References
Ailor E, Betenbaugh MJ. 1999. Modifying secretion and post-translational
processing in insect cells. Current Opinion in Biotechnology10 :142–145.
Ayres MD, Howard SC, Kuzio J, Lopez-Ferber M, Possee RD. 1994. The
Complete DNA Sequence of Autographa californica Nuclear Polyhedrosis
Virus. Virology 202 :586–605.
Beperet I, Irons SL, Simón O, King LA, Williams T, Possee RD,
López-Ferber M, Caballero P. 2014. Superinfection Exclusion in
Alphabaculovirus Infections Is Concomitant with Actin Reorganization.J Virol 88 :3548–3556.
Bernal V, Carinhas N, Yokomizo AY, Carrondo MJT, Alves PM. 2009. Cell
density effect in the baculovirus-insect cells system: A quantitative
analysis of energetic metabolism. Biotechnology and
Bioengineering 104 :162–180.
Bernal V, Monteiro F, Carinhas N, Ambrósio R, Alves PM. 2010. An
integrated analysis of enzyme activities, cofactor pools and metabolic
fluxes in baculovirus-infected Spodoptera frugiperda Sf9 cells.Journal of Biotechnology 150 :332–342.
Carinhas N, Bernal V, Monteiro F, Carrondo MJT, Oliveira R, Alves PM.
2010. Improving baculovirus production at high cell density through
manipulation of energy metabolism. Metabolic Engineering12 :39–52.
Carinhas N, Robitaille AM, Moes S, Carrondo MJT, Jenoe P, Oliveira R,
Alves PM. 2011. Quantitative Proteomics of Spodoptera frugiperda Cells
during Growth and Baculovirus Infection. PLOS ONE6 :e26444.
Cecchini S, Virag T, Kotin RM. 2011. Reproducible High Yields of
Recombinant Adeno-Associated Virus Produced Using Invertebrate Cells in
0.02- to 200-Liter Cultures. Hum Gene Ther22 :1021–1030.
Chen W, Yang X, Tetreau G, Song X, Coutu C, Hegedus D, Blissard G, Fei
Z, Wang P. 2019. A high-quality chromosome-level genome assembly of a
generalist herbivore, Trichoplusia ni. Molecular Ecology
Resources 19 :485–496.
Chen Y-R, Zhong S, Fei Z, Gao S, Zhang S, Li Z, Wang P, Blissard GW.
2014. Transcriptome Responses of the Host Trichoplusia ni to Infection
by the Baculovirus Autographa californica Multiple Nucleopolyhedrovirus.Journal of Virology 88 :13781–13797.
Correia R, Fernandes B, Alves PM, Carrondo MJT, Roldão A. 2020.
Improving Influenza HA-Vlps Production in Insect High Five Cells via
Adaptive Laboratory Evolution. Vaccines 8 :589.
Correia R, Fernandes B, Castro R, Nagaoka H, Takashima E, Tsuboi T,
Fukushima A, Viebig NK, Depraetere H, Alves PM, Roldão A. 2022. Asexual
Blood-Stage Malaria Vaccine Candidate PfRipr5: Enhanced Production in
Insect Cells. Frontiers in Bioengineering and Biotechnology10 .
https://www.frontiersin.org/articles/10.3389/fbioe.2022.908509.
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P,
Chaisson M, Gingeras TR. 2013. STAR: ultrafast universal RNA-seq
aligner. Bioinformatics 29 :15–21.
Doverskog M, Jacobsson U, Chapman BE, Kuchel PW, Häggström L. 2000.
Determination of NADH-dependent glutamate synthase (GOGAT) in Spodoptera
frugiperda (Sf9) insect cells by a selective 1H/15N NMR in vitro assay.Journal of Biotechnology 79 :87–97.
Fernandes B, Castro R, Bhoelan F, Bemelman D, Gomes RA, Costa J,
Gomes-Alves P, Stegmann T, Amacker M, Alves PM, Fleury S, Roldão A.
