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Morbidity and mortality from ischaemic heart disease (IHD) and heart failure (HF) remain significant in Europe and are increasing worldwide. Patients with IHD or HF might benefit from novel therapeutic strategies, such as cell-based therapies. We recently discussed the therapeutic potential of cell-based therapies and provided recommendations on how to improve the therapeutic translation of these novel strategies for effective cardiac regeneration and repair. Despite major advances in optimizing these strategies with respect to cell source and delivery method, the clinical outcome of cell-based therapy remains unsatisfactory. Major obstacles are the low engraftment and survival rate of transplanted cells in the harmful microenvironment of the host tissue, and the paucity or even lack of endogenous cells with repair capacity. Therefore, new ways of delivering cells and their derivatives are required in order to empower cell-based cardiac repair and regeneration in patients with IHD or HF. Strategies using tissue engineering (TE) combine cells with matrix materials to enhance cell retention or cell delivery in the transplanted area, and have recently received much attention for this purpose. Here, we summarize knowledge on novel approaches emerging from the TE scenario. In particular, we will discuss how combinations of cell/bio-materials (e.g. hydrogels, cell sheets, prefabricated matrices, microspheres, and injectable matrices) combinations might enhance cell retention or cell delivery in the transplantation areas, thereby increase the success rate of cell therapies for IHD and HF. We will not focus on the use of classical engineering approaches, employing fully synthetic materials, because of their unsatisfactory material properties which render them not clinically applicable. The overall aim of this Position Paper from the ESC Working Group Cellular Biology of the Heart is to provide recommendations on how to proceed in research with these novel TE strategies combined with cell-based therapies to boost cardiac repair in the clinical settings of IHD and HF. [ABSTRACT FROM AUTHOR]

The aim of this study was to develop a PCR-based rapid method to detect Bacillus cereus group cells from paper and cardboard. Primers targeting the 16S rDNA and real-time PCR with SYBR green I detection were used in order to be able to also quantify the target. Both autoclaved cardboard samples spiked with B. cereus vegetative cells or spores and naturally contaminated paper and cardboard samples were studied. Results were compared with culturing verified by commercial (API) tests. Several different methods were tested for DNA isolation from the paper and cardboard samples. Two commercial kits intended for soils, the UltraClean soil DNA kit and the FastDNA spin kit for soil, gave the most reproducible results. In spiked samples, the average yield was 50% of added vegetative cells, but spore yield was only about 10%. PCR results from adding vegetative cells correlated with added colony-forming unit (cfu) values (r=0.93, P <0.001) in the range 100–10,000 cfu g-1. Three out of nine studied paper and cardboard samples contained B. cereus group bacteria, based both on culturing and real-time PCR. The numbers were 102–103 bacteria g-1; and PCR gave somewhat higher results than culturing. Thus, real-time PCR can be used as a rapid semi-quantitative method to screen paper and cardboard samples for contamination with B. cereus group bacteria. [ABSTRACT FROM AUTHOR]

Conventional methods for purifying PCR-grade fungal genomic DNA typically require cell disruption (either physical or enzymatic) coupled with laborious organic extraction and precipitation stages, or expensive column-based technologies. Here we present an easy and extremely rapid method of preparing yeast and mould genomic DNAs from living cultures using Whatman FTA filter matrix technology. Aqueous suspensions of yeast cells or hyphal fragments and conidia (in the case of moulds) are applied directly (or after freeze-thawing) to dry FTA filters. Inoculated filters are then subjected to brief microwave treatment, to dry the filters and inactivate the organisms. Filter punches are removed, washed rapidly, dried and placed directly into PCR reactions. We show that this procedure inactivated all of the 38 yeast and 75 mould species tested, and generated PCR-grade DNA preparations in around 15 minutes. A total of 218 out of 226 fungal isolates tested liberated amplifiable DNA after application to FTA filters. Detection limits with yeast cultures were approximately 10 colony-forming units per punch. Moreover, we demonstrate that filter punches can be recovered after PCR, washed and used in fresh PCR reactions without detectable cross-contamination. Whatman FTA technology thus represents a cheap, ultra-rapid method of fungal genomic DNA preparation, and also potentially represents a powerful fungal DNA archiving and storage system. [ABSTRACT FROM AUTHOR]

The article presents abstracts from papers related to animal behavior that were published in the February 2005 issue of the "Journal of Animal Science." The paper "Effects of Dried Distillers Grains on Heifer Consumption of Low or High Quality Forage," was presented by S. Morik, T. Klopfenstein and D. Adams. The paper "Developmental Potential of Porcine Nuclear Transfer Embryos Using Non-Differentiated Donor Cells," by K. Lee, investigated the developmental potential of early embryos reconstructed using olfactory unsheathing cells (OECs). OECs are located in the olfactory bulb and thought to have remarkable developmental plasticity. The paper "Endocrine and Follicular Dynamics in Beef Heifers Divergently Selected for Peripheral IGF-1 Concentrations," by D. Dauch, K. Fike, M. Mussard, G. Bridges, C. Gasser, D. Grum, M. Davis, and M. Day, compared estradiol concentrations and ovarian follicular dynamics prior to ovulation and subsequent luteal progesterone concentrations between genetic lines of beef heifers divergently selected for peripheral concentrations of insulin-like growth factor-1.

