A Case Study of Eukaryogenesis: The Evolution of Photoreception by Photolyase/Cryptochrome Proteins

Eukaryogenesis, the origin of the eukaryotes, is still poorly understood. Herein, we show how a detailed all-kingdom phylogenetic analysis overlaid with a map of key biochemical features can provide valuable clues. The photolyase/cryptochrome family of proteins are well known to repair DNA in response to potentially harmful effects of sunlight and to entrain circadian rhythms. Phylogenetic analysis of photolyase/cryptochrome protein sequences from a wide range of prokaryotes and eukaryotes points to a number of horizontal gene transfer events between ancestral bacteria and ancestral eukaryotes. Previous experimental research has characterised patterns of tryptophan residues in these proteins that are important for photoreception, specifically a tryptophan dyad, a canonical tryptophan triad, an alternative tryptophan triad, a tryptophan tetrad and an alternative tetrad. Our results suggest that the spread of the different triad and tetrad motifs across the kingdoms of life accompanied the putative horizontal gene transfers and is consistent with multiple bacterial contributions to eukaryogenesis

Issues in the Pharmacokinetics of Trichloroethylene and Its Metabolites

Much progress has been made in understanding the complex pharmacokinetics of trichloroethylene (TCE). Qualitatively, it is clear that TCE is metabolized to multiple metabolites either locally or into systemic circulation. Many of these metabolites are thought to have toxicologic importance. In addition, efforts to develop physiologically based pharmacokinetic (PBPK) models have led to a better quantitative assessment of the dosimetry of TCE and several of its metabolites. As part of a mini-monograph on key issues in the health risk assessment of TCE, this article is a review of a number of the current scientific issues in TCE pharmacokinetics and recent PBPK modeling efforts with a focus on literature published since 2000. Particular attention is paid to factors affecting PBPK modeling for application to risk assessment. Recent TCE PBPK modeling efforts, coupled with methodologic advances in characterizing uncertainty and variability, suggest that rigorous application of PBPK modeling to TCE risk assessment appears feasible at least for TCE and its major oxidative metabolites trichloroacetic acid and trichloroethanol. However, a number of basic structural hypotheses such as enterohepatic recirculation, plasma binding, and flow- or diffusion-limited treatment of tissue distribution require additional evaluation and analysis. Moreover, there are a number of metabolites of potential toxicologic interest, such as chloral, dichloroacetic acid, and those derived from glutathione conjugation, for which reliable pharmacokinetic data is sparse because of analytical difficulties or low concentrations in systemic circulation. It will be a challenge to develop reliable dosimetry for such cases

Does oral sodium bicarbonate therapy improve function and quality of life in older patients with chronic kidney disease and low-grade acidosis (the BiCARB trial)? Study protocol for a randomized controlled trial

Date of acceptance: 01/07/2015 © 2015 Witham et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Acknowledgements UK NIHR HTA grant 10/71/01. We acknowledge the financial support of NHS Research Scotland in conducting this trial.Peer reviewedPublisher PD

Host microenvironment in breast cancer development: Inflammatory cells, cytokines and chemokines in breast cancer progression: reciprocal tumor–microenvironment interactions

A comprehensive overview of breast cancer development and progression suggests that the process is influenced by intrinsic properties of the tumor cells, as well as by microenvironmental factors. Indeed, in breast carcinoma, an intensive interplay exists between the tumor cells on one hand, and inflammatory cells/cytokines/chemokines on the other. The purpose of the present review is to outline the reciprocal interactions that exist between these different elements, and to shed light on their potential involvement in breast cancer development and progression

Environmental Factors in the Relapse and Recurrence of Inflammatory Bowel Disease:A Review of the Literature

