Singhania RR, Patel AK, Thomas L et al (2015) Industrial enzymes. In: Pandey A, Höfer R, Taherzadeh M et al (eds) Industrial biorefineries & white biotechnology. Elsevier, London, pp 473–497
Damborsky J, Brezovsky J (2013) ScienceDirect computational tools for designing and engineering enzymes. Curr Opin Chem Biol 19:8–16. doi:10.1016/j.cbpa.2013.12.003
Heux S, Donohue MJO, Dumon C (2015) White biotechnology: state of the art strategies for the development of biocatalysts for biore fi ning. Biotechnol Adv 33:1653–1670. doi:10.1016/j.biotechadv.2015.08.004
Tiwari MK, Singh R, Singh RK et al (2012) Computational approaches for rational design of proteins with novel functionalities structural, catalytic, sensory, and regulatory functions. Rational design of enzymes is a great challenge to our understanding of design or engineer proteins that fold. Comput Struct Biotechnol 2:1–13. doi:10.5936/csbj.201209002
Wölcke J, Ullmann D (2001) Miniaturized HTS technologies—uHTS. Drug Discov Today 6:637–646. doi:10.1016/S1359-6446(01)01807-4
Cacho RA, Tang Y, Chooi Y-H (2015) Next-generation sequencing approach for connecting secondary metabolites to biosynthetic gene clusters in fungi. Frontiers Microbiol 5:774. doi:10.3389/fmicb.2014.00774
Weber T, Kim HU (2016) The secondary metabolite bioinformatics portal: computational tools to facilitate synthetic biology of secondary metabolite production. Synth Syst Biotechnol. doi:10.1016/j.synbio.2015.12.002
Medema MH, Kottmann R, Yilmaz P et al (2015) The minimum information about a biosynthetic gene cluster (MIBiG) specification. Nat Chem Biol 11:625–631. doi:10.1038/nchembio.1890
Caradec T, Pupin M, Vanvlassenbroeck A et al (2014) Prediction of monomer isomery in florine: a workflow dedicated to nonribosomal peptide discovery. PLoS One. doi:10.1371/journal.pone.0085667
Leclère V, Weber T, Jacques P, Pupin M (2016) Bioinformatics tools for the discovery of new nonribosomal peptides. Methods in molecular biology (Clifton, NJ) 1401:209–232. doi:10.1007/978-1-4939-3375-4_14
Flissi A, Dufresne Y, Michalik J et al (2015) Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing. Nucleic Acids Res 44:D1113–D1118. doi:10.1093/nar/gkv1143
Conway KR, Boddy CN (2013) ClusterMine360: a database of microbial PKS/NRPS biosynthesis. Nucleic Acids Res 41:402–407. doi:10.1093/nar/gks993
Pupin M, Esmaeel Q, Flissi A et al (2015) Norine: a powerful resource for novel nonribosomal peptide discovery. Synth Syst Biotechnol. doi:10.1016/j.synbio.2015.11.001
Weber T, Blin K, Duddela S et al (2015) AntiSMASH 3. 0—a comprehensive resource for the genome mining of biosynthetic gene clusters. 43:237–243. doi:10.1093/nar/gkv437
Starcevic A, Zucko J, Simunkovic J et al (2008) ClustScan: an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures. Nucleic Acids Res 36:6882–6892. doi:10.1093/nar/gkn685
Khaldi N, Seifuddin FT, Turner G et al (2010) SMURF: genomic mapping of fungal secondary metabolite clusters. Fungal Genet Biol 47:736–741. doi:10.1016/j.fgb.2010.06.003
Esmaeel Q, Pupin M, Kieu NP et al (2016) Burkholderia genome mining for nonribosomal peptide synthetases reveals a great potential for novel siderophores and lipopeptides synthesis. MicrobiologyOpen. doi:10.1002/mbo3.347
Rohe P, Venkanna D, Kleine B et al (2012) An automated workflow for enhancing microbial bioprocess optimization on a novel microbioreactor platform. Microb Cell Fact 11:144. doi:10.1186/1475-2859-11-144
Zhao J, Li Y, Zhang C et al (2012) Genome shuffling of Bacillus amyloliquefaciens for improving antimicrobial lipopeptide production and an analysis of relative gene expression using FQ RT-PCR. J Ind Microbiol Biotechnol 39:889–896. doi:10.1007/s10295-012-1098-9
Mali P, Yang L, Esvelt KM et al (2013) RNA-guided human genome engineering via Cas9. Science 339:823–826. doi:10.1126/science.1232033
Le Cong F, Ran A, Cox D et al (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339:819–823. doi:10.1126/science.1231143
Mei Y, Wang Y, Chen H et al (2016) Recent progress in CRISPR/Cas9 technology. J Genet Genomics 43:63–75. doi:10.1016/j.jgg.2016.01.001
Kanaar R, Wyman C, Rothstein R (2008) Quality control of DNA break metabolism: in the “end”, it’s a good thing. EMBO J 27:581–588. doi:10.1038/emboj.2008.11
