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Overview of mathematical approaches used to model bacterial chemotaxis I: the single cell
Mathematical modeling of bacterial chemotaxis systems has been influential and insightful in helping to understand experimental observations. We provide here a comprehensive overview of the range of mathematical approaches used for modeling, within a single bacterium, chemotactic processes caused by changes to external gradients in its environment. Specific areas of the bacterial system which have been studied and modeled are discussed in detail, including the modeling of adaptation in response to attractant gradients, the intracellular phosphorylation cascade, membrane receptor clustering, and spatial modeling of intracellular protein signal transduction. The importance of producing robust models that address adaptation, gain, and sensitivity are also discussed. This review highlights that while mathematical modeling has aided in understanding bacterial chemotaxis on the individual cell scale and guiding experimental design, no single model succeeds in robustly describing all of the basic elements of the cell. We conclude by discussing the importance of this and the future of modeling in this area
Expression of VjbR under Nutrient Limitation Conditions Is Regulated at the Post-Transcriptional Level by Specific Acidic pH Values and Urocanic Acid
VjbR is a LuxR homolog that regulates transcription of many genes including important virulence determinants of the facultative intracellular pathogen Brucella abortus. This transcription factor belongs to a family of regulators that participate in a cell-cell communication process called quorum sensing, which enables bacteria to respond to changes in cell population density by monitoring concentration of self produced autoinducer molecules. Unlike almost all other LuxR-type proteins, VjbR binds to DNA and activates transcription in the absence of any autoinducer signal. To investigate the mechanisms by which Brucella induces VjbR-mediated transcriptional activation, and to determine how inappropriate spatio-temporal expression of the VjbR target genes is prevented, we focused on the study of expression of vjbR itself. By assaying different parameters related to the intracellular lifestyle of Brucella, we identified a restricted set of conditions that triggers VjbR protein expression. Such conditions required the convergence of two signals of different nature: a specific pH value of 5.5 and the presence of urocanic acid, a metabolite involved in the connection between virulence and metabolism of Brucella. In addition, we also observed an urocanic acid, pH-dependent expression of RibH2 and VirB7, two additional intracellular survival-related proteins of Brucella. Analysis of promoter activities and determination of mRNA levels demonstrated that the urocanic acid-dependent mechanisms that induced expression of VjbR, RibH2, and VirB7 act at the post-transcriptional level. Taken together, our findings support a model whereby Brucella induces VjbR-mediated transcription by modulating expression of VjbR in response to specific signals related to the changing environment encountered within the host
Enrichment of trace elements in the clay size fraction of mining soils
Reactive waste dumps with sulfide minerals pro-
14 mote acid mine drainage (AMD), which results in water and
15 soil contamination by metals and metalloids. In these systems,
16 contamination is regulated by many factors, such as mineral-
17 ogical composition of soil and the presence of sorption sites
18 on specific mineral phases. So, the present study dedicates
19 itself to understanding the distribution of trace elements in
20 different size fractions (<2-mm and <2-μm fractions) of min-
21 ing soils and to evaluate the relationship between chemical
22 and mineralogical composition. Cerdeirinha and Penedono,
23 located in Portugal, were the waste dumps under study. The
24 results revealed that the two waste dumps have high degree of
25 contamination by metals and arsenic and that these elements
26 are concentrated in the clay size fraction. Hence, the higher
27 degree of contamination by toxic elements, especially arsenic
28 in Penedono as well as the role of clay minerals, jarosite, and
29 goethite in retaining trace elements has management implica-
