Chinese herbal formulae and non-alcoholic fatty liver disease : a preliminary investigation in an experimental animal model

University of Technology, Sydney. Faculty of Science.Background: Non-alcoholic Fatty Liver Disease (NAFLD) embodies the hepatic manifestation of metabolic syndrome, commonly associated with obesity, hyperinsulinaemia, peripheral insulin resistance, diabetes, hypertension, hypercholesterolaemia and hypertriglyceridaemia (Sanyal, 2002). NAFLD is recently conceded to be a global epidemic burden, being ranked as the second leading cause of preventative death (Younossi, 2008). Since the pathogenesis of NAFLD remains controversial, no established pharmacological agent has been developed that effectively targets or prevents excessive fat accumulation in the hepatocytes and, as a result, current treatments are primarily symptomatic. Chinese herbal medicine has become a growing focus for Western medical research in the quest for more effective treatments since various Chinese herbal formulae are used in Asian countries for hepatic and metabolic syndromes (Chen et al, 2006, Hollander and Merchanick 2008). Objective: To determine whether obesity related NAFLD could be induced in healthy rats by dietary manipulation alone and to investigate the effects of three Chinese herbal formulae in these animals on relevant variables on in vivo measures and on tissue analyses post mortem. Design: The research comprised of two related studies. Study one was a between subjects equivalent group experiment with repeated measures, with the rats randomly divided among six intervention groups. Five groups were continuously fed a high fat diet (HFD) and one group fed a standard laboratory chow for 11 weeks until sacrifice. Study two entailed the collection of liver and adipose tissues immediately post mortem. These tissue weights were recorded and the livers were used to measure hepatic triglyceride content and for histological examination of the rat liver. Participants and interventions: 56 male Sprague Dawley rats, six weeks old and weighing between 170 - 210g were randomly divided among six intervention groups. Five groups were continuously fed a HFD and one group, a standard laboratory chow for 11 weeks until sacrifice. After a five week induction period, the six week intervention phase commenced with the allocated intervention administered daily by oral gavage. Blood collection occurred in the last week before sacrifice for subsequent analyses. The pharmacological interventions comprised Rosiglitazone (RSG); antidiabetic medication, SK0504 (S4), SK0506 (S6) and a decoction of SK0506 (DS6) as well as water for the two control groups. Note: S4 combines Jiao Gu Lan (Gynostemma pentaphyllum), San Qi (Panax notoginseng), Huang Lian (Rhizoma Coptidis) and Dan Shen (Salvia miltiorrhiza) and S6 combines Dan Shen (Salvia miltiorrhiza) and Zhi Zi (Fructus Gardenia Jasminodis). Main outcome measures: Bodyweight, food and energy food intake; biochemical and hepatic analyses (plasma glucose, Non-esterified Fatty Acids (NEFA), cholesterol, triglycerides (TG), High Density Lipoprotein-Cholesterol (HDL-C), Alanine Transaminase (ALT), Aspartate Transaminase (AST) and hepatic triglycerides); and histopathological staining (to observe hepatic morphology) were measured. Results: The results for the five week induction phase suggest that despite the difference in diet (HFD or standard chow) the rats regulated their energy intake as there was no significant difference in the increase in mean weight for the two diets. During the intervention phase there were further increases in body weight that plateaued after four weeks, quite independent of diet or intervention. However, there was no clear relationship between caloric intake and weight gain in that there were significant differences between the two S6 groups and the others and yet this did not equate to any difference in weight gain. At the end of the intervention period there was no significant difference between most groups in blood glucose levels and typically animals were within the healthy range. Therefore high fat feeding alone, particularly in a short period of time of ten weeks did not cause hyperglycaemia. Within the intervention groups there was evidence of marked hyperlipidaemia with the HFD as evidenced by significant increases in NEFA, TG and cholesterol. In general, this was attenuated by the interventions. Notably both forms of the S6 intervention had a cardioprotective effect illustrated by the elevation of levels of HDL-C. There were potentially hepatotoxic effects indicated by elevation of liver enzymes associated with HFD feeding alone that were supported by histopathological changes in the liver. Post mortem comparisons included weights of adipose tissues, hepatic tissue and hepatic morphology for evidence of NAFLD. With the epidydimal, subcutaneous and inguinal fat deposits, there was a significant degree of fat accumulation in the HFD group compared with the chow group. RSG showed no beneficial effect with regard to fat accumulation, which contrasts with the effects of the two herbal formulae S4 and S6. There was no evidence of hepatomegaly in any group. High fat feeding resulted in excess hepatic triglyceride levels which was attenuated by RSG, S4 and S6, with S6 being the most effective. Note that no intervention completely prevented this high fat feeding accumulation. The significant increase in hepatic TG accumulation and plasma biochemical analysis (NEFA, TG and cholesterol) with the high fat feeding in control groups was supported from the histological findings of macro- and microvesicular steatosis fed the HFD alone. These histological changes were absent in animals fed the other HFD based interventions (S6, S4 and RSG). There was no discernible fibrosis in any of the groups. Conclusion: HFD feeding alone produced NAFLD as hypertriglyceraemia, hypercholesterolaemia and histological evidence of steatosis was observed. The three herbal formulae all attenuated the HFD’s hyperlipidaemic effects in relation to plasma TG, NEFA, cholesterol, HDL-C and hepatic TG as no steatosis was formed. However lack of difference in weights between standard chow and HFD fed rats during the induction and intervention phases suggests the model failed to produce obesity which may be due to the short period of 11 weeks of the dietary manipulation. S4 and S6 both attenuated the effects on liver enzymes of the high fat diet, possibly indicating possible hepatoprotective effects with the values falling towards those for the Chow group. RSG by contrast elevated AST levels above those for HFD. The two forms of S6; powder and decoction, compared in study one showed generally similar results

