Phaeomelanin- and carotenoid-based pigmentation reflect oxidative status in two populations of the yellow warbler (Setophaga petechia)

Carotenoid- and phaeomelanin-based sexual pigmentation may signal a capacity to maintain oxidative balance and viability. However, diverse empirical results leave the association between pigmentation and oxidative stress (OS) unclear. We assessed the hypothesis that population-specific levels of oxidative challenge, or strategies for managing OS, affect relationships between sexual pigmentation and OS. Specifically, intense oxidative challenge in migratory, temperate breeding birds might enhance correlations between pigmentation and OS relative to allied tropical breeders, since quality-based differences in OS may arise only under intense oxidative challenge. Alternatively, in temperate breeders with intense within-season reproductive effort, high-quality birds may invest in reproduction over oxidative balance, dampening negative correlations between pigmentation and OS. To assess these alternatives, we compared prenesting relationships between pigmentation and OS in a migratory, Californian population of yellow warblers (Setophaga petechia brewsteri) and in a resident, Mexican population (Setophaga petechia bryanti, "mangrove warblers"). Yellow warblers displayed higher OS than mangrove warblers. However, year of capture and sex had bigger influences on correlations between pigmentation and OS than population. Males with more intense melanin pigmentation had lower OS among mangrove warblers and yellow warblers captured in 2011, but not among yellow warblers captured in 2012. In females only, lower OS levels were associated with more colorful carotenoid pigmentation. Results suggest that both phaeomelanin- and carotenoid-based pigmentation have the potential to correlate with OS levels, but that the signaling potential of pigmentation may shift with inter-annual variation in environmental conditions and display sex-specific dynamics. © 2014 Springer-Verlag Berlin Heidelberg

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

©2008 Pandit and Skolnick; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This article is available from: http://www.biomedcentral.com/1471-2105/9/531doi:10.1186/1471-2105-9-531Background: Protein tertiary structure comparisons are employed in various fields of contemporary structural biology. Most structure comparison methods involve generation of an initial seed alignment, which is extended and/or refined to provide the best structural superposition between a pair of protein structures as assessed by a structure comparison metric. One such metric, the TM-score, was recently introduced to provide a combined structure quality measure of the coordinate root mean square deviation between a pair of structures and coverage. Using the TM-score, the TM-align structure alignment algorithm was developed that was often found to have better accuracy and coverage than the most commonly used structural alignment programs; however, there were a number of situations when this was not true. Results: To further improve structure alignment quality, the Fr-TM-align algorithm has been developed where aligned fragment pairs are used to generate the initial seed alignments that are then refined using dynamic programming to maximize the TM-score. For the assessment of the structural alignment quality from Fr-TM-align in comparison to other programs such as CE and TMalign, we examined various alignment quality assessment scores such as PSI and TM-score. The assessment showed that the structural alignment quality from Fr-TM-align is better in comparison to both CE and TM-align. On average, the structural alignments generated using Fr-TM-align have a higher TM-score (~9%) and coverage (~7%) in comparison to those generated by TM-align. Fr- TM-align uses an exhaustive procedure to generate initial seed alignments. Hence, the algorithm is computationally more expensive than TM-align. Conclusion: Fr-TM-align, a new algorithm that employs fragment alignment and assembly provides better structural alignments in comparison to TM-align. The source code and executables of Fr- TM-align are freely downloadable at: http://cssb.biology.gatech.edu/skolnick/files/FrTMalign/

Hydrocarbons Are Essential for Optimal Cell Size, Division, and Growth of Cyanobacteria.

Cyanobacteria are intricately organized, incorporating an array of internal thylakoid membranes, the site of photosynthesis, into cells no larger than other bacteria. They also synthesize C15-C19 alkanes and alkenes, which results in substantial production of hydrocarbons in the environment. All sequenced cyanobacteria encode hydrocarbon biosynthesis pathways, suggesting an important, undefined physiological role for these compounds. Here, we demonstrate that hydrocarbon-deficient mutants of $\textit{Synechocystis }$ sp. PCC 7002 and $\textit{Synechocystis }$ sp. PCC 6803 exhibit significant phenotypic differences from wild type, including enlarged cell size, reduced growth, and increased division defects. Photosynthetic rates were similar between strains, although a minor reduction in energy transfer between the soluble light harvesting phycobilisome complex and membrane-bound photosystems was observed. Hydrocarbons were shown to accumulate in thylakoid and cytoplasmic membranes. Modeling of membranes suggests these compounds aggregate in the center of the lipid bilayer, potentially promoting membrane flexibility and facilitating curvature. In vivo measurements confirmed that $\textit{Synechocystis }$ sp. PCC 7002 mutants lacking hydrocarbons exhibit reduced thylakoid membrane curvature compared to wild type. We propose that hydrocarbons may have a role in inducing the flexibility in membranes required for optimal cell division, size, and growth, and efficient association of soluble and membrane bound proteins. The recent identification of C15-C17 alkanes and alkenes in microalgal species suggests hydrocarbons may serve a similar function in a broad range of photosynthetic organisms.T.L. was supported by BBSRC Research Grant BB/J016985/1 to C.W.M. D.J.L-S. was supported by the Environmental Services Association Education Trust. L.L.B was supported by a BBSRC Doctoral Training Grant (BB/F017464/1)

