Only need revise a little words, less than 275 words.

 

1) would you please combine “lesson learned” and “intern” section together?

 

2) would you please briefly summarize my previous research on biotechnology in the conclusion part as well?

PLANTS IN DIGITAL AGE 10

Plants in Digital Age: Using Biotechnology and Digitization in the Herbarium

Internship

Student’s Name

Running head: PLANTS IN DIGITAL AGE 1

Institutional Affiliation

Table of Contents Internship Experience 3 Lessons Learnt 4 Research 5 Conclusion 10 References 11

Plants in Digital Age: Using biotechnology and digitization in the Herbarium

Internship

Internship Experience

This semester, I interned at the Wisconsin State Herbarium(WIS) under the supervision of Mr. Mark Allen Wetter, who is the senior academic curator of the WIS. My project was all about the curation of Japanese and Chinese plants from 1980s, including mounting, filing and imaging them. It was such a meaningful experience that allowed me to have a better understanding of the workflow of the herbarium. This is in an effort to strengthen my career of pursuing museum study in the future. Therefore, this paper seeks to provide a comprehensive report of my experiences at Wisconsin State Herbarium (WIS) while citing the impacts of current technologies used in herbariums, their limitations and concerns.

The first thing I learned at the WIS is the technique of mounting. We always glued the label of the specimen at the bottom right corner and then decided how to position the plant on the mounting paper. After establishing the position of the plant, we glued the plant, then put a piece of hard cardboard under the plant and a film of wax paper above the plant. The process followed with placing two bags of rocks on the plant for a night. Although this process sounds easy, it can be challenging. For instance, at times, it became a challenge when dealing with specimens with brittle flowers or specimens with many extreme tiny leaves. However, even with this, I am glad that the experience helped me to improve and learn more on the technique of mounting in this semester. For instance, with the help of Mr. Mark and other volunteers at the herbarium, I learned different methods and useful tips used when applying glue on the plants. For example, I discovered that when dealing with plants that are not flat, people put leads wrapped with tapes on the part, which is not flat, to force that part stick on the paper.

The second thing I learned is that after the plants have been mounted on the mounting paper, the next step is to fill the plants’ data into an Excel spreadsheet. Before filling the data, a unique barcode is attached to the specimen. All the information related to the plants are manually typed into the computer. Though, for the plant species I was working with, their labels did not contain a family name, therefore I had to use the database to search their family names and copy them to the spreadsheet. Throughout my course, I have come to understand that filing is a process that needs extra carefulness and multiple times of proofreading. This is because the accuracy of one’s data entry can directly affect the quality of information in the whole database. During the filing process, however, I noticed some typos on the labels that were as a result of misspelling of Japanese or Chinese local location. The typos can cause a huge impact on the accuracy of information recorded in the database, more especially if the person filling the data is not familiar with the Chinese or Japanese language or geography.

The final part of my project involved taking photos of the collected specimens and storing them in a computer with a file name corresponding to that of their barcode number. Here, I learned that is necessary to place a color card on top of the specimen and a Bucky badger stamp seal on the mounting paper before imaging. We will use this color card later to determine if the photo we took met the accepted standards: that is, the values of red, green, and blue color of the specimen should be about 240 but less than 245. Finally, we sealed the specimens with another stamp showing that imaging has already taken place to complete the process.

Lessons Learnt

Normally the project takes a period of three weeks to be complete. I went through the cycle four times during this semester since there are large amounts of Japanese and Chinese plants need to be curated. I really enjoyed the experience at WIS because of the use of technology that facilitated the availability of resources to people even further from the herbarium. In general, I got inspired by the high efficiency and corporation portrayed by both the organization and the management during the entire time I practiced as an intern at the Wisconsin State Herbarium.

During the entire internship period, I adopted new improved skills that will help me in my future career. Precisely, I mastered the skill of recording and mounting, which for a long time has had me worrying. I put the skills I had learnt in the classrooms setting to test and I am glad people around me were of great help in improving the practical part of the skill. I can confidently do mounting without the help of anyone or fear of doing it wrong. I just discovered I needed to be a little bit confident as well as get maximum exposure. In addition, I got to discover that this internship had a huge relationship with my research. Over time, most herbariums had had a challenge in acquiring a technology that could be helpful in the collection and storage of specimen. For instance, some of the available technologies are not up to date making most herbariums to avail unreliable records that are unfit for use.