From Flood to Drip Irrigation Under Climate Change: Impacts on Evapotranspiration and Groundwater Recharge in the Mediterranean Region of Valencia (Spain)

[EN] Agricultural irrigation is the major water consumer in the Mediterranean region. In response to the growing pressure on freshwater resources, more efficient irrigation technologies have been widely promoted. In this study, we assess the impact of the ongoing transition from flood to drip irrigation on future hydroclimatic regimes under various climate change scenarios, with a particular focus on actual evapotranspiration and groundwater recharge in the Mediterranean region of Valencia, Spain. Hydroclimatic predictions for the near-term future (2020-2049) and the mid-term future (2045-2074) were made under two emission scenarios (RCP 4.5 and RCP 8.5) using a hydrological model that was forced with data from five GCM-RCM combinations and field-based irrigation volume and frequency observations. Our findings suggest that climate change could lead to statistically significant changes in the regional hydroclimatic regime despite projection uncertainties. Major changes include a statistically significant decrease in mean groundwater recharge of up to -6.6% under flood irrigation and -9.3% under drip irrigation and contrasting changes in mean actual evapotranspiration for flood and drip irrigation in the order of +1% and -2.1%, respectively. Since sustainably available water resources in the Valencia region are entirely allocated, the expected changes and associated uncertainties create a challenging context for future water management. Our simulations further indicate that, rather than climate change, the choice of irrigation technique may have a greater impact on actual evapotranspiration and groundwater recharge. Our findings therefore highlight the importance of considering both climate change and irrigation technique when assessing future water resources in irrigated Mediterranean agriculture.The authors thank the Coop Research Program on "Sustainability in Food Value Chains" of the ETH Zurich World Food System Center and the ETH Zurich Foundation for supporting this project. The Coop Research Program is supported by the Coop Sustainability Fund. The authors further thank the Spanish Ministry of Science and Innovation through the research project TE-TISCHANGE (RTI2018-093717-B-100) for financial support. This work was also supported by the ADAPTAMED research project funded by the Spanish Ministry of Science and Innovation (RTI2018-101483-B-I00) with European FEDER funds.Pool, S.; Francés, F.; Garcia-Prats, A.; Pulido-Velazquez, M.; Sanchis Ibor, C.; Schirmer, M.; Yang, H.... (2021). From Flood to Drip Irrigation Under Climate Change: Impacts on Evapotranspiration and Groundwater Recharge in the Mediterranean Region of Valencia (Spain). Earth's Future. 9(5):1-20. https://doi.org/10.1029/2020EF001859S1209

