FAQ

Category Question
nanoCLAMPs

Why does Nectagen ship nanoCLAMPs in lyophilized form?


Nectagen ships nanoCLAMPs in lyophilized form so that users can resuspend the nanoCLAMP in their buffer of choice.  The lyophilized cake is packaged under nitrogen to minimize oxidation.  The lyophilized formulation is expected to have superior stability and temperature tolerance compared to a liquid formulation.  Long-term testing is underway to determine the shelf-life of the lyophilized form. 

nanoCLAMPs

How did Nectagen choose CBM32-2 as the scaffold for nanoCLAMPs?


Nectagen chose CBM32-2 based on its suitability for use for research, not for therapeutics as is the case for many other antibody substitutes.

Several candidate scaffolds were screened according to the following criteria:

3D structure available to enable rational design

Beta sheet sandwich domain to mimic immunoglobulin domain

Size <5 nanometers to improve performance in super-resolution applications

Several loops tolerant to substitution to enable variabilization

N- and C-termini on the end opposite the variabilized loops to minimize interference by fusion proteins

Lack of disulfides to facilitate intracellular expression

Compatibility with phage display to allow in vitro screening

>20 mg/l expression in E. coli to facilitate low cost production

Polyol sensitivity to allow for protein purification under gentle conditions

Unlike scaffolds intended for therapeutic applications, Nectagen did not screen for low antigenicity, tissue penetrance, in vivo half-life, or compatibility with therapeutic production processes.  

Nectagen characterized the performance of more than a dozen potential scaffolds to identify NagH CBM32-2 as meeting the criteria above.   

 

 

 

nanoCLAMPs

What is known about the toxicity of the nanoCLAMP scaffold?


The toxicity of nanoCLAMPs has not been directly tested. nanoCLAMPs should be treated like any other protein with unknown effects on humans.  The scaffold is derived from NagH CBM32-2, a 148 amino acid domain from the 1627 amino acid NagH gene from Clostridium perfringens. NagH is a hyaluronidase and is also known as mu-toxin. The CBM32-2 domain is distinct from the hyaluronidase catalytic domain and is a carbohydrate binding module recognizing N-acetylglucosamine. The domain is not known to have any catalytic activity on its own. nanoCLAMPs are not expected to bind N-acetylglucosamine because the loops responsible for binding N-acetylglucosamine have been randomized.  More information about the scaffold can be found in Ficko-Blean and Boralston, J. Mol. Biol. 2009.

General Products, Terminology, nanoCLAMPs

What is a "lot"?


Nectagen uses "lot" to refer to the group of products produced by a single manufacturing run. Products within each lot are expected to have indistinguishable performance.

Each lot is subject to a quality control procedure to confirm identity, purity, quantity, and function. 

Site, nanoCLAMPs, Policies

Why can't I see the amino acid sequences for nanoCLAMPs?


nanoCLAMP sequences are visible to authenticated users who agree to Nectagen's terms of use.  The sequences are hidden for anonymous users.  Users can gain access by creating an account and agreeing to the terms.  

nanoCLAMPs

How can I attach dyes or enzymes to nanoCLAMPs?


nanoCLAMPs have a unique cysteine at their C-terminus.  Sulfhydryl-reactive cross-linkers such as maleimide bind site-specifically with a defined stoichiometry. Maleimide-dye and maleimide-enzymes are commercially available from many suppliers.  Users can also make gene fusions using the amino acid sequences provided under the terms of use. 

nanoCLAMPs

Why do nanoCLAMPs release bound protein when exposed to polyols?


It is not known why nanoCLAMPs and some monoclonal antibodies are polyol sensitive.  This property is characteristic of some monoclonal antibodies.  Thompson et al. Methods Enzymol. 2009.  Nectagen uses propylene glycol in its standard elution buffers.  Glycerol is an alternative polyol that may be gentler but less efficient at elution.  

nanoCLAMPs

How has the nanoCLAMP scaffold been modified from NagH CBM 32-2?


The nanoCLAMP scaffold contains a M929L mutation to eliminate a methionine potentially subject to oxidation and an N-terminal his-tag to faciliate purification. Three loops on the face opposite the N- and C-termini are randomized to generate diversity.

