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20 results on '"Mystikou, Alexandra"'

1. LA4SR: illuminating the dark proteome with generative AI

Author

Nelson, David R., Jaiswal, Ashish Kumar, Ismail, Noha, Mystikou, Alexandra, and Salehi-Ashtiani, Kourosh

Subjects
Quantitative Biology - Genomics, Computer Science - Artificial Intelligence, Computer Science - Computation and Language, Quantitative Biology - Quantitative Methods
Abstract

AI language models (LMs) show promise for biological sequence analysis. We re-engineered open-source LMs (GPT-2, BLOOM, DistilRoBERTa, ELECTRA, and Mamba, ranging from 70M to 12B parameters) for microbial sequence classification. The models achieved F1 scores up to 95 and operated 16,580x faster and at 2.9x the recall of BLASTP. They effectively classified the algal dark proteome - uncharacterized proteins comprising about 65% of total proteins - validated on new data including a new, complete Hi-C/Pacbio Chlamydomonas genome. Larger (>1B) LA4SR models reached high accuracy (F1 > 86) when trained on less than 2% of available data, rapidly achieving strong generalization capacity. High accuracy was achieved when training data had intact or scrambled terminal information, demonstrating robust generalization to incomplete sequences. Finally, we provide custom AI explainability software tools for attributing amino acid patterns to AI generative processes and interpret their outputs in evolutionary and biophysical contexts.

Published
2024

4. Rediscovery of the rare <italic>Cladochroa chnoosporiformis</italic> Skottsberg from the Falkland Islands and its merger with <italic>Utriculidium durvillei</italic> Skottsberg.

Author

Mystikou, Alexandra, Asensi, Aldo O., Peters, Akira F., Kytinou, Eleni, Amin, Shady A., Brickle, Paul, van West, Pieter, and Küpper, Frithjof C.

Subjects
*BROWN algae, *MERGERS & acquisitions, *MATERIAL culture, *ISLANDS, *MORPHOLOGY
Abstract

The Subantarctic brown alga Cladochroa chnoosporiformis had been collected only on one occasion by Carl Skottsberg in 1907 from Port Philomel, West Falkland, Falkland Islands, resulting in its formal taxonomic description. Due to the lack of reports since then, doubts remained about its existence and identity. Within the framework of this study, Cladochroa was rediscovered 106 years after its original description at its type locality, confirming its existence and the morphological features described by Skottsberg. The re-collection enabled molecular studies on field material and isolated cultures. Sequences of nrDNA, rbcL, and 5′-COI suggest that C. chnoosporiformis is conspecific with Utriculidium durvillei, which has nomenclatural priority. However, the morphologies of C. chnoosporiformis and U. durvillei are significantly different. Utriculidium may be the gametophyte generation of Cladochroa, or hitherto unknown factors cause highly different morphologies without alternating generations. [ABSTRACT FROM AUTHOR]

Published
2024
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7. Seaweed biodiversity around the Antarctic Convergence in the South Atlantic

Author

Mystikou, Alexandra

Subjects
579.8, Marine algae
Abstract

This study focuses on the seaweed biodiversity around the Antarctic Convergence in the South Atlantic. It integrates field work in the Falkland Islands and surrounding regions with algal culturing, molecular techniques, microscopy and morphological identification. Chapter 2 explores the diversity of seaweeds of the south-western Antarctic Peninsula which is poorly studied, contrasting with the substantial knowledge available for the northern parts of the Peninsula. A baseline seaweed species checklist for the southern Adelaide Island and northern Marguerite Bay region is presented here, combining data obtained during a small number of surveys in 1973-5 and a six week intensive diving-based field campaign in 2010-2011. Subantarctic and Antarctic regions remain little studied in their seaweed diversity. Chapter 3 is based upon field collections in the early 1970s and 2007-2013. It is supported by sequencing COI and reports new records of several macroalgal species and an oomycete. Chapter 4 revisits the enigmatic Subantarctic brown alga Cladochroa chnoosporiformis, which had been collected only on one occasion by Carl Skottsberg in 1907 from Port Philomel, West Falkland, resulting in its formal taxonomic description. Within the framework of this study, Cladochroa was rediscovered after 106 years at its type locality, confirming its existence and morphological features as described by Skottsberg. The recollection enabled molecular studies of its phylogenetic placement by DNA sequencing, suggesting that C. chnoosporiformis is conspecific with Utriculidium durvillei. In Chapter 5, DNA barcoding was applied to both seaweed tissue samples taken while preparing herbarium specimens during 2 expeditions to the Falkland Islands, and to live macroalgal isolates obtained from substratum samples using the Germling Emergence Method. In several cases, this enabled detection of previously unsequenced or undescribed taxa, respectively. The potential and challenges of applying DNA barcoding for cataloguing the biodiversity of remote bioregions such as the Falklands are discussed.

