Appendix| Fungi Data Inventory 146

Neurospora crassa is one of the most extensively studied biological species. Thus, I began the study of collecting all relevant information on that organism that was already accessible at that time. I built a database in FileMaker that allows to easily sort, filter, extract, and share the data with others. Every movie has assigned its unique identification number (ID). It allows easily find the Intellectual Property (IP) information, the name of the researcher who recorded the movie, and all relevant laboratory and technical documentation. Importantly, in FileMaker it is possible to attach multimedia, pdf, or even sound in each database cell, what makes it easy to sort. Also, the data is encrypted when sent over the internet.

Figure 130 Breakdown of the movies collected in the Fungi Data Inventory: (A) fungi moving in restricted geometries (Poly-Di-Methylo-Siloxane mazes) – a kind gift of prof. Dan Nicolau; (B)

Neurospora crassa (wild type) growing on agar- a kind gift of prof Roger Lew; (C) Neurospora crassa tip- confocal microscopy movies – a kind gift of prof. Nicolau (D) visualizing microtubules in vivo –

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Fungi Data Inventory exists of 84 movies in total. It includes 33 phase contrast microscopy movies introducing filamentous fungi growing in PDMS (Poly-Di-Methylo-

Siloxane) mazes, 26 confocal microscopy movies showing the hyphal tip (more precisely the Spitzenkörper), and 2 movies introducing the microtubules motility in vivo – all recorded at the University of Liverpool (Prof. Dan Nicolau nanobiotechnology Lab, Department of Electrical Engineering & Electronics), 19 phase contrast microscopy movies recorded at the University of York (Prof. Roger Lew biophysics lab, Department of Biology). For the visual reference, please see Figure 131. The Fungi Data Inventory - FileMaker Database consists of the fields grouped within the two main sections: part I – Administrative Data and part II – Experimental and Technical Information. The part I consists of the following database fields: MovieID (numerical field) – containing the number generated according to the creation order), AuthorName (text field) – the name of the person in charge of the experiments, recording the movies, proper calibration, Year (numerical field) – the year when the movie was recorded, Institution

(text field) – name of the institution that owns the Intellectual Property rights,

ProjectTitle (text field) – the name of the project/grant under which the experiments were run, Species (text field) – the name of the biological species studies, wild- type/mutant(text field) – classification of the information, the field indicated whether the study organism is a wild type of genetically manipulated, FileSize (numerical field) – specifies the file size, this is a very helpful feature while sharing data with others or putting the movie into the PowerPoint or Prezi presentations. The part II consists of the following database fields: ,Attachments (container field) – any word or pdf files with information related to the experimental settings/methods, Description (text field) – temporal (time between consecutive frames, total recording time) and or spatial information (calibration), Picture (container field) – snapshot of one of the movie frames, Play movie (container field) – movie file for download, Digital design

(container field) – digital representation (map) of the physical maze, Comments (text field) – any comments related to the movie, MATLAB code (container field) – any MATLAB code related to the movie, Geometrical structure (text field) – geometrical design used for the experiment, Imaging aim (text field) – whether the experiment focused on visualization of the mycelium, tip, or microtubules, Working set (text field) – movie classification according to the set of experiments run in the laboratory.

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The database is available in 2 modes: Table View (designed for searching, sorting, and filtering records) and Interface View (designed for a single-record view).The idea of managing data that way is introduced in Figure 132, on the next page. Another useful feature of this database is making use of container fields. Container field is any field that contains a movie, Word, Excel, Notepad, multimedia file. Storing the data that way allows to find the necessary movies or technical documentation easily according to the ID number instead of digging through the several folders and subfolders, when the data is stored in the traditional ways on Apple or Windows computers. The database FMP files are available under the following hyperlink: Fungi Data Inventory.The account username to the database is: ‘filamentous fungi’ and the password is ‘Neurosporacrassa’.

Figure 131 Introduction to the Fungi Inventory FileMaker Database: (A) the database

fields can be easily controlled by the Fields’ Manager, (B) explanation of the Fields/Record structure in the database.

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Here, I introduce the simple database that was further developed by adding movies and information including bacterial species as well; that can be further developed towards an international laboratory data repository. This solution can be easily deployed worldwide by installing FileMaker Go on iPads for the constant electronic data capture. The data can be then collected on the remote server and further downloaded into the individual PCs and analyzed by various researchers in different countries. Moreover, it is possible to write scripts in FileMaker that allow for automating complex searches. Once I collected all relevant data and processed the movies to the satisfactory quality, I have looked into the universal patterns displayed in the Neurospora crassa behaviour. The data collected here is evidence for existing directional memory in fungi, corner-specific branching, and ceasing growth reported by Marie Held in 2011 (Held, 2011a). Also, there is evidence in the movies that two hyphae can move on top of each other (Held, 2011a). Other observations are that Neurospora crassa hyphae extending on a polymer surface can be

Figure 132 Illustrating the idea of Table view and Interface view in the FileMaker. (A) Table View

– ideal for running database queries, searching and extracting the information, and for filtering the data. (B) Interface View – once the accurate record has been identified, this mode is perfect for data analysis.

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even stickier compared to yeast. It is important to bear in mind hypha is not sliding, and that adhesion is important in the context of the tip pressure and sub-apical bending also observable in the documentation included.

Figure 133 Explaining the functionality of the container field type while switching between the table and interface view. The data architecture allows to easily find the movies and associated them with other digital files or administrative information. This is often crucial for the data monitoring and evaluation. The containers in the Fungi Data Inventory comprise the AVI and TIFF movie files, the first frame of every movie collected, the digital engineering design file, where applicable (for the programming and modelling purposes), Word and other types of text files (e.g. csv or tab delimited). Also, the interface with the Dropbox has been established here. All files stored in the container fields can be downloaded via exporting field contents.

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Other important observations involve the acute hyphal tip contact dynamics of a Spitzenkörper, analysis of approach angle (the hyphae often go the opposite way to the original approach angle), changing extension rate after reorientation, force displayed during hyphal tip penetration, hyphal indentation (a deep recess or notch on the edge of surface), or stochastic membrane deformation. Another specific feature of Neurospora crassa is the presence of the perforated septa. Hyphae are only partially separated by septa so that a colony is essentially one large cell containing many nuclei. Importantly, parameters that were measured for the needs of this study were highly unlikely taken from the somatic hyphae in the peripheral growth zone. The probability of leading hypha entering the microfluidic PDMS channels was negligible, and, therefore, their contribution to the average growth parameters on agar was excluded from the statistical analysis. Other interesting observations made are that some hyphae shift to the left side, many of the further generations (young) branches ceases growth probably because of lack of space, hyphae growing on top of, underneath, or in parallel to each other are more likely to stop extending. Hyphae can also hit and push each other, what might cause the shift of the whole branching sector.