Integration of aqueous (micellar) two-phase systems on the proteins separation

A two-step approach combining an aqueous two-phase system (ATPS) and an aqueous micellar two-phase system (AMTPS), both based on the thermo-responsive copolymer Pluronic L-35, is here proposed for the purification of proteins and tested on the sequential separation of three model proteins, cytochrome c, ovalbumin and azocasein. Phase diagrams were established for the ATPS, as well as co-existence curves for the AMTPS. Then, by scanning and choosing the most promising systems, the separation of the three model proteins was performed. The aqueous systems based on Pluronic L-35 and potassium phosphate buffer (pH = 6.6) proved to be the most selective platform to separate the proteins (SAzo/Cyt = 1667; SOva/Cyt = 5.33 e SAzo/Ova = 1676). The consecutive fractionation of these proteins as well as their isolation from the aqueous phases was proposed, envisaging the industrial application of this downstream strategy. The environmental impact of this downstream process was studied, considering the carbon footprint as the final output. The main contribution to the total carbon footprint comes from the ultrafiltration (~ 49%) and the acid precipitation (~ 33%) due to the energy consumption in the centrifugation. The ATPS step contributes to ~ 17% while the AMTPS only accounts for 0.30% of the total carbon footprint.publishe

Cisluminator for agarose gel.

The CisIluminator. it is just a simple epiiluminator, for biology labs, or any lab that use agarose gels. Updates at: https://gitlab.com/Molino/CisLuminator/tree/master Features: UVB lamps for fluorophores excitation Lamps are positioned at 45º angle from gels position Image documentation can be taken by a Smartphone This project can be made using acrylyc or other laser cutable material, as MDF. It was tested with crude MDF (6 mm) and 4 mm transparent acrylic. Door hinge was printed with a open hinge fyle from Thingverse (http://www.thingiverse.com/thing:1396038)

Como calcular a quantidade de proteína/DNA em uma banda com o ImageJ

Esse vídeo é sobre como realizar análise de densitometria utilizando o ImageJ. Link no youtube: https://www.youtube.com/watch?v=NJO0CLwwpmw Info: Lingua: Português Programa: FIJI - Fiji is just ImageJ Imagem gel utilizada: File: SDS-PAGE with Taq DNA Polymerase.JPG Author: Marta Ferreira (MPCF) Multi-licensed under the GFDL and all CC-By-SA Link: https://commons.wikimedia.org/wiki/File:SDS-PAGE_with_Taq_DNA_Polymerase.JPG Imagem gel artificial File: Fake_gel.png Author: Molino, JVD Made in: Inkscap

Microcentrifuge tube rack

<p>A microcentrifuge rack.</p> <p>it is just a simple rack, for biology labs, or any lab that use microcentrifuge tubes.</p> <p>Updates at: https://gitlab.com/Molino/CisLuminator/tree/master</p> <p>Features:</p> <p><br> 65 holes for 1.5-2.0 mL microcentrifuge tubes<br> 36 holes for 0.6 mL microcentrifuge tubes<br> 37 holes for 0.2 mL microcentrifuge tubes</p> <p><br> This project can be made using acrylyc or other laser cutable material. It was tested with transparent acrylic (3 and 5 mm).</p> <p>The ticker the acrylic, more stable the structure.</p

OpenCyclop - a in situ microscope

<p>OpenCyclop.</p> <p>it is just a simple ISM (in situ microscope), for biology labs, or any lab that measure cell density in a culture.</p> <p>Updates at: https://gitlab.com/Molino/OpenCyclop</p> <p>Features:</p> <p>DIY microscope by webcam lens invertion<br> Structure to microscope coupling and microfluidic slide<br> Analysis sofware written in MATLAB </p> <p>This project can be made using simple webcam and 3D printed parts. Microfluidic slides can be purchased.</p

Fluorescence microscopy of Chlamydomonas reinhardtii for mCherry detection: secretion peptides strains.