The causes of relapse in patients with Crohn's disease (CD) and ulcerative colitis (UC) are largely unknown. This paper reviews the epidemiological and clinical data on how medications (non-steroidal anti-inflammatory drugs, estrogens and antibiotics), lifestyle factors (smoking, psychological stress, diet and air pollution) may precipitate clinical relapses and recurrence. Potential biological mechanisms include: increasing thrombotic tendency, imbalances in prostaglandin synthesis, alterations in the composition of gut microbiota, and mucosal damage causing increased permeability

Acetate Kinase Isozymes Confer Robustness in Acetate Metabolism

Acetate kinase (ACK) (EC no: 2.7.2.1) interconverts acetyl-phosphate and acetate to either catabolize or synthesize acetyl-CoA dependent on the metabolic requirement. Among all ACK entries available in UniProt, we found that around 45% are multiple ACKs in some organisms including more than 300 species but surprisingly, little work has been done to clarify whether this has any significance. In an attempt to gain further insight we have studied the two ACKs (AckA1, AckA2) encoded by two neighboring genes conserved in Lactococcus lactis (L. lactis) by analyzing protein sequences, characterizing transcription structure, determining enzyme characteristics and effect on growth physiology. The results show that the two ACKs are most likely individually transcribed. AckA1 has a much higher turnover number and AckA2 has a much higher affinity for acetate in vitro. Consistently, growth experiments of mutant strains reveal that AckA1 has a higher capacity for acetate production which allows faster growth in an environment with high acetate concentration. Meanwhile, AckA2 is important for fast acetate-dependent growth at low concentration of acetate. The results demonstrate that the two ACKs have complementary physiological roles in L. lactis to maintain a robust acetate metabolism for fast growth at different extracellular acetate concentrations. The existence of ACK isozymes may reflect a common evolutionary strategy in bacteria in an environment with varying concentrations of acetate

A conceptual framework for crop-based agri-food supply chain characterization under uncertainty

