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Smith MK, Buhr DL, Dhlakama TA, Dupraw D, Fitz-Coy S, Francisco A, Ganesan A, Hubbard SA, Nederlof A, Newman LJ, Stoner MR, Teichmann J, Voyta JC, Wooster R, Zeygerman A, Zwilling MF, Kiss MM. Corrigendum to "Automated enumeration of Eimeria oocysts in feces for rapid coccidiosis monitoring" [Poult. Sci. 102 (1) (2023) 102252]. Poult Sci 2023; 102:102892. [PMID: 37478621 PMCID: PMC10387592 DOI: 10.1016/j.psj.2023.102892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2023] Open
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Smith MK, Buhr DL, Dhlakama TA, Dupraw D, Fitz-Coy S, Francisco A, Ganesan A, Hubbard SA, Nederlof A, Newman LJ, Stoner MR, Teichmann J, Voyta JC, Wooster R, Zeygerman A, Zwilling MF, Kiss MM. Corrigendum to "Automated enumeration of Eimeria oocysts in feces for rapid coccidiosis monitoring" [Poultry Science, Volume 102, Issue 1, January 2023, 102252]. Poult Sci 2023; 102:102446. [PMID: 36624016 PMCID: PMC10014328 DOI: 10.1016/j.psj.2022.102446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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Smith MK, Buhr DL, Dhlakama TA, Dupraw D, Fitz-Coy S, Francisco A, Ganesan A, Hubbard SA, Nederlof A, Newman LJ, Stoner MR, Teichmann J, Voyta JC, Wooster R, Zeygerman A, Zwilling MF, Kiss MM. Automated enumeration of Eimeria oocysts in feces for rapid coccidiosis monitoring. Poult Sci 2022; 102:102252. [PMID: 36463777 PMCID: PMC9719016 DOI: 10.1016/j.psj.2022.102252] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022] Open
Abstract
Coccidiosis represents a major driver in the economic performance of poultry operations, as coccidia control is expensive, and infections can result in increased feed conversion ratios, uneven growth rates, increased co-morbidities with pathogens such as Salmonella, and mortality within flocks. Shifts in broiler production to antibiotic-free strategies, increased attention on pre-harvest food safety, and growing incidence of anti-coccidial drug resistance has created a need for increased understanding of interventional efficacy and methods of coccidia control. Conventional methods to quantify coccidia oocysts in fecal samples involve manual microscopy processes that are time and labor intensive and subject to operator error, limiting their use as a diagnostic and monitoring tool in animal parasite control. To address the need for a high-throughput, robust, and reliable method to enumerate coccidia oocysts from poultry fecal samples, a novel diagnostic tool was developed. Utilizing the PIPER instrument and MagDrive technology, the diagnostic eliminates the requirement for extensive training and manual counting which currently limits the application of conventional microscopic methods of oocysts per gram (OPG) measurement. Automated microscopy to identify and count oocysts and report OPG simplifies analysis and removes potential sources of operator error. Morphometric analysis on identified oocysts allows for the oocyst counts to be separated into 3 size categories, which were shown to discriminate the 3 most common Eimeria species in commercial broilers, E. acervulina, E. tenella, and E. maxima. For 75% of the samples tested, the counts obtained by the PIPER and hemocytometer methods were within 2-fold of each other. Additionally, the PIPER method showed less variability than the hemocytometer counting method when OPG levels were below 100,000. By automated identification and counting of oocysts from 12 individual fecal samples in less than one hour, this tool could enable routine, noninvasive diagnostic monitoring of coccidia in poultry operations. This approach can generate large, uniform, and accurate data sets that create new opportunities for understanding the epidemiology and economics of coccidia infections and interventional efficacy.