Motivation: Quantitative models are increasingly used in systems biology. Usually, these quantitative models involve many molecular species and their associated reactions. When simulating a tissue with thousands of cells, using these large models becomes computationally and time limiting. Results: In this paper, we propose to construct abstractions using information theory notions. Entropy is used to discretize the state space and mutual information is used to select a subset of all original variables and their mutual dependencies. We apply our method to an hybrid model of TRAIL-induced apoptosis in HeLa cell. Our abstraction, represented as a Dynamic Bayesian Network (DBN), reduces the number of variables from 92 to 10, and accelerates numerical simulation by an order of magnitude, yet preserving essential features of cell death time distributions. [ABSTRACT FROM AUTHOR]

The article discusses a research paper in which the researchers found bactericidal activity of nukacin ISK-1 against Micrococcus luteus DSM 1790 and Staphylococcus simulans 22 which shows decrease in cell viability, cell lysis, and dissipation of the membrane potential. Topics discussed include nukacin ISK-1 against Bacillus subtilis JCM 1465T, leakage of small molecules, and daptomycin, a lipopeptide antibiotic.

Ferrous ion biooxidation is a process with many promising industrial applications: mainly regeneration of ferric ion as an oxidizing reagent in bioleaching processes and depuration of acid mine drainage. The flooded packed-bed bioreactor (FPB) is the design that leads to the highest biooxidation rate. In this bioreactor, biomass is immobilized in a biofilm that consists of an inorganic matrix, formed by precipitated ferric compounds, in the pores of which cells are attached. This biofilm covers the surface of particles (siliceous stone) that form the bed. The chemical stability of this inorganic matrix defines the widest possible pH range in FPBs. At pH below 1, ferric matrix is dissolved and cells are washed out. At pH higher than 2, ferric ion precipitates massively, greatly hindering mass transfer to cells. Thus, among other parameters, pH is recognised as a key factor for operational control in FPBs. This paper aims to explain the effect of pH on FPB operation, with an emphasis on microbial population behaviour. FPBs seeded with mixed inocula were assayed in the pH range from 2.3 to 0.8 and the microbial population was characterised. The microbial consortium in the bioreactor is modified by pH; at pH above 1.3 Acidithiobacillus ferrooxidans is the dominant microorganism, whereas at pH below 1.3 Leptospirillum ferrooxidans dominates. Inoculum can be adapted to acidity during continuous operation by progressively decreasing the pH of the inlet solution. Thus, in the pH range from 2.3 to 1, the biotic factor does not compromise the bioreactor performance. [ABSTRACT FROM AUTHOR]

Yeast flocculation has been found to be important in many biotechnological processes. It has been suggested that flocculation is promoted by decreasing electrostatic repulsion between cells. In this study, we used an unconventional rapid technique-permittivity test-for determination of the flocculation properties and surface charge values of three industrial yeast strains with well-known flocculation characteristics: Saccharomyces cerevisiae NCYC 1017 (brewery, ale), S. pastorianus NCYC 680 (brewery, lager), and Debaryomyces occidentalis LOCK 0251 (unconventional amylolytic yeast). The measurements of permittivity were compared with the results from two classical methods for determination of surface charge: Alcian blue retention and Sephadex DEAE attachment. The permittivity values for particular strains correlated directly with the results of Alcian blue retention ( r = 0.9). The results also confirmed a strong negative relationship between the capacitance of yeast suspensions and their flocculation abilities. The highest permittivity was noted for the ale strain NCYC 1017, with weak flocculation abilities, and the lowest for the flocculating lager yeast NCYC 680. This paper is the first to describe the possibility of using a rapid permittivity test to evaluate the surface charge of yeast cells and their flocculation abilities. This method is of practical value in various biotechnological industries where flocculation is applied as a major method of cell separation. [ABSTRACT FROM AUTHOR]

In this paper, we analyze the pattern of distribution of three populations of picoplanktonic autotrophs measured using flow cytometry. Prochlorococcus sp., Synechococcus sp. and eukaryotic picoplankton were investigated at 58 stations to the south of the Iberian Peninsula including the northeastern Gulf of Cádiz, Strait of Gibraltar and northwestern Alborán Sea, during July 1995. There were important differences in the oceanographic conditions in these regions, with warmer, low-nutrient and low-chlorophyll waters in the Atlantic sector and colder, high-nutrient and high-chlorophyll waters in the Alborán sector in which upwelling occurred. The biomass concentration of picoplanktonic cells was two times higher in the Atlantic area than in the richer Alborán Sea waters. The average integrated abundance of picophytoplankton was negatively correlated with chlorophyll a concentration as well as with inorganic nitrogen availability. Prochlorococcus and Synechococcus were the most abundant groups, and they showed a complementarity in their spatial distribution, with a shallower and more coastal distribution of Synechococcus and the presence of Prochlorococcus mainly at offshore stations and at deeper depths. The ratio of autotrophic picoplankton/total autotrophic biomass showed significant differences on both sides of the Strait, with much higher values in the Gulf of Cádiz sector. [ABSTRACT FROM PUBLISHER]

The comet assay is a technique used to quantify DNA damage and repair at a cellular level. In the assay, cells are embedded in agarose and the cellular content is stripped away leaving only the DNA trapped in an agarose cavity which can then be electrophoresed. The damaged DNA can enter the agarose and migrate while the undamaged DNA cannot and is retained. DNA damage is measured as the proportion of the migratory ‘tail’ DNA compared to the total DNA in the cell. The fundamental basis of these arbitrary values is obtained in the comet acquisition phase using fluorescence microscopy with a stoichiometric stain in tandem with image analysis software. Current methods deployed in such an acquisition are expected to be both objectively and randomly obtained. In this paper we examine the ‘randomness’ of the acquisition phase and suggest an alternative method that offers both objective and unbiased comet selection. In order to achieve this, we have adopted a survey sampling approach widely used in stereology, which offers a method of systematic random sampling (SRS). This is desirable as it offers an impartial and reproducible method of comet analysis that can be used both manually or automated. By making use of an unbiased sampling frame and using microscope verniers, we are able to increase the precision of estimates of DNA damage. Results obtained from a multiple-user pooled variation experiment showed that the SRS technique attained a lower variability than that of the traditional approach. The analysis of a single user with repetition experiment showed greater individual variances while not being detrimental to overall averages. This would suggest that the SRS method offers a better reflection of DNA damage for a given slide and also offers better user reproducibility. [ABSTRACT FROM PUBLISHER]

