The Use of Aptamers and Molecularly Imprinted Polymers in Biosensors for Environmental Monitoring: A Tale of Two Receptors

Round 1

Reviewer 1 Report

The authors have reviewed the use of aptamers and MIPs in biosensor for environmental monitoring in this manuscript, which is a quite interesting topic. Both synthetic receptors and their use in sensors have been compared throughout the manuscript. The major issue regarding this manuscript is the lack of scientific depth. The more detail and concrete explanations are necessary while describing the works involved in the review as well as while comparing the aptamers and MIPs. In addition to this, the following comments should be addressed:

• Line 4 and line 133, full stop is not necessary in the end of the titles.
• Inconsistencies in lower and upper cases of titles/subtitles need to be corrected.
• Line 40, “inclusion of functional monomers”
• Line 52, the number is missing in the caption.
• Introduction is superficial. It needs to be improved. Aptamers and MIPs should also be concretely compared in a table as well.
• Figure 1, Figure 2, and Figure 3 are taken from the Ref 78, 82, and 88, respectively. However, they are not cited. They must be properly cited based on the rules of MDPI as well as the other publishing houses. The other schemes and figures should also be checked by the authors.
• All display items have very poor resolution. They all need to be substantially improved.
• Line 95 & 96, the reason/s for non-specific binding should be given.
• Line 149-150, the last part of the sentence needs to be corrected.
• Line 248, “aptasensors suffer from low stability”. The reasons for this low stability should be mentioned.
• Line 257, “are skill-oriented”.
• Line 267, the difficulty in whole cell imprinting is not only depend on the selection of right functional monomers. There exist several other important drawbacks, which need to be addressed critically.
• Line 269-272, the results of different works must be compared concretely with important values. For example, the linear range and LOD were not provided in Ref 76. The reader would not able to compare the efficiency of MIP and aptamer for the same analyte. This must be taken into account in the entire manuscript.
• Line 274, the four different materials need to be defined in the brackets.
• The conclusion section must cover the solutions and future prospects towards the current limitations in both aptamer and MIP technologies.

Author Response

Reviewer 1

The authors have reviewed the use of aptamers and MIPs in biosensor for environmental monitoring in this manuscript, which is a quite interesting topic. Both synthetic receptors and their use in sensors have been compared throughout the manuscript. The major issue regarding this manuscript is the lack of scientific depth. The more detail and concrete explanations are necessary while describing the works involved in the review as well as while comparing the aptamers and MIPs. In addition to this, the following comments should be addressed:

- We thank the reviewer for his helpful comments and constructive criticism of our paper. We have made the following changes to the manuscript to improve the overall quality and readability.

Line 4 and line 133, full stop is not necessary in the end of the titles.

- Full stops have been removed from lines 4 and 133.

Inconsistencies in lower and upper cases of titles/subtitles need to be corrected.

- The titles have been corrected for consistency

Line 40, “inclusion of functional monomers”

- The sentence has been corrected on line 40

Line 52, the number is missing in the caption.

- The sentence has been corrected on line 52

Introduction is superficial. It needs to be improved. Aptamers and MIPs should also be concretely compared in a table as well.

- We have substantially expanded the introduction and added a table to compare the performance of antibodies, MIPs and aptamers (Table 1)

Figure 1, Figure 2, and Figure 3 are taken from the Ref 78, 82, and 88, respectively. However, they are not cited. They must be properly cited based on the rules of MDPI as well as the other publishing houses. The other schemes and figures should also be checked by the authors.

- All prior copyright has been obtained from the prospective publishers for figure 1, 2 and 3 and citations given in line with fair use.

All display items have very poor resolution. They all need to be substantially improved.

- The figures have been replaced with ones of a higher resolution.  

Line 95 & 96, the reason/s for non-specific binding should be given.

- We have added an explanation for the non-specific binding on line 95 and 96

Line 149-150, the last part of the sentence needs to be corrected.