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Zhao Q, Buhr D, Gunter C, Frenette J, Ferguson M, Sanford E, Holland E, Rajagopal C, Batonick M, Kiss MM, Weiner MP. Rational library design by functional CDR resampling. N Biotechnol 2017; 45:89-97. [PMID: 29242049 DOI: 10.1016/j.nbt.2017.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/17/2017] [Accepted: 12/09/2017] [Indexed: 12/18/2022]
Abstract
Successful antibody discovery relies on diversified libraries, where two aspects are implied, namely the absolute number of unique clones and the percentage of functional clones. Instead of pursuing the absolute quantity thresholded by current display technology, we have sought to maximize the effective diversity by improving functional clone percentage. With the combined effort of bioinformatics, structural biology, molecular immunology and phage display technology, we devised a bioinformatic pipeline to construct and validate libraries via combinatorial assembly of sequences from a database of experimentally validated antibodies. Furthermore, we showed that the libraries constructed as such yielded a significantly increased success rate against different antigen types and generated over 20-fold more unique hits per targets compared with libraries based on traditional degenerate nucleotide methods. Our study indicated that predefined CDR sequences with optimized CDR-framework compatibility could be a productive direction of functional library construction for in vitro antibody development.
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Affiliation(s)
- Qi Zhao
- Abcam plc, 688 E. Main Street, Branford, CT, 06405, USA.
| | - Diane Buhr
- Abcam plc, 688 E. Main Street, Branford, CT, 06405, USA
| | | | | | - Mary Ferguson
- Abcam plc, 688 E. Main Street, Branford, CT, 06405, USA
| | - Eric Sanford
- Abcam plc, 688 E. Main Street, Branford, CT, 06405, USA
| | - Erika Holland
- Abcam plc, 688 E. Main Street, Branford, CT, 06405, USA
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Huang R, Kiss MM, Batonick M, Weiner MP, Kay BK. Generating Recombinant Antibodies to Membrane Proteins through Phage Display. Antibodies (Basel) 2016; 5:antib5020011. [PMID: 31557992 PMCID: PMC6698964 DOI: 10.3390/antib5020011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 04/21/2016] [Accepted: 04/21/2016] [Indexed: 01/03/2023] Open
Abstract
One of the most important classes of proteins in terms of drug targets is cell surface membrane proteins, and yet it is a challenging set of proteins for generating high-quality affinity reagents. In this review, we focus on the use of phage libraries, which display antibody fragments, for generating recombinant antibodies to membrane proteins. Such affinity reagents generally have high specificity and affinity for their targets. They have been used for cell staining, for promoting protein crystallization to solve three-dimensional structures, for diagnostics, and for treating diseases as therapeutics. We cover publications on this topic from the past 10 years, with a focus on the various formats of membrane proteins for affinity selection and the diverse affinity selection strategies used. Lastly, we discuss the challenges faced in this field and provide possible directions for future efforts.
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Affiliation(s)
- Renhua Huang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607-7060, USA.
| | - Margaret M Kiss
- AxioMx Inc., a subsidiary of Abcam Plc, Branford, CT 06405, USA.
| | - Melissa Batonick
- AxioMx Inc., a subsidiary of Abcam Plc, Branford, CT 06405, USA.
| | - Michael P Weiner
- AxioMx Inc., a subsidiary of Abcam Plc, Branford, CT 06405, USA.
| | - Brian K Kay
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607-7060, USA.
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Batonick M, Holland EG, Busygina V, Alderman D, Kay BK, Weiner MP, Kiss MM. Platform for high-throughput antibody selection using synthetically-designed antibody libraries. N Biotechnol 2015; 33:565-73. [PMID: 26607994 DOI: 10.1016/j.nbt.2015.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/04/2015] [Accepted: 11/09/2015] [Indexed: 11/30/2022]
Abstract
Synthetic humanized antibody libraries are frequently generated by random incorporation of changes at multiple positions in the antibody hypervariable regions. Although these libraries have very large theoretical diversities (>10(20)), the practical diversity that can be achieved by transformation of Escherichia coli is limited to about 10(10). To constrain the practical diversity to sequences that more closely mimic the diversity of natural human antibodies, we generated a scFv phage library using entirely pre-defined complementarity determining regions (CDR). We have used this library to select for novel antibodies against four human protein targets and demonstrate that identification of enriched sequences at each of the six CDRs in early selection rounds can be used to reconstruct a consensus antibody with selectivity for the target.