The Saccharomyces cerevisiae BDF1 gene encodes a bromodomain-containing transcription factor. We previously reported that deletion of Bdf1p in yeast cells resulted in increased sensitivity to NaCl stress. In this paper, we show that the function of Bdf1p in salt tolerance is not directly linked with the Ena1p-mediated Na+ extrusion system, and a number of other well-characterized stress-response pathways. Interestingly, however, our data demonstrate that, under the NaCl stress, the absence of Bdf1p leads to mitochondrial dysfunction, including decreasing of mitochondrial membrane potential (ΔΨ) and accumulation of reactive oxygen species, and chromatin fragmentation and condensation. These results indicate that the bromodomain-containing protein, Bdf1p, is involved in the regulation of apoptosis in yeast cells. [ABSTRACT FROM AUTHOR]

Chlamydia has long been studied as an intracellular pathogen causing widespread diseases. In the last three decades, the field of apoptosis has rapidly emerged, and as a consequence, research on infectious diseases in general and on Chlamydia–host interaction in particular shifted to apoptosis modulation. Ten years ago, the first paper describing the drastic inhibition of apoptosis in Chlamydia-infected cells was published. In a reversal of roles, here was a pathogen that was strongly protecting cells in an organism against destruction by the organism's immune system. Since then, numerous studies have described apoptosis inhibition by Chlamydia and the mechanisms involved, but still there is a lack of general consensus on the subject. With a section of studies even reporting the induction of cell death by Chlamydia and not its inhibition, the field became even more diverse and complicated. In this review, an attempt is made to discuss the recent findings on apoptosis modulation by chlamydial species. [ABSTRACT FROM AUTHOR]

Recent technical and conceptual advances in the biological sciences opened the possibility of the construction of newly designed cells. In this paper we review the state of the art of cell engineering in the context of genome research, paying particular attention to what we can learn on naturally reduced genomes from either symbiotic or free living bacteria. Different minimal hypothetically viable cells can be defined on the basis of several computational and experimental approaches. Projects aiming at simplifying living cells converge with efforts to make synthetic genomes for minimal cells. The panorama of this particular view of synthetic biology lead us to consider the use of defined minimal cells to be applied in biomedical, bioremediation, or bioenergy application by taking advantage of existing naturally minimized cells. [ABSTRACT FROM AUTHOR]

Aims: To investigate the effects of anthrax lethal toxin (LeTx) on human primary keratinocytes. Methods and Results: We show here that human primary keratinocytes are resistant to LeTx-triggered cytotoxicity. All but one of the MEKs (mitogen-activated protein kinase kinases) are cleaved within 3 h, and the cleavage of MEKs in keratinocytes leads to their subsequent proteasome-mediated degradation at different rates. Moreover, LeTx reduced the concentration of several cytokines except RANTES in culture. Conclusions: Our results indicate that primary keratinocytes are resistant to LeTx cytotoxicity, and MEK cleavage does not correlate with LeTx cytotoxicity. Although LeTx is considered as an anti-inflammatory agent, it upregulates RANTES. Significance and Impact of the Study: According to a current view, the action of LeTx results in downregulation of the inflammatory response, as evidenced by diminished expression of several inflammatory biomarkers. Paradoxically, LeTx has been reported to attract neutrophils to cutaneous infection sites. This paper, which shows that RANTES, a chemoattractant for immune cells, is upregulated after exposure of keratinocytes to LeTx, although a number of other markers of the inflammatory response are downregulated. Our results might explain why the exposure of keratinocytes to LeTx results in the recruitment of neutrophils to cutaneous infection sites, while the expression of several inflammatory biomarkers is diminished. [ABSTRACT FROM AUTHOR]

Chemotaxis is the process by which cells behave in a way that follows the chemical gradient. Applications to bacteria growth, tissue inflammation and vascular tumours provide a focus on optimization strategies. Experiments can characterize the form of possible chemotactic sensitivities. This paper addresses the recovery of the chemotactic sensitivity from these experiments while allowing for non-linear dependence of the parameter on the state variables. The existence of solutions to the forward problem is analysed. The identification of a chemotactic parameter is determined by inverse problem techniques. Tikhonov regularization is investigated and appropriate convergence results are obtained. Numerical results of concentration-dependent chemotactic terms are explored. [ABSTRACT FROM AUTHOR]

Aims: The aim of this paper was to develop a loop-mediated isothermal amplification (LAMP) method for rapid, sensitive and inexpensive detection of Singapore grouper iridovirus (SGIV) in grouper (GP), Epinephelus sp. Methods and Results: A set of six specific primers was designed by targeting the SGIV ORF-014L. With Bst DNA polymerase large fragment, the target DNA can be amplified as early as 20 min at 65°C in a simple water bath. The detection limit is about 0·02 fg (equivalent to 6·3 copies) of plasmid ORF-014L. LAMP products could be judged with three different methods. There were no cross-reactions with seven other aquatic animal viruses indicating high specificity of the LAMP. The LAMP method was applied to detect SGIV in virus-infected GP cells and GP tissues effectively. Conclusions: The LAMP described in this study is a cheap, sensitive, specific and rapid protocol for the detection of SGIV in cells and in GP tissues. Significance and Impact of the Study: The developed LAMP method can be simply applied both in field condition and in laboratory operation for specific detection of SGIV infection. [ABSTRACT FROM AUTHOR]