Controls on gut phosphatisation : the trilobites from the Weeks Formation Lagerstätte (Cambrian; Utah)

Despite being internal organs, digestive structures are frequently preserved in Cambrian Lagerstätten. However, the reasons for their fossilisation and their biological implications remain to be thoroughly explored. This is particularly true with arthropods--typically the most diverse fossilised organisms in Cambrian ecosystems--where digestive structures represent an as-yet underexploited alternative to appendage morphology for inferences on their biology. Here we describe the phosphatised digestive structures of three trilobite species from the Cambrian Weeks Formation Lagerstätte (Utah). Their exquisite, three-dimensional preservation reveals unique details on trilobite internal anatomy, such as the position of the mouth and the absence of a differentiated crop. In addition, the presence of paired pygidial organs of an unknown function is reported for the first time. This exceptional material enables exploration of the relationships between gut phosphatisation and the biology of organisms. Indeed, soft-tissue preservation is unusual in these fossils as it is restricted to the digestive structures, which indicates that the gut played a central role in its own phosphatisation. We hypothesize that the gut provided a microenvironment where special conditions could develop and harboured a source of phosphorus. The fact that gut phosphatization has almost exclusively been observed in arthropods could be explained by their uncommon ability to store ions (including phosphorous) in their digestive tissues. However, in some specimens from the Weeks Formation, the phosphatisation extends to the entire digestive system, suggesting that trilobites might have had some biological particularities not observed in modern arthropods. We speculate that one of them might have been an increased capacity for ion storage in the gut tissues, related to the moulting of their heavily-mineralised carapace

Translating metaphors into Afrikaans in a source language-oriented translation of the Hebrew Bible

No Abstract

Validation of a new three-dimensional imaging system using comparative craniofacial anthropometry

Abstract Background The aim of this study is to validate a new three-dimensional craniofacial stereophotogrammetry imaging system (3dMDface) through comparison with manual facial surface anthropometry. The null hypothesis was that there is no difference between craniofacial measurements using anthropometry vs. the 3dMDface system. Methods Facial images using the new 3dMDface system were taken from six randomly selected subjects, sitting in natural head position, on six separate occasions each 1 week apart, repeated twice at each sitting. Exclusion criteria were excess facial hair, facial piercings and undergoing current dentofacial treatment. 3dMDvultus software allowed facial landmarks to be marked and measurements recorded. The same measurements were taken using manual anthropometry, using soluble eyeliner to pinpoint landmarks, and sliding and spreading callipers and measuring tape to measure distances. The setting for the investigation was a dental teaching hospital and regional (secondary and tertiary care) cleft centre. The main outcome measure was comparison of the craniofacial measurements using the two aforementioned techniques. Results The results showed good agreement between craniofacial measurements using the 3dMDface system compared with manual anthropometry. For all measurements, except chin height and labial fissure width, there was a greater variability with the manual method compared to 3D assessment. Overall, there was a significantly greater variability in manual compared with 3D assessments (p < 0.02). Conclusions The 3dMDface system is validated for craniofacial measurements

Gene-modified T cells for adoptive immunotherapy of renal cell cancer maintain transgene-specific immune functions in vivo