- The sentence has been corrected on line 149-150

Line 248, “aptasensors suffer from low stability”. The reasons for this low stability should be mentioned.

- The sentence has been amended on line 248.

Line 257, “are skill-oriented”.

- “are skill-oriented” has been changed to  “labour intensive”  on line 257

Line 267, the difficulty in whole cell imprinting is not only depend on the selection of right functional monomers. There exist several other important drawbacks, which need to be addressed critically.

- The other main drawbacks related the use of MIP for whole cell imprinting are provided and highlighted in the new version of the manuscript on line 267 and 317.

Line 269-272, the results of different works must be compared concretely with important values. For example, the linear range and LOD were not provided in Ref 76. The reader would not able to compare the efficiency of MIP and aptamer for the same analyte. This must be taken into account in the entire manuscript.

- The issues are addressed and highlighted in the new version of the manuscript on Lines line 269-272.

Line 274, the four different materials need to be defined in the brackets.

- The issue is addressed and highlighted in the new version of the manuscript on line 274.

The conclusion section must cover the solutions and future prospects towards the current limitations in both aptamer and MIP technologies.

- The conclusion has been further expanded on to discuss the future prospects of the two technologies in the conclusion Section.

Reviewer 2 Report

This review reports on the recent developments in the field of aptamer and MIP sensors for the environmental monitoring area, with a focus of the detection of various contaminants: antibiotics, pesticides, heavy metals and pathogens. This work is interesting because it covers two fields which only rarely meet for the design of biosensors. Before acceptance, the authors should address the points summarized below:

1. It would have been helpful for the reader to know which period the review covers?
2. Since many aptamer and MIP based sensors have been developed, it would be interesting to comment also on commercial applications in the area of environmental monitoring, if any. Ref 4 tackles this question for MIPs. It would be interesting to clearly mention the achievements which lead or are promising for potential industrial used not only for MIPs but also for aptamers. At lines 73-74, the authors say that limitations hindered their commercial development. This is not true for all the applications because MIPs have been developed or are developed for industrial use, like for example, solid-phase extraction and explosives detection (PolyIntell, Biotage, Supelco MIP (Sigma Aldrich), Wheatley SPI LLC American company who developed a portable device for rapid detection of traces of explosives). So, it’s important to be more specific here.
3. What about the synergic use of aptamer and MIP to improve the performance of such synthetic receptors for environmental pollutants detection?
4. Could authors comment on the wide range of the limit of detection of the different sensors described in this review?
5. In order to use the figures from published work, editor permission has to be obtained. The resolution of the figures is very low and requires improvement!
6. Additional typos and editing comments:

• Lines 32 and 33 “complementary”: Please, be more precise. “complementary” in shape, functionality, etc…
• Lines 80-90: for traces detection and to avoid template leakage issues, dummy templates can be used for the imprinting.
• Line 109: The authors focused on examples of sensors targeting tetracycline. Could they mention briefly if sensors for other antibiotic targets have been developed?
• Line 115: “recently” used twice in the same sentence
• Lines 118-121: long sentence; the message would be clearer if presented in 2 sentences!
• Line 125: remove dot after the reference [31]!
• Line 135: “As such, the number…” instead of “As such a number …”
• Lines 141-142: Use “The nanozymes, which is based on Ag nanoparticules, was found…”
• Line 145: “based” used twice in the same sentence
• Line 145: “nanotube… was synthetized…”
• Lines 149-150: please revise the end of the sentence
• Line 179: use “fulfils”
• Line 222: use comma to separate references or merge them
• Lines 226 & 230: for consistency sake, the refs should be added after the dot
• Lines: 224-232: which is the limits of detection for these two sensors
• Lines 243-246: please revise this sentence
• Line 277: LOD is used for limit of detection whereas, in the tables previously introduced, LD is used instead!
• Line 327: for consistency sake, please use a dot after “et al”
• Line 347: please revise the sentence

Author Response

Reviewer 2

This review reports on the recent developments in the field of aptamer and MIP sensors for the environmental monitoring area, with a focus of the detection of various contaminants: antibiotics, pesticides, heavy metals and pathogens. This work is interesting because it covers two fields which only rarely meet for the design of biosensors. Before acceptance, the authors should address the points summarized below:

- We thank the reviewer for his helpful comments and constructive criticism, we have amended the manuscript as mentioned by the reviewer.

