Id4 proteins show dynamic changes in expression during vibrissae follicle developmentDEVELOPMENTAL DYNAMICS, Issue 6 2008Nigel L. Hammond Abstract Id proteins are involved in the transcriptional control of many fundamental biological processes, including differentiation and lineage commitment. We studied Id2, Id3, and Id4 protein expression during different stages of rat vibrissa follicle development using immunohistochemistry. Id2 was highly expressed in the cytoplasm of specialized cells in the basal epidermis and outer root sheath during early stages of follicle development. These cells were identified as Merkel cells (MCs) by means of double-immunolabeling with synaptophysin and cytokeratin-20, and persisted in neonatal follicles. Id3 immunofluorescence was characterized by membrane-associated expression in basal epithelial cells of follicles early in development. Subsequently follicle epithelial cells switched to have strong nuclear labeling, also a feature of newly forming dermal papilla cells. Id4 expression was primarily associated with innervation of the developing follicle musculature. These observations illustrate dynamic expression patterns of Id2 and Id3 proteins in developing follicles and specifically link Id2 expression to Merkel cell specification. Developmental Dynamics 237:1653,1661, 2008. © 2008 Wiley-Liss, Inc. [source] Spontaneous mutation in mice provides new insight into the genetic mechanisms that pattern the seminal vesicles and prostate glandDEVELOPMENTAL DYNAMICS, Issue 4 2003Paul C. Marker Abstract The seminal vesicles and prostate gland are anatomically adjacent male sex-accessory glands. Although they arise from different embryonic precursor structures and express distinct sets of secretory proteins, these organs share common features in their developmental biology. A key shared developmental feature is the elaboration of complex secretory epithelia with tremendous surface area from simple precursor structures with juxtaposed epithelial and mesenchymal cells. In this study, new insight into the nature of the biological processes that underlie glandular morphogenesis is achieved by analyzing the phenotypes present in mice that harbor a spontaneous mutation, seminal vesicle shape (svs), previously identified for causing altered seminal vesicle morphology in adults. An examination of seminal vesicle development in svs mice provides the first evidence that the concurrent processes of epithelial branching and epithelial infolding are distinct processes under separate genetic control. It also provides the first direct evidence that the thickness and topology of the smooth muscle layer in the seminal vesicles are determined by interaction with the glandular epithelium during the branching process. In addition, the seminal vesicle phenotype in svs mice is shown to phenocopy the morphologic form present in certain other mammals such as the guinea pig, raising the possibility that the svs mutation is the sort of variant that arises during evolution. By also including an investigation of the prostate gland, this study also identifies previously unrecognized phenotypes in svs prostates, including increased gland size and dramatically reduced levels of branching morphogenesis. Finally, this study advances the goal of identifying the svs gene by mapping the svs mutation relative to known molecular markers and testing Fgfr2 as a candidate gene. The finding that the svs mutation maps to a genomic region syntenic to a region frequently deleted in human prostate tumors, together with the prostatic phenotype present in svs mice, further raises the interesting possibility that the svs mutation will identify a candidate prostate tumor suppressor gene. Developmental Dynamics 226:643,653, 2003. © 2003 Wiley-Liss, Inc. [source] Suspended sediment transport in a small Mediterranean agricultural catchmentEARTH SURFACE PROCESSES AND LANDFORMS, Issue 7 2009Joan Estrany Abstract The aim of this study is to analyze suspended sediment transport in a Mediterranean agricultural catchment under traditional soil and water conservation practices. Field measurements were conducted in Can Revull, a small ephemeral catchment (1.03 km2) on the island of Mallorca. This study uses continuous turbidity records to analyse suspended sediment transport regimes, construct and interpret multiple regression models of total suspended sediment concentration (SSC) and of SSC related to stormflow discharge, and assess the sediment loads and yields of three hydrological years (2004,2005 to 2006,2007). An annual average SSC of 17.3 mg l,1, with a maximum of 2270 mg l,1, was recorded in the middle of the winter period when rainfall intensities are high and headwater slopes are ploughed and thus bare. Strong seasonal contrasts of baseflow dynamics associated with different degrees of dilution provide a large scatter in SSC and in the derived rating curves, reflecting that other factors control the supply of suspended sediment. Multiple regression models identify rainfall intensity as the most significant variable in sediment supply. However, under baseflow conditions, physical and biological processes generate sediment in the channel that is subsequently removed during high flow. In contrast, when baseflow is not present, rainfall intensity is the only process that supplies sediment to the channel, mostly from hillslopes. Considering the study period as average in terms of total annual rainfall and intensities, suspended sediment yields were an order of magnitude lower than those obtained in other Mediterranean catchments, a factor that can be related to the historical use of soil conservation practices. Copyright © 2009 John Wiley & Sons, Ltd. [source] Nuclear proteome analysis of undifferentiated mouse embryonic stem and germ cellsELECTROPHORESIS, Issue 11 2008Nicolas Buhr Abstract Embryonic stem cells (ESCs) and embryonic germ cells (EGCs) provide exciting models for understanding the underlying mechanisms that make a cell pluripotent. Indeed, such understanding would enable dedifferentiation and reprogrammation of any cell type from a patient needing a cell