Abstract BACKGROUND: We have treated three patients with carboxy-anhydrase-IX (CAIX) positive metastatic renal cell cancer (RCC) by adoptive transfer of autologous T-cells that had been gene-transduced to express a single-chain antibody-G250 chimeric receptor [scFv(G250)], and encountered liver toxicity necessitating adaptation of the treatment protocol. Here, we investigate whether or not the in vivo activity of the infused scFv(G250)(+) T cells is reflected by changes of selected immune parameters measured in peripheral blood. METHODS: ScFv(G250)-chimeric receptor-mediated functions of peripheral blood mononuclear cells (PBMC) obtained from three patients during and after treatment were compared to the same functions of scFv(G250)(+) T lymphocytes prior to infusion, and were correlated with plasma cytokine levels. RESULTS: Prior to infusion, scFv(G250)(+) T lymphocytes showed in vitro high levels of scFv(G250)-chimeric receptor-mediated functions such as killing of CAIX(+) RCC cell lines and cytokine production upon exposure to these cells. High levels of IFN-gamma were produced, whilst production of TNF-alpha, interleukin-4 (IL-4), IL-5 and IL-10 was variable and to lower levels, and that of IL-2 virtually absent. PBMC taken from patients during therapy showed lower levels of in vitro scFv(G250)-receptor-mediated functions as compared to pre-infusion, whilst IFN-gamma was the only detectable cytokine upon in vitro PBMC exposure to CAIX. During treatment, plasma levels of IFN-gamma increased only in the patient with the most prominent liver toxicity. IL-5 plasma levels increased transiently during treatment in all patients, which may have been triggered by the co-administration of IL-2. CONCLUSION: ScFv(G250)-receptor-mediated functions of the scFv(G250)(+) T lymphocytes are, by and large, preserved in vivo upon administration, and may be reflected by fluctuations in plasma IFN-gamma levels

Vector assembly of colloids on monolayer substrates

The key to spontaneous and directed assembly is to encode the desired assembly information to building blocks in a programmable and efficient way. In computer graphics, raster graphics encodes images on a single-pixel level, conferring fine details at the expense of large file sizes, whereas vector graphics encrypts shape information into vectors that allow small file sizes and operational transformations. Here, we adapt this raster/vector concept to a 2D colloidal system and realize &apos;vector assembly&apos; by manipulating particles on a colloidal monolayer substrate with optical tweezers. In contrast to raster assembly that assigns optical tweezers to each particle, vector assembly requires a minimal number of optical tweezers that allow operations like chain elongation and shortening. This vector approach enables simple uniform particles to form a vast collection of colloidal arenes and colloidenes, the spontaneous dissociation of which is achieved with precision and stage-by-stage complexity by simply removing the optical tweezers

The social construction and consequences of groundwater modelling: insight from the Mancha Oriental aquifer, Spain