Research

A herbarium is a collection of preserved plant specimens and associated data used for scientific study. The oldest traditions of making herbarium collection can be traced back to Italy. Luca Ghini, who is an Italian physicians and botanists created herbaria with his students. The oldest extant plant specimen is GheradoCibo from around 1532 in the herbaria created by Luca (Bellorini, 2016). Nowadays, with the development of modern technologies such as DNA sequencing, digitization, and fine-scale geography, these advanced technologies are employed into the research and management of many contemporary herbariums to for accuracy purposes(Meineke, 2018). This paper will use the Wisconsin State Herbarium (WIS) as an example to highlight several technologies that have been used in current herbariums, and then explore the impacts of these technologies on the herbariums and finally discuss limitations and concerns of these technologies.

According to Mr. Mark Allen Wetter, the senior academic curator of WIS, almost every specimen (native and introduced) has provided two sequenced genes for a project named “Dimension of Biodiversity (DOB)”. The goal of this project is to better understand the evolutionary and genetic bases for plant diversity by integrating contemporary understanding of genetic, phylogenetic and functional diversity in temperate plants. Currently, researchers participating in this project are sequencing 2-3 identifier genes for most of the vascular plant specimens in Wisconsin to generate a robust phylogeny, thus inferring patterns of trait evolution and diversification as well as phylogenetic patterns in community assembly (Erickson et al, 2014). The researchers will then use the data generated by the DNA barcoding subproject to examine the association of ecological traits with phylogenetic tree, so that people can have deeper understanding of important ecological topics such as recent habitat fragmentation, colonization/extinction and geographic range.

However, it is very time consuming and costly to extract DNA from plants for sequencing. According to Foundation Plant Services (2018), it will cost $345 and three to four weeks to identify an unknown specimen. Therefore, the WIS does not use DNA sequencing to identify unknown specimen. Instead, faculty at the WIS uses the traditional method that has been used in the last few centuries: keying the specimens with floras and monographs, and then comparing the unknown to other verified specimens in the collection. However, one of the problems of this method is that if the specimen is sterile or relatively young, it is always impossible to identify the specimen successfully (Pace et al., 2018). Another problem of this technique is that the accuracy of the result of identification, sometimes, depends more on the level of expertise and flora knowledge of the person who identifies the plants. That is, the more exposure to the flora, the higher the chance a person can identify a specimen correctly.

Apart from using biotechnology to conduct research study, the WIS also use advanced electronic technology to digitize the specimens in the herbarium. It is noteworthy to point out that the WIS contributes specimen records to the repository of Integrated Digitized Biocollections (iDigBio) of the USA’s National Resources for Advancing Digitization of Biodiversity Collections (ADBC) funded by the National Science Foundation (Nelson et al., 2015). Through ADBC, data and images for millions of biological specimens are available in electronic format for the research community, government agencies, students, educators and the general public.

First, to digitize a specimen, volunteers and faculties at WIS attach a unique bar code to it. No two specimens anywhere in the world will have the exact same barcode, which minimizes confusion and makes retrieval of these specimens much easier than what was experienced in the past (WIS, 2018). After that, volunteers and faculties at WIS will record all of the information related to the specimens into the database. This information includes who collected the specimens, how many specimens have been assigned to this collection, where and when it was collected, as well as a brief description of the plant, habitat, GPS coordinates, other plants growing in the vicinity, etc.

The next step of digitization is the imaging of specimens. The photographers will use SLR camera to take pictures of the specimens. Before the shooting, a color card is putbelow the specimen. This is because the color card can be used to a calibrate computer monitor or adjust color if the specimen image is printed. Additionally, a herbarium stamp is also sealed on the specimen before imaging. Here, the WIS makes use of university’s mascot Bucky Badger. If this specimen is ever lent to other organizations, it is more likely to be returned to WIS because the stamp identifies it by origin.After imaging the specimen, the photographers will scan the bar code on the specimen and rename the filename so that the file name corresponds to the bar code. The photographers will also seal another stamp on the specimen to indicate that this specimen has been imaged. The final step of digitization is organizing specimens into different cabinets according to their phylogeny.