therapy treatment. Proteome analysis has emerged as an important technology for deciphering these biological processes and thereby ESC and EGC proteomes are increasingly studied. Nevertheless, their nuclear proteomes have only been poorly investigated up to now. In order to investigate signaling pathways potentially involved in pluripotency, proteomic analyses have been performed on mouse ESC and EGC nuclear proteins. Nuclei from ESCs and EGCs at undifferentiated stage were purified by subcellular fractionation. After 2-D separation, a subtractive strategy (subtracting culture environment contaminating spots) was applied and a comparison of ESC, (8.5 day post coïtum (dpc))-EGC and (11.5,dpc)-EGC specific nuclear proteomes was performed. A total of 33 ESC, 53 (8.5,dpc)-EGC, and 36 (11.5,dpc)-EGC spots were identified by MALDI-TOF-MS and/or nano-LC-MS/MS. This approach led to the identification of two isoforms (with and without N -terminal acetylation) of a known pluripotency marker, namely developmental pluripotency associated 5 (DPPA5), which has never been identified before in 2-D gel-MS studies of ESCs and EGCs. Furthermore, we demonstrated the efficiency of our subtracting strategy, in association with a nuclear subfractionation by the identification of a new protein (protein arginine N -methyltransferase 7; PRMT7) behaving as proteins involved in pluripotency. [source] Simultaneous detection of S -adenosylmethionine and S -adenosylhomocysteine in mouse and rat tissues by capillary electrophoresisELECTROPHORESIS, Issue 7-8 2003Eric O. Uthus Abstract A capillary electrophoresis method for the determination of S -adenosylmethionine (SAM) and S -adenosylhomocysteine (SAH) in rat liver and kidney and mouse liver is described. The method can also be used to determine SAM in whole blood. The method provides rapid (approximately 16 min sample to sample) resolution of both compounds in perchloric extracts of tissues. Separation was performed by using an uncoated 50 ,m ID capillary with 60 cm total length (50 cm to the detector window). Samples were separated at 22.5 kV and the separation running buffer was 200 mM glycine pH 1.8 (with HCl). The method compares favorably to HPLC methods (r,2 = 0.994 for SAM, r,2 = 0.998 for SAH) and has a mass detection limit of about 10 fmol for both SAM and SAH at a signal-to-noise ratio of 3. The method is linear over ranges of 1,100 ,M SAM and 1,250 ,M SAH. This method can be used to determine tissue concentrations of SAM and SAH, two metabolites that can provide insight into many biological processes. [source] Data Mining for Bioprocess OptimizationENGINEERING IN LIFE SCIENCES (ELECTRONIC), Issue 3 2004S. Rommel Abstract Although developed for completely different applications, the great technological potential of data analysis methods called "data mining" has increasingly been realized as a method for efficiently analyzing potentials for optimization and for troubleshooting within many application areas of process, technology. This paper presents the successful application of data mining methods for the optimization of a fermentation process, and discusses diverse characteristics of data mining for biological processes. For the optimization of biological processes a huge amount of possibly relevant process parameters exist. Those input variables can be parameters from devices as well as process control parameters. The main challenge of such optimizations is to robustly identify relevant combinations of parameters among a huge amount of process parameters. For the underlying process we found with the application of data mining methods, that the moment a special carbohydrate component is added has a strong impact on the formation of secondary components. The yield could also be increased by using 2 m3 fermentors instead of 1 m3 fermentors. [source] Factors affecting the evolution of development strategies in parasitoid wasps: the importance of functional constraints and incorporating complexityENTOMOLOGIA EXPERIMENTALIS ET APPLICATA, Issue 1 2005Jeffrey A. Harvey Abstract Parasitoid wasps have long been considered as model organisms for examining optimal resource allocation to different fitness functions, such as body size and development time. Unlike insect predators, which may need to consume many prey items to attain maturity, parasitoids generally rely on a limited amount of resources that are obtained from a single source (the host). This review discusses a range of ecophysiological constraints that affect host quality and concomitantly the evolution of development strategies in parasitoids. Two macroevolutionary differences in host usage strategies (idiobiosis, koinobiosis) are initially described. Over many years, particular attention has been paid in examining a range of quantitative host attributes such as size, age, or stage, as these affect idiobiont and koinobiont parasitoid development. Parasitoids and their hosts, however, constitute only a small part of an ecological community. Consequently, host quality may be affected by a broad range of factors that may operate over variable spatial and temporal scales. Intimate factors include aggressive competition with other parasitoids and pathogens for access to host resources, whereas less intimate factors include the effects of toxic plant compounds (allelochemicals) on parasitoid performance as mediated through primary and/or secondary hosts. It is suggested that future experiments should increase the levels of trophic complexity as these influence the evolution of life history and development strategies in parasitoids. This includes integration of a suite of direct and indirect mechanisms, including biological processes occurring in different ecological realms, such as above-ground and below-ground interactions. [source] Anthropogenic disturbance affects the structure of bacterial communitiesENVIRONMENTAL MICROBIOLOGY, Issue 3 2010Duane Ager Summary Patterns of taxa abundance distributions are the result of the combined effects of historical and biological processes and as such are central to ecology. It is accepted that a taxa abundance distribution for