Deep Affordance-grounded Sensorimotor Object Recognition

It is well-established by cognitive neuroscience that human perception of objects constitutes a complex process, where object appearance information is combined with evidence about the so-called object "affordances", namely the types of actions that humans typically perform when interacting with them. This fact has recently motivated the "sensorimotor" approach to the challenging task of automatic object recognition, where both information sources are fused to improve robustness. In this work, the aforementioned paradigm is adopted, surpassing current limitations of sensorimotor object recognition research. Specifically, the deep learning paradigm is introduced to the problem for the first time, developing a number of novel neuro-biologically and neuro-physiologically inspired architectures that utilize state-of-the-art neural networks for fusing the available information sources in multiple ways. The proposed methods are evaluated using a large RGB-D corpus, which is specifically collected for the task of sensorimotor object recognition and is made publicly available. Experimental results demonstrate the utility of affordance information to object recognition, achieving an up to 29% relative error reduction by its inclusion.Comment: 9 pages, 7 figures, dataset link included, accepted to CVPR 201

A Deep Learning Approach to Object Affordance Segmentation

Learning to understand and infer object functionalities is an important step towards robust visual intelligence. Significant research efforts have recently focused on segmenting the object parts that enable specific types of human-object interaction, the so-called "object affordances". However, most works treat it as a static semantic segmentation problem, focusing solely on object appearance and relying on strong supervision and object detection. In this paper, we propose a novel approach that exploits the spatio-temporal nature of human-object interaction for affordance segmentation. In particular, we design an autoencoder that is trained using ground-truth labels of only the last frame of the sequence, and is able to infer pixel-wise affordance labels in both videos and static images. Our model surpasses the need for object labels and bounding boxes by using a soft-attention mechanism that enables the implicit localization of the interaction hotspot. For evaluation purposes, we introduce the SOR3D-AFF corpus, which consists of human-object interaction sequences and supports 9 types of affordances in terms of pixel-wise annotation, covering typical manipulations of tool-like objects. We show that our model achieves competitive results compared to strongly supervised methods on SOR3D-AFF, while being able to predict affordances for similar unseen objects in two affordance image-only datasets.Comment: 5 pages, 4 figures, ICASSP 202

Arabidopsis Coexpression Tool:a tool for gene coexpression analysis in Arabidopsis thaliana

Gene coexpression analysis refers to the discovery of sets of genes which exhibit similar expression patterns across multiple transcriptomic data sets, such as microarray experiment data of public repositories. Arabidopsis Coexpression Tool (ACT), a gene coexpression analysis web tool for Arabidopsis thaliana, identifies genes which are correlated to a driver gene. Primary microarray data from ATH1 Affymetrix platform were processed with Single-Channel Array Normalization algorithm and combined to produce a coexpression tree which contains ∼21,000 A. thaliana genes. ACT was developed to present subclades of coexpressed genes, as well as to perform gene set enrichment analysis, being unique in revealing enriched transcription factors targeting coexpressed genes. ACT offers a simple and user-friendly interface producing working hypotheses which can be experimentally verified for the discovery of gene partnership, pathway membership, and transcriptional regulation. ACT analyses have been successful in identifying not only genes with coordinated ubiquitous expressions but also genes with tissue-specific expressions

Clavibacter michiganensis downregulates photosynthesis and modifies monolignols metabolism revealing a crosstalk with tomato immune responses