Although the process of digitization at WIS is not a smooth one, it is relatively smooth and continuous. WIS faces a number of challenges in the day-to-day basis of collection in other natural history collection of specimen.The digitization does not meet the accepted standards. The organization faces similar challenges other herbarium across the globe face in their operations (Vollmar et al., 2010). For instance, the imaging technique available in the herbarium is good, but it is not perfect. Adopting the new imaging could help taking perfect shots that will provide better photos of specimens to make learning easier and efficient. On the same note, another challenge that WIS is having is lack of automated systems of recording data especially during collection. Developed herbariums have working automated systems that do require there staff to apply anything manual in the whole process of specimen collection. Even though, there are some process that might require manual input of data, it better if the firm had more improvised ways data entry. Many at times, unnoticeable mistakes are likely to occur affecting the credibility of the recorded data. Many at times, this uneven digitization landscape can have a negative variation of data hence compromising it in the end and rendering unfit for use (Vollmar et al., 2010).

According to Vollmar et al (2010), 44 interviewed respondents gave their reasons as to why they thought digitization was not going on in their institutions. The table below provided the reasons in terms of most important to the less significant cause. It is evident that from the research, funding, time, and staff were the major reasons while collection permits, sensitive data, and indigenous rights had the least impact on digitization. For instance, funding was linked to salaries, buying of the technology and infrastructure to accommodate the digitization. Interestingly, over 70% of the interviewed respondents had requested funds for digitization of which some never secured at all (Vollmar et al., 2010). The funds requested were to cater for upgrading their systems, buying new equipment, and salaries to pay people in charge of the technology.

Additionally, among 171 respondents from collection facilities in which digitization was either ongoing or had occurred within the past two years, the major hinders to digitization were similar to the reasons proposed by other respondents as to why digitization was not ongoing (Vollmar et al., 2010). Funding, time and staff were consistently the top three challenges faced by most of collections.

Conclusion

Digitization is still a major issue in natural history collections. There is a bunch of challenges and concerns that hinder the transformation as addressed in this paper. The challenges, if not addressed appropriately, could lead to exact and valid data but unfit for use by the public. Research indicates that most facilities are unable to digitize because of limited funding, time, staff, time, lack of institutional support, data sharing, collection permits, and indigenous rights. However, funding was established to be the major challenge to many of the respondents that were interviewed during the survey(Vollmar et al., 2010). Institutions responsible for natural specimen collections should be able to establish measures to address the barriers to digitization.

References

Bellorini, C. (2016). New Ways of Studying Plants.In The World of Plants in Renaissance Tuscany (pp. 101-136).Routledge.

Erickson, D. L., Jones, F. A., Swenson, N. G., Pei, N., Bourg, N. A., Chen, W., …& Huang, C. L. (2014). Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach.Frontiers in genetics, 5, 358.

Foundation Plant Services.(2018).FPS DNA-Based Grape varietal identification &pProfiling services.The Regents of the University of California. Retrieved from 

Meineke, E. K., Davis, C. C., & Davies, T. J. (2018).The unrealized potential of herbaria for global change biology. Ecological Monographs, 88(4), 505-525.

Nelson, G., Sweeney, P., Wallace, L. E., Rabeler, R. K., Allard, D., Brown, H., …& Gilbert, E. (2015). Digitization workflows for flat sheets and packets of plants, algae, and fungi.Applications in plant sciences, 3(9), 1500065.

Pace, M. C., Giraldo, G., Frericks, J., Lehnebach, C. A., & Cameron, K. M. (2018).Illuminating the systematics of the Spiranthessinensis species complex (Orchidaceae): ecological speciation with little morphological differentiation.Botanical Journal of the Linnean Society.

Wisconsin State Herbarium.(2018). Integrated Digitized Biocollections (iDigBio).Board of Regents of the University of Wisconsin System. Retrieved from https://herbarium.wisc.edu/databases/idigbio/