Morphogenesis in streptomycetes is characterized by the formation of aerial hyphae that emerge from the substrate mycelium. Despite many years of study, a detailed picture of the events that occur during the transition from substrate to aerial mycelium has yet to be defined. In this paper, it was shown that a specific cell death event takes place during early growth of the substrate mycelium in Streptomyces coelicolor and Streptomyces lividans. Subsequently, a second mycelium starts to develop from the remaining viable segments of these substrate hyphae in the form of islands, which progressively cover the plate surface. Interestingly, the genes coding for the chaplin and rodlin proteins, which are involved in the formation of the hydrophobic layer characteristic of aerial structures, are specifically expressed in the second mycelium islands, strongly suggesting that this second mycelium should be considered the early precursor of the mature hydrophobic aerial mycelium. [ABSTRACT FROM AUTHOR]

Size regulation is a crucial feature in many biological systems, with misregulation leading to dysplasia or hyperplasia. The recent discovery of counting factor (CF) in Dictyostelium discoideum will lead to a greater understanding of how the system regulates the size of a group of cells. In this paper we mathematically model the known effects of CF using two different models: a cellular automata model and a discrete continuum hybrid model. With the use of these models we are able to understand how modulation of adhesion and motile forces by CF can facilitate stream breakup. In addition, the modelling suggests a new possible mechanism for stream breakup involving the frequency of cell reorientation. [ABSTRACT FROM AUTHOR]

In this paper we report that stimulation of mAChRs in PC12D cells activates Ca2+ channels that are regulated independently of intracellular Ca2+ stores. In nominally Ca2+-free medium, exposure of PC12D cells to carbachol stimulates a robust influx of Ba2+, a Ca2+ substitute. This influx is blocked by atropine, but not by inhibitors of the nicotinic acetylcholine receptor or L-, N-, or T-type voltage-regulated Ca2+ channels. By contrast, depletion of intracellular Ca2+ stores with thapsigargin only weakly stimulates Ba2+ influx. Unlike store-operated Ca2+ channels (SOCCs), which close only after intracellular Ca2+ stores refill, channels mediating carbachol-stimulated Ba2+ influx rapidly close following the inactivation of mAChRs with atropine. Ba2+ influx is inhibited by extracellular Ca2+, by the Ca2+ channel blocker SKF-96365, and by activation of protein kinase C (PKC). Exogenous expression of antisense RNA encoding the rat canonical-transient receptor potential Ca2+ channel subtype 6 (TRPC6) or the N-terminal domain of TRPC6 blocks carbachol-stimulated Ba2+ influx in PC12D cells. Expression of TRPC6 antisense RNA or the TRPC6 N-terminal domain also blocks Ba2+ influx stimulated by 1-oleoyl-2-acetyl-sn-glycerol (OAG), a diacylglycerol analog previously shown to activate exogenously expressed TRPC6 channels. These data show that mAChRs in PC12D cells activate endogenous Ca2+ channels that are regulated independently of Ca2+ stores and require the expression of TRPC6. [ABSTRACT FROM PUBLISHER]

A previous paper demonstrated that indinavir affects the virulence of Cryptococcus neoformans , thereby rendering the fungus more susceptible to killing by natural effector cells. This study demonstrates that inoculation of immunosuppressed mice with C. neoformans previously exposed to indinavir, in comparison to untreated C. neoformans , results in: (i) a more pronounced secretion of interleukin-12 by splenic dendritic cells; (ii) reduction of CD14 and Fc γ Rs expression on splenic dendritic cells, and upregulation of CD86 and CD40 molecules; (iii) enhancement of interferon-γ and interleukin-2 production by splenic T cells and increase of their proliferation in response to fungal antigens; and (iv) survival from an otherwise lethal challenge, correlated with a drastic decrease in colony forming units from brain and liver. In conclusion, these data indicate that indinavir interaction with C. neoformans could be beneficial because of its direct influence on fungal virulence and blunting of the deleterious effects exerted by C. neoformans on host immune response. Thus, indinavir could be crucial in addressing the outcome of cryptococcosis in immunocompromised hosts. [ABSTRACT FROM AUTHOR]

This paper attempts to determine an optimal fixation protocol for stabilizing RNA during microdissection so as to obtain high-quality RNA from specific cell populations procured from esophageal carcinoma specimens, and to develop a manual microdissection that can facilitate the procurement. The special features of our protocol include one-step dehydration of tissue sections in 100% ethanol immediately after cryosectioning, a self-made T-shape plate (T plate) and “exclusion microdissection” procedure. The quality of RNA isolated from dissected cells was analyzed by neutral agarose gel electrophoresis and reverse transcription-polymerase chain reaction (RT-PCR) to detect genes of different abundance levels. One-step 100% ethanol fixation of cryosections effectively stabilized RNA integrity for agelong period of time while maintaining histological morphology comparable to that using the conventional procedure, indicating that it is a valid protocol for preservation of RNA in microdissected samples. In conjunction with the application of the T plate and ‘exclusion microdissection’ procedure, which efficiently simplifies manual microdissection procedure, allowing maximal procurement of target cells from complex primary tissues, full use of every single specimen for maximal procurement of target cells from the sections was allowed. The RNA isolated from 5 different stage-specific cell populations of an esophageal carcinoma specimen was of high quality and sufficient in quantity for various downstream molecular analyses. Our method is suitable for a wide spectrum of expression analysis in diverse clinical settings. [ABSTRACT FROM AUTHOR]