It would have been helpful for the reader to know which period the review covers?

- The following sentence has been added to the review to reflect the time period of the review. “The review covers the developments of the last 5-10 years of aptamer and MIP development”.

Since many aptamer and MIP based sensors have been developed, it would be interesting to comment also on commercial applications in the area of environmental monitoring, if any. Ref 4 tackles this question for MIPs. It would be interesting to clearly mention the achievements which lead or are promising for potential industrial used not only for MIPs but also for aptamers. At lines 73-74, the authors say that limitations hindered their commercial development. This is not true for all the applications because MIPs have been developed or are developed for industrial use, like for example, solid-phase extraction and explosives detection (PolyIntell, Biotage, Supelco MIP (Sigma Aldrich), Wheatley SPI LLC American company who developed a portable device for rapid detection of traces of explosives). So, it’s important to be more specific here.

- We have amended this section to give a brief discussion on the current commercial development in aptamers and MIPs. 

What about the synergic use of aptamer and MIP to improve the performance of such synthetic receptors for environmental pollutants detection?

- The synergic effect of aptamers and MIPs has been briefly addressed in the antibiotic section and introduction section.

Could authors comment on the wide range of the limit of detection of the different sensors described in this review?

- It is extremely challenging to draw a conclusion from the wide variation in detection limits observed for some biosensors.  I would assume as a fair guess, that systematic errors are to blame.  In terms of MIPs, polymerization is not a very controllable reaction and hence you can get variation in batch to batch performance.  For aptamers, even though you can synthesize the aptamers with low batch to batch variation, their performance is sensitive to the buffer conditions used in the application and any deviation from the original buffer conditions used can adversely affect their performance. We have added a brief sentence on systematic errors.

In order to use the figures from published work, editor permission has to be obtained. The resolution of the figures is very low and requires improvement!

- The figures are either replaced with high resolution ones or redrawn by the authors. 

- About the copyright permissions: (i) Scheme is drawn by the authors, (ii) Figures 1 permission is granted and provided, (iii) Figures 2-4 are attributed to the open access journals.

Additional typos and editing comments:

Lines 32 and 33 “complementary”: Please, be more precise. “complementary” in shape, functionality, etc…

- The sentence has been amended

Lines 80-90: for traces detection and to avoid template leakage issues, dummy templates can be used for the imprinting.

-We have added a sentence to acknowledge dummy templates to specifically address this problem.

Line 109: The authors focused on examples of sensors targeting tetracycline. Could they mention briefly if sensors for other antibiotic targets have been developed?

-A brief discussion of other antibiotics has been added to the

Line 115: “recently” used twice in the same sentence

-The sentence has been amended.

Lines 118-121: long sentence; the message would be clearer if presented in 2 sentences!

-The sentences have been split into two for clarity to the reader.

Line 125: remove dot after the reference [31]!

-Formatting has been changed to have the full stop after the reference. 

Line 135: “As such, the number…” instead of “As such a number …”

-The sentence has been amended.

Lines 141-142: Use “The nanozymes, which is based on Ag nanoparticles, was found…”

-The sentence has been amended

Line 145: “based” used twice in the same sentence

-The word has based has been deleted.

Line 145: “nanotube… was synthetized…”

-The sentence was amended.

Lines 149-150: please revise the end of the sentence

-The sentence has been amended.

Line 179: use “fulfils”

-The usage of “fulfils” appears to be correct here.  No changes were made.

Line 222: use comma to separate references or merge them

-The references have been merged together.

Lines 226 & 230: for consistency sake, the refs should be added after the dot

-For consistency and following other formatted papers, the full stops have been placed after the reference brackets.