Jiang W, Bikard D, Cox D et al (2013) RNA-guided editing of bacterial genomes using CRISPR–Cas systems. Nat Biotechnol 31:233–239. doi:10.1038/nbt.2508
Cobb RE, Wang Y, Zhao H (2014) High-efficiency multiplex genome editing of Streptomyces species using an engineered CRISPR/Cas system. ACS Synth Biol. doi:10.1021/sb500351f
Tong Y, Charusanti P, Zhang L et al (2015) CRISPR–Cas9 based engineering of actinomycetal genomes. ACS Synth Biol 4:1020–1029. doi:10.1021/acssynbio.5b00038
Hodgkins A, Farne A, Perera S et al (2015) WGE: a CRISPR database for genome engineering. Bioinformatics 31:3078–3080. doi:10.1093/bioinformatics/btv308
Xu H, Xiao T, Chen CH et al (2015) Sequence determinants of improved CRISPR sgRNA design. Genome Res 25:1147–1157. doi:10.1101/gr.191452.115
Blin K, Pedersen LE, Weber T, Lee SY (2016) CRISPy-web: an online resource to design sgRNAs for CRISPR applications. Synth Syst Biotechnol. doi:10.1016/j.synbio.2016.01.003
Weber T, Blin K, Duddela S et al (2015) AntiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 43:1–7. doi:10.1093/nar/gkv437
Bikard D, Euler CW, Jiang W et al (2014) Exploiting CRISPR–Cas nucleases to produce sequence-specific antimicrobials. Nat Biotechnol 32:1146–1150. doi:10.1038/nbt.3043
Citorik RJ, Mimee M, Lu TK (2014) Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. Nat Biotechnol 32:1141–1145. doi:10.1038/nbt.3011
Beisel CL, Gomaa AA, Barrangou R (2014) A CRISPR design for next-generation antimicrobials. Genome Biol 15:516. doi:10.1186/s13059-014-0516-x
Peng J, Zhou Y, Zhu S, Wei W (2015) High-throughput screens in mammalian cells using the CRISPR–Cas9 system. FEBS J 282:2089–2096. doi:10.1111/febs.13251
Shi J, Wang E, Milazzo JP et al (2015) Discovery of cancer drug targets by CRISPR–Cas9 screening of protein domains. Nat Biotechnol 33:1–10. doi:10.1038/nbt.3235
Kilian KA, Moghe PV (2016) High throughput strategies for the design, discovery, and analysis of biomaterials. Acta Biomater 34:v–vi. doi:10.1016/j.actbio.2016.03.019
Bertin PN, Heinrich-Salmeron A, Pelletier E et al (2011) Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta- and proteo-genomics. ISME J 5:1735–1747. doi:10.1038/ismej.2011.51
Piel J (2002) A polyketide synthase-peptide synthetase gene cluster from an uncultured bacterial symbiont of Paederus beetles. Proc Natl Acad Sci USA 99:14002–14007. doi:10.1073/pnas.222481399
Wierzbicka-Woś A, Bartasun P, Cieśliński H et al (2013) Cloning and characterization of a novel cold-active glycoside hydrolase family 1 enzyme with β-glucosidase, β-fucosidase and β-galactosidase activities. BMC Biotechnol 13:22. doi:10.1186/1472-6750-13-22
Schröder C, Elleuche S, Blank S, Antranikian G (2014) Characterization of a heat-active archaeal β-glucosidase from a hydrothermal spring metagenome. Enzyme Microb Technol 57:48–54. doi:10.1016/j.enzmictec.2014.01.010
Zhu Y, Li J, Cai H et al (2013) Characterization of a new and thermostable esterase from a metagenomic library. Microbiol Res 168:589–597. doi:10.1016/j.micres.2013.04.004
Harris AD (2012) Soil metagenomics: a prospective approach for novel enzyme discovery. Int J Curr Res 4:88–92
Hawksworth DL (1991) The fungal dimension of biodiversity: magnitude, significance, and conservation. Mycol Res 95:641–655. doi:10.1016/S0953-7562(09)80810-1
Blackwell M (2011) The fungi: 1, 2, 3… 5.1 million species? Am J Bot 98:426–438. doi:10.3732/ajb.1000298
Reeder J, Knight R (2009) The “rare biosphere”: a reality check. Nat Methods 6:636–637. doi:10.1038/nmeth0909-636
Ling LL, Schneider T, Peoples AJ et al (2015) A new antibiotic kills pathogens without detectable resistance. Nature 517:455–459. doi:10.1038/nature14098
Lewis K, Epstein S, D’Onofrio A, Ling LL (2010) Uncultured microorganisms as a source of secondary metabolites. J Antibiot 63:468–476. doi:10.1038/ja.2010.87
Wohlgemuth R, Plazl I, Žnidaršič-Plazl P et al (2015) Microscale technology and biocatalytic processes: opportunities and challenges for synthesis. Trends Biotechnol 33:302–314. doi:10.1016/j.tibtech.2015.02.010
Tušek A, Šalić A, Kurtanjek Ž, Zelić B (2012) Modeling and kinetic parameter estimation of alcohol dehydrogenase-catalyzed hexanol oxidation in a microreactor. Eng Life Sci 12:49–56. doi:10.1002/elsc.201100020