Hydrocarbons Are Essential for Optimal Cell Size, Division, and Growth of Cyanobacteria.

Cyanobacteria are intricately organized, incorporating an array of internal thylakoid membranes, the site of photosynthesis, into cells no larger than other bacteria. They also synthesize C15-C19 alkanes and alkenes, which results in substantial production of hydrocarbons in the environment. All sequenced cyanobacteria encode hydrocarbon biosynthesis pathways, suggesting an important, undefined physiological role for these compounds. Here, we demonstrate that hydrocarbon-deficient mutants of $\textit{Synechocystis }$ sp. PCC 7002 and $\textit{Synechocystis }$ sp. PCC 6803 exhibit significant phenotypic differences from wild type, including enlarged cell size, reduced growth, and increased division defects. Photosynthetic rates were similar between strains, although a minor reduction in energy transfer between the soluble light harvesting phycobilisome complex and membrane-bound photosystems was observed. Hydrocarbons were shown to accumulate in thylakoid and cytoplasmic membranes. Modeling of membranes suggests these compounds aggregate in the center of the lipid bilayer, potentially promoting membrane flexibility and facilitating curvature. In vivo measurements confirmed that $\textit{Synechocystis }$ sp. PCC 7002 mutants lacking hydrocarbons exhibit reduced thylakoid membrane curvature compared to wild type. We propose that hydrocarbons may have a role in inducing the flexibility in membranes required for optimal cell division, size, and growth, and efficient association of soluble and membrane bound proteins. The recent identification of C15-C17 alkanes and alkenes in microalgal species suggests hydrocarbons may serve a similar function in a broad range of photosynthetic organisms.T.L. was supported by BBSRC Research Grant BB/J016985/1 to C.W.M. D.J.L-S. was supported by the Environmental Services Association Education Trust. L.L.B was supported by a BBSRC Doctoral Training Grant (BB/F017464/1)

Morphological characterization of sweet and sour cherry cultivars in a germplasm bank at Portugal

Nine sweet cherry and eight sour cherry varieties located in a germplasm bank at Fundauo, Portugal, were studied from the viewpoint of characterization. Most of them were autochthonous cultivars that have a high risk of extinction since at the present they are markedly minor varieties. Morphological characteristics were evaluated in different organs: crown and trunk of the trees, leaves, flowers and fruits, over a three consecutive years period. Statistical analyses were carried out in order to detect similarities between cultivars as well as the existence of synonymies. Qualitative characteristics of the fruits were scored in order to carry out the multivariate analysis. A dendrogram of the evaluated characters shows the marked differentiation between sour and sweet cherries and suggests the existing synonymies. Conservation of the autochthonous cultivars in the future is highly recommended

Cortical microstructure in primary progressive aphasia: a multicenter study

Cortical mean diffusivity is a novel imaging metric sensitive to early changes in neurodegenerative syndromes. Higher cortical mean diffusivity values reflect microstructural disorganization and have been proposed as a sensitive biomarker that might antedate macroscopic cortical changes. We aimed to test the hypothesis that cortical mean diffusivity is more sensitive than cortical thickness to detect cortical changes in primary progressive aphasia (PPA).In this multicenter, case-control study, we recruited 120 patients with PPA (52 non-fluent, 31 semantic, and 32 logopenic variants; and 5 GRN-related PPA) as well as 89 controls from three centers. The 3-Tesla MRI protocol included structural and diffusion-weighted sequences. Disease severity was assessed with the Clinical Dementia Rating scale. Cortical thickness and cortical mean diffusivity were computed using a surface-based approach.The comparison between each PPA variant and controls revealed cortical mean diffusivity increases and cortical thinning in overlapping regions, reflecting the canonical loci of neurodegeneration of each variant. Importantly, cortical mean diffusivity increases also expanded to other PPA-related areas and correlated with disease severity in all PPA groups. Cortical mean diffusivity was also increased in patients with very mild PPA when only minimal cortical thinning was observed and showed a good correlation with measures of disease severity.Cortical mean diffusivity shows promise as a sensitive biomarker for the study of the neurodegeneration-related microstructural changes in PPA.© 2022. The Author(s)