Lines: 224-232: which is the limits of detection for these two sensors

- The LOD of these two sensors were reported in Table 1 and Table 2. For the first sensor [60], sensor-based on RGO–IIP, it was 0.02 µgL^-1. Moreover, for the second sensor, gold inkjet-printed aptasenor [46], it was 10 µgL^-1 and 5 µgL^-1 in water and DMSO, respectively.

Lines 243-246: please revise this sentence

-This sentence was revised.

Line 277: LOD is used for the limit of detection whereas, in the tables previously introduced, LD is used instead!

-The term LD has been replaced with LOD in all cases.

Line 327: for consistency sake, please use a dot after “et al”

- The issue is addressed and highlighted in the new version of manuscript. Lines 376.

Line 347: please revise the sentence

-The sentence has been amended

Reviewer 3 Report

the paper is a review on the use of Aptamers and Molecularly Imprinted
Polymers in Biosensor for Environmental Monitoring.

The review is well organised and clear in each section. The authors should report the work of Giusti and Ciardelli, that worked a lot on this research area and developed also different polymers imprinted structure working as biosensors and tissue engineering scaffolds.

Author Response

Reviewer 3

The review is well organised and clear in each section. The authors should report the work of Giusti and Ciardelli, that worked a lot on this research area and developed also different polymers imprinted structure working as biosensors and tissue engineering scaffolds.

- We thank the reviewer for his supportive comments. We have added the following papers to reflect the work of  Giusti and Ciardelli.

https://doi.org/10.1163/1568562053115417

https://doi.org/10.1016/j.memsci.2006.05.031

Round 2

Reviewer 1 Report

The authors have addressed the comments convincingly. There are some typing errors, which can be corrected during the proof-reading process. I recommend the publication of this manuscript in Chemosensors.

Author Response

The manuscript has been further proofread.  Thank you to the reviewer for helping us to improve the manuscript.

Reviewer 2 Report

Few minor suggestions for the revised version of the review:

Lines 49, 76, 89, 117, 186, 222, 344, 353: extra space needed before the reference

Line 60: use small case for "biomimetic"

Line 137: “The same can be said…”

Line 143: “Although, their development is often achieved in a trial and error manner to find the optimal monomer, template and cross linker ratios.” Rational MIP design approaches are more and more common nowadays.

Line 185: For consistency sake, use MIPs instead of MIPS.

Line 329: Bacillus cereus should be in italic

Line 359: please give the correct range for the linear response

Line 425, 426: The name of the pathogens should be in italic

Line 449: To remain consistent with the additions in the section on “The Development of Aptamers and MIPs” about the commercial developments, I would suggest to talk about “the lack of large scale commercial development.”

Author Response

Lines 49, 76, 89, 117, 186, 222, 344, 353: extra space needed before the reference

Corrected

Line 60: use small case for "biomimetic"

Corrected

Line 137: “The same can be said…”

Corrected

Line 143: “Although, their development is often achieved in a trial and error manner to find the optimal monomer, template and cross-linker ratios.” Rational MIP design approaches are more and more common nowadays.

The sentence has been amended and reference added to reflect this development

Line 185: For consistency sake, use MIPs instead of MIPS.

Corrected

Line 329: Bacillus cereus should be in italic

Corrected

Line 359: please give the correct range for the linear response

Corrected

Line 425, 426: The name of the pathogens should be in italic

Corrected 

Line 449: To remain consistent with the additions in the section on “The Development of Aptamers and MIPs” about the commercial developments, I should suggest talking about “the lack of large scale commercial development.”

We have amended the sentence to reflect the current commercial development of MIPs and aptamers.  I think we can agree that there is some commercial development of both MIPs and aptamers but they are still relatively young industries, respectively.   

Reviewer 3 Report

the paper was revised as required

Author Response

The paper has been further proofread for typo errors. We thank the reviewer for helping us to improve the manuscript.