[EN] Crop-based Agri-food Supply Chains (AFSCs) are complex systems that face multiple sources of uncertainty that can cause a significant imbalance between supply and demand in terms of product varieties, quantities, qualities, customer requirements, times and prices, all of which greatly complicate their management. Poor management of these sources of uncertainty in these AFSCs can have negative impact on quality, safety, and sustainability by reducing the logistic efficiency and increasing the waste. Therefore, it becomes crucial to develop models in order to deal with the key sources of uncertainty. For this purpose, it is necessary to precisely understand and define the problem under study. Even, the characterisation process of this domains is also a difficult and time-consuming task, especially when the right directions and standards are not in place. In this chapter, a Conceptual Framework is proposed that systematically collects those aspects that are relevant for an adequate crop-based AFSC management under uncertainty.Authors of this publication acknowledge the contribution of the Project 691249, RUC-APS "Enhancing and implementing Knowledge based ICT solutions within high Risk and Uncertain Conditions for Agriculture Production Systems" (www.ruc-aps.eu), funded by the European Union under their funding scheme H2020-MSCA-RISE-2015Alemany Díaz, MDM.; Esteso, A.; Ortiz Bas, Á.; Hernández Hormazabal, JE.; Fernández, A.; Garrido, A.; Martin, J.... (2021). A conceptual framework for crop-based agri-food supply chain characterization under uncertainty. Studies in Systems, Decision and Control. 280:19-33. https://doi.org/10.1007/978-3-030-51047-3_2S1933280Taylor, D.H., Fearne, A.: Towards a framework for improvement in the management of demand in agri-food supply chains. Supply Chain Manage. 11, 379–384 (2006)Matopoulos, A., Vlachopoulou, M., Manthou, V., Manos, B.: A conceptual framework for supply chain collaboration: empirical evidence from the agri-food industry. Supply Chain Manage. 12, 177–186 (2007)Ahumada, O., Villalobos, J.R.: Application of planning models in the agri-food supply chain: a review. Eur. J. Oper. Res. 196, 1–20 (2009)Iakovou, E., Vlachos, D., Achillas, C., Anastasiadis, F.: A methodological framework for the design of green supply chains for the agrifood sector. Paper presented at the 2nd international conference on supply chains, Katerini, 5–7 Oct 2012Manzini, R., Accorsi, R.: The new conceptual framework for food supply chain assessment. J. Food Eng. 115, 251–263 (2013)Shukla, M., Jharkharia, S.: Agri-fresh produce supply chain management: a state-of-the-art literature review. Int. J. Oper. Prod. Manage. 33, 114–158 (2013)Lemma, Y., Kitaw, D., Gatew, G.: Loss in perishable food supply chain: an optimization approach literature review. Int. J. Sci. Eng. Res. 5, 302–311 (2014)Tsolakis, N.K., Keramydas, C.A., Toka, A.K., Aidonis, D.A., Iakovou, E.T.: Agrifood supply chain management: a comprehensive hierarchical decision-making framework and a critical taxonomy. Biosyst. Eng. 120, 47–64 (2014)Van der Vorst, J.G., Da Silva, C.A., Trienekens, J.H.: Agro-industrial Supply Chain Management: Concepts and Applications. FAO (2007)Hernandez, J., Mortimer, M., Patelli, E., Liu, S., Drummond, C., Kehr, E., Calabrese, N., Iannacone, R., Kacprzyk, J., Alemany, M.M.E., Gardner, D.: RUC-APS: enhancing and implementing knowledge based ICT solutions within high risk and uncertain conditions for agriculture production systems. In: 11th International Conference on Industrial Engineering and Industrial Management, Valencia, Spain (2017)Miles, M.B., Huberman, A.M.: Qualitative Data Analysis: An Expanded Sourcebook. Sage Publications, Thousand Oaks (1994)Alemany, M.M.E., Alarcón, F., Lario, F.C., Boj, J.J.: An application to support the temporal and spatial distributed decision-making process in supply chain collaborative planning. Comput. Ind. 62, 519–540 (2011)Teimoury, E., Nedaei, H., Ansari, S., Sabbaghi, M.: A multi-objective analysis for import quota policy making in a perishable fruit and vegetable supply chain: a system dynamics approach. Comput. Electron. Agric. 