30 tions. Such information must be carefully thought in the reha-
31 bilitation projects to be planned for both waste dumps
The effectiveness of a multidisciplinary intervention strategy for the treatment of symptomatic joint hypermobility in childhood:A randomised, single Centre parallel group trial (The Bendy Study)
Introduction: Joint hypermobility is common in childhood and can be associated with musculoskeletal pain and dysfunction. Current management is delivered by a multidisciplinary team, but evidence of effectiveness is limited. This clinical trial aimed to determine whether a structured multidisciplinary, multisite intervention resulted in improved clinical outcomes compared with standard care. Method: A prospective randomised, single centre parallel group trial comparing an 8-week individualised multidisciplinary intervention programme (bespoke physiotherapy and occupational therapy in the clinical, home and school environment) with current standard management (advice, information and therapy referral if deemed necessary). The primary endpoint of the study was between group difference in child reported pain from baseline to 12 months as assessed using the Wong Baker faces pain scale. Secondary endpoints were parent reported pain (100 mm visual analogue scale), parent reported function (child health assessment questionnaire), child reported quality of life (child health utility 9-dimensional assessment), coordination (movement assessment battery for children version 2) and grip strength (handheld dynamometer). Results: 119 children aged 5 to 16 years, with symptomatic hypermobility were randomised to receive an individualised multidisciplinary intervention (I) (n = 59) or standard management (S) (n = 60). Of these, 105 completed follow up at 12 months. No additional significant benefit could be shown from the intervention compared to standard management. However, there was a statistically significant improvement in child and parent reported pain, coordination and grip strength in both groups. The response was independent of the degree of hypermobility. Conclusion: This is the first randomised controlled trial to compare a structured multidisciplinary, multisite intervention with standard care in symptomatic childhood hypermobility. For the majority, the provision of education and positive interventions aimed at promoting healthy exercise and self-management was associated with significant benefit without the need for more complex interventions. Trial registration: The trial was registered prospectively with the national database at the Clinical Research Network (UKCRN Portfolio 9366). The trial was registered retrospectively with ISRCTN (ISRCTN86573140)
Exchange of nutrients and oxygen across the sediment-water interface below a Sparus aurata marine fish farm in the north-western Mediterranean Sea
Purpose: This study analyzes the effects of aquaculture activities in open seawater in the north-western coastal waters of the Mediterranean Sea. It is the first of its kind to be based on benthic flux data gathered in situ below fish farms for this particular area. Materials and methods: Samples were collected on four sampling campaigns over a 1-year cycle under a Sparus aurata fish farm facility where benthic fluxes were measured in situ using light and dark benthic chambers. Bottom water and sediment samples were also collected. Data were compared to those for a nearby control station. Results and discussion: Significant differences were found (ANOVA, p < 0. 05) between concentrations of organic matter (OM), total phosphorus and redox potentials in sediments located under the cages and those of the control station. The consumption of dissolved oxygen (DO) by sediment and positive ammonium (NH4 +) fluxes was stimulated by OM content, with correlations of r = -0. 60 (p < 0. 01) and r = 0. 70 (p < 0. 01), respectively. The OM content of sediments was found to be consistently higher under the cages than at the control station, with the highest value (1. 8 ± 0. 7 %) under the cages observed during the early summer; values of DO and NH4 + fluxes were -64 ± 17 and 12. 7 ± 1. 0 mmol m-2 day-1, respectively. PO4 3- fluxes were consistently higher in the fish farm sediments (between 0. 58 and 0. 