The gram-positive pathogenic bacterium Clavibacter michiganensis subsp. michiganensis (Cmm) causes bacterial canker disease in tomato, affecting crop yield and fruit quality. To understand how tomato plants respond, the dynamic expression profile of host genes was analyzed upon Cmm infection. Symptoms of bacterial canker became evident from the third day. As the disease progressed, the bacterial population increased in planta, reaching the highest level at six days and remained constant till the twelfth day post inoculation. These two time points were selected for transcriptomics. A progressive down-regulation of key genes encoding for components of the photosynthetic apparatus was observed. Two temporally separated defense responses were observed, which were to an extent interdependent. During the primary response, genes of the phenylpropanoid pathway were diverted towards the synthesis of monolignols away from S-lignin. In dicots, lignin polymers mainly consist of G- and S-units, playing an important role in defense. The twist towards G-lignin enrichment is consistent with previous findings, highlighting a response to generate an early protective barrier and to achieve a tight interplay between lignin recomposition and the primary defense response mechanism. Upon progression of Cmm infection, the temporal deactivation of phenylpropanoids coincided with the upregulation of genes that belong in a secondary response mechanism, supporting an elegant reprogramming of the host transcriptome to establish a robust defense apparatus and suppress pathogen invasion. This high-throughput analysis reveals a dynamic reorganization of plant defense mechanisms upon bacterial infection to implement an array of barriers preventing pathogen invasion and spread