[EN] Groundwater flow models have been increasingly used to support policy making. A substantial amount of research has been dedicated to improving, validating and calibrating models and including stakeholders in the modelling process. However, little research has been done to analyze how the choices of model makers and steering by policy makers result in models with specific characteristics, which only allow specific modelling outcomes, and how the use of these modelling outcomes leads to specific social, economic and environmental consequences. In this study, we use the social construction of technology framework to explore the development, characteristics and uses of the groundwater model of the Mancha Oriental aquifer in Spain. The specific characteristics and functioning of this model influenced the policy implementation, implying that involving stakeholders in the development and use of models is crucial for improved democratic policy making.This work was carried out as part of the collaboration agreement between the University of Castilla–La Mancha and Wageningen University. The research is also part of Femke Rambags’ MSc Thesis. David Sanz was supported by the Grants for Stays at Other Universities and Research Centres (UCLM). Special thanks go to the Júcar Water Authority (CHJ) and stakeholders (JCRMO) in the Mancha Oriental System for the necessary information. We would also like to thank Dr A. Sahuquillo of the Universitat Politècnica de València de Valencia and Dr S. Castaño of the University of Castilla–La Mancha for comments and participation in the first stage of modelling. The contents of this paper do not represent the views of CHJ or JCRMO. Finally, we thank the two anonymous reviewers of this article for their valuable comments and suggestions.Sanz Martínez, D.; Vos, J.; Rambags, F.; Hoogesteger, J.; Cassiraga, EF.; Gómez-Alday, JJ. (2018). The social construction and consequences of groundwater modelling: insight from the Mancha Oriental aquifer, Spain. International Journal of Water Resources Development. 1-22. https://doi.org/10.1080/07900627.2018.1495619S122Beall, A. M., & Ford, A. (2010). Reports from the Field. International Journal of Information Systems and Social Change, 1(2), 72-89. doi:10.4018/jissc.2010040105Beven, K. (2000). On model uncertainty, risk and decision making. Hydrological Processes, 14(14), 2605-2606. doi:10.1002/1099-1085(20001015)14:143.0.co;2-wBijker, W. E. (s. f.). Social Construction of Technology. A Companion to the Philosophy of Technology, 88-94. doi:10.1002/9781444310795.ch15Bots, P. W. G., Bijlsma, R., von Korff, Y., Van der Fluit, N., & Wolters, H. (2011). Supporting the Constructive Use of Existing Hydrological Models in Participatory Settings: a Set of &#8220;Rules of the Game&#8221; Ecology and Society, 16(2). doi:10.5751/es-03643-160216Budds, J. (2009). Contested H2O: Science, policy and politics in water resources management in Chile. Geoforum, 40(3), 418-430. doi:10.1016/j.geoforum.2008.12.008CALERA, A., GARRIDO-RUBIO, J., BELMONTE, M., ARELLANO, I., FRAILE, L., CAMPOS, I., & OSANN, A. (2017). REMOTE SENSING-BASED WATER ACCOUNTING TO SUPPORT GOVERNANCE FOR GROUNDWATER MANAGEMENT FOR IRRIGATION IN LA MANCHA ORIENTAL AQUIFER, SPAIN. Water Resources Management IX. doi:10.2495/wrm170121Cassiraga, E., Sanz, D., Castaño, S. Álvarez, O. & Sahuquillo, A. (2013). Modelo de flujo subterráneo de los acuíferos de la Mancha Oriental y sus relaciones con el río Júcar [Groundwater model flow of the Mancha Oriental Aquifer and their relations with the Júcar River]. Unpublished report (pp 77). Confederación Hidrográfica del Júcar.Castaño, S., Sanz, D., & Gómez-Alday, J. J. (2009). Methodology for Quantifying Groundwater Abstractions for Agriculture via Remote Sensing and GIS. Water Resources Management, 24(4), 795-814. doi:10.1007/s11269-009-9473-7Castaño, S., Sanz, D., & Gómez-Alday, J. J. (2013). Sensitivity of a Groundwater Flow Model to Both Climatic Variations and Management Scenarios in a Semi-arid Region of SE Spain. Water Resources Management, 27(7), 2089-2101. doi:10.1007/s11269-013-0277-4Castilla-Rho, J. C. (2017). Groundwater Modeling with Stakeholders: Finding the Complexity that Matters. Groundwater, 55(5), 620-625. doi:10.1111/gwat.12569Doherty, J., & Simmons, C. T. (2013). Groundwater modelling in decision support: reflections on a unified conceptual framework. Hydrogeology Journal, 21(7), 1531-1537. doi:10.1007/s10040-013-1027-7Ferrer, J. & Garijo, L. (2013). Mercados del agua y flexibilización del marco concesional [Water markets and flexibilization of the concessional framework]. XI Semin. Nac. “Transparencia y concesiones” Obs. del Agua la Fund. Botín.Forsyth, T. (2004). Critical Political Ecology. doi:10.4324/9780203017562Giordano, M. (2009). Global Groundwater? Issues and Solutions. Annual Review of Environment and Resources, 34(1), 153-178. doi:10.1146/annurev.environ.030308.100251Hernández-Mora, N., del Moral Ituarte, L., La-Roca, F., La Calle, A., & Schmidt, G. (2014). Interbasin Water Transfers in Spain: Interregional Conflicts and Governance Responses. Globalized Water, 175-194. doi:10.1007/978-94-007-7323-3_13Holley, C., Sinclair, D., Lopez-Gunn, E., & Schlager, E. (2016). Conjunctive Management Through Collective Action. Integrated Groundwater Management, 229-252. doi:10.1007/978-3-319-23576-9_9Hoogesteger, J., & Wester, P. (2015). Intensive groundwater use and (in)equity: Processes and governance challenges. Environmental Science & Policy, 51, 117-124. doi:10.1016/j.envsci.2015.04.004Hoogesteger, J., & Wester, P. (2017). Regulating groundwater use: The challenges of policy implementation in Guanajuato, Central Mexico. Environmental Science & Policy, 77, 107-113. doi:10.1016/j.envsci.2017.08.002Jakeman, A. J., Barreteau, O., Hunt, R. J., Rinaudo, J.