98 mmol m-2 day-1) than those observed at the control station. Nitrate (NO3 -) fluxes were found to be consistently negative due to denitrification occurring in the sediments and were related to the concentration of NO3 - in bottom waters (r = 0. 92, p < 0. 01). Si fluxes were shown to be associated with water temperature (r = 0. 59, p < 0. 05). Conclusions: The results imply that sediments located below cages accumulate organic matter originating from aquaculture activities, especially during summer months when this activity increases. Sediments undergo biogeochemical changes that mainly affect fluxes of DO, NH4 + and soluble reactive phosphorus, although these do not seem to have a significant impact on the quality of the water column due to the hydrodynamic characteristics of the area. © 2012 Springer-Verlag.We would like to thank the Caja del Mediterraneo for a predoctoral fellowship fund for this research and Antonio Asuncion Acuigroup Maremar manager for the facilities and support in conducting the study. The translation of this paper was funded by the Universidad Politecnica de Valencia, Spain. We are grateful for the valuable comments of the anonymous reviewers on previous versions of the manuscript.Morata Higón, T.; Sospedra, J.; Falco Giaccaglia, SL.; Rodilla Alama, M. (2012). Exchange of nutrients and oxygen across the sediment-water interface below a Sparus aurata marine fish farm in the north-western Mediterranean Sea. Journal of Soils and Sediments. 12(10):1623-1632. doi:10.1007/s11368-012-0581-2S162316321210APHA, AWWA, and WEF (2005) Standard methods for the examination of water wastewater, 21st edn. American Public Health Association, WashingtonAksu M, Kocatas A (2007) Environmental effects of the three fish farms in Izmir Bay (Aegean Sea-Turkey) on water column and sediment. Rapport du 38e Congrés de la Commission Internationale Pour L’exploration Scientifique de la Mer Méditerranée 38, 414Aminot A, Chaussepied M (1983) Manuel des analyses chimiques en milieu marin. Centre National pour l’Explotation des Oceans, BrestArocena R, Conde D (1999) Sedimento. Métodos en ecología de aguas continentales. Universidad de la República, Montevideo, pp 40–52Asociación Empresarial de Productores de Cultivos Marinas (APROMAR) (2010) La Acuicultura Marina de Peces en España, pp. 69Baumgarten MGZ, Rocha JM, Niencheski LFH (1996) Manual de análises em oceanografia química, Rio GrandeBelias C, Dassenakis M, Scoullos M (2007) Study of the N, P and Si fluxes between fish farm sediment and seawater. Results of simulation experiments employing a benthic chamber under various redox conditions. Mar Chem 103:266–275Berelson WM, McManus J, Coale KH, Johnson KS, Burdige D, Kilgore T, Colodner D, Chavez F, Kudela R, Boucher J (2003) A time series of benthic flux measurements from Monterey Bay, CA. Cont Shelf Res 23:457–481Black KD, McDougall N (2002) Hydrography of four Mediterranean marine cage sites. J Appl Ichthyol 18:129–133Borja A, Rodríguez JG, Black K, Bodoy A, Emblow C, Fernandes TF, Forte J, Karakassis I, Muxika I, Nickell TD, Papageorgiou N, Pranovi F, Sevastou K, Tomassetti P, Angel D (2009) Assessing the suitability of a range of benthic indices in the evaluation of environmental impact of fin and shellfish aquaculture located in sites across Europe. Aquaculture 293:231–240Cermelj B, Ogrinc N, Faganeli J (2001) Anoxic mineralization of biogenic debris in near-shore marine sediments (Gulf of Trieste, northern Adriatic). Sci Total Environ 266:143–152Dell’Anno A, Mei ML, Pusceddu A, Danovaro R (2002) Assessing the trophic state and eutrophication of coastal marine systems: a new approach based on the biochemical composition of sediment organic matter. Mar Pollut Bull 44:611–622Dosdat A (2001) Environmental impact of aquaculture in the Mediterranean: nutritional and feeding aspects. Environmental impact assessment of Mediterranean aquaculture farms. Cah Options Méditerr CIHEAM-FAO 55:23–36Ferrón S, Ortega T, Forja JM (2009) Benthic fluxes in a tidal salt marsh creek by fish farm activities: Río San Pedro (Bay of Cádiz, SW Spain). Mar Chem 113:50–62Freitas U, Niencheski LFH, Zarzur S, Manzolli RP, Vieira JPP, Rosa LC (2008) Influência de um cultivo de camaraô sobre o metabolismo béntico e a qualidade da agua. Rev Bras Eng Agríc Ambient 12:293–301Hall POJ, Holby O, Kollberg S, Samuelsson MO (1992) Chemical fluxes and mass balances in a