Site, Terminology

What does "ISBN" mean?


ISBN stands for International Standard Book Number and is a book's unique identifier with the country registration agencies.  ISBN's issued after 2006 contain 13 digits vs. 10 previously.  Use of the ISBN allows Nectagen to connect book references to outside databases.  Currently ISBN's connect to Amazon so that users can review comprehensive information on a book and order a copy conveniently.  Nectagen does not receive any consideration from Amazon.  

The ISBN can typically be found on the back of a book's inside title page or underneath the image of the book cover in the Amazon listing.

Site, Policies

Why does Nectagen link to outside data sources?


Whenever possible, Nectagen links its data to outside data sources such Genbank, Uniprot, or Wikipedia.  Nectagen believes that the utility of its own database increases when it can build upon the work of others.  Whenever possible, Nectagen provides links to make it easier for users to access outside data.  Nectagen does not seek to hold its users captive to its database. 

Site, Policies

Why does Nectagen provide links to outside vendors and their products?


Nectagen provides these links for the convenience of its user community.  Nectagen does not endorse any vendors or their products and does not receive any consideration from the listed vendors. 

Site

How do I provide feedback to other community members and Nectagen?


Nectagen provides structured forms for community members to rate content, review content, report problems with the site, and report quality issues with products.  The data is structured and open so that members can find and review feedback contributed by others.  For instance, Nectagen records and publicizes reports of quality issues so that other members become aware of information relevant to their work as quickly as possible.  

Site, nanoCLAMPs, Policies

Why can't I see the amino acid sequences for nanoCLAMPs?


nanoCLAMP sequences are visible to authenticated users who agree to Nectagen's terms of use.  The sequences are hidden for anonymous users.  Users can gain access by creating an account and agreeing to the terms.  

Site

How does Nectagen's messaging system work?


Nectagen offers a messaging service to strengthen its community by providing users with a convenient way to contact each other.  In each user's account settings, users may opt-in to receive messages from other users and receive an e-mail notification of new messages.  Messages may be exchanged through the system without revealing a user's e-mail address.

Nectagen will not use the messaging system for promotional purposes.  Users may not send bulk messages or use messages to solicit businesses.

Users should expect their messages to be as confidential as when using an employer's e-mail system.  Nectagen does not monitor messages but reserves the right to review messages when abuse or policy violations are suspected.  Nectagen's system uses password protection and access controls to secure the contents of e-mails but does not encrypt or otherwise secure the content.  

For private or non-professional communications, users should use Nectagen's messaging system to exchange e-mail addresses and communicate directly. 

Site

Why aren't I receiving messages or notifications?


You may not be receiving messages or notifications because you have not opted in or because your spam filter is catching the notifications.

To receive messages and notifications, go to your account settings via your dashboard.  Under "Private Messages," check one or both boxes.

To make sure you receive notification e-mails, send yourself a message. Identify the resulting notification message from support@nectagen.com as "Not spam." 

Site

Why do the links on the right sidebar change as I view different pages?


The links on the right sidebar represent available actions.  The visible links change depending upon the type of page being viewed and the role of the user.  Please contact support if you believe a link should be available but is missing. 

Site

Why doesn't new content  that I draft get saved to the database?


One possible reason is that you closed the window or tab before hitting the "Save" button, usually near the bottom of the screen.

Another possible reason is that you are not logged in. Anonymous users are not permitted to add content.

Site, Policies

Why does Nectagen require authors, reviewers, raters and commenters to use their real name?


 

Authors, reviewers, raters and commenters are required to disclose their real name because Nectagen believes the use of real names promotes accountability and transparency, both of which strengthen its community.   Knowing authors, reviewers, raters and commenters experience and past history helps a reader to assess the credibility and validity of their contributions. Individuals may opt to have a public profile to share their credentials and past contributions with the community.  Requiring attribution for all contributions also promotes responsible and balanced behavior by contributors. 

Unlike contributors, readers and purchasers are not required to disclose their identity.  Individuals may choose to purchase products and use the site without disclosing their use. 