2022a. Insect Cells for High-Yield Production of SARS-CoV-2 Spike
Protein: Building a Virosome-Based COVID-19 Vaccine Candidate.Pharmaceutics 14 :854.
Fernandes B, Sousa M, Castro R, Schäfer A, Hauser J, Schulze K, Amacker
M, Tamborrini M, Pluschke G, Alves PM, Fleury S, Roldão A. 2022b.
Scalable Process for High-Yield Production of PfCyRPA Using Insect Cells
for Inclusion in a Malaria Virosome-Based Vaccine Candidate.Frontiers in Bioengineering and Biotechnology 10 .
https://www.frontiersin.org/articles/10.3389/fbioe.2022.879078.
Finak G, McDavid A, Yajima M, Deng J, Gersuk V, Shalek AK, Slichter CK,
Miller HW, McElrath MJ, Prlic M, Linsley PS, Gottardo R. 2015. MAST: a
flexible statistical framework for assessing transcriptional changes and
characterizing heterogeneity in single-cell RNA sequencing data.Genome Biol 16 :278.
Folimonova SY. 2012. Superinfection Exclusion Is an Active
Virus-Controlled Function That Requires a Specific Viral Protein.Journal of Virology 86 :5554–5561.
Galibert L, Jacob A, Savy A, Dickx Y, Bonnin D, Lecomte C, Rivollet L,
Sanatine P, Boutin Fontaine M, Le Bec C, Merten O-W. 2021. Monobac
System–A Single Baculovirus for the Production of rAAV.Microorganisms 9 :1799.
Gotoh T, Ando N, Kikuchi K-I. 2008. Re-Infection Profile of
Baculoviruses to Sf-9 Insect Cells that Have Already Been Infected:
Virus Binding and Recombinant Protein Production. Journal of
Chemical Engineering of Japan 41 :804–808.
Hao Y, Hao S, Andersen-Nissen E, Mauck WM, Zheng S, Butler A, Lee MJ,
Wilk AJ, Darby C, Zager M, Hoffman P, Stoeckius M, Papalexi E, Mimitou
EP, Jain J, Srivastava A, Stuart T, Fleming LM, Yeung B, Rogers AJ,
McElrath JM, Blish CA, Gottardo R, Smibert P, Satija R. 2021. Integrated
analysis of multimodal single-cell data. Cell 0 .
https://www.cell.com/cell/abstract/S0092-8674(21)00583-3.
Ke M, Elshenawy B, Sheldon H, Arora A, Buffa FM. 2022. Single cell
RNA-sequencing: A powerful yet still challenging technology to study
cellular heterogeneity. BioEssays 44 :2200084.
Koczka K, Peters P, Ernst W, Himmelbauer H, Nika L, Grabherr R. 2018.
Comparative transcriptome analysis of a Trichoplusia ni cell line
reveals distinct host responses to intracellular and secreted protein
products expressed by recombinant baculoviruses. Journal of
Biotechnology 270 :61–69.
Mena JA, Ramírez OT, Palomares LA. 2003. Titration of Non-Occluded
Baculovirus Using a Cell Viability Assay. BioTechniques34 :260–264.
Mena JA, Ramírez OT, Palomares LA. 2007. Population kinetics during
simultaneous infection of insect cells with two different recombinant
baculoviruses for the production of rotavirus-like particles. BMC
Biotechnology 7 :39.
Merten O-W. 2016. AAV vector production: state of the art developments
and remaining challenges. In: .
Monteiro F, Bernal V, Alves P. 2016. Metabolic drivers of IC-BEVS
productivity: Tackling the production of enveloped viral particles.Vaccine Technology VI .
https://dc.engconfintl.org/vaccine_vi/110.