Published
2015

14. New records of the rare deep-water alga Sebdenia monnardiana (Rhodophyta) and the alien Dictyota cyanoloma (Phaeophyceae) and the unresolved case of deep-water kelp in the Ionian and Aegean Seas (Greece)

Author

Küpper, Frithjof C., primary, Tsiamis, Konstantinos, additional, Johansson, Niko Rainer, additional, Peters, Akira F., additional, Salomidi, Maria, additional, Manousakis, Leonidas, additional, Kallergis, Manolis, additional, Graham, Michael H., additional, Kinlan, Brian, additional, Mystikou, Alexandra, additional, Žuljević, Ante, additional, Nikolić, Vedran, additional, Gerakaris, Vasilis, additional, Katsaros, Christos, additional, and Panayotidis, Panayotis, additional

Published
2019
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16. Arctic marine phytobenthos of northern Baffin Island

Author

Küpper, Frithjof C., primary, Peters, Akira F., additional, Shewring, Dawn M., additional, Sayer, Martin D. J., additional, Mystikou, Alexandra, additional, Brown, Hugh, additional, Azzopardi, Elaine, additional, Dargent, Olivier, additional, Strittmatter, Martina, additional, Brennan, Debra, additional, Asensi, Aldo O., additional, West, Pieter, additional, and Wilce, Robert T., additional

Published
2016
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17. New records and observations of macroalgae and associated pathogens from the Falkland Islands, Patagonia and Tierra del Fuego

Author

Mystikou, Alexandra, primary, Asensi, Aldo O., additional, DeClerck, Olivier, additional, Müller, Dieter G., additional, Peters, Akira F., additional, Tsiamis, Konstantinos, additional, Fletcher, Kyle I., additional, Westermeier, Renato, additional, Brickle, Paul, additional, van West, Pieter, additional, and Küpper, Frithjof C., additional

Published
2016
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18. Further expansion of the alien seaweed Caulerpa taxifolia var. distichophylla (Sonder) Verlaque, Huisman & Procacini (Ulvophyceae, Bryopsidales) in the Eastern Mediterranean Sea

Author

Aplikioti, Marilena, primary, Louizidou, Paraskevi, additional, Mystikou, Alexandra, additional, Marcou, Melina, additional, Stavrou, Petros, additional, Kalogirou, Stefanos, additional, Tsiamis, Konstantinos, additional, Panayotidis, Panayotis, additional, and Küpper, Frithjof, additional

Published
2016
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19. Seaweed biodiversity in the south-western Antarctic Peninsula: Surveying macroalgal community composition in the Adelaide Island / Marguerite Bay region over a 35-year time span

Author

Mystikou, Alexandra, Peters, Akira F., Asensi, Aldo O., Brickle, Paul, van West, Pieter, Convey, Peter, Kupper, Frithjof C., Mystikou, Alexandra, Peters, Akira F., Asensi, Aldo O., Brickle, Paul, van West, Pieter, Convey, Peter, and Kupper, Frithjof C.

Abstract

The diversity of seaweed species of the south-western Antarctic Peninsula region is poorly studied, contrasting with the substantial knowledge available for the northern parts of the Peninsula. However, this is a key region affected by contemporary climate change. Significant consequences of this change include sea ice recession, increased iceberg scouring and increased inputs of glacial melt water, all of which can have major impacts on benthic communities. We present a baseline seaweed species checklist for the southern Adelaide Island and northern Marguerite Bay region, combining data obtained during a small number of surveys completed in 1973–1975 and a 6-week intensive diving-based field campaign in 2010–2011. Overall, with a total of 41 macroalgal species recorded (7 brown, 27 red, 6 green, 1 chrysophyte), the region is species-poor compared to the north of the Antarctic Peninsula, and even more so in comparison with the sub-Antarctic. The key canopy-forming species is Desmarestia menziesii, which is abundant in Antarctic Peninsula waters, but lacking in the sub-Antarctic. Himantothallus grandifolius, which is a common species further north in the Antarctic phytobenthos, was absent in our recent collections. This paper also reports the first record of Aplanochytrium sp. (Labyrinthulomycetes) from this part of Antarctica and in association with Elachista sp.

Published
2014

20. Algal Cell Factories: Approaches, Applications, and Potentials.

Author

Weiqi Fu, Chaiboonchoe, Amphun, Khraiwesh, Basel, Nelson, David R., Al-Khairy, Dina, Mystikou, Alexandra, Alzahmi, Amnah, and Salehi-Ashtiani, Kourosh

Abstract

With the advent of modern biotechnology, microorganisms from diverse lineages have been used to produce bio-based feedstocks and bioactive compounds. Many of these compounds are currently commodities of interest, in a variety of markets and their utility warrants investigation into improving their production through strain development. In this review, we address the issue of strain improvement in a group of organisms with strong potential to be productive "cell factories": the photosynthetic microalgae. Microalgae are a diverse group of phytoplankton, involving polyphyletic lineage such as green algae and diatoms that are commonly used in the industry. The photosynthetic microalgae have been under intense investigation recently for their ability to produce commercial compounds using only light, CO2, and basic nutrients. However, their strain improvement is still a relatively recent area of work that is under development. Importantly, it is only through appropriate engineering methods that we may see the full biotechnological potential of microalgae come to fruition. Thus, in this review, we address past and present endeavors towards the aim of creating productive algal cell factories and describe possible advantageous future directions for the field. [ABSTRACT FROM AUTHOR]

Published
2016
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