Overview Life-cell imaging was performed with a confocal fluorescence microscopy to observe mCherry in the secretion vacuoles. mCherry fluorescence compartmentalization was observed by a Confocal Zeiss LSM 780-NLO, using an argon laser 543 nm to excite mCherry and a spectral detector set approximately to 610-650 nm range. For chlorophyll, we used a laser at 405 nm for excitation, and spectral detector set to 680 nm region. All pictures were taken with the same system configuration and analyzed by Fiji, an ImageJ distribution software. Cells images were acquired in bundles of 0.4 μm afar photos per channel in the z-axis. Files info: Each file is the raw image obtained from fluorescent microscopy. Organization Construct_name.czi - Ex: "pAH04mCherry.czi" pAH04mCherry -> construct without signal peptide pJP22mCherry -> construct with signal peptide from arylsulfatase 1 (Chlamydomonas reinhardtii) pJP26mCherry -> construct with signal peptide from binding protein 1 (C. reinhardtii) pJP28mCherry -> construct with signal peptide from carbonic anhydrase 1 (C. reinhardtii) pJP29 mCherry -> construct with signal peptide from ice-binding protein 1 (Artic Chlamydomonas sp) pJP30-35mCherry -> construct with signal peptide from in silico identified list (DOI 10.5281/zenodo.556792). Wildtype cc1690 -> parental strain used for transformation. For more information on the constructs, check our paper. Consider citing our work. Molino JVD, de Carvalho JCM, Mayfield SP (2018) Comparison of secretory signal peptides for heterologous protein expression in microalgae: Expanding the secretion portfolio for Chlamydomonas reinhardtii. PLoS ONE 13(2): e0192433. https://doi.org/10.1371/journal. pone.019243

Data - Effect of electrolytes as adjuvants in GFP and LPS partitioning on aqueous two-phase systems: 1. Polymer-polymer systems