marine fish cage farm: IV. Nitrogen. Mar Ecol Prog Ser 89:81–91Hargrave B (2005) Environmental effects of marine finfish aquaculture. The handbook of environmental. chemistry, vol. 5. Part M. Springer, BerlinHargrave BT, Phillips GA, Doucette LI, White MJ, Milligan TG, Wildish DJ, Cranston RE (1997) Assessing benthic impacts of organic enrichment from marine aquaculture. Water Air Soil Pollut 99:641–650Heilskov AC, Holmer M (2001) Effects of benthic fauna on organic matter mineralization in fish-farm sediments: importance of size and abundance. ICES J Mar Sci 58:427–434Herbert RA (1999) Nitrogen cycling in coastal marine ecosystems. FEMS Microbiol Rev 23:563–590Holby O, Hall POJ (1991) Chemical fluxes and mass balances in a marine fish cage farm. 11. Phosphorus. Mar Ecol Prog Ser 70:263–272Holby O, Hall POJ (1994) Chemical fluxes and mass balances in a marine fish cage farm. III. Silicon. Aquaculture 120:305–318Jackson C, Preston N, Thompson PJ (2004) Intake and discharge nutrient loads at three intensive shrimp farms. Aquacult Res 35:1053–1061Karakassis I, Tsapakis M, Hatziyanni E (1998) Seasonal variability in sediment profiles beneath fish farm cages in the Mediterranean. Mar Ecol Prog Ser 162:243–252Kaymakci A, Aksu M, Egemen O (2010) Impacts of the fish farms on the water column nutrient concentrations and accumulation of heavy metals in the sediments in the eastern Aegean Sea (Turkey). Environ Monit Assess 162:439–451Lorenti M, De Falco G (2004) Measurements and characterization of abiotic variables. In: Gambi MC, Diappiano M (eds) Mediterranean marine benthos: a manual of methods for its sampling and study. Societa Italiana di Biologia Marina, Genova, pp 1–37Maldonado M, Carmona MC, Echeverría Y, Riesgo A (2005) The environmental impact of Mediterranean cage fish farms at semi-exposed locations: does it need a re-assessment? Helgol Mar Res 59:121–135Mantzavrakos E, Kornaros M, Lyberatos G, Kaspiris P (2007) Impacts of a marine fish farm in Argolikos Gulf (Greece) on the water column and the sediment. Desalination 210:110–124Mazzola A, Mirto S, La Rosa T, Fabiano M, Danovaro R (2000) Fish-farming effects on benthic community structure in coastal sediments: analysis of meiofaunal recovery. ICES J Mar Sci 57:1454–1461Molina L, Vergara JM (2005) Impacto ambiental de jaulas flotantes: estado actual de conocimientos y conclusiones prácticas. Bol Inst Esp Oceanogr 21:75–81Morán XAG, Estrada M (2005) Winter pelagic photosynthesis in the NW Mediterranean Deep-Sea. Research I 52:1806–1822Neofitou N, Klaoudatos S (2008) Effect of fish farming on the water column nutrient concentration in a semi-enclosed gulf of the Eastern Mediterranean. Aquac Res 39:482–490Niencheski LF, Jahnke RA (2002) Benthic respiration and inorganic nutrient fluxes in the estuarine región of Patos Lagoon (Brazil). Aquat Geochem 8:135–152Nizzoli D, Bartoli M, Viaroli P (2007) Oxygen and ammonium dynamics during a farming cycle of the bivalve Tapes philippinarum. Hydrobiologia 587:25–36Pergent-Martini C, Boudouresque CF, Pasqualini V, Pergent G (2006) Impact of fish farming facilities on Posidonia oceanica meadows: a review. Mar Ecol 27:310–319Pitta P, Karakassis I, Tsapakis M, Zivanovic S (1999) Natural versus mariculture induced variability in nutrients and plankton in the Eastern Mediterranean. Hydrobiologia 391:181–194Redfield AC, Ketchum BH, Richards FA (1963) The influence of organisms on the composition of seawater. In: Hill MN (ed) The sea, vol 2. Interscience, New YorkRiise JC, Roos N (1997) Benthic metabolism and the effects of bioturbation in a fertilized polyculture fish pond in northeast Thailand. Aquaculture 150:45–62Rodríguez J (1999) Ecología. Ed. Pirámide. pp 411Sakamaki T, Nishimura O, Sudo R (2006) Tidal time-scale variation in nutrient flux across the sediment-water interface of an estuarine tidal flat. Estuar Coast Shelf Sci 67:653–663Sarà G, Scilipoti D, Milazzo M, Modica A (2006) Use of stable isotopes to investigate dispersal of waste from fish farms as a function of hydrodynamics. Mar Ecol Prog Ser 313:261–270Shepard FP (1954) Nomenclature based on sand-silt-clay relations. J Sediment Petrol 24:151–158Siokou-Frangou I, Christaki U, Mazzocchi MG, Montresor M, Ribera d’Alcalá M, Vaqué D, Zingone A (2010) Plankton in the open Mediterranean Sea: a review. BG 7:1543–1586Warnken KW, Gill GA, Lehman R, Dellapenna T, Allison MA (2002) The effects of shrimp trawling on sediment oxygen demand and the release of trace metals and nutrients from estuarine sediments. Estuar Coast Shelf Sci 57:25–42Yucel-Gier G, Kucuksezgin F, Kocak F (2007) Effects of fish farming on nutrients and benthic community structure in the Eastern Aegean (Turkey). Aquac Res 38:256–26