Molecular mechanisms of development in plants

Η παρούσα διατριβή αποδεικνύει ότι το πυρηνικό γονίδιο AtLOn1 περιέχει δύο ενάρξεις της μετάφρασης στο ίδιο αναγνωστικό πλαίσιο κωδικοποιώντας για δύο ισόμορφα. Το πλασιδιακό ισόμορφο Lon1L που ξεκινά στην πρώτη Μεθειονίνη και το μιτοχονδριακό ισόμορφο Lon1S το οποίο ξεκινά στη Μεθειονίνη 46. In vivo μικροσκοπία φθορισμού του AtLon1 γονιδίου σε σύντηξη με το YFP έδειξε ότι συμβαίνει ολίσθηση του μηχανισμού σάρωσης του ριβοσώματος στην περιοχή του πρώτου AUG, οδηγώντας σε εναλλακτική έναρξη της μετάφρασης στο δεύτερο κωδικόνιο έναρξης. Επίσης παρουσιάζεται ρύθμιση και σε μεταγραφικό επίπεδο αφού υπάρχει και εναλλακτική έναρξη της μεταγραφής σε συνδυασμό με την ανάπτυξη ή περιβαλλοντικές συνθήκες. Το γονίδιο AtLon1 επιτυχώς συμπλήρωσε το φαινότυπο του μεταλλάγματος Pim1 στη ζύμη ανεξάρτητα του πεπτιδίου οδηγού. Ακόμη, το πεπτίδιο οδηγός του AtLon1 είναι αρκετα συντηρημένο και σε άλλους φυτικούς οργανισμούς. Οι πρωτεΐνες που περιέχουν το τμήμα PORR (Plant Organelle RNA Recognition) εμπλέκονται στο μάτισμα των πλαστιδιακών γονιδίων της ομάδας ΙΙ. Το γονίδιο Leukothea1 περιέχει το τμήμα PORR και είναι αναγκαίο την ανάπτυξη του εμβρύου. Το μετάλλαγμα leuko1-1 εμφανίζει λευκές κοτυληδόνες, ενώ η ολική έλλειψη της πρωτεΐνης οδηγεί στη θνησιμότητα του εμβρύου, όπως εμφανίζεται στο μετάλλαγμα leuko1-2. Η πρωτεΐνη Leuko1 έχει πεπτίδιο οδηγό για τον χλωροπλάστη, αλλά και σινιάλα εισόδου και εξόδου από τον πυρήνα, τα NLS και NES αντίστοιχα. Μικροσκοπική ανάλυση των κατασκευών του γονιδίου με YFP έδειξε ότι η πρωτεΐνη μπορεί να τοποθετείται στον πυρήνα, αλλά και στον χλωροπλάστη και μάλιστα διακινούμενη από τον πυρήνα στον χλωροπλάστη. Ο φαινότυπος του μεταλλάγματος leuko1-1 οφείλεται στην έλλειψη της πρωτεΐνης από τον πυρήνα. Για αυτό το λόγο, η αποκλειστική τοποθέτηση της πρωτεΐνης Leuko1 στον πυρήνα συμπλήρωσε το φαινότυπο του μεταλλάγματος leuko1-1. Η παρούσα διατριβή παρέχει πληροφορίες και αποτελέσματα που έχουν να κάνουν με τους μηχανισμούς τοποθέτησης και λειτουργίας των γονιδίων Lon1 και Leukothea αναφορικά της ανάπτυξης του φυτικού σώματος. Η πολλαπλή επανοτοποθέτηση των παραπάνω πρωτεϊνών παρέχει ένα εξελιγμένο δίκτυο σηματοδότησης μέσα στο φυτό έναnτι της ανάπτυξη ή και των περιβαλλοντικών συνθηκών που επικρατούν.Cellular homeostasis and survival relies on components of protein quality control mechanism including chaperones for proper folding of non-native polypeptides and proteases to eliminate the irreparably damaged proteins. In bacteria and eukaryotic organelles the ATP-dependent Lon protease plays a critical role in the removal of oxidised proteins and hence prevents cumulative damage by deleterious degradation-resistant aggregates. This report demonstrates that nuclear AtLon1 gene contains two in-frame translation initiation codons encoding for a long plastidial isoform (Lon1L) starting at Met1 and a short mitochondrial targeted isoform (Lon1S) starting at Met46. In vivo fluorescence microscopy of AtLon1 N-terminal deletion variants fused to YFP revealed leaky ribosome scanning around the first AUG, which deviates extensively from the optimum Kozak consensus, leading to alternative translation initiation at the second initiation codon. Additional complexity results from differential selection of transcription start sites (TSS) depending on tissue specificity and stress-response. The TSS for Lon1S devoid of the first AUG context is predominant, whereas the upstream TSS containing the two in-frame AUGs is highly expressed only in leaves and under shortage of light. The twin N-terminal presequences of AtLon1 are highly conserved among various plant species. Interestingly, AtLon1 successfully complemented the mitochondrial mutant phenotype of the yeast PIM1 gene homolog through an AUG context-dependent but N-terminal targeting domain independent mechanism. In line with the widely-held theory that dual-targeted condition is a gain-of-function derived from gene duplication, the AtLon1 twin presequences may represent an intermediate in the evolution of dual-targeting affecting post-germinative growth. Recent studies have shown that proteins containing the PORR (Plant Organelle RNA Recognition) domain are implicated in group II intron splicing mechanism of chloroplast encoded genes. Leukothea1 gene that contains the PORR domain is necessary for embryo development. The leuko1-1 mutant allele caused by single nucleotide change of G to A resulting in amino acid substitution of Glycine 373 to Aspartic acid. The leuko1-1 seedlings have typical white-cotyledon phenotype. The total loss of Leukothea1 function in leuko1-2 mutant alleles results in embryo arrest upon transition from the globular to the heart-stage embryo. In silico analysis has shown that Leuko1 protein has a putative transit peptide for chloroplast targeting and signals for nuclear localization NLS and export NES. Microscopic analysis of Leuko1 gene constructs fused to YFP confirmed the dual targeting properties of Leuko1 to both chloroplasts and the nucleus. Furthermore, the Leuko1 roadmap to the nucleus and back to the cytoplasm from the nucleus depends on the Importin1α and Exportin1 mechanisms, respectively. The leuko1-1 phenotype results from the disturbed equilibrium of the protein in the nucleus due to enhanced protein export. Therefore, the truncated version of Leuko1 protein missing the transit peptide at the N-terminus complements the leuko1-1 phenotype, highlighting the crucial role of Leuko1 in the nucleus. Leuko1 protein targeting to the nucleus is associated with the mRNA processing and splicing of nuclear-encoded genes targeted to the chloroplasts. This study provides information regarding the mechanisms of two nuclear-encoded proteins translocation to distinct subcellular compartments. Plant organelles originate for endosymbiosys of bacteria in the primitive eukