Συστηματική εξελικτική μελέτη των σχέσεων δομής-λειτουργίας και εξειδίκευσης στους βακτηριακούς μεταφορείς πουρινών-πυριμιδινών

2021 ◽  
Author(s):  
Αικατερίνη Τατσάκη
Keyword(s):  
Sequence Reconstruction

Η μελέτη των διαφορών εξειδίκευσης μεταξύ διαμεμβρανικών μεταφορέων πουρινών από διαφορετικούς οργανισμούς είναι ένα πεδίο έρευνας με δυνατότητες εφαρμογών (α) στην κατανόηση της μοριακής βάσης των διαφορών εξειδίκευσης μεταξύ εξελικτικά διαφορετικών ομάδων οργανισμών, (β) στο σχεδιασμό/επιλογή κυτταροτοξικών αναλόγων πουρινών με μεγαλύτερη εξειδίκευση έναντι κυττάρων-στόχων, (γ) στη βελτίωση της δράσης συγκεκριμένων χημειοθεραπευτικών αναλόγων πουρινών βάσει της ανάλυσης των μηχανισμών πρόσληψης των φαρμάκων αυτών από βακτήρια του μικροβιώματος. Οι έως τώρα μελέτες για την κατανόηση των διαφορών εξειδίκευσης των μεταφορέων αυτών έχουν στηριχθεί σε συγκριτική ανάλυση και διεξοδική μεταλλαξιγένεση σημερινών ομολόγων. Στην παρούσα Διδακτορική Διατριβή, εφαρμόστηκε μία διαφορετική προσέγγιση που βασίζεται σε διερεύνηση της εξελικτικής βάσης των διαφορών εξειδίκευσης μετά από φυλογενετική ανάλυση και ανασύσταση προγονικών αλληλουχιών (Αncestral Sequence Reconstruction). Ειδικότερα, η διατριβή αναφέρεται στην εξέλιξη των εξειδικεύσεων της οικογένειας NAT/NCS2 (Nucleobase-Ascorbate Transporter/Nucleobase-Cation Symporter-2), της κυριότερης και εξελικτικά ευρύτερης οικογένειας μεταφορέων πουρινών-πυριμιδινών. Αρχικά, πραγματοποιήθηκε εκτενής φυλογενετική ανάλυση, ανασύσταση και λειτουργική ανάλυση των προγονικών αλληλουχιών που αντιπροσωπεύουν την «κοινή ρίζα» τριών μονοφυλετικών κλάδων βακτηριακών NAT/NCS2 ομολόγων με διακριτά προφίλ εξειδίκευσης. Ακολούθησε ανάλυση μεταλλαξιγένεσης στο υπόβαθρο των προγονικών αλληλουχιών με κριτήριο τις διαφορές στην αλληλουχία των προγονικών αλληλουχιών σε σχέση με τις σημερινές ομόλογες πρωτεΐνες διαφορετικής εξειδίκευσης και αναλύσεις μοριακής δυναμικής των προγονικών αλληλουχιών για την κατανόηση σε δομικό πλαίσιο του ρόλου των μεταλλαγών που βρέθηκε να έχουν σημαντική επίπτωση στην εξειδίκευση. Από τα αποτελέσματα της Διατριβής που βασίστηκε στην εφαρμογή της στρατηγικής της ανασύστασης προγονικών αλληλουχιών, αποκαλύφθηκαν λειτουργικά προφίλ και προφίλ εξειδίκευσης που δεν θα μπορούσαν να προβλεφθούν μόνο από τη σύγκριση των σημερινών ομολόγων. Η εφαρμογή τέτοιων εξελικτικών μεθόδων θα μπορούσε να προσφέρει ένα νέο αποτελεσματικό τρόπο για την ανάλυση των σχέσεων δομής-λειτουργίας και εξειδίκευσης στις πρωτεΐνες διαμεμβρανικής μεταφοράς.

scholarly journals Paracellular and Transcellular Leukocytes Diapedesis Are Divergent but Interconnected Evolutionary Events

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 254
Author(s):  
Michel-Edwar Mickael ◽  
Norwin Kubick ◽  
Pavel Klimovich ◽  
Patrick Henckell Flournoy ◽  
Irmina Bieńkowska ◽  
...  
Keyword(s):  
Immune Cell ◽  
Critical Role ◽  
Cellular Polarity ◽  
Endothelial Layer ◽  
Trichoplax Adhaerens ◽  
Migration Pathway ◽  
Two Systems ◽  
Sequence Reconstruction ◽  
Rhoa Protein ◽  
Migration Pathways

Infiltration of the endothelial layer of the blood-brain barrier by leukocytes plays a critical role in health and disease. When passing through the endothelial layer during the diapedesis process lymphocytes can either follow a paracellular route or a transcellular one. There is a debate whether these two processes constitute one mechanism, or they form two evolutionary distinct migration pathways. We used artificial intelligence, phylogenetic analysis, HH search, ancestor sequence reconstruction to investigate further this intriguing question. We found that the two systems share several ancient components, such as RhoA protein that plays a critical role in controlling actin movement in both mechanisms. However, some of the key components differ between these two transmigration processes. CAV1 genes emerged during Trichoplax adhaerens, and it was only reported in transcellular process. Paracellular process is dependent on PECAM1. PECAM1 emerged from FASL5 during Zebrafish divergence. Lastly, both systems employ late divergent genes such as ICAM1 and VECAM1. Taken together, our results suggest that these two systems constitute two different mechanical sensing mechanisms of immune cell infiltrations of the brain, yet these two systems are connected. We postulate that the mechanical properties of the cellular polarity is the main driving force determining the migration pathway. Our analysis indicates that both systems coevolved with immune cells, evolving to a higher level of complexity in association with the evolution of the immune system.

Ancestral sequence reconstruction for protein engineers

2021 ◽  
Vol 69 ◽  
pp. 131-141
Author(s):  
Matthew A. Spence ◽  
Joe A. Kaczmarski ◽  
Jake W. Saunders ◽  
Colin J. Jackson
Keyword(s):  
Ancestral Sequence ◽  
Ancestral Sequence Reconstruction ◽  
Sequence Reconstruction

scholarly journals circtools—a one-stop software solution for circular RNA research

2018 ◽  
Vol 35 (13) ◽  
pp. 2326-2328 ◽  
Author(s):  
Tobias Jakobi ◽  
Alexey Uvarovskii ◽  
Christoph Dieterich
Keyword(s):  
High Throughput Sequencing ◽  
Circular Rna ◽  
Statistical Testing ◽  
Supplementary Information ◽  
Circular Rnas ◽  
Sequencing Data ◽  
High Throughput Sequencing Data ◽  
Multi Stage ◽  
Sequence Reconstruction ◽  
One Stop

Abstract Motivation Circular RNAs (circRNAs) originate through back-splicing events from linear primary transcripts, are resistant to exonucleases, are not polyadenylated and have been shown to be highly specific for cell type and developmental stage. CircRNA detection starts from high-throughput sequencing data and is a multi-stage bioinformatics process yielding sets of potential circRNA candidates that require further analyses. While a number of tools for the prediction process already exist, publicly available analysis tools for further characterization are rare. Our work provides researchers with a harmonized workflow that covers different stages of in silico circRNA analyses, from prediction to first functional insights. Results Here, we present circtools, a modular, Python-based framework for computational circRNA analyses. The software includes modules for circRNA detection, internal sequence reconstruction, quality checking, statistical testing, screening for enrichment of RBP binding sites, differential exon RNase R resistance and circRNA-specific primer design. circtools supports researchers with visualization options and data export into commonly used formats. Availability and implementation circtools is available via https://github.com/dieterich-lab/circtools and http://circ.tools under GPLv3.0. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Para-cellular and transcellular diapedesis are divergent but inter-connected evolutionary events

2020 ◽  
Author(s):  
Norwin Kubick ◽  
Pavel Klimovich ◽  
Patrick Henckel ◽  
Michel-Edwar Mickael
Keyword(s):  
Immune Cells ◽  
Critical Role ◽  
Adaptive Immune System ◽  
Cellular Process ◽  
Endothelial Layer ◽  
Trichoplax Adhaerens ◽  
Core Proteins ◽  
Two Systems ◽  
Sequence Reconstruction ◽  
Migration Pathways

AbstractInfiltration of the endothelial layer of the blood-brain barrier by leukocytes plays a critical role in health and disease. When passing through the endothelial layer during the diapedesis process lymphocytes can either follow a para-cellular route or a transcellular one. There is a debate whether these two processes constitute one mechanism, or they form two evolutionary distinct migration pathways. We used phylogenetic analysis, HH search, ancestor sequence reconstruction together with functional specificity and positive selection analysis to investigate this intriguing question further. We found that the two systems share several ancient components, such as RhoA protein that plays an important role in controlling actin movement in both mechanisms. However, some of the key components differ between these two transmigration processes. CAV1 genes emerged during Trichoplax adhaerens and it was only reported in trans-cellular process. Para-cellular process core proteins had at least two distinct starting points. First, during drosophila emergence, Tre1 which is homologous to melatonin GPCR receptor diverged. Secondly, PECAM1 emerged from FASL5/3 during elephant shark divergence. Lastly, both systems employ late divergent genes such as ICAM1 and PECAM1. Taken together our results suggest that these two systems constitute different yet interconnected mechanisms of immune cells infiltrations of the brain. Our analysis indicates that this system coevolved with immune cells, evolving to a higher level of complexity in association with the evolution of the adaptive immune system.