Assessing the Impact of Pumpkins Plantation, Harvest and Storage Decisions on a Collaborative Supply Chain with Data Analysis Tools

[EN] Successful pumpkins production requires the use of varieties that jointly with other factors yield well and produce pumpkins of the size, shape, color, and quality demanded by the market. But not only these issues are important. The perishable nature of pumpkins makes other issues such as how to prevent deterioration after harvest to become also relevant. In this paper the pumpkins plantation, harvest and storage (PHS) process is described and how some decisions affect certain goals, such as yield or conservation time. Additionally, some decision-making insights in a supply chain collaborative scenario made up of two stages: plantation/harvest and storage are given, where yield and conservation time trade-offs are outlined to develop win-win strategies. A real case using data analysis tools is analyzed. Results provide guidelines not only to make decisions independently on each stage but also to collaboratively work.The authors acknowledge the support of the project 691249, RUCAPS: "Enhancing and implementing knowledge based ICT solutions within high risk and uncertain conditions for agriculture production systems", funded by the European Union's research and innovation programme under the H2020 Marie Skodowska-Curie Actions.Pérez Perales, D.; Rodríguez-Sánchez, MDLÁ.; Ortiz Bas, Á.; Guyon, C. (2020). Assessing the Impact of Pumpkins Plantation, Harvest and Storage Decisions on a Collaborative Supply Chain with Data Analysis Tools. IFIP Advances in Information and Communication Technology. 598:511-523. https://doi.org/10.1007/978-3-030-62412-5_42S511523598Prima, W.A., Xing, K., Amer, Y.: Collaboration and sustainable agri-food supply chain: a literature review. MATEC, 5802004 (2016)Pérez Perales, D., Alarcón Valero, F., Drummond, C., Ortiz, Á.: Towards a sustainable agri-food supply chain model. the case of LEAF. In: Ortiz, Á., Andrés Romano, C., Poler, R., García-Sabater, J.-P. (eds.) Engineering Digital Transformation. LNMIE, pp. 333–341. Springer, Cham (2019). https://doi.org/10.1007/978-3-319-96005-0_40Esteso, 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. 56(13), 4418–4446 (2018)Bahrami, R., Khodadadi, M., Piry, S., Hassanpanah, D.: The effects of planting methods and head pruning on seed yield and yield components of medicinal pumpkin (Cucurbita Pepo Subsp. Pepo Convar. Pepo Var. Styriaca) at low temperature areas. Pak. J. Bio. Sci. 12(6), 538–541 (2009)Tarus, W.J., Ochuodho, J.O., Rop, N.K.: Influence of harvesting stage on seed quality aspects of pumpkin (Cucurbita Pepo L.). J. Exp. Agr. 18(2), 1–9 (2017)Amodio, M.L., Rinaldi, R., Colell, G.: Extending shelf life of fresh-cut pumpkin (Cucurbita Maxima): effect of pre-treatments and storage conditions. Acta Hortic. 876, 333–340 (2010)Pimentel, D., et al.: Annual vs perennial grain production. Agric. Ecosyst. Environ. 161, 1–9 (2012)Biesiada, A., Nawirska, A., Kucharska, A., Sokół-Łętowska, A.: The effect of nitrogen fertilization methods on yield and chemical composition of pumpkin (Cucurbita maxima) fruits before and after storage. Veg. Crops. Res. B. 70, 203–211 (2009)Gwenael, J., Paul, Ch., Sau, I., Saurabh, S., Thomasse, S.: Hitting and harvesting pumpkins. Siam. J. Discrete. Math. 28(3), 1363–1390 (2014)Oluoch, M.O.: Production practices of pumpkins for improved productivity. Scripta. Hort. 15, 181–189 (2012)Ondigi, A., Toili, W., Ijani, A., Omuterema, S.: Comparative analysis of production practices and utilization of pumpkins (Cucurbita Pepo and Cucurbita Maxima) by smallholder farmers in the lake victoria basin, East Africa. Afr. J. Environ. Sci. Tech. 2(9), 