<p><strong>Overview</strong></p> <p>The production of recombinant biopharmaceuticals is highly dependent of a proper choice of the downstream processing stages. Particularly, the purification that must ensure that all the endotoxins (lipopolysaccharide - LPS) are efficiently removed from the final product. This dataset contains the raw data and statistical analysis for the research entitled - "Effect of electrolytes as adjuvants in GFP and LPS partitioning on aqueous two-phase systems: 1. Polymer-polymer systems". </p> <p><strong>Info</strong></p> <p>ANOVA_Turkey_Sub.R <- code for ANOVA analysis in R statistic 3.3.3    <br> glm.R <- code for GLM analysis in R statistic 3.3.3<br> K&REC_LPS_PEG_NaPA.xlsx <- File with raw values organized in a spreadsheet of GFP partition coefficient (K) and recover (REC) for ANOVA analysis<br> K&REC_LPS_PEG_NaPA_K.docx <- File with ANOVA result of partition coefficient (K) for GFP<br> K&REC_LPS_PEG_NaPA_REC.docx <- File with ANOVA result of recover (REC) for GFP         <br> K_GFP_Pol_005.csv <- File with raw values organized in a spreadsheet of GFP partition coefficient (K) for GLM analysis in 0.05M salt assays    <br> K_GFP_Pol_005.doc <- File with GLM analysis of GFP partition coefficient (K) in 0.05M salt assays  <br> K_GFP_Pol_005_QQ.png <- Residual quantile plot of GLM analysis for partition coefficient (K) in 0.05M salt assays  <br> K_GFP_Pol_025.csv <- File with raw values organized in a spreadsheet of GFP partition coefficient (K) for GLM analysis in 0.25M salt assays  <br> K_GFP_Pol_025.doc  <- File with GLM analysis of GFP partition coefficient (K) in 0.25M salt assays  <br> K_GFP_Pol_025_QQ.png <- Residual quantile plot of GLM analysis for partition coefficient (K) in 0.25M salt assays         <br> REC_GFP_Pol_005.csv <- File with raw values organized in a spreadsheet of GFP recover (REC) for GLM analysis in 0.05M salt assays         <br> REC_GFP_Pol_005.doc  <- File with GLM analysis of GFP recover (REC) in 0.05M salt assays    <br> REC_GFP_Pol_005_QQ.png <- Residual quantile plot of GLM analysis of GFP recover (REC) in 0.05M salt assays   <br> REC_GFP_Pol_025.csv <- File with raw values organized in a spreadsheet of GFP recover (REC) for GLM analysis in 0.25M salt assays          <br> REC_GFP_Pol_025.doc  <- File with GLM analysis of GFP recover (REC) in 0.25M salt assays <br> REC_GFP_Pol_025_QQ.png <- Residual quantile plot of GLM analysis of GFP recover (REC) in 0.25M salt assays        <br> REM_LPS_PEG_NaPA.docx  <- File with ANOVA result of LPS removal          <br> REM_LPS_PEG_NaPA.xlsx <- File with raw values organized in a spreadsheet of LPS removal for ANOVA analysis<br> Stability_GFP_PEG_NaPA.docx <- File with ANOVA result of GFP stability<br> Stability_GFP_PEG_NaPA.xlsx <- File with raw values organized in a spreadsheet of GFP stability results for ANOVA analysis</p> <p>REM_LPS_Pol_005.csv  <- File with raw values organized in a spreadsheet of LPS removal (REM) for GLM analysis in 0.05M salt assays         <br> REM_LPS_Pol_005.doc  <- File with GLM analysis of LPS removal (REM) in 0.05M salt assays    <br> REM_LPS_Pol_005_QQ.png <- Residual quantile plot of GLM analysis of LPS removal (REM) in 0.05M salt assays  <br> REM_LPS_Pol_025.csv  <- File with raw values organized in a spreadsheet of LPS removal (REM) for GLM analysis in 0.25M salt assays         <br> REM_LPS_Pol_025.doc   <- File with GLM analysis of LPS removal (REM) in 0.25M salt assays    <br> REM_LPS_Pol_025_QQ.png <- Residual quantile plot of GLM analysis of LPS removal (REM) in 0.25M salt