Dear Dr Lindner,

Thank you for submitting your manuscript entitled "qByte: Open-source isothermal fluorimeter for democratizing analysis of nucleic acids, proteins and cells" for consideration as a Methods and Resources Article by PLOS Biology. Please accept my sincere apologies for the delay in getting back to you with feedback this week.

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Richard Hodge, PhD

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rhodge@plos.org

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Dear Dr Lindner,

Thank you for your patience while your manuscript "qByte: Open-source isothermal fluorimeter for democratizing analysis of nucleic acids, proteins and cells" went through peer-review at PLOS Biology. Apologies for the delay in sending our decision on your submission. Unfortunately we encountered some delays during the review process. Your manuscript has now been evaluated by the PLOS Biology editors, an Academic Editor with relevant expertise, and by several independent reviewers.

In light of the reviews, which you will find at the end of this email, we are pleased to offer you the opportunity to address the comments from the reviewers in a revision that we anticipate should not take you very long. Some of the technical points made by Reviewer 1 will be important to address by inclusion of additional data, but most other points can be addressed by textual revisions changes. We will assess your revised manuscript and your response to the reviewers' comments with our Academic Editor aiming to avoid further rounds of peer-review, although might need to consult with the reviewers, depending on the nature of the revisions.

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Sincerely,

Christian

Christian Schnell

Senior Editor

PLOS Biology

cschnell@plos.org

on behalf of

Richard Hodge, PhD

Senior Editor

PLOS Biology

rhodge@plos.org

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REVIEWS:

Reviewer #1: see pdf

Reviewer #2: The authors have presented a compelling device that can significantly democratize access to biotechnology research. They present application examples with results that show a diversity of successful uses. There are some minor points which might be addressable: a) Lines 312-332 "Specifically, we identified two main possible implementations…." in which the authors describe absolute versus fluorescence change within the samples and so forth. Further in line 324 they describe a second potential improvement. Overall, this paragraph is confusing because the as a reader, I am not sure if you are describing a set of design choices (First vs Second) that you had to take. I am not sure exactly which one you actually took. It left me with more questions about how the device works than answers. Or if you are discussing future considerations. I would restructure that paragraph in a way that it becomes clear and not intermingle theoretical improvements with actual choices. The data speaks for itself and the work is good, this *paragraph* did not increase confidence in your choices. I am sure that was not your intention.

b) Your selection of a wide variety of protocols and applications was refreshing to see beyond a diagnostic approach. Perhaps consider framing the selection in terms of diversity (given the versatile nature of your device) or another theme. Otherwise the use of TX-TL reactions seems to be slotted in.

c) Given your focus on field deployability: The deployment of the device in Ghana is very well explained, as is the work in the UK (Cambridge), Switzerland (Gaudi Labs), France ("Universit´e Paris Cit´e, INSERM U1284, Center for Research and Interdisciplinarity, F-75006 Paris, France) and in Chile ("Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Catolica de Chile, Santiago, Chile"). This alone is a powerful demonstration of international technology transfer. On the other hand, Line 336 (and its summary in the abstract) detracts from this claim since you omit results (Line 337) in the paper. It seems to be a distraction. Suggestion: Omit references to field work whose results you are not showing or position it as future work.

In summary, the authors have assembled a formidable interdisciplinary team resulting in a real-world, affordable devices with remarkable international results and implications for democratized biotechnology. This work should be published as soon as possible.

Attachments

Attachment

Submitted filename: qByte review 2025 - Saad bhamla.pdf

Dear Dr Lindner,

Thank you for your patience while we considered your revised manuscript "qByte: Open-source isothermal fluorimeter for democratizing analysis of nucleic acids, proteins and cells" for publication as a Methods and Resources Article at PLOS Biology. This revised version of your manuscript has been evaluated by the PLOS Biology editors, the Academic Editor and the original reviewers.

Based on the reviews, I am pleased to say that we are likely to accept this manuscript for publication, provided you satisfactorily address the following data and other policy-related requests that I have provided below (A-E):

(A) We would like to suggest the following minor edit to the title:

“qByte: an open-source isothermal fluorimeter for democratizing analysis of nucleic acids, proteins and cells”

(B) You may be aware of the PLOS Data Policy, which requires that all data be made available without restriction: http://journals.plos.org/plosbiology/s/data-availability. For more information, please also see this editorial: http://dx.doi.org/10.1371/journal.pbio.1001797

Note that we do not require all raw data. Rather, we ask that all individual quantitative observations that underlie the data summarized in the figures and results of your paper be made available in one of the following forms:

-Supplementary files (e.g., excel). Please ensure that all data files are uploaded as 'Supporting Information' and are invariably referred to (in the manuscript, figure legends, and the Description field when uploading your files) using the following format verbatim: S1 Data, S2 Data, etc. Multiple panels of a single or even several figures can be included as multiple sheets in one excel file that is saved using exactly the following convention: S1_Data.xlsx (using an underscore).

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Figure 2A-G, 3A-D, S1C (Figures 2 and 3)

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(E) Please ensure that your Data Statement in the submission system accurately describes where your data can be found and is in final format, as it will be published as written there.

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As you address these items, please take this last chance to review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the cover letter that accompanies your revised manuscript.

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*Protocols deposition*

To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols

Please do not hesitate to contact me should you have any questions.

Best wishes,

Richard

Richard Hodge, PhD

Senior Editor, PLOS Biology

rhodge@plos.org

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Reviewer remarks:

Reviewer #1 (Saad Bhamla, signs review): Authors have addressed all my comments

Reviewer #2: Congratulations!

Dear Ariel,

On behalf of my colleagues and the Academic Editor, Tom Misteli, I am pleased to say that we can accept your manuscript for publication, provided you address any remaining formatting and reporting issues. These will be detailed in an email you should receive within 2-3 business days from our colleagues in the journal operations team; no action is required from you until then. Please note that we will not be able to formally accept your manuscript and schedule it for publication until you have completed any requested changes.

In addition, please include a sentence in the figure legend for S1C Figure 3 in the S1 Data file that states where the underlying data can be found (‘The raw data supporting all figures can be found in S2 File’). This can be included during the production process. I have also included the PDF version of the manuscript in the File Inventory as a Supplementary File. This can be removed from the File Inventory if needed during production.

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PRESS

We frequently collaborate with press offices. If your institution or institutions have a press office, please notify them about your upcoming paper at this point, to enable them to help maximise its impact. If the press office is planning to promote your findings, we would be grateful if they could coordinate with biologypress@plos.org. If you have previously opted in to the early version process, we ask that you notify us immediately of any press plans so that we may opt out on your behalf.

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Thank you again for choosing PLOS Biology for publication and supporting Open Access publishing. We look forward to publishing your study. 

Best wishes, 

Richard

Richard Hodge, PhD

Senior Editor, PLOS Biology

rhodge@plos.org

PLOS

Empowering researchers to transform science

Carlyle House, Carlyle Road, Cambridge, CB4 3DN, United Kingdom

California (U.S.) corporation #C2354500, based in San Francisco