a given community of animals or plants following a perturbation will typically change in structure from one of high evenness to increasing dominance. Subsequently, such changes in evenness have been used as indicators of biological integrity and environmental assessment. Here, using replicated experimental treehole microcosms perturbed with different concentrations of the pollutant pentachlorophenol, we investigated whether changes in bacterial community structure would reflect the effects of anthropogenic stress in a similar manner to larger organisms. Community structure was visualized using rank,abundance plots fitted with linear regression models. The slopes of the regression models were used as a descriptive statistic of changes in evenness over time. Our findings showed that bacterial community structure reflected the impact and the recovery from an anthropogenic disturbance. In addition, the intensity of impact and the rate of recovery to pre-perturbation structure were dose-dependent. These properties of bacterial community structures may potentially provide a metric for environmental assessment and regulation. [source] Interactions between arbuscular mycorrhizal fungi and bacteria and their potential for stimulating plant growthENVIRONMENTAL MICROBIOLOGY, Issue 1 2006Veronica Artursson Summary Arbuscular mycorrhizal (AM) fungi and bacteria can interact synergistically to stimulate plant growth through a range of mechanisms that include improved nutrient acquisition and inhibition of fungal plant pathogens. These interactions may be of crucial importance within sustainable, low-input agricultural cropping systems that rely on biological processes rather than agrochemicals to maintain soil fertility and plant health. Although there are many studies concerning interactions between AM fungi and bacteria, the underlying mechanisms behind these associations are in general not very well understood, and their functional properties still require further experimental confirmation. Future mycorrhizal research should therefore strive towards an improved understanding of the functional mechanisms behind such microbial interactions, so that optimized combinations of microorganisms can be applied as effective inoculants within sustainable crop production systems. In this context, the present article seeks to review and discuss the current knowledge concerning interactions between AM fungi and plant growth-promoting rhizobacteria, the physical interactions between AM fungi and bacteria, enhancement of phosphorus and nitrogen bioavailability through such interactions, and finally the associations between AM fungi and their bacterial endosymbionts. Overall, this review summarizes what is known to date within the present field, and attempts to identify promising lines of future research. [source] Ultrasonic treatment of waste activated sludgeENVIRONMENTAL PROGRESS & SUSTAINABLE ENERGY, Issue 2 2006Raf Dewil Abstract Activated sludge processes are key technologies to treat wastewater. These biological processes produce huge amounts of waste activated sludge (WAS), now commonly called biosolids. Mechanical, thermal, and/or chemical WAS conditioning techniques have been proposed to reduce the sludge burden. The ultrasonic treatment of WAS is quite novel. The present paper reports on extensive investigations using an ultrasonic treatment of WAS, to study its potential to meet one or all of four objectives: (1) reduce WAS quantities; (2) achieve a better dewaterability; (3) provoke a release of soluble chemical oxygen demand (COD) from the biosolids, preferably transformed into biodegradable organics; and (4) possibly destroy the filamentous microorganisms responsible for sludge bulking. Although meeting these objectives would help to solve the problems cited, the energy consumption could be a considerable drawback: the paper will thus assess whether all or some objectives are met, and at what operational cost. A literature survey defines the occurring phenomena (cavitation) and the important operation parameters [such as frequency, duration, specific energy input (SE)]. The experiments are carried out in a batch reactor of volume up to 2.3 L. The ultrasonic equipment consisted of a generator, a converter, and a sonotrode, supplied by Alpha Ultrasonics under the brand name of Telsonic. Three different kinds of sludge were tested, with different concentrations of dry solids (DS) between approximately 3.5 and 14 g DS/L WAS. Ultrasonic energy was introduced in a continuous manner (against possible pulsed operation). The major operational parameters studied include duration of the ultrasonic treatment and specific energy input. The applied frequency was set at 20 kHz. The release of COD from the WAS phase into the filtrate phase is a function of the specific energy input with yields of nearly 30% achievable at SE values of 30,000 kJ/kg DS. A major fraction of the COD is transformed into biodegradable organics (BOD). The reduction in DS fraction of the sludge is proportional to the COD release rates. Although the DS content is reduced, the dewaterability of the sludge is not improved. This reflects itself in increased filtration times during vacuum filtration and in increased values of the capillary suction time (CST). This more difficult dewaterability is the result of considerably reduced floc sizes, offering an extended surface area: more surface water is bound (CST increases) and the filterability decreases as a result of clogging of the cake. To reach the same dryness as for the untreated cake, the required dosage of polyelectrolyte is nearly doubled when the SE of the ultrasound treatment is increased from 7500 to 20,000 kJ/kg DS. The ultrasonic reduction of filamentous WAS organisms is not conclusive and very little effect is seen at low intensities and short treatment durations. Microscopic analysis of the WAS identified the dominant presence of Actynomyces. The release of soluble COD and BOD certainly merit further research. © 2006 American Institute of Chemical Engineers Environ Prog, 2006 [source] | |||||||||||||||||||||||||||||||||||||||||||||||||