assays</p> <p>K_GFP_Pol_025_NaCl_Li2SO4.csv <- File with raw values organized in a spreadsheet of GFP partition coefficient (K) for GLM analysis in 0.25M salt assays comparing NaCl and Li2SO4 effect <br> K_GFP_Pol_025_NaCl_Li2SO4.doc  <- File with GLM analysis of GFP partition coefficient (K) in 0.25M salt assays comparing NaCl and Li2SO4 effect <br> K_GFP_Pol_025_NaCl_Li2SO4_QQ.png <- Residual quantile plot of GLM analysis of GFP recover (REC) in 0.25M salt assays comparing NaCl and Li2SO4 effect   </p> <p>REM_LPS_Pol_KI_0.05_vs_0.25.csv <- File with raw values organized in a spreadsheet of GFP partition coefficient (K) for GLM analysis in KI assays comparing salt concentration effect  <br> REM_LPS_Pol_KI_0.05_vs_0.25.doc <- File with GLM analysis of GFP partition coefficient (K) in KI assays comparing salt concentration effect<br> REM_LPS_Pol_KI_0.05_vs_0.25_QQ.png <- Residual quantile plot of GLM analysis of GFP recover (REC) in KI assays comparing salt concentration effect<br> REM_LPS_Pol_KNO3_0.05_vs_0.25.csv  <- File with raw values organized in a spreadsheet of GFP partition coefficient (K) for GLM analysis in KNO3 assays comparing salt concentration effect  <br> REM_LPS_Pol_KNO3_0.05_vs_0.25.doc <- File with GLM analysis of GFP partition coefficient (K) in KNO3 assays comparing salt concentration effect<br> REM_LPS_Pol_KNO3_0.05_vs_0.25_QQ.png <- Residual quantile plot of GLM analysis of GFP recover (REC) in KNO3 assays comparing salt concentration effect<br> REM_LPS_Pol_Li2SO4_0.05_vs_0.25.csv <- File with raw values organized in a spreadsheet of GFP partition coefficient (K) for GLM analysis in Li2SO4 assays comparing salt concentration effect  <br> REM_LPS_Pol_Li2SO4_0.05_vs_0.25.doc <- File with GLM analysis of GFP partition coefficient (K) in Li2SO4 assays comparing salt concentration effect<br> REM_LPS_Pol_Li2SO4_0.05_vs_0.25_QQ.png <- Residual quantile plot of GLM analysis of GFP recover (REC) in Li2SO4 assays comparing salt concentration effect<br> REM_LPS_Pol_NaCl_0.05_vs_0.25.csv <- File with raw values organized in a spreadsheet of GFP partition coefficient (K) for GLM analysis in NaCl assays comparing salt concentration effect  <br> REM_LPS_Pol_NaCl_0.05_vs_0.25.doc <- File with GLM analysis of GFP partition coefficient (K) in NaCl assays comparing salt concentration effect <br> REM_LPS_Pol_NaCl_0.05_vs_0.25_QQ.png <- Residual quantile plot of GLM analysis of GFP recover (REC) in NaCl assays comparing salt concentration effect</p> <p> </p> <p><strong>Annotation</strong></p> <p>12/12 - Concentration of 12% of each polymer PEG/NaPA</p> <p>16/16 - Concentration of 16% of each polymer PEG/NaPA</p> <p>P/N -  PEG/NaPA</p> <p>10e4, 10e5, 10e6 - Concentration of LPS in scientific notation - 10000, 100000, 100000 EU/mL</p> <p>poly - Polymer</p> <p>salt - Salt concentration in the assay</p> <p>tsalt - Type of salt in the assay (NaCl, KNO3, KI and Li2SO4)</p> <p>lps - lipopolysaccharide</p> <p>K - GFP partition coefficient</p> <p>REM - LPS removal</p> <p>REC - GFP recover</p> <p>wo_salt - Assay without salt addition</p> <p><strong>Acknowledgements</strong></p> <p>The authors are grateful for financial support from FAPESP (São Paulo Research Foundation, Brazil) through the following projects: 2005/60159-7; 2007/51978-0; 2014/16424-7; and 2014/19793-3. The authors also acknowledge the support from CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Brazil) through the process #0366/09-9 and CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brazil).</p> <p><strong>Consider citing our work. </strong></p> <p>1. Work in progress...</p