Kintses B, Hein C, Mohamed MF et al (2012) Picoliter cell lysate assays in microfluidic droplet compartments for directed enzyme evolution. Chem Biol 19:1001–1009. doi:10.1016/j.chembiol.2012.06.009
Wójcik M, Telzerow A, Quax WJ, Boersma YL (2015) High-throughput screening in protein engineering: recent advances and future perspectives. Int J Mol Sci 16:24918–24945. doi:10.3390/ijms161024918
Pitzler C, Wirtz G, Vojcic L et al (2014) A fluorescent hydrogel-based flow cytometry high-throughput screening platform for hydrolytic enzymes. Chem Biol 21:1733–1742. doi:10.1016/j.chembiol.2014.10.018
Tu R, Martinez R, Prodanovic R et al (2011) A flow cytometry-based screening system for directed evolution of proteases. J Biomol Screen 16:285–294. doi:10.1177/1087057110396361
Becker S, Höbenreich H, Vogel A et al (2008) Single-cell high-throughput screening to identify enantioselective hydrolytic enzymes. Angew Chem Int Ed 47:5085–5088. doi:10.1002/anie.200705236
Fernández-Álvaro E, Snajdrova R, Jochens H et al (2011) A combination of in vivo selection and cell sorting for the identification of enantioselective biocatalysts. Angew Chem Int Ed 50:8584–8587. doi:10.1002/anie.201102360
Davids T, Schmidt M, Böttcher D, Bornscheuer UT (2013) Strategies for the discovery and engineering of enzymes for biocatalysis. Curr Opin Chem Biol 17:215–220. doi:10.1016/j.cbpa.2013.02.022
Yoo TH, Pogson M, Iverson BL, Georgiou G (2012) Directed evolution of highly selective proteases by using a novel FACS-based screen that capitalizes on the p53 regulator MDM2. ChemBioChem 13:649–653. doi:10.1002/cbic.201100718
Agresti JJ, Antipov E, Abate AR et al (2010) Ultrahigh-throughput screening in drop-based microfluidics for directed evolution. Proc Natl Acad Sci USA 107:4004–4009. doi:10.1073/pnas.0910781107
Deal KS, Easley CJ (2012) Self-regulated, droplet-based sample chopper for microfluidic absorbance detection. Anal Chem 84:1510–1516. doi:10.1021/ac202791d
Cecchini MP, Hong J, Lim C et al (2011) Ultrafast surface enhanced resonance raman scattering detection in droplet-based microfluidic systems. Anal Chem 83:3076–3081. doi:10.1021/ac103329b
Lee SA, Zheng G, Mukherjee N, Yang C (2012) On-chip continuous monitoring of motile microorganisms on an ePetri platform. Lab Chip 12:2385–2390. doi:10.1039/C2LC40090A
Salisbury CM, Maly DJ, Ellman JA (2002) Peptide microarrays for the determination of protease substrate specificity. J Am Chem Soc 124:14868–14870. doi:10.1021/ja027477q
Zhu Q, Uttamchandani M, Li D et al (2003) Enzymatic profiling system in a small-molecule microarray. Org Lett 5:1257–1260. doi:10.1021/ol034233h
Houseman BT, Mrksich M (2002) Carbohydrate arrays for the evaluation of protein binding and enzyme activity. Chem Biol 9:443–454
Yeo WS, Mrksich M (2003) Self-assembled monolayers that transduce enzymatic activities to electrical signals. Angew Chem Int Ed 42:3121–3124. doi:10.1002/anie.200250862
Gosalia DN, Diamond SL (2003) Printing chemical libraries on microarrays for fluid phase nanoliter reactions. Proc Natl Acad Sci USA 100:8721–8726. doi:10.1073/pnas.1530261100
Park CB, Clark DS (2002) Sol-gel encapsulated enzyme arrays for high-throughput screening of biocatalytic activity. Biotechnol Bioeng 78:229–235. doi:10.1002/bit.10238
Bisswanger H (2014) Enzyme assays. Perspectives. Science 1:41–55. doi:10.1016/j.pisc.2014.02.005
Haswell SJ, Middleton RJ, O’Sullivan B et al (2001) The application of micro reactors to synthetic chemistry. Chem Commun 80:391–398. doi:10.1039/b008496o
Abbas A, Treizebre A, Supiot P et al (2009) Cold plasma functionalized TeraHertz BioMEMS for enzyme reaction analysis. Biosens Bioelectron 25:154–160. doi:10.1016/j.bios.2009.06.029
Kim DN, Lee Y, Koh W-G (2009) Fabrication of microfluidic devices incorporating bead-based reaction and microarray-based detection system for enzymatic assay. Sens Actuat B Chem 137:305–312. doi:10.1016/j.snb.2008.12.042
Draper MC, Niu X, Cho S et al (2012) Compartmentalization of electrophoretically separated analytes in a multiphase microfluidic platform. Anal Chem 84:5801–5808. doi:10.1021/ac301141x
DeMello AJ (2006) Control and detection of chemical reactions in microfluidic systems. Nature 442:394–402. doi:10.1038/nature05062