Accountability and transparency do not necessarily come at the cost of privacy. To promote privacy, Nectagen does not publish e-mail or other contact information.  Members may opt to an internal messaging system to communicate without disclosing e-mail addresses. Members may opt to disclose their contact information in a biosketch or C.V.

 

Site, Policies

Why does Nectagen ask users to enter data in forms instead of allowing cutting and pasting the entire text?


Nectagen's database is highly structured to capture, organize and display data.  While cut and paste data entry would be faster and easier, Nectagen believes the long-term investment in structured data is more useful to its community.  The burden is higher for individuals initially, but ultimately the structured data makes it easier for other users to build upon each piece of data so that the community benefits more over time.  

Where possible, Nectagen has entered as much data as possible to remove the burden from users.  For example, Nectagen has entered taxonomy data for model organisms, STR profiles for commonly used cell lines, and reference information for commonly used solution ingredients.    

Site, Terminology

What does "clone content" mean?


"Clone content" means making an editable copy of an entry in the database. This action makes data entry more efficient for variants.  For some content, e.g. applications, solutions or protocols, the current database design requires each ingredient or step to be added again with the current database structure. Unfortunately, a one step "cloning" process is challenging because these data reside in multiple tables in the database.  These tables enable features such as having a specialized template for different kinds of results, reordering steps and reusing ingredients.  The database structure make a tradeoff between the convenience of these features and the convenience of full cloning capability.  The rationale is that the features requiring different tables will be used for each new entry while the cloning feature will only be used occasionally.   Automating the entry of variants for these kinds of content will require developing a script.  Nectagen will do so as soon as resources are available. 

Site, Apps

Why does Nectagen ask users to enter protocols as individual steps?


Nectagen is developing web and mobile apps to make it easier for users to follow protocols.  These apps will have features such as integrated timers, record keeping and exporting.  The structured entry of steps in protocols facilitates the development of these features.  

Site

How can I delete content?


If you have permission to edit a form, you will see a link that says "Edit" either at the end of the row in a table or in the right side bar.  Follow the link.  There is typically a "Delete" link in the lower right corner.

Typically, the original author of content may delete content if the content is "Unlocked." If the content has already been referenced by others, the content will be "Locked" and cannot be deleted.  Non-authors do not have permission to delete content. 

Site

Why does Nectagen ask users to enter solutions as individual ingredients?


Entering solutions as individual ingredients enables other users to take advantage of a calculator for making their solutions.  After the author has made the initial investment in entering the data, subsequent users can enter the volume desired and have the required volumes of stock solutions automatically calculated. 

Site, Terminology

What is a "PubMed ID" or "PMID"?


Pubmed ID is an article's unique identifier in Medline.  It can be found at the bottom of the abstract.

Terminology, Apps

What is an "application" or "app"?


Nectagen uses "application" or "app" to refer to a documented use of its products.  Applications may be posted by any user, are reviewed by Nectagen or users and then rated by users.  

Terminology, Apps

What is an "ingredient"?


Nectagen uses "ingredients" to refer to components of solutions. Typically, ingredients are stock solutions.  

Terminology, Apps

What is a "specimen"?


Nectagen uses "specimen" to refer to the source material treated with the nanoCLAMP. The specimen can be an extract loaded on a column, a histological preparation or a serum sample assayed by an ELISA. Nectagen describes the specimen according to the following hierarchy:  Organism, Strain, Organ, Tissue, Cell Type, Cell Line, and Subcellular Compartment. The hierarchy is intended to allow users to readily identify the specimens most similar to their intended application. 

Site, Apps

Why does Nectagen ask users to enter protocols as individual steps?


Nectagen is developing web and mobile apps to make it easier for users to follow protocols.  These apps will have features such as integrated timers, record keeping and exporting.  The structured entry of steps in protocols facilitates the development of these features.  

Terminology, Apps

What is a "target"?


Nectagen uses "target" to refer to the protein bound by the nanoCLAMP.  Nectagen does not use "antigen" because nanoCLAMPs are not derived from an immunological response. Nectaen typically identifies the target by the gene name or the common name.  

Apps

Why do solution names include the author?