Data - Effect of electrolytes as adjuvants in GFP and LPS partitioning on aqueous two-phase systems: 2. Nonionic micellar systems

<p><strong>Overview</strong></p> <p>The production of recombinant biopharmaceuticals is highly dependent of a proper choice of the downstream processing stages. Particularly, the purification that must ensure that all the endotoxins (lipopolysaccharide - LPS) are efficiently removed from the final product. This dataset contains the raw data and statistical analysis for the research entitled - "Effect of electrolytes as adjuvants in GFP and LPS partitioning on aqueous two-phase systems: 2. Nonionic micellar systems". </p> <p><strong>Info</strong></p> <p>ANOVA_Turkey_Sub.R <- code for ANOVA analysis in R statistic 3.3.3    <br> glm.R <- code for GLM analysis in R statistic 3.3.3<br> K&REC_ORG_ANOVA.csv  <- File with raw values organized in a spreadsheet of GFP partition coefficient (K) and recover (REC) for ANOVA analysis</p> <p>K_ORG_ANOVA.docx <-  File with ANOVA result of partition coefficient (K) for GFP</p> <p>REC_ORG_ANOVA.docx  <- File with ANOVA result of partition coefficient (REC) for GFP</p> <p>REM_LPS_ORG_ANOVA.csv  <- File with raw values organized in a spreadsheet of LPS removal for ANOVA analysis</p> <p>REM_LPS_ORG_ANOVA.docx  <- File with ANOVA result of removal of LPS</p> <p>Stability__ORG_ANOVA.csv <- File with raw values organized in a spreadsheet of GFP stability for ANOVA analysis</p> <p>Stability__ORG_ANOVA.docx  <- File with ANOVA result of GFP stability</p> <p>K_ORG_glm_005.csv  <- File with raw values organized in a spreadsheet of GFP partition coefficient (K) for GLM analysis in 0.05M salt assays    </p> <p>K_ORG_glm_005.doc <- File with GLM analysis of GFP partition coefficient (K) in 0.05M salt assays  </p> <p>K_ORG_glm_005_QQ.png <- Residual quantile plot of GLM analysis for partition coefficient (K) in 0.05M salt assays  </p> <p>K_ORG_glm_025.csv  <- File with raw values organized in a spreadsheet of GFP partition coefficient (K) for GLM analysis in 0.25M salt assays    </p> <p>K_ORG_glm_025.doc <- File with GLM analysis of GFP partition coefficient (K) in 0.25M salt assays  </p> <p>K_ORG_glm_025_QQ.png <- Residual quantile plot of GLM analysis for partition coefficient (K) in 0.25M salt assays  </p> <p>REC_ORG_glm_005.csv <- File with raw values organized in a spreadsheet of GFP recover (REC) for GLM analysis in 0.05M salt assays</p> <p>REC_ORG_glm_005.doc <-  File with GLM analysis of GFP recover (REC) in 0.05M salt assays    </p> <p>REC_ORG_glm_005_QQ.png <- Residual quantile plot of GLM analysis of GFP recover (REC) in 0.05M salt assays   </p> <p>REC_ORG_glm_025.csv <- File with raw values organized in a spreadsheet of GFP recover (REC) for GLM analysis in 0.25M salt assays</p> <p>REC_ORG_glm_025.doc <-  File with GLM analysis of GFP recover (REC) in 0.25M salt assays    </p> <p>REC_ORG_glm_025_QQ.png <- Residual quantile plot of GLM analysis of GFP recover (REC) in 0.25M salt assays   </p> <p>REM_ORG_glm_005.csv <- File with raw values organized in a spreadsheet of LPS removal (REM) for GLM analysis in 0.05M salt assays</p> <p>REM_ORG_glm_005.doc <-  File with GLM analysis of LPS removal (REM) in 0.05M salt assays  </p> <p>REM_ORG_glm_005_QQ.png <-  Residual quantile plot of GLM analysis of LPS removal (REM) in 0.25M salt assays</p> <p>REM_ORG_glm_025.csv <- File with raw values organized in a spreadsheet of LPS removal (REM) for GLM analysis in 0.25M salt assays</p> <p>REM_ORG_glm_025.doc <-  File with GLM analysis of LPS removal (REM) in 0.25M salt assays </p> <p>REM_ORG_glm_025_QQ.png <-  Residual quantile plot of GLM analysis of LPS removal (REM) in 0.25M salt assays</p> <p> </p> <p><strong>Annotation</strong></p> <p>12/12 - Concentration of 12% of each polymer PEG/NaPA</p> <p>16/16 - Concentration of 16% of each polymer PEG/NaPA</p> <p>P/N -  PEG/NaPA</p> <p>10e4, 10e5, 10e6 - Concentration of LPS in scientific notation - 10000, 100000, 100000 EU/mL</p> <p>poly - Polymer</p> <p>salt - Salt concentration in the assay</p> <p>tsalt - Type of salt in the assay (NaCl, KNO3, KI and Li2SO4)</p> <p>lps - lipopolysaccharide</p> <p>K - GFP partition coefficient</p> <p>REM - LPS removal</p> <p>REC - GFP recover</p> <p>wo_salt - Assay without salt addition</p> <p><strong>Acknowledgements</strong></p> <p>The authors are grateful for financial support from FAPESP (São Paulo Research Foundation, Brazil) through the following projects: 2005/60159-7; 2007/51978-0; 2014/16424-7; and 2014/19793-3. The authors also acknowledge the support from CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Brazil) through the process #0366/09-9 and CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brazil).</p> <p><strong>Consider citing our work. </strong></p> <p>1. Work in progress...</p