Elagli A, Laurette S, Treizebre A et al (2014) Diffusion based kinetic selectivity modulation of enzymatic proteolysis in a microfluidic reactor: experimental analysis and stochastic modeling. RSC Adv 4:3873–3882. doi:10.1039/C3RA46005C
Honda T, Miyazaki M, Nakamura H, Maeda H (2006) Facile preparation of an enzyme-immobilized microreactor using a cross-linking enzyme membrane on a microchannel surface. Adv Synth Catal 348:2163–2171. doi:10.1002/adsc.200606224
Song YS, Shin HY, Lee JY et al (2012) β-Galactosidase-immobilised microreactor fabricated using a novel technique for enzyme immobilisation and its application for continuous synthesis of lactulose. Food Chem 133:611–617. doi:10.1016/j.foodchem.2012.01.096
Anuar ST, Zhao Y-Y, Mugo SM, Curtis JM (2013) The development of a capillary microreactor for transesterification reactions using lipase immobilized onto a silica monolith. J Mol Catal B Enzym 92:62–70. doi:10.1016/j.molcatb.2013.03.013
Ogończyk D, Jankowski P, Garstecki P et al (2012) Functionalization of polycarbonate with proteins; open-tubular enzymatic microreactors. Lab Chip 12:2743. doi:10.1039/c2lc40204a
Laurette S, Treizebre A, Elagli A et al (2012) Highly sensitive terahertz spectroscopy in microsystem. RSC Adv 2:10064. doi:10.1039/c2ra21320f
Elagli A, Belhacene K, Vivien C et al (2014) Facile immobilization of enzyme by entrapment using a plasma-deposited organosilicon thin film. J Mol Catal B Enzym 110:77–86. doi:10.1016/j.molcatb.2014.09.014
Büchs J (2001) Introduction to advantages and problems of shaken cultures. Biochem Eng J 7:91–98. doi:10.1016/S1369-703X(00)00106-6
Lattermann C, Büchs J (2015) Microscale and miniscale fermentation and screening. Curr Opin Biotechnol 35:1–6. doi:10.1016/j.copbio.2014.12.005
Bhambure R, Kumar K, Rathore AS (2011) High-throughput process development for biopharmaceutical drug substances. Trends Biotechnol 29:127–135. doi:10.1016/j.tibtech.2010.12.001
Marques M, Cabral J, Fernandes P (2009) High throughput in biotechnology: from shake-flasks to fully instrumented microfermentors. Recent Pat Biotechnol 3:124–140. doi:10.2174/187220809788700193
Käß F, Prasad A, Tillack J et al (2014) Rapid assessment of oxygen transfer impact for Corynebacterium glutamicum. Bioprocess Biosyst Eng. doi:10.1007/s00449-014-1234-1
Duetz WA (2007) Microtiter plates as mini-bioreactors: miniaturization of fermentation methods. Trends Microbiol 15:469–475. doi:10.1016/j.tim.2007.09.004
Huber R, Roth S, Rahmen N, Büchs J (2011) Utilizing high-throughput experimentation to enhance specific productivity of an E. coli T7 expression system by phosphate limitation. BMC Biotechnol 11:22. doi:10.1186/1472-6750-11-22
Sundstrom ER, Criddle CS (2015) Optimization of methanotrophic growth and production of poly(3-hydroxybutyrate) in a high-throughput microbioreactor system. Appl Environ Microbiol 81:4767–4773. doi:10.1128/aem.00025-15
Huber R, Ritter D, Hering T et al (2009) Robo-Lector—a novel platform for automated high-throughput cultivations in microtiter plates with high information content. Microb Cell Fact 8:42. doi:10.1186/1475-2859-8-42
Huber R, Wulfhorst H, Maksym L et al (2011) Screening for enzyme activity in turbid suspensions with scattered light. Biotechnol Prog 27:555–561. doi:10.1002/btpr.519
Jäger G, Wulfhorst H, Zeithammel EU et al (2011) Screening of cellulases for biofuel production: online monitoring of the enzymatic hydrolysis of insoluble cellulose using high-throughput scattered light detection. Biotechnol J 6:74–85. doi:10.1002/biot.201000387
Oliveira AF, Pessoa ACSN, Bastos RG, de la Torre LG (2016) Microfluidic tools toward industrial biotechnology. Biotechnol Prog. doi:10.1002/btpr.2350
Blesken C, Olfers T, Grimm A, Frische N (2016) The microfluidic bioreactor for a new era of bioprocess development. Eng Life Sci 16:190–193. doi:10.1002/elsc.201500026
Hegab HM, ElMekawy A, Stakenborg T (2013) Review of microfluidic microbioreactor technology for high-throughput submerged microbiological cultivation. Biomicrofluidics. doi:10.1063/1.4799966
Puskeiler R, Kusterer A, John GT, Weuster-Botz D (2005) Miniature bioreactors for automated high-throughput bioprocess design (HTBD): reproducibility of parallel fed-batch cultivations with Escherichia coli. Biotechnol Appl Biochem 42:227–235. doi:10.1042/BA20040197