Different studies dealing with the start of progesterone supplementation in assisted reproduction treatment cycles have shown that the problem apparently is the correct timing. We therefore would like to discuss the data on: (i) the start of progesterone replacement in oocyte donation programmes; (ii) the start of progesterone replacement in frozenthawed hormone-supplemented cycles; (ii) the problem of too early a rise of progesterone in fresh IVF cycles as a model of too early an administration of progesterone; and (iv) the benefit of high progesterone levels on the day of embryo transfer in fresh IVF cycles. From the data reviewed in this paper it seems to be appropriate to start progesterone administration before transfer in oocyte donation programmes as well as transfer of cryopreserved/thawed cells as soon as the endometrium is developed sufficiently (=8?mm, trilaminar pattern), and to perform the embryo transfer not before day 34 of progesterone treatment, i.e. embryo development on day 23. Studies dealing with the influence of too early a rise of progesterone in fresh IVF cycles have shown different results. In fact high progesterone levels seem to reflect a high response but not a lower probability of conception. Furthermore, high progesterone levels on the day of embryo transfer in fresh IVF cycles could lower myometrial contractility and therefore increase implantation rates. Since the experience from oocyte donation programes shows the benefit of a longer preparation time using progesterone, and high progesterone levels seem to have a benefit during embryo transfer, this would suggest extending progesterone administration before transfer. However, we have to find the optimal individual transfer protocol after mock cycles, for example with pinopode detection or other methods applicable in routine IVF programmes. We need more studies to be sure whether reproductive outcome after transfer of cryopreservedthawed cells in estrogen/progesterone supplement cycles is influenced by the duration of progesterone pretreatment. If this is so, we must look for practicable methods to modify the protocols according to the individual patient, the embryonic developmental stage during transfer and other variables. [ABSTRACT FROM AUTHOR]

s. guobin, x. jianmin, g. chen, l. huizhou and c. jiayong. 2004.To immobilizePseudomonas delafieldiiR-8 cells in magnetic polyvinyl alcohol (PVA) beads for biodesulfurization.Magnetic PVA beads were prepared by a freezing–thawing technique under liquid nitrogen. The beads have distinct super-paramagnetic properties and their saturation magnetization is 8·02 emu g−1. The desulfurization rate of the immobilized cells could reach 40·2 mmol kg−1 h−1. Desulfurization patterns of dibenzothiophene in model oil with the immobilized and free cells were represented by the Michaelis–Menten equation. The Michaelis constant for both immobilized and free cells was 1·3 mmol l−1.The cells immobilized in magnetic PVA beads could be stably stored and be repeatedly used over 12 times for biodesulfurization. The immobilized cells could be easily separated by magnetic field.Magnetic PVA beads are easy to prepare. The immobilization process in the paper is to increase the efficiency of cells and to decrease the cost of operations. [ABSTRACT FROM AUTHOR]

Messenger RNA (mRNA) localisation is a widespread mechanism within eukaryotic cells that provides local synthesis of proteins close to where they function. In general, this mRNA targeting involves the cytoskeleton and signals within the 3 untranslated region (3 UTR) of the transcript. In this paper, the authors review what is known of the nature of the localisation signals and the proteins that interact with them in animal cells. Specific examples are selected to illustrate the emerging pattern of how these signals are formed by the mRNA and the key RNA-binding proteins. The signals are usually restricted to relatively short regions of the 3 UTR, but their precise nature varies, with both sequence and structure playing key roles. Repeat motifs and functional redundancy also appear as common features of these signals. The trans-acting factors involved in localisation include proteins having other roles in nuclear events, proteins that shuttle between the nucleus and the cytoplasm and translational factors. In addition, there is evidence of homology among these proteins and the mechanisms of localisation across eukaryotic species. [ABSTRACT FROM AUTHOR]

In this paper we expand on two mathematical models for investigating the role of three distinct repression mechanisms within the so-called quorum sensing (QS) cell-signalling process of bacterial colonies growing (1) in liquid cultures and (2) in biofilms. The repression mechanisms studied are (I) reduction of cell signalling molecule (QSM) production by a constitutively produced agent degrading the messenger RNA of a crucial enzyme (QSE), (ii) lower QSM production rate due to a negative feedback process and (iii) loss of QSMs by binding directly to a constitutively produced agent; the first two mechanisms are known to be employed by the pathogenic bacterium Pseudomonas aeruginosa and the last is relevant to the plant pathogen Agrobacterium tumefaciens. The modelling approach assumes that the bacterial colony consists of two sub-populations, namely down- and up-regulated cells, that differ in the rates at which they produce QSMs, while QSM concentration governs the switching between subpopulations. Parameter estimates are obtained by curve-fitting experimental data (involving P. aeruginosa growth in liquid culture, obtained as part of this study) to solutions of model (1). Asymptotic analysis of the model (1) shows that mechanism (I) is necessary, but not sufficient, to predict the observed saturation of QSM levels in an exponentially growing colony; either mechanism (ii) or (iii) also needs to be incorporated to obtain saturation. Consequently, only a fraction of the population will become up-regulated. Furthermore, only mechanisms (I) and (iii) affect the main timescales for upregulation. Repression was found to play a less significant role in a biofilms, but mechanisms (I)-(iii) were nevertheless found to reduce the ultimate up-regulated cell fraction and mechanisms (I) and (iii) to increase the timescale for substantial up-regulation and to decrease the wave speed of an expanding front of QS activity. [ABSTRACT FROM AUTHOR]