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Affiliation(s)
- Melissa Batonick
- AxioMx, Inc., 688 East Main Street, Branford, CT 06405, United States.
| | - Erika G Holland
- AxioMx, Inc., 688 East Main Street, Branford, CT 06405, United States
| | - Valeria Busygina
- AxioMx, Inc., 688 East Main Street, Branford, CT 06405, United States
| | - Dawn Alderman
- AxioMx, Inc., 688 East Main Street, Branford, CT 06405, United States
| | - Brian K Kay
- University of Illinois at Chicago, 845 West Taylor Street Chicago, IL 60607, United States
| | - Michael P Weiner
- AxioMx, Inc., 688 East Main Street, Branford, CT 06405, United States
| | - Margaret M Kiss
- AxioMx, Inc., 688 East Main Street, Branford, CT 06405, United States
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Holland EG, Acca FE, Belanger KM, Bylo ME, Kay BK, Weiner MP, Kiss MM. In vivo elimination of parental clones in general and site-directed mutagenesis. J Immunol Methods 2014; 417:67-75. [PMID: 25523926 DOI: 10.1016/j.jim.2014.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 12/09/2014] [Accepted: 12/10/2014] [Indexed: 11/27/2022]
Abstract
The Eco29k I restriction endonuclease is a Sac II isoschizomer that recognizes the sequence 5'-CCGCGG-3' and is encoded, along with the Eco29k I methylase, in the Escherichia coli strain 29k. We have expressed the Eco29k I restriction-methylation system (RM2) in E. coli strain TG1 to produce the strain AXE688. We have developed a directed molecular evolution (DME) mutagenesis method that uses Eco29k I to restrict incoming parental DNA in transformed cells. Using our DME method, we have demonstrated that our AXE688 strain results in mutated directed molecular evolution libraries with diversity greater than 10(7) from a single transformation and with greater than 90% recombinant clones.
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Affiliation(s)
- Erika G Holland
- AxioMx, Inc., 688 E. Main St., Branford, CT 06405, United States
| | - Felicity E Acca
- AxioMx, Inc., 688 E. Main St., Branford, CT 06405, United States
| | | | - Mary E Bylo
- AxioMx, Inc., 688 E. Main St., Branford, CT 06405, United States
| | - Brian K Kay
- University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL 60607, United States
| | - Michael P Weiner
- AxioMx, Inc., 688 E. Main St., Branford, CT 06405, United States
| | - Margaret M Kiss
- AxioMx, Inc., 688 E. Main St., Branford, CT 06405, United States.
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Holland EG, Buhr DL, Acca FE, Alderman D, Bovat K, Busygina V, Kay BK, Weiner MP, Kiss MM. AXM mutagenesis: an efficient means for the production of libraries for directed evolution of proteins. J Immunol Methods 2013; 394:55-61. [PMID: 23680235 DOI: 10.1016/j.jim.2013.05.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 05/02/2013] [Accepted: 05/06/2013] [Indexed: 12/31/2022]
Abstract
Affinity maturation is an important part of the recombinant antibody development process. There are several well-established approaches for generating libraries of mutated antibody genes for affinity maturation, but these approaches are generally too laborious or expensive to allow high-throughput, parallel processing of multiple antibodies. Here, we describe a scalable approach that enables the generation of libraries with greater than 10(8) clones from a single Escherichia coli transformation. In our method, a mutated DNA fragment is produced using PCR conditions that promote nucleotide misincorporation into newly synthesized DNA. In the PCR reaction, one of the primers contains at least three phosphorothioate linkages at its 5' end, and treatment of the PCR product with a 5' to 3' exonuclease is used to preferentially remove the strand synthesized with the non-modified primer, resulting in a single-stranded DNA fragment. This fragment then serves as a megaprimer to prime DNA synthesis on a uracilated, circular, single-stranded template in a Kunkel-like mutagenesis reaction that biases nucleotide base-changes between the megaprimer and uracilated DNA sequence in favor of the in vitro synthesized megaprimer. This method eliminates the inefficient subcloning steps that are normally required for the construction of affinity maturation libraries from randomly mutagenized antibody genes.
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