Funke M, Buchenauer A, Schnakenberg U et al (2010) Microfluidic biolector-microfluidic bioprocess control in microtiter plates. Biotechnol Bioeng 107:497–505. doi:10.1002/bit.22825
Gebhardt G, Hortsch R, Kaufmann K et al (2011) A new microfluidic concept for parallel operated milliliter-scale stirred tank bioreactors. Biotechnol Prog 27:684–690. doi:10.1002/btpr.570
Bras EJS, Chu V, Aires-Barros MR et al (2016) A microfluidic platform for physical entrapment of yeast cells with continuous production of invertase. J Chem Technol Biotechnol. doi:10.1002/jctb.5010
Schäpper D, Alam MNHZ, Szita N et al (2009) Application of microbioreactors in fermentation process development: a review. Anal Bioanal Chem 395:679–695. doi:10.1007/s00216-009-2955-x
de Jong J, Lammertink RGH, Wessling M (2006) Membranes and microfluidics: a review. Lab Chip 6:1125–1139. doi:10.1039/b603275c
Coutte F, Lecouturier D, Leclère V et al (2013) New integrated bioprocess for the continuous production, extraction and purification of lipopeptides produced by Bacillus subtilis in membrane bioreactor. Process Biochem 48:25–32. doi:10.1016/j.procbio.2012.10.005
Zanzotto A, Szita N, Boccazzi P et al (2004) Membrane-aerated microbioreactor for high-throughput bioprocessing. Biotechnol Bioeng 87:243–254. doi:10.1002/bit.20140
Daubert I, Mercier-Bonin M, Maranges C et al (2003) Why and how membrane bioreactors with unsteady filtration conditions can improve the efficiency of biological processes. Ann N Y Acad Sci 984:420–435
Alam MNHZ, Pinelo M, Samanta K et al (2011) A continuous membrane microbioreactor system for development of integrated pectin modification and separation processes. Chem Eng J 167:418–426. doi:10.1016/j.cej.2010.09.082
Coutte F, Lecouturier D, Firdaous L et al (2016) Recent trends in membrane bioreactors. Current developments in biotechnology and bioengineering. Recent Trends Membr Bioreact (In press)
Zavrel M, Bross D, Funke M et al (2009) High-throughput screening for ionic liquids dissolving (ligno-)cellulose. Bioresour Technol 100:2580–2587. doi:10.1016/j.biortech.2008.11.052
Kirk TV, Szita N (2013) Oxygen transfer characteristics of miniaturized bioreactor systems. Biotechnol Bioeng 110:1005–1019. doi:10.1002/bit.24824
Betts JI, Baganz F (2006) Miniature bioreactors: current practices and future opportunities. Microb Cell Fact 5:21. doi:10.1186/1475-2859-5-21
Kim BJ, Diao J, Shuler ML (2012) Mini-scale bioprocessing systems for highly parallel animal cell cultures. Biotechnol Prog 28:595–607. doi:10.1002/btpr.1554
Frachon E, Bondet V, Munier-Lehmann H, Bellalou J (2006) Multiple microfermentor battery: a versatile tool for use with automated parallel cultures of microorganisms producing recombinant proteins and for optimization of cultivation protocols. Appl Environ Microbiol 72:5225–5231. doi:10.1128/AEM.00239-06
Motta Dos Santos LF, Coutte F, Ravallec R et al (2016) An improvement of surfactin production by B. subtilis BBG131 using design of experiments in microbioreactors and continuous process in bubbleless membrane bioreactor. Bioresour Technol. doi:10.1016/j.biortech.2016.07.053
Riedlberger P, Weuster-Botz D (2012) New miniature stirred-tank bioreactors for parallel study of enzymatic biomass hydrolysis. Bioresour Technol 106:138–146. doi:10.1016/j.biortech.2011.12.019
Nunes MAP, Fernandes PCB, Ribeiro MHL (2013) Microtiter plates versus stirred mini-bioreactors in biocatalysis: a scalable approach. Bioresour Technol 136:30–40. doi:10.1016/j.biortech.2013.02.057
Delvigne F, Brognaux A, Francis F et al (2011) Green fluorescent protein (GFP) leakage from microbial biosensors provides useful information for the evaluation of the scale-down effect. Biotechnol J 6:968–978. doi:10.1002/biot.201000410
Brognaux A, Thonart P, Delvigne F et al (2013) Direct and indirect use of GFP whole cell biosensors for the assessment of bioprocess performances: design of milliliter scale-down bioreactors. Biotechnol Prog 29:48–59. doi:10.1002/btpr.1660
Guiochon G, Beaver LA (2011) Separation science is the key to successful biopharmaceuticals. J Chromatogr A 1218:8836–8858. doi:10.1016/j.chroma.2011.09.008
Shukla AA, Hubbard B, Tressel T et al (2007) Downstream processing of monoclonal antibodies—application of platform approaches. J Chromatogr B Anal Technol Biomed Life Sci 848:28–39. doi:10.1016/j.jchromb.2006.09.026