-D., Ross, A., Arshad, M., & Hamilton, S. (2016). Integrated Groundwater Management: An Overview of Concepts and Challenges. Integrated Groundwater Management, 3-20. doi:10.1007/978-3-319-23576-9_1Kahil, M. T., Ward, F. A., Albiac, J., Eggleston, J., & Sanz, D. (2016). Hydro-economic modeling with aquifer–river interactions to guide sustainable basin management. Journal of Hydrology, 539, 510-524. doi:10.1016/j.jhydrol.2016.05.057Konikow, L. F., & Bredehoeft, J. D. (1992). Ground-water models cannot be validated. Advances in Water Resources, 15(1), 75-83. doi:10.1016/0309-1708(92)90033-xKonikow, L. F., & Kendy, E. (2005). Groundwater depletion: A global problem. Hydrogeology Journal, 13(1), 317-320. doi:10.1007/s10040-004-0411-8Lopez-Gunn, E. (2003). The Role of Collective Action in Water Governance: A Comparative Study of Groundwater User Associations in La Mancha Aquifers in Spain. Water International, 28(3), 367-378. doi:10.1080/02508060308691711Massuel, S., Cappelaere, B., Favreau, G., Leduc, C., Lebel, T., & Vischel, T. (2011). Integrated surface water–groundwater modelling in the context of increasing water reserves of a regional Sahelian aquifer. Hydrological Sciences Journal, 56(7), 1242-1264. doi:10.1080/02626667.2011.609171Melsen, L. A., Addor, N., Mizukami, N., Newman, A. J., Torfs, P. J. J. F., Clark, M. P., … Teuling, A. J. (2018). Mapping (dis)agreement in hydrologic projections. Hydrology and Earth System Sciences, 22(3), 1775-1791. doi:10.5194/hess-22-1775-2018MOLLE, F. (2008). Why Enough Is Never Enough: The Societal Determinants of River Basin Closure. International Journal of Water Resources Development, 24(2), 217-226. doi:10.1080/07900620701723646Narain, V., & Singh, A. K. (2017). Flowing against the current: The socio-technical mediation of water (in)security in periurban Gurgaon, India. Geoforum, 81, 66-75. doi:10.1016/j.geoforum.2017.02.010Pérez, M. A. (2005). Modelo distribuido de simulación del ciclo hidrológico con calidad de aguas integrado en sistemas de información geográfica para grandes cuencas [Distributed model of simulation of the hydrological cycle with water quality integrated in geographic information systems for large basins]. (Ph.D. Thesis). Universidad Politécnica de Valencia, Spain.Rambags, F. (2014). The social shaping of the hydrological model of the Mancha Oriental System. (Msc Thesis Water resources management). Wageningen University.Refsgaard, J. C., & Henriksen, H. J. (2004). Modelling guidelines––terminology and guiding principles. Advances in Water Resources, 27(1), 71-82. doi:10.1016/j.advwatres.2003.08.006Sanz, D., Calera, A., Castaño, S., & Gómez-Alday, J. J. (2015). Knowledge, participation, and transparency in groundwater management. Water Policy, wp2015024. doi:10.2166/wp.2015.024Sanz, D., Castaño, S., Cassiraga, E., Sahuquillo, A., Gómez-Alday, J. J., Peña, S., & Calera, A. (2011). Modeling aquifer–river interactions under the influence of groundwater abstraction in the Mancha Oriental System (SE Spain). Hydrogeology Journal, 19(2), 475-487. doi:10.1007/s10040-010-0694-xSanz, D., Gómez-Alday, J. J., Castaño, S., Moratalla, A., De las Heras, J., & Martínez-Alfaro, P. E. (2009). Hydrostratigraphic framework and hydrogeological behaviour of the Mancha Oriental System (SE Spain). Hydrogeology Journal, 17(6), 1375-1391. doi:10.1007/s10040-009-0446-yTortajada, C. (2010). Water Governance: Some Critical Issues. International Journal of Water Resources Development, 26(2), 297-307. doi:10.1080/07900621003683298Vaux, H. (2010). Groundwater under stress: the importance of management. Environmental Earth Sciences, 62(1), 19-23. doi:10.1007/s12665-010-0490-xVoinov, A., & Bousquet, F. (2010). Modelling with stakeholders☆. Environmental Modelling & Software, 25(11), 1268-1281. doi:10.1016/j.envsoft.2010.03.007Voinov, A., Kolagani, N., McCall, M. K., Glynn, P. D., Kragt, M. E., Ostermann, F. O., … Ramu, P. (2016). Modelling with stakeholders – Next generation. Environmental Modelling & Software, 77, 196-220. doi:10.1016/j.envsoft.2015.11.016Voss, C. I. (2011). Editor’s message: Groundwater modeling fantasies —part 1, adrift in the details. Hydrogeology Journal, 19(7), 1281-1284. doi:10.1007/s10040-011-0789-zWester, P., Hoogesteger, J. & Vincent, L. (2009). Local IWRM organizations for groundwater regulation: The experiences of the Aquifer Management Councils (COTAS) in Guanajuato, Mexico. Natural Resources Forum 33(1), 29–38. doi.org/10.1111/j.1477-8947.2009.01206.

Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome

<p>Abstract</p> <p>Background</p> <p>Alternative splicing (AS) is a widespread phenomenon in higher eukaryotes but the extent to which it leads to functional protein isoforms and to proteome expansion at large is still a matter of debate. In contrast to animal species, for which AS has been studied extensively at the protein and functional level, protein-centered studies of AS in plant species are scarce. Here we investigate the functional impact of AS in dicot and monocot plant species using a comparative approach.</p> <p>Results</p> <p>Detailed comparison of AS events in alternative spliced orthologs from the dicot <it>Arabidopsis thaliana </it>and the monocot <it>Oryza sativa </it>(rice) revealed that the vast majority of AS events in both species do not result from functional conservation. Transcript isoforms that are putative targets for the nonsense-mediated decay (NMD) pathway are as likely to contain conserved AS events as isoforms that are translated into proteins. Similar results were obtained when the same comparison was performed between the two more closely related monocot species rice and <it>Zea mays </it>(maize).</p> <p>Genome-wide computational analysis of functional protein domains encoded in alternatively and constitutively spliced genes revealed that only the RNA recognition motif (RRM) is overrepresented in alternatively spliced genes in all species analyzed. In contrast, three domain types were overrepresented in constitutively spliced genes. AS events were found to be less frequent within than outside predicted protein domains and no domain type was found to be enriched with AS introns. Analysis of AS events that result in the removal of complete protein domains revealed that only a small number of domain types is spliced-out in all species analyzed. Finally, in a substantial fraction of cases where a domain is completely removed, this domain appeared to be a unit of a tandem repeat.</p> <p>Conclusion</p> <p>The results from the ortholog comparisons suggest that the ability of a gene to produce more than one functional protein through AS does not persist during evolution. Cross-species comparison of the results of the protein-domain oriented analyses indicates little correspondence between the analyzed species. Based on the premise that functional genetic features are most likely to be conserved during evolution, we conclude that AS has only a limited role in functional expansion of the proteome in plants.</p