scholarly journals Time-stretch microscopy based on time-wavelength sequence reconstruction from wideband incoherent source

2014 ◽  
Vol 105 (4) ◽  
pp. 041113 ◽  
Author(s):  
Chi Zhang ◽  
Yiqing Xu ◽  
Xiaoming Wei ◽  
Kevin K. Tsia ◽  
Kenneth K. Y. Wong
Keyword(s):  
Sequence Reconstruction ◽  
Incoherent Source

scholarly journals Ancestral sequence reconstruction produces thermally stable enzymes with mesophilic enzyme-like catalytic properties

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ryutaro Furukawa ◽  
Wakako Toma ◽  
Koji Yamazaki ◽  
Satoshi Akanuma
Keyword(s):  
Low Temperature ◽  
Catalytic Properties ◽  
Amino Acid Sequences ◽  
Ancestral Sequence ◽  
Kinetic Properties ◽  
Reconstruction Technique ◽  
Thermally Stable ◽  
Ancestral Sequence Reconstruction ◽  
Ancestral Sequences ◽  
Sequence Reconstruction

Abstract Enzymes have high catalytic efficiency and low environmental impact, and are therefore potentially useful tools for various industrial processes. Crucially, however, natural enzymes do not always have the properties required for specific processes. It may be necessary, therefore, to design, engineer, and evolve enzymes with properties that are not found in natural enzymes. In particular, the creation of enzymes that are thermally stable and catalytically active at low temperature is desirable for processes involving both high and low temperatures. In the current study, we designed two ancestral sequences of 3-isopropylmalate dehydrogenase by an ancestral sequence reconstruction technique based on a phylogenetic analysis of extant homologous amino acid sequences. Genes encoding the designed sequences were artificially synthesized and expressed in Escherichia coli. The reconstructed enzymes were found to be slightly more thermally stable than the extant thermophilic homologue from Thermus thermophilus. Moreover, they had considerably higher low-temperature catalytic activity as compared with the T. thermophilus enzyme. Detailed analyses of their temperature-dependent specific activities and kinetic properties showed that the reconstructed enzymes have catalytic properties similar to those of mesophilic homologues. Collectively, our study demonstrates that ancestral sequence reconstruction can produce a thermally stable enzyme with catalytic properties adapted to low-temperature reactions.

scholarly journals Spatio-temporal silhouette sequence reconstruction for gait recognition against occlusion

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Md. Zasim Uddin ◽  
Daigo Muramatsu ◽  
Noriko Takemura ◽  
Md. Atiqur Rahman Ahad ◽  
Yasushi Yagi
Keyword(s):  
Gait Cycle ◽  
Gait Recognition ◽  
Real Life ◽  
Image Sequence ◽  
Body Parts ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
Hinge Loss ◽  
Sequence Reconstruction ◽  
Spatio Temporal

AbstractGait-based features provide the potential for a subject to be recognized even from a low-resolution image sequence, and they can be captured at a distance without the subject’s cooperation. Person recognition using gait-based features (gait recognition) is a promising real-life application. However, several body parts of the subjects are often occluded because of beams, pillars, cars and trees, or another walking person. Therefore, gait-based features are not applicable to approaches that require an unoccluded gait image sequence. Occlusion handling is a challenging but important issue for gait recognition. In this paper, we propose silhouette sequence reconstruction from an occluded sequence (sVideo) based on a conditional deep generative adversarial network (GAN). From the reconstructed sequence, we estimate the gait cycle and extract the gait features from a one gait cycle image sequence. To regularize the training of the proposed generative network, we use adversarial loss based on triplet hinge loss incorporating Wasserstein GAN (WGAN-hinge). To the best of our knowledge, WGAN-hinge is the first adversarial loss that supervises the generator network during training by incorporating pairwise similarity ranking information. The proposed approach was evaluated on multiple challenging occlusion patterns. The experimental results demonstrate that the proposed approach outperforms the existing state-of-the-art benchmarks.

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