296–304 (2008)Naik, M.L., Prasad, V.M., Raya, L.P.: A study on character association and path analysis in pumpkin (Cucurbita Moschata Duch. Ex Poir.). Int. J. Adv. Res. 3(1), 1030–1034 (2015)Nerson, H., Paris, H.S., Paris, E.P.: Fruit shape, size and seed yield in Cucurbita Pepo. Acta Hort. 510, 227–230 (2000)Ortiz, A., Alarcón, F., Pérez, D., Alemany, M.M.E.: Identifying the main uncertainties in the agri-food supply chain. In: Mula, J., Barbastefano, R., Díaz-Madroñero, M., Poler, R. (eds.) New global perspectives on industrial engineering and management. LNMIE, pp. 221–229. Springer, Cham (2019). https://doi.org/10.1007/978-3-319-93488-4_25Khalid, E., Mohammed, E.: Dependence of pumpkin yield on plant density and variety. Am. J. Plant. Sci. 2, 636–643 (2011)Jakop, M., et al.: Yield performance and agronomic efficiency in oil pumpkins (Cucurbita Pepo L. Group Pepo) depending on production systems and varieties. Agr. 14(1), 25–36 (2017)Ahmed, B., Masud, M.A.T., Zakaria, M., Hossain, M.M., Mian, M.A.K.: Evaluation of pumpkin (Cucurbita Moschata Duch. Ex Poir.) for yield and other characters. Bangl. J. Agr. Res. 42(1), 1–11 (2017)Zhao, J., et al.: Physicochemical and antioxidant properties of different pumpkin cultivars grown in China. Food Sci. Technol. 9(4), 308–316 (2015)Zhou, C., et al.: The effect of high hydrostatic pressure on the microbiological quality and physical–chemical characteristics of pumpkin (Cucurbita Maxima Duch.) during refrigerated storage. Innov. Food. Sci. Emerg. 21, 24–34 (2014)Loy, J.B.: Harvest period and storage affect biomass partitioning and attributes of eating quality in acorn squash (Cucurbita Pepo), Présenté à Cucurbitaceae, Asheville, North Carolina, USA, pp. 568–577 (2006)Nagao, A., Indou, T., Dohi, H.: Effects of curing condition and storage temperature on postharvest quality of squash fruit. J. Jpn. Soc. Hort. Sci. 60(1), 175–181 (1991)Habibunnisa, R., Prasad, R., Shivaiah, K.M.: Storage behaviour of minimally processed pumpkin (Cucurbita Maxima) under modified atmosphere packaging conditions. Eur. Food Res. Technol. 212(2), 165–169 (2001)Sharrock, K.R., Parkes, S.L.: Physiological changes during development and storage of fruit of buttercup squash in relation to their susceptibility to Rot. New. Zeal. J. Crop. Hort. 18(4), 185–196 (1990)Muzzaffar, S., Baba, W.N., Nazir, N., Masoodi, F.A., Bhat, M.M., Bazaz, R.: Effect of storage on physicochemical, microbial and antioxidant properties of pumpkin (Cucurbita Moschata) candy. Cog. Food. Agr. 2(1), 1163650 (2016)Rahman, M.A., Miaruddin, M., Khan, M.H.H., Masud, M.A.T., Begum, M.M.: Effect of storage periods on postharvest quality of pumpkin. Bangl. J. Agr. Res. 38(2), 247–255 (2013)Song, J., Wei, Q., Wang, X., Li, D., Liu, C., Zhang, M., Meng, L.: Degradation of carotenoids in dehydrated pumpkins as affected by different storage conditions. Food. Res. Int. 107, 130–136 (2018)Matová, A.: the influence of genotype and storage condition on the content of selected bioactive substances in the fruit of pumpkin (Cucurbita Moschata Duch.). J. Microbiol. Bioech. Food. Sci. 9(2), 288–292 (2019)Tilman, D., Balzer, C., Hill, J., Befort, B.L.: Global food demand and the sustainable intensification of agricultura. Proc. Natl. Acad. Sci. U. S. A. 108, 20260–20264 (2011)Wang, W., et al.: Multiple trade‐offs between maximizing yield and minimizing greenhouse gas production in Chinese rice croplands. Land. Degrad. Dev. (2020)Pleijel, H., Uddling, J.: Yield vs. quality trade-offs for wheat in response to carbon dioxide and ozone. Glob. Change. Biol. 18(2), 596–n/a (2011)Pedhazur, E.J., Schmelkin, L.P.: Measurement, Design, and Analysis: an Integrated Approach. Lawrence Erlbaum Associates, Hillsdale (1991