Embryos, seeds and fruits of four species of Capparis L. (Capparaceae) from Argentina are described in this paper: C. flexuosa (L.) L. sensu lato, C. retusa Griseb., C. speciosa Griseb. and C. tweediana Eichl. Chlorophyllous embryos are found in C. flexuosa and C. retusa, species with thin seed coats, dehiscent siliques, and somewhat fleshy red endocarps. Nonchlorophyllous embryos are found in the berry-fruited C. speciosa and C. tweediana, the former with leathery indehiscent fruit wall, the latter with thin-walled dehiscent berries with massive fleshy pulp. The pulp is permeated by seed coat hairs in C. tweediana. The embryos of C. flexuosa, C. retusa and C. tweediana belong to the ‘Axile Division, Foliate Subdivision, and Folded Type’ of the classification devised by A. C. Martin in 1946. Some features of the embryo of C. speciosa (which are not considered in Martin's classification), support a new subdivision (Massive) and a new morphological type (Unequal cotyledons), characterized by profound anisocotyly, globose shape of the major cotyledon, presence of suberized cells and an undeveloped radicle. Anatomical studies of embryos and seedlings confirm the anisocotyly. © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society, 2004, 145, 209−218. [ABSTRACT FROM AUTHOR]

The mapping of protein-protein interactions is key to understanding biological processes. Many technologies have been reported to map interactions and these have been systematically applied in yeast. To date, the number of reported yeast protein interactions that have been truly validated by at least one other approach is low. The mapping of human protein interaction networks is even more complicated. Thus, it is unreasonable to try to map the human interactome; instead, interaction mapping in human cell lines should be focused along the lines of diseases or changes that can be associated with specific cells. In this paper, an approach for combining different 'omics' technologies to achieve efficient mapping and validation of protein interactions in human cell lines is presented. [ABSTRACT FROM AUTHOR]

Genome-scale molecular networks, including protein interaction and gene regulatory networks, have taken centre stage in the investigation of the burgeoning disciplines of systems biology and biocomplexity. What do networks tell us? Some see in networks simply the comprehensive, detailed description of all cellular pathways, others seek in networks simple, higher-order qualities that emerge from the collective action of the individual pathways. This paper discusses networks from an encompassing category of thinking that will hopefully help readers to bridge the gap between these polarised viewpoints. Systems biology so far has emphasised the characterisation of large pathway maps. Now one has to ask: where is the actual biology in 'systems biology'? As structures midway between genome and phenome, and by serving as an 'extended genotype' or an 'elementary phenotype', molecular networks open a new window to the study of evolution and gene function in complex living systems. For the study of evolution, features in network topology offer a novel starting point for addressing the old debate on the relative contributions of natural selection versus intrinsic constraints to a particular trait. To study the function of genes, it is necessary not only to see them in the context of gene networks, but also to reach beyond describing network topology and to embrace the global dynamics of networks that will reveal higher-order, collective behaviour of the interacting genes. This will pave the way to understanding how the complexity of genome-wide molecular networks collapses to produce a robust whole-cell behaviour that manifests as tightly-regulated switching between distinct cell fates--the basis for multicellular life. [ABSTRACT FROM AUTHOR]

The use of cell-free expression systems as an alternative to cell-based methods for protein production is greatly facilitating studies of protein functions. Recent improvements to cell-free systems, and the development of cell-free protein display and microarray technologies, have led to cell-free protein synthesis becoming a powerful tool for large-scale analysis of proteins. This paper reviews the most commonly used cell-free systems and their applications in proteomics. [ABSTRACT FROM AUTHOR]

The molecular networks regulating basic physiological processes in a cell can be converted into mathematical equations (eg differential equations) and solved by a computer. The division cycle of eukaryotic cells is an important example of such a control system, and fission yeast is an excellent test organism for the computational modelling approach. The mathematical model is tested by simulating wild-type cells and many known cell cycle mutants. This paper describes an example where this approach is useful in understanding multiple rounds of DNA synthesis (endoreplication) in fission yeast cells that lack the main (B-type) mitotic cyclin, Cdc13. It is proposed that the key physiological variable driving progression through the cell cycle during balanced growth and division is the mass/DNA ratio, rather than the mass/nucleus ratio. [ABSTRACT FROM AUTHOR]

All living cells accumulate high concentrations of K+ in order to keep themselves alive. To this end they have developed a great diversity of transporters. The internal level of K+ is the result of the net balance between the activities of the K+ influx and the K+ efflux transporters. Potassium fluxes have been extensively studied and characterized in Saccharomyces cerevisiae. However, this is not the case in the fission yeast and, in addition, the information available indicates that both yeasts present substantial and interesting differences. In this paper we have reviewed and summarized the information on K+ fluxes in Schizosaccharomyces pombe. We have included some unpublished results recently obtained in our laboratory and, in particular, we have highlighted the significant differences found between the well-known yeast S. cerevisiae and the fission yeast Sch. pombe. [Copyright &y& Elsevier]

Background: Peritoneal mesothelial cells have a remarkable capacity to respond to peritoneal insults. They generate an intense biological response and play an important role in the formation of adhesions. This review describes these activities and comments on their relationship to surgical drainage, peritoneal lavage and laparostomy in the management of patients with peritonitis. Methods and results: Material was identified from previous review articles, references cited in original papers and a Medline search of the literature. The peritoneal mesothelium adapts to peritonitis by facilitating the clearance of contaminated fluid from the peritoneal cavity and inducing the formation of fibrinous adhesions that support the localization of contaminants. In addition, the fluid within the peritoneal cavity is a battleground in which effector mechanisms generated with the involvement of peritoneal mesothelial cells meet the contaminants. The result is a complex mix of cascading processes that have evolved to protect life in the absence of surgery. Conclusion: Future advances in the management of patients with severe peritonitis may depend upon molecular strategies that modify the activity of peritoneal mesothelial cells. [ABSTRACT FROM AUTHOR]