DIfferent authors may use the same solution name to refer to different solutions.  For example, there are multiple versions of PBS with different pH or amounts of potassium.  To avoid confusion, the author's name is appended to the solution to increase the likelihood that there is a one-to-one correspondence between solution name and solution composition.  The author's name is used instead of a unique identifying number because it is easier to remember. 

Points

How do I earn Nectagen points?


Nectagen points are awarded to provide an incentive for users to contribute to the Nectagen community.  Points are awarded to users for contributing applications and screens that are validated by reviewers and users.  

Policies

How does Nectagen market its products?


Nectagen believes that scientists make purchasing decisions based on problems they need to solve not problems they didn't know they had.  The Nectagen website is designed to provide users with as much information as possible to determine whether its products will work in the intended application. Nectagen does not have a sales force or marketing department and instead focuses its resources on developing new products and supporting its user community.  

Policies

Why does Nectagen only accept Paypal?


Nectagen uses Paypal exclusively so that Nectagen does not hold user's confidential payment information.  Nectagen focuses on developing and maintaining a website to promote the open exchange of scientific information not a website to secure financial information.  Nectagen has chosen Paypal as the payment gateway because Paypal is the most established and widely used vendor and conforms to legal requirements for handling financial information.  

Site, Policies

Why does Nectagen link to outside data sources?


Whenever possible, Nectagen links its data to outside data sources such Genbank, Uniprot, or Wikipedia.  Nectagen believes that the utility of its own database increases when it can build upon the work of others.  Whenever possible, Nectagen provides links to make it easier for users to access outside data.  Nectagen does not seek to hold its users captive to its database. 

Policies

Why does Nectagen link to outside databases like Wikipedia, Genbank, Swissprot, PubMed, the Gene Ontology Consortium and Amazon?


Nectagen has designed its database to maximize the use of outside reference data.  For instance, Nectagen links "Ingredients" to their Wikipedia page, which has information such as chemical formula, physical properties and comon uses.  Rather than relying upon Nectagen or its members re-entering and curating the data, Nectagen can take advantage of the ongoing efforts of the Wikipedia community.  Likewise, Nectagen's database benefits from the past and ongoing efforts of Genbank, GO, SwissProt and Amazon.  Where possible, Nectagen links to well established databases that are run by government agencies, non-profit groups or consortia, which focus on disseminating data rather than commercial considerations.  On occasion, Nectagen will use an open access commercial database such as Amazon when the quality and scope of the data is superior to other alternatives. 

Site, Policies

Why does Nectagen provide links to outside vendors and their products?


Nectagen provides these links for the convenience of its user community.  Nectagen does not endorse any vendors or their products and does not receive any consideration from the listed vendors. 

Policies

How does Nectagen provide technical support?


Nectagen's database aims to serve as the first source of support. The Nectagen forum serves as the next source of support.  These searchable and open support systems aim to build a community-sourced body of knowledge that will be deeper, broader and timelier than a closed system. In unusual circumstances, please contact Nectagen directly and privately at support@nectagen.com.  Nectagen does not have a dedicated technical support team so inquiries will be handled by a member of the research team.  

Site, nanoCLAMPs, Policies

Why can't I see the amino acid sequences for nanoCLAMPs?


nanoCLAMP sequences are visible to authenticated users who agree to Nectagen's terms of use.  The sequences are hidden for anonymous users.  Users can gain access by creating an account and agreeing to the terms.  

General Products, Policies

Why does Nectagen ship products in 1.6 ml screw cap tubes?


Nectagen chose 1.6 ml conical screw cap tubes because they have a secure closure, resist breakage, and are compatible with standard microcentrifuges.  

Site, Policies

Why does Nectagen require authors, reviewers, raters and commenters to use their real name?


 

Authors, reviewers, raters and commenters are required to disclose their real name because Nectagen believes the use of real names promotes accountability and transparency, both of which strengthen its community.   Knowing authors, reviewers, raters and commenters experience and past history helps a reader to assess the credibility and validity of their contributions. Individuals may opt to have a public profile to share their credentials and past contributions with the community.  Requiring attribution for all contributions also promotes responsible and balanced behavior by contributors. 

Unlike contributors, readers and purchasers are not required to disclose their identity.  Individuals may choose to purchase products and use the site without disclosing their use. 