Histone deacetylases suppress cgg repeat-induced neurodegeneration via transcriptional silencing in models of Fragile X Tremor Ataxia Syndrome
Fragile X Tremor Ataxia Syndrome (FXTAS) is a common inherited neurodegenerative disorder caused by expansion of a CGG trinucleotide repeat in the 59UTR of the fragile X syndrome (FXS) gene, FMR1. The expanded CGG repeat is thought to induce toxicity as RNA, and in FXTAS patients mRNA levels for FMR1 are markedly increased. Despite the critical role of FMR1 mRNA in disease pathogenesis, the basis for the increase in FMR1 mRNA expression is unknown. Here we show that overexpressing any of three histone deacetylases (HDACs 3, 6, or 11) suppresses CGG repeat-induced neurodegeneration in a Drosophila model of FXTAS. This suppression results from selective transcriptional repression of the CGG repeat-containing transgene. These findings led us to evaluate the acetylation state of histones at the human FMR1 locus. In patient-derived lymphoblasts and fibroblasts, we determined by chromatin immunoprecipitation that there is increased acetylation of histones at the FMR1 locus in pre-mutation carriers compared to control or FXS derived cell lines. These epigenetic changes correlate with elevated FMR1 mRNA expression in pre-mutation cell lines. Consistent with this finding, histone acetyltransferase (HAT) inhibitors repress FMR1 mRNA expression to control levels in pre-mutation carrier cell lines and extend lifespan in CGG repeat-expressing Drosophila. These findings support a disease model whereby the CGG repeat expansion in FXTAS promotes chromatin remodeling in cis, which in turn increases expression of the toxic FMR1 mRNA. Moreover, these results provide proof of principle that HAT inhibitors or HDAC activators might be used to selectively repress transcription at the FMR1 locus.open293
Estimating economies of scale and scope with flexible technology
The final publication is available at Springer via http://dx.doi.org/10.1007/s11123-016-0467-1Economies of scope are typically modelled and estimated using a cost function that is common to all firms in an industry irrespective of their type, e.g. whether they specialize in a single output or produce multiple outputs. Instead, we estimate a flexible technology model that allows for type-specific technologies and show how it can be estimated using linear parametric forms including the translog. A common technology remains a special case of our model and is testable econometrically. Our sample, of publicly owned US electric utilities, does not support a common technology for integrated and specialized firms. Our empirical results therefore suggest that assuming a common technology might bias estimates of economies of scale and scope. Thus, how we model the production technology clearly influences the policy conclusions we draw from its characteristics
The nucleoporin ALADIN regulates Aurora A localization to ensure robust mitotic spindle formation
The formation of the mitotic spindle is a complex process that requires massive cellular reorganization. Regulation by mitotic kinases controls this entire process. One of these mitotic controllers is Aurora A kinase, which is itself highly regulated. In this study, we show that the nuclear pore protein ALADIN is a novel spatial regulator of Aurora A. Without ALADIN, Aurora A spreads from centrosomes onto spindle microtubules, which affects the distribution of a subset of microtubule regulators and slows spindle assembly and chromosome alignment. ALADIN interacts with inactive Aurora A and is recruited to the spindle pole after Aurora A inhibition. Of interest, mutations in ALADIN cause triple A syndrome. We find that some of the mitotic phenotypes that we observe after ALADIN depletion also occur in cells from triple A syndrome patients, which raises the possibility that mitotic errors may underlie part of the etiology of this syndrome
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