This paper describes a method for imaging the endogenous release of glutamate from cerebral neurons. This method is based on the reactions of glutamate oxidase and peroxidase, and on the detection of hydrogen peroxide by a fluorescent substrate of peroxidase. Glutamate has been sensitively measured in vitro in the range of 20 nM to 1 µM. We used two types of Ca2+ channel inhibitors, MK-801 and ω-Conotoxin GVIA, which act to suppress Ca2+ transport at postsynaptic and presynaptic neurons, respectively. MK-801 did not inhibit the increase in glutamate release after KCl stimulation, while there was no increase in glutamate release after KCl stimulation when ω-Conotoxin GVIA was used, probably due to the inhibition of voltage-activated Ca2+ channels in the presynapse. Glutamate release and Ca2+ flow in the synaptic regions were imaged using a laser confocal fluorescence microscope. KCl-evoked glutamate release was localized around cell bodies linked to axon terminals. This procedure allows imaging that can be sensitively detected by the fluorometric enzymatic assay of endogenous glutamate release in synapses. [ABSTRACT FROM PUBLISHER]

This paper describes how biological function can be represented in terms of molecular activities and processes. It presents several key features of a data model that is based on a conceptual description of the network of interactions between molecular entities within the cell and between cells. This model is implemented in the aMAZE database that presently deals with information on metabolic pathways, gene regulation, sub- or supracellular locations, and transport. It is shown that this model constitutes a useful generalisation of data representations currently implemented in metabolic pathway databases, and that it can furthermore include multiple schemes for categorising and classifying molecular entities, activities, processes and localisations. In particular, we highlight the flexibility offered by our system in representing multiple molecular activities and their control, in viewing biological function at different levels of resolution and in updating this view as our knowledge evolves. [ABSTRACT FROM AUTHOR]

This paper demonstrates that CD40 is expressed on rheumatoid synovial pannus and primary fibroblast cell lines established from rheumatoid and osteoarthritic synovium as well as normal skin. Among various tested cytokines, interferon-gamma (IFN-γ) and lo a lower extent, tumour necrosis factor-alpha (TNE-α) were found to upregulate CD40 expression on fibroblasts. Synovial and skin fibroblasts cultured over CD40 Ligand transfected L cells (L-CD40L) demonstrate a CD40 specific increase of DNA synthesis as measured by tritiated thymidine incorporation. Cell-cycle analysis and enumeration of viable cells further show that CD40 induced fibroblast proliferation. Costimulation with L-CD40 L and IFN-γ, resulted in maximal proliferation. Engagement of fibroblasts CD40 increased the IL-l-induced production of granulocyte macrophage-colony stimulating factor and macrophage inflammatory protein-Iα MIP-lα, CD40L activated fibroblasts showed decreased levels of CD40, but only marginal alterations of other cell-surface antigens. Taken together, the present results indicate that fibroblasts express functional CD40 and suggest a possible role of CD40L expressing cells, such as activated T cells and mast cells, in the development of synovium hyperplasia. [ABSTRACT FROM AUTHOR]

The arihritogenic properties of adjuvant oil upon percutaneous administration in DA rats was investigated. Groups of rats were administered single or repeated percutaneous applications of Freund's incomplete adjuvant (FIA) or olive oil on shaved skin with or without prior abrasion of the skin. Control rats were shaved and abrased only. A transient arthritis developed in 8/16 animals after repeated applications of FIA on abrased skin. The incidence of arthritis increased to 7/8 animals when FIA was repeatedly administered via filter paper on abrased skin and covered with a bandage. Histological examination of the arthritic joints showed proliferation of the synovial lining layer, infiltration of mononuclear cells and polymorphonuclear cells in the subsynovial tissue. Some bone and cartilage destruction was also seen. Repeated treatment with olive oil on abrased skin induced joint swelling in 3/15 animals, which did not, however, correspond to any microscopically observable signs of inflammation. Also, a single application of FIA on abrased skin or repeated applications of FIA without abrasion induced arthritis, although with low penetration, whereas control animals had no clinical signs of joint involvement. These findings demonstrate that percutaneous administration of adjuvant oil can cause arthritis in genetically susceptible animals. [ABSTRACT FROM AUTHOR]

The article presents various research papers related to inhibitory proteins and non-lethal effects, published in an earlier issue of the journal "Clinical & Experimental Immunology". One of the abstracts talk about role of inhibitory membrane proteins in the complement dependent killing of trophoblast cells. Trophoblast cells are known to be highly resistant to killing by decidual NK cells. HRF20 is deficient in a patient suffering from paroxysmal nocturnal hemoglobinuria. This deficiency in HRF20 is not only on blood cells but also other tissues including endothelial cells and peripheral nerves.

Patients affected by AIDS-related complex (ARC) show several immunological abnormalities which may lead to a disregulation of immunosurveillance against viral latent infections. In this paper evidence for Epstein-Barr virus (EBV) reactivation in seven out of eight affected by persistent generalized lymphadenopathy is given. These patients showed either elevated levels of circulating EBNA-positive transformed cells or depressed EBV-specific T cell cytotoxicity, as assessed by the regression assay, or both. A direct involvement of EBV in the pathogenesis of ARC is thus suggested. Natural killer cell activity was found decreased, correlating to the evidence of circulating EBV-infected cells and of impaired EBV-specific immune control. These data provide evidence that, when specific immune mechanisms lose control on ubiquitous latent viruses, the risk for reactivation becomes higher. In the case of EBV, direct evidence of this event is provided by the emergence in the peripheral blood of clones of infected cells with unlimited growth potential. [ABSTRACT FROM AUTHOR]