Accountability and transparency do not necessarily come at the cost of privacy. To promote privacy, Nectagen does not publish e-mail or other contact information.  Members may opt to an internal messaging system to communicate without disclosing e-mail addresses. Members may opt to disclose their contact information in a biosketch or C.V.

 

Site, Policies

Why does Nectagen ask users to enter data in forms instead of allowing cutting and pasting the entire text?


Nectagen's database is highly structured to capture, organize and display data.  While cut and paste data entry would be faster and easier, Nectagen believes the long-term investment in structured data is more useful to its community.  The burden is higher for individuals initially, but ultimately the structured data makes it easier for other users to build upon each piece of data so that the community benefits more over time.  

Where possible, Nectagen has entered as much data as possible to remove the burden from users.  For example, Nectagen has entered taxonomy data for model organisms, STR profiles for commonly used cell lines, and reference information for commonly used solution ingredients.    

General Products, Terminology, nanoCLAMPs

What is a "lot"?


Nectagen uses "lot" to refer to the group of products produced by a single manufacturing run. Products within each lot are expected to have indistinguishable performance.

Each lot is subject to a quality control procedure to confirm identity, purity, quantity, and function. 

General Products, Policies

Why does Nectagen ship products in 1.6 ml screw cap tubes?


Nectagen chose 1.6 ml conical screw cap tubes because they have a secure closure, resist breakage, and are compatible with standard microcentrifuges.  

Terminology, Apps

What is an "ingredient"?


Nectagen uses "ingredients" to refer to components of solutions. Typically, ingredients are stock solutions.  

Site, Terminology

What does "ISBN" mean?


ISBN stands for International Standard Book Number and is a book's unique identifier with the country registration agencies.  ISBN's issued after 2006 contain 13 digits vs. 10 previously.  Use of the ISBN allows Nectagen to connect book references to outside databases.  Currently ISBN's connect to Amazon so that users can review comprehensive information on a book and order a copy conveniently.  Nectagen does not receive any consideration from Amazon.  

The ISBN can typically be found on the back of a book's inside title page or underneath the image of the book cover in the Amazon listing.

General Products, Terminology, nanoCLAMPs

What is a "lot"?


Nectagen uses "lot" to refer to the group of products produced by a single manufacturing run. Products within each lot are expected to have indistinguishable performance.

Each lot is subject to a quality control procedure to confirm identity, purity, quantity, and function. 

Terminology, Apps

What is a "specimen"?


Nectagen uses "specimen" to refer to the source material treated with the nanoCLAMP. The specimen can be an extract loaded on a column, a histological preparation or a serum sample assayed by an ELISA. Nectagen describes the specimen according to the following hierarchy:  Organism, Strain, Organ, Tissue, Cell Type, Cell Line, and Subcellular Compartment. The hierarchy is intended to allow users to readily identify the specimens most similar to their intended application. 

Site, Terminology

What does "clone content" mean?


"Clone content" means making an editable copy of an entry in the database. This action makes data entry more efficient for variants.  For some content, e.g. applications, solutions or protocols, the current database design requires each ingredient or step to be added again with the current database structure. Unfortunately, a one step "cloning" process is challenging because these data reside in multiple tables in the database.  These tables enable features such as having a specialized template for different kinds of results, reordering steps and reusing ingredients.  The database structure make a tradeoff between the convenience of these features and the convenience of full cloning capability.  The rationale is that the features requiring different tables will be used for each new entry while the cloning feature will only be used occasionally.   Automating the entry of variants for these kinds of content will require developing a script.  Nectagen will do so as soon as resources are available. 

Terminology, Apps

What is a "target"?


Nectagen uses "target" to refer to the protein bound by the nanoCLAMP.  Nectagen does not use "antigen" because nanoCLAMPs are not derived from an immunological response. Nectaen typically identifies the target by the gene name or the common name.  

Terminology, Apps

What is an "application" or "app"?


Nectagen uses "application" or "app" to refer to a documented use of its products.  Applications may be posted by any user, are reviewed by Nectagen or users and then rated by users.  

Site, Terminology

What is a "PubMed ID" or "PMID"?


Pubmed ID is an article's unique identifier in Medline.  It can be found at the bottom of the abstract.