Kuhad RC, Deswal D, Sharma S et al (2016) Revisiting cellulase production and redefining current strategies based on major challenges. Renew Sustain Energy Rev 55:249–272. doi:10.1016/j.rser.2015.10.132
Nfor BK, Verhaert PDEM, van der Wielen LAM et al (2009) Rational and systematic protein purification process development: the next generation. Trends Biotechnol 27:673–679. doi:10.1016/j.tibtech.2009.09.002
Łacki KM, Lacki KM (2014) High throughput process development in biomanufacturing. Curr Opin Chem Eng 6:25–32. doi:10.1016/j.coche.2014.08.004
Hanke AT, Ottens M (2014) Purifying biopharmaceuticals: knowledge-based chromatographic process development. Trends Biotechnol 32:210–220. doi:10.1016/j.tibtech.2014.02.001
Jungbauer A (2013) Continuous downstream processing of biopharmaceuticals. Trends Biotechnol 31:479–492. doi:10.1016/j.tibtech.2013.05.011
Carapito R, Gallet B, Zapun A, Vernet T (2006) Automated high-throughput process for site-directed mutagenesis, production, purification, and kinetic characterization of enzymes. Anal Biochem 355:110–116. doi:10.1016/j.ab.2006.04.047
Yoo D, Provchy J, Park C et al (2014) Automated high-throughput protein purification using an ÄKTApurifier and a CETAC autosampler. J Chromatogr A 1344:23–30. doi:10.1016/j.chroma.2014.04.014
Merrill AH, Sullards MC, Allegood JC et al (2005) Sphingolipidomics: high-throughput, structure-specific, and quantitative analysis of sphingolipids by liquid chromatography tandem mass spectrometry. Methods 36:207–224. doi:10.1016/j.ymeth.2005.01.009
de Boer AR, Letzel T, van Elswijk DA et al (2004) On-line coupling of high-performance liquid chromatography to a continuous-flow enzyme assay based on electrospray ionization mass spectrometry. Anal Chem 76:3155–3161. doi:10.1021/ac035380w
Gillet LC, Leitner A, Aebersold R (2015) Mass spectrometry applied to bottom-up proteomics: entering the high-throughput era for hypothesis testing
Swaney DL, Villén J (2016) Proteomic analysis of protein posttranslational modifications by mass spectrometry. Cold Spring Harbor Protoc 2016:pdb.top077743. doi:10.1101/pdb.top077743
McCullough B, Gaskell S (2009) Using electrospray ionisation mass spectrometry to study non-covalent interactions. Comb Chem High Throughput Screen 12:203–211. doi:10.2174/138620709787315463
Gingras A-C, Gstaiger M, Raught B, Aebersold R (2007) Analysis of protein complexes using mass spectrometry. Nat Rev Mol Cell Biol 8:645–654. doi:10.1038/nrm2208
Smits AH, Vermeulen M (2016) Characterizing protein–protein interactions using mass spectrometry: challenges and opportunities. Trends Biotechnol. doi:10.1016/j.tibtech.2016.02.014
Van Veen SQ, Claas ECJ, Kuijper EJ (2010) High-throughput identification of bacteria and yeast by matrix-assisted laser desorption ionization-time of flight mass spectrometry in conventional medical microbiology laboratories. J Clin Microbiol 48:900–907. doi:10.1128/JCM.02071-09
Sandrin TR, Goldstein JE, Schumaker S (2013) MALDI TOF MS profiling of bacteria at the strain level: a review. Mass Spectrom Rev. doi:10.1002/mas
Bodzon-Kulakowska A, Bierczynska-Krzysik A, Dylag T et al (2006) Methods for samples preparation in proteomic research. J Chromatogr B Analyt Technol Biomed Life Sci 849:1–31
Barkal LJ, Theberge AB, Guo C et al (2016) Microbial metabolomics in open microscale platforms. Nat Commun 7:1–11. doi:10.1038/ncomms10610
de Raad M, Fischer CR, Northen TR (2015) High-throughput platforms for metabolomics. Curr Opin Chem Biol 30:7–13. doi:10.1016/j.cbpa.2015.10.012
Welker M (2011) Proteomics for routine identification of microorganisms. Proteomics 11:3143–3153. doi:10.1002/pmic.201100049
Schey KL, Hachey AJ, Rose KM, Grey AC (2016) MALDI imaging mass spectrometry of Pacific White Shrimp L. vannamei and identification of abdominal muscle. Proteins. doi:10.1002/pmic.201500531
De Rond T, Peralta-Yahya P, Cheng X et al (2013) Versatile synthesis of probes for high-throughput enzyme activity screening. Anal Bioanal Chem 405:4969–4973. doi:10.1007/s00216-013-6888-z
Chen B, Peng Y, Valeja SG et al (2016) Online hydrophobic interaction chromatography–mass spectrometry for top-down proteomics. Anal Chem. doi:10.1021/acs.analchem.5b04285
Catherman AD, Skinner OS, Kelleher NL (2014) Top down proteomics: facts and perspectives. Biochem Biophys Res Commun 445:683–693. doi:10.1016/j.bbrc.2014.02.041