The presence of J chain in human immunocytes containing various immunoglobulin classes has already been reported and in this paper we investigated the presence of J chain in human myeloma cells using light and electron microscopy. Myeloma cells were positive for cytoplasmic J chain in thirteen cases six of fifteen IgG myeloma, two of seven IgA myeloma, two of nine B J myeloma and three of three primary macroglobulinaemia. None of the four with benign monoclonal gammopathy was positive for J chain. The ultrastructural localization of J chain in IgG myeloma cells was similar to that γ chain, i.e. around the nuclear membrane, in the endoplasmic reticulum (ER) and it the Golgi apparatus. The latter finding is compatible with the presence of J chain in the urine of the same patient. We examined the urine from nine patients with J chain-positive cells and secretion of J chain was confirmed in three patients two with IgG myeloma and one with B J myeloma. In none of twelve in whom the immunocytochemical findings were negative for J chain was there evidence of urinary J chain. [ABSTRACT FROM AUTHOR]

In this paper we report a study of the effects of splenectomy on the immunosuppressive action of essential fatty acids (EFA) which is thought to be mediated through prostaglandins (PG) produced in the spleen. Experimental allergic encephalomyelitis (EAE) was induced in normal, splenectomized and sham splenectomized Lewis rats. EFA were administered orally, the animals in the control groups being treated with liquid paraffin. Treatment with EFA significantly suppressed clinical disease in those animals in which EAE was induced by the inoculation of central nervous system material of guinea-pigs or by passive transfer by Con A-stimulated spleen cells. Splenectomy abrogated the suppressive effect of EFA. This observation, together with previous results showing the abrogation of EFA immunosuppression by an inhibitor of the biosynthesis of PG from EFA, led us to postulate a close relationship between EFA, PG and a splenic factor suppressing immunopathological mechanisms in EAE. [ABSTRACT FROM AUTHOR]

This paper describes further confirmation of the successful application of the macrophage electrophoretic mobility (MEM) test to the detection of malignant disease. Results from fifty-one patients and eighteen controls are presented. The apparatus and technique used for the measurement of macrophage elctrophoretic mobility differed from those previously used in other investigations. Further information is presented on the nature and behaviour of macrophage slowing factor(s), and experiments concerning the possible use of cells other than guinea-pig macrophages as indicators of slowing factor production are also described. [ABSTRACT FROM AUTHOR]

Patients with small cell carcinoma of the esophagus have a poor prognosis and have generally been treated by chemotherapy. However, all reported cases were at advanced stages. We need to establish an adequate treatment for patients with small cell carcinoma of the esophagus with invasion limited to the submucosal layer. In this paper, five cases of small cell carcinomas, which accounted for 2.8% of 180 surgically treated esophageal carcinomas, were reviewed for pathological findings, treatment, and outcome. Among three patients who had a small cell carcinoma of the esophagus with invasion limited to the submucosal layer, two patients survived for 7 and 9 years after surgery with no evidence of the disease. One of them was treated using surgery alone. Consequently, surgery may be considered as a possible choice of treatment for small cell carcinoma of the esophagus with invasion limited to the submucosa. [ABSTRACT FROM AUTHOR]

Glycomics is a developing field that provides structural information on complex populations of glycans isolated from tissues, cells and organs. Strategies employing matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) are central to glycomic analysis. Current MALDI-based glycomic strategies are capable of efficiently analyzing glycoprotein and glycosphingolipid glycomes but little attention has been paid to devising glycomic methodologies suited to the analysis of glycosaminoglycan (GAG) polysaccharides which pose special problems for MALDI analysis because of their high level of sulfation and large size. In this paper, we describe MALDI strategies that have been optimized for the analysis of highly sulfated GAG-derived oligosaccharides. A crystalline matrix norharmane, as well as an ionic liquid 1-methylimidazolium α-cyano-4-hydroxycinnamate (ImCHCA), have been used for the analysis of heparin di-, tetra-, hexa- and decasaccharides carrying from 2 to 13 sulfate groups. Information about the maximum number of sulfate groups is obtained using the ionic liquid whereas MALDI-TOF/TOF MS/MS experiments using norharmane allowed the determination of the nature of the glycosidic backbone, and more precise information about the presence and the position in the sequence of N-acetylated residues. [ABSTRACT FROM AUTHOR]

Up to prescribed limits, the maximum test compound concentrations used in mammalian cell genotoxicity assays in vitro are determined by cytotoxicity, unless limited by solubility in solvents or culture medium. However, ‘cytotoxicity’ is different in the various test systems, both in the methods used to estimate it and the levels of toxicity that must be achieved. For example, in cytogenetic assays, the acceptable level of toxicity is defined as a ‘significant reduction (>50%)’ in cell number, culture confluency or mitotic index (MI) (OECD 473, ICH S2A), whereas mutation tests require relative total growth or cloning efficiency (CE) to be reduced by 80–90% (OECD 476, ICH S2A). In this study using mouse lymphoma cells, it was shown that, for a variety of agents with differing modes of action, cytotoxicity varies considerably depending on the method used to estimate it. Specifically, trypan blue exclusion, MI and binucleate incidence all grossly underestimate cytotoxicity in comparison with cell growth or CE. If the performance of different test systems is to be compared, or if data from different assays are to be used for the meaningful assessment of a novel chemical entity, it is essential that similar methods to determine cytotoxicity are used for them all. The purpose of this paper is not to recommend a specific method to determine cytotoxicity, although it can be argued that any such method must quantify the proportion of cells capable of division following treatment, but rather to draw attention to the fact that apparent toxicity depends upon the method used to estimate it. [ABSTRACT FROM AUTHOR]