Monteiro F, Bernal V, Alves PM. 2017. The role of host cell physiology
in the productivity of the baculovirus-insect cell system: Fluxome
analysis of Trichoplusia ni and Spodoptera frugiperda cell lines.Biotechnology and Bioengineering 114 :674–684.
Monteiro F, Carinhas N, Carrondo MJT, Bernal V, Alves PM. 2012. Toward
system-level understanding of baculovirus–host cell interactions: from
molecular fundamental studies to large-scale proteomics approaches.Front. Microbiol. 3 .
https://www.frontiersin.org/articles/10.3389/fmicb.2012.00391/full.
Nayyar N, Kaur I, Malhotra P, Bhatnagar RK. 2017. Quantitative
proteomics of Sf21 cells during Baculovirus infection reveals
progressive host proteome changes and its regulation by viral miRNA.Sci Rep 7 :10902.
Pais DAM, Galrão PRS, Kryzhanska A, Barbau J, Isidro IA, Alves PM. 2020.
Holographic Imaging of Insect Cell Cultures: Online Non-Invasive
Monitoring of Adeno-Associated Virus Production and Cell Concentration.Processes 8 :487.
Pais DAM, Portela RMC, Carrondo MJT, Isidro IA, Alves PM. 2019. Enabling
PAT in insect cell bioprocesses: In situ monitoring of recombinant
adeno-associated virus production by fluorescence spectroscopy.Biotechnology and Bioengineering 116 :2803–2814.
Palomares LA, López S, Ramírez OT. 2002. Strategies for manipulating the
relative concentration of recombinant rotavirus structural proteins
during simultaneous production by insect cells. Biotechnology and
Bioengineering 78 :635–644.
Penaud-Budloo M, François A, Clément N, Ayuso E. 2018. Pharmacology of
Recombinant Adeno-associated Virus Production. Mol Ther Methods
Clin Dev 8 :166–180.
Rohrmann GF. 2013. Baculovirus Molecular Biology 3rd ed. Bethesda (MD):
National Center for Biotechnology Information (US).
http://www.ncbi.nlm.nih.gov/books/NBK114593/.
Rohrmann GF. 2019. Baculovirus infection: The cell cycle and apoptosis.Baculovirus Molecular Biology [Internet]. 4th edition .
National Center for Biotechnology Information (US).
https://www.ncbi.nlm.nih.gov/books/NBK543456/.
Roldão A, Oliveira R, Carrondo MJT, Alves PM. 2009. Error assessment in
recombinant baculovirus titration: Evaluation of different methods.Journal of Virological Methods 159 :69–80.
Russell AB, Trapnell C, Bloom JD. 2018. Extreme heterogeneity of
influenza virus infection in single cells. Ed. Arup K Chakraborty.eLife 7 :e32303.
Silvano M, Correia R, Virgolini N, Clarke C, Alves PM, Isidro IA, Roldão
A. 2022. Gene Expression Analysis of Adapted Insect Cells during
Influenza VLP Production Using RNA-Sequencing. Viruses14 :2238.
Smith GE, Summers MD, Fraser MJ. 1983. Production of human beta
interferon in insect cells infected with a baculovirus expression
vector. Mol Cell Biol 3 :2156–2165.
Smith RH, Levy JR, Kotin RM. 2009. A simplified baculovirus-AAV
expression vector system coupled with one-step affinity purification
yields high-titer rAAV stocks from insect cells. Mol Ther17 :1888–1896.
Sokolenko S, George S, Wagner A, Tuladhar A, Andrich JMS, Aucoin MG.
2012. Co-expression vs. co-infection using baculovirus expression
vectors in insect cell culture: Benefits and drawbacks.Biotechnology Advances 30 :766–781.
Srivastava A, Mallela KMG, Deorkar N, Brophy G. 2021. Manufacturing
Challenges and Rational Formulation Development for AAV Viral Vectors.Journal of Pharmaceutical Sciences 110 :2609–2624.