Mayne J, Ning Z, Zhang X et al (2016) Bottom-up proteomics (2013–2015): keeping up in the era of systems biology. Anal Chem 88:95–121. doi:10.1021/acs.analchem.5b04230
Qi Y, Volmer DA (2016) Structural analysis of small to medium-sized molecules by mass spectrometry after electron-ion fragmentation (ExD) reactions. Analyst 141:794–806. doi:10.1039/c5an02171e
Hu A, Noble WS, Wolf-Yadlin A (2016) Technical advances in proteomics: new developments in data-independent acquisition. F1000Research. doi:10.12688/f1000research.7042.1
Chen P (2003) Electrospray ionization tandem mass spectrometry in high-throughput screening of homogeneous catalysts. Angew Chem Int Ed 42:2832–2847. doi:10.1002/anie.200200560
Ng ESM, Yang F, Kameyama A et al (2005) High-throughput screening for enzyme inhibitors using frontal affinity chromatography with liquid chromatography and mass spectrometry. Anal Chem 77:6125–6133. doi:10.1021/ac051131r
Yi X, Hao Y, Xia N et al (2013) Sensitive and continuous screening of inhibitors of β-site amyloid precursor protein cleaving enzyme 1 (BACE1) at single SPR chips. Anal Chem 85:3660–3666. doi:10.1021/ac303624z
Ahmad S, Hughes MA, Johnson GL, Scott JE (2013) Development and validation of a high-throughput intrinsic ATPase activity assay for the discovery of MEKK2 inhibitors. J Biomol Screen 18:388–399. doi:10.1177/1087057112466430
Greis KD (2006) Mass spectrometry for enzyme assays and inhibitor screening: an emerging application in pharmaceutical research. Mass Spectrom Rev 26:324–339. doi:10.1002/mas.20127
Domínguez JM, Fuertes A, Orozco L et al (2012) Evidence for irreversible inhibition of glycogen synthase kinase-3β by tideglusib. J Biol Chem 287:893–904. doi:10.1074/jbc.M111.306472
Song XS, Zhang J, Chen X et al (2015) Identification of DGAT2 inhibitors using mass spectrometry. J Biomol Screen. doi:10.1177/1087057115607463
Schrader W, Eipper A, Pugh DJ, Reetz MT (2002) Second-generation MS-based high-throughput screening system for enantioselective catalysts and biocatalysts. Can J Chem 80:626–632. doi:10.1139/v02-069
Bakhtiar R, Ramos L, Tse FL (2001) Use of atmospheric pressure ionization mass spectrometry in enantioselective liquid chromatography. Chirality 13:63–74. doi:10.1002/1520-636X(2001)13:2<63:AID-CHIR1000>3.0.CO;2-5
Schug K (2007) Solution phase enantioselective recognition and discrimination by electrospray ionization–mass spectrometry: state-of-the-art, methods, and an eye towards increased throughput measurements. Comb Chem High Throughput Screen 10:301–316. doi:10.2174/138620707781662790
Kanie O, Shioiri Y, Ogata K et al (2016) Diastereomeric resolution directed towards chirality determination focussing on gas-phase energetics of coordinated sodium dissociation. Sci Rep 6:24005. doi:10.1038/srep24005
Lepère V, Le Barbu-Debus K, Clavaguéra C et al (2015) Chirality-dependent structuration of protonated or sodiated polyphenylalanines: IRMPD and ion mobility studies. Phys Chem Chem Phys. doi:10.1039/C5CP06768E.10.1039/C5CP06768E
Dancík V, Addona TA, Clauser KR et al (2004) De novo peptide sequencing via tandem mass spectrometry. J Comput Biol J Comput Mol Cell Biol 6:327–342. doi:10.1089/106652799318300
Trimpin S (2016) “Magic” ionization mass spectrometry. J Am Soc Mass Spectrom 27:4–21. doi:10.1007/s13361-015-1253-4
Cramer R (2015) Advances in MALDI and laser-induced soft ionization mass spectrometry. Adv MALDI Laser Induc Soft Ioniz Mass Spectrom. doi:10.1007/978-3-319-04819-2
Smoluch M, Mielczarek P, Silberring J (2016) Plasma-based ambient ionization mass spectrometry in bioanalytical sciences. Mass Spectrom Rev 35:22–34. doi:10.1002/mas.21460
Gordon LJ, Allen M, Artursson P et al (2016) Direct measurement of intracellular compound concentration by rapidfire mass spectrometry offers insights into cell permeability. J Biomol Screen 21:156–164. doi:10.1177/1087057115604141
Chumbley CW, Reyzer ML, Allen JL et al (2016) Absolute quantitative MALDI imaging mass spectrometry: a case of rifampicin in liver tissues. Anal Chem 88:2392–2398. doi:10.1021/acs.analchem.5b04409
Holding AN (2015) XL-MS: protein cross-linking coupled with mass spectrometry. Methods 89:54–63. doi:10.1016/j.ymeth.2015.06.010
Leitner A, Faini M, Stengel F, Aebersold R (2016) Crosslinking and mass spectrometry: an integrated technology to understand the structure and function of molecular machines. Trends Biochem Sci 41:20–32. doi:10.1016/j.tibs.2015.10.008
Ghaste M, Mistrik R, Shulaev V (2016) Applications of Fourier transform ion cyclotron resonance (FT-ICR) and orbitrap based high resolution mass spectrometry in metabolomics and lipidomics. Int J Mol Sci 17:816. doi:10.3390/ijms17060816
Ma X, Ouyang Z (2016) Ambient ionization and miniature mass spectrometry system for chemical and biological analysis. TrAC Trends Anal Chem. doi:10.1016/j.trac.2016.04.009
Cetina DM, Giraldo GI, Orrego CE (2011) Application of response surface design to solvent, temperature and lipase selection for optimal monoglyceride production. J Mol Catal B Enzym 72:13–19. doi:10.1016/j.molcatb.2011.04.017
Corrêa FDA, Sutili FK, Miranda LSM et al (2012) Epoxidation of oleic acid catalyzed by PSCI-amano lipase optimized by experimental design. J Mol Catal B Enzym 81:7–11. doi:10.1016/j.molcatb.2012.03.011
Gonçalves KM, Sutili FK, Leite SGF et al (2012) Palm oil hydrolysis catalyzed by lipases under ultrasound irradiation—the use of experimental design as a tool for variables evaluation. Ultrason Sonochem 19:232–236. doi:10.1016/j.ultsonch.2011.06.017
Lee A, Chaibakhsh N, Rahman MBA et al (2010) Optimized enzymatic synthesis of levulinate ester in solvent-free system. Ind Crops Prod 32:246–251. doi:10.1016/j.indcrop.2010.04.022
Heuson E, Petit J-L, Debard A et al (2016) Continuous colorimetric screening assays for the detection of specific l- or d-α-amino acid transaminases in enzyme libraries. Appl Microbiol Biotechnol 100:397–408. doi:10.1007/s00253-015-6988-0
Lerin LA, Richetti A, Dallago R et al (2012) Enzymatic synthesis of ascorbyl palmitate in organic solvents: process optimization and kinetic evaluation. Food Bioprocess Technol 5:1068–1076. doi:10.1007/s11947-010-0398-1
Abildskov J, Van Leeuwen MB, Boeriu CG, Van Den Broek LAM (2013) Computer-aided solvent screening for biocatalysis. J Mol Catal B Enzym 85–86:200–213. doi:10.1016/j.molcatb.2012.09.012
Rosa SM, Soria MA, Vlez CG, Galvagno MA (2010) Improvement of a two-stage fermentation process for docosahexaenoic acid production by Aurantiochytrium limacinum SR21 applying statistical experimental designs and data analysis. Bioresour Technol 101:2367–2374. doi:10.1016/j.biortech.2009.11.056
Godoy MG, Gutarra MLE, Castro AM et al (2011) Adding value to a toxic residue from the biodiesel industry: production of two distinct pool of lipases from Penicillium simplicissimum in castor bean waste. J Ind Microbiol Biotechnol 38:945–953. doi:10.1007/s10295-010-0865-8
Malik M, Ganguli A, Ghosh M (2012) Modeling of permeabilization process in Pseudomonas putida G7 for enhanced limonin bioconversion. Appl Microbiol Biotechnol 95:223–231. doi:10.1007/s00253-012-3880-z
Lattanzio VMT, Von Holst C, Visconti A (2013) Experimental design for in-house validation of a screening immunoassay kit. The case of a multiplex dipstick for Fusarium mycotoxins in cereals. Anal Bioanal Chem 405:7773–7782. doi:10.1007/s00216-013-6922-1
Rios-Solis L, Bayir N, Halim M et al (2013) Non-linear kinetic modelling of reversible bioconversions: application to the transaminase catalyzed synthesis of chiral amino-alcohols. Biochem Eng J 73:38–48. doi:10.1016/j.bej.2013.01.010
Fu Q, Zhang C, Lin Z et al (2016) Rapid screening and identification of compounds with DNA-binding activity from folium citri reticulatae using on-line HPLC-DAD-MS(n) coupled with a post column fluorescence detection system. Food Chem 192:250–259. doi:10.1016/j.foodchem.2015.07.009
Müller MM, Hausmann R (2011) Regulatory and metabolic network of rhamnolipid biosynthesis: traditional and advanced engineering towards biotechnological production. Appl Microbiol Biotechnol 91:251–264. doi:10.1007/s00253-011-3368-2
Brooks KM, Hampel KJ (2011) Rapid steps in the glmS ribozyme catalytic pathway: cation and ligand requirements. Biochemistry 50:2424–2433. doi:10.1021/bi101842u
Bøjstrup M, Marri L, Lok F, Hindsgaul O (2015) A chromogenic assay suitable for high-throughput determination of limit dextrinase activity in barley malt extracts. J Agric Food Chem 63:10873–10878. doi:10.1021/acs.jafc.5b04596