93, 37–45 (2013)Kusumastuti, R.D., van Donk, D.P., Teunter, R.: Crop-related harvesting and processing planning: a review. Int. J. Prod. Econ. 174, 76–92 (2016)Zhang, W., Wilhelm, W.E.: OR/MS decision support models for the specialty crops industry: a literature review. Ann. Oper. Res. 190, 131–148 (2011)Grillo, H., Alemany, M.M.E., Ortiz, A.: A review of mathematical models for supporting the order promising process under lack of homogeneity in product and other sources of uncertainty. Comput. Ind. Eng. 91, 239–261 (2016)Blanco, A.M., Masini, G., Petracci, N., Bandoni, J.A.: Operations management of a packaging plant in the fruit industry. J. Food Eng. 70, 299–307 (2005)Grillo, H., Alemany, M.M.E., Ortiz, A., Fuertes-Miquel, V.S.: Mathematical modelling of the order-promising process for fruit supply chains considering the perishability and subtypes of products. Appl. Math. Model. 49, 255–278 (2017)Verdouw, C.N., Beulens, A.J.M., Trienekens, J.H., Wolferta, J.: Process modelling in demand-driven supply chains: a reference model for the fruit industry. Comput. Electron. Agric. 73, 174–187 (2010)Amorim, P., Günther, H., Almada-Lobo, B.: Multi-objective integrated production and distribution planning of perishable products. Int. J. Prod. Econ. 138, 89–101 (2012)Nahmias, S.: Perishable inventory theory: a review. Oper. Res. 30, 680–708 (1982)Mowat, A., Collins, R.: Consumer behavior and fruit quality: supply chain management in an emerging industry. Supply Chain Manage. 5, 45–54 (2000)Kazaz, B., Webster, S.: The impact of yield-dependent trading costs on pricing and production planning under supply uncertainty. M&SOM Manuf. Serv. Oper. Manage. 13, 404–417 (2011)Van der Vorst, J.G.: Effective food supply chains: generating, modelling and evaluating supply chain scenarios (2000)Fuertes-Miquel, V.S., Cuenca, L., Boza, A., Guyon, C., Alemany, M.M.E.: Conceptual framework for the characterization of vegetable breton supply chain sustainability in an uncertain context. In: 12th International Conference on Industrial Engineering and Industrial Management, XXII Congreso de Ingeniería de Organización, Girona, Spain, 12–13 July 2018Kummu, M., de Moel, H., Porkka, M., Siebert, S., Varis, O., Ward, P.J.: Lost food, wasted resources: global food supply chain losses and their impacts on freshwater, cropland, and fertiliser use. Sci. Total Environ. 438, 477–489 (2012)Hoekstra, S., Romme, J.: Integral Logistic Structures: Developing Customer-Oriented Goods Flow. Industrial Press Inc., New York (1992)Borodin, V., Bourtembourg, J., Hnaien, F., Labadie, N.: Handling uncertainty in agricultural supply chain management: a state of the art. Eur. J. Oper. Res. 254, 348–359 (2016)Handayati, Y., Simatupang, T.M., Perdana, T.: Agri-food supply chain coordination: the state-of-the-art and recent developments. Logist. Res. 8, 1–15 (2015)Mintzberg, H.: The Structuring of Organisations. Prentice-Hall, Upper Saddle River (1979)Keuning, D.: Grondslagen Van Het Management. Stenfert Kroese, Houten (1995) (in Dutch)Esteso, A., Alemany, M.M.E., Ortiz, A.: Conceptual framework for designing agri-food supply chains under uncertainty by mathematical programming models. Int. J. Prod. Res. (2018)Backus, G.B.C., Eidman, V.R., Dijkhuizen, A.A.: Farm decision making under risk and uncertainty. Neth. J. Agr. Sci. 45, 307–328 (1997)Esteso, A., Alemany, M.M.E., Ortiz, A.: Conceptual framework for managing uncertainty in a collaborative agri-food supply chain context. In: IFIP Advances in Information and Communication Technology, vol. 506, pp. 715–724 (2017)Mundi, I., Alemany, M.M.E., Poler, R., Fuertes-Miquel, V.S.: Review of mathematical models for production planning under uncertainty due to lack of homogeneity: proposal of a conceptual model. Int. J. Prod. Res. (2019)Grillo, H., Alemany, M.M.E., Ortiz, A., De Baets, B.: Possibilistic compositions and state functions: application to the order promising process for perishables. Int. J. Prod. Res. (2019)Soto-Silva, W.E., Nadal-Roig, E., González-Araya, M.C., Pla-Aragones, L.M.: Operational research models applied to the fresh fruit supply chain. Eur. J. Oper. Res. 251, 345–355 (2016)Farahani, R.Z., Rezapour, S., Drezner, T., Fallah, S.: Competitive supply chain network design: an overview of classifications, models, solution techniques and applications. Omega 45, 92–118 (2014)Banasik, A., Bloemhof-Ruwaard, J.M., Kanellopoulos, A., Claassen, G.D.H., van der Vorst, J.G.: Multi-criteria decision making approaches for green supply chains: a review. Flex. Serv. Manuf. J. 1–31 (2016)Paam, P., Berretta, R., Heydar, M., Middleton, R.H., García-Flores, R., Juliano, P.: Planning models to optimize the agri-fresh food supply chain for loss minimization: a review. In: Reference Module in Food Science (2016)Soysal, M., Bloemhof-Ruwaard, J.M., Meuwissen, M.P., van der Vorst, J.G.: A review on quantitative models for sustainable food logistics management. Int. J. Food Syst. Dyn. 3, 136–155 (2012