Sun J, Vera JC, Drnevich J, Lin YT, Ke R, Brooke CB. 2020. Single cell
heterogeneity in influenza A virus gene expression shapes the innate
antiviral response to infection. PLoS Pathog16 :e1008671.
Tennant JR. 1964. EVALUATION OF THE TRYPAN BLUE TECHNIQUE FOR
DETERMINATION OF CELL VIABILITY. Transplantation2 :685–694.
Tirosh I, Izar B, Prakadan SM, Wadsworth MH, Treacy D, Trombetta JJ,
Rotem A, Rodman C, Lian C, Murphy G, Fallahi-Sichani M, Dutton-Regester
K, Lin J-R, Cohen O, Shah P, Lu D, Genshaft AS, Hughes TK, Ziegler CGK,
Kazer SW, Gaillard A, Kolb KE, Villani A-C, Johannessen CM, Andreev AY,
Allen EMV, Bertagnolli M, Sorger PK, Sullivan RJ, Flaherty KT, Frederick
DT, Jané-Valbuena J, Yoon CH, Rozenblatt-Rosen O, Shalek AK, Regev A,
Garraway LA. 2016. Dissecting the multicellular ecosystem of metastatic
melanoma by single-cell RNA-seq. Science 352 :189–196.
Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, Lennon
NJ, Livak KJ, Mikkelsen TS, Rinn JL. 2014. Pseudo-temporal ordering of
individual cells reveals dynamics and regulators of cell fate decisions.Nat Biotechnol 32 :381–386.
Tzani I, Herrmann N, Carillo S, Spargo CA, Hagan R, Barron N, Bones J,
Dillmore WS, Clarke C. 2021. Tracing production instability in a
clonally derived CHO cell line using single-cell transcriptomics.Biotechnology and Bioengineering 118 :2016–2030.
Virag T, Cecchini S, Kotin RM. 2009. Producing Recombinant
Adeno-Associated Virus in Foster Cells: Overcoming Production
Limitations Using a Baculovirus–Insect Cell Expression Strategy.Hum Gene Ther 20 :807–817.
Virgolini N, Hagan R, Correia R, Silvano M, Fernandes S, Alves PM,
Clarke C, Roldão A, Isidro IA. 2022. Transcriptome analysis of Sf9
insect cells during production of recombinant Adeno-associated virus.Biotechnology Journal n/a :2200466.
Wei L, Cao L, Miao Y, Wu S, Xu S, Wang R, Du J, Liang A, Fu Y. 2017.
Transcriptome analysis of Spodoptera frugiperda 9 (Sf9) cells infected
with baculovirus, AcMNPV or AcMNPV-BmK IT. Biotechnol Lett39 :1129–1139.
Xiao H, Ye X, Xu H, Mei Y, Yang Y, Chen X, Yang Y, Liu T, Yu Y, Yang W,
Lu Z, Li F. 2020. The genetic adaptations of fall armyworm Spodoptera
frugiperda facilitated its rapid global dispersal and invasion.Molecular Ecology Resources 20 :1050–1068.
Xue J, Qiao N, Zhang W, Cheng R-L, Zhang X-Q, Bao Y-Y, Xu Y-P, Gu L-Z,
Han J-DJ, Zhang C-X. 2012. Dynamic Interactions between Bombyx mori
Nucleopolyhedrovirus and Its Host Cells Revealed by Transcriptome
Analysis. Journal of Virology 86 :7345–7359.
Yu G, Wang L-G, Han Y, He Q-Y. 2012. clusterProfiler: an R Package for
Comparing Biological Themes Among Gene Clusters. OMICS16 :284–287.
Yu Q, Xiong Y, Liu J, Wang Q, Qiu Y, Wen D. 2016. Comparative proteomics
analysis of apoptotic Spodoptera frugiperda cells during p35 knockout
Autographa californica multiple nucleopolyhedrovirus infection.Comparative Biochemistry and Physiology Part D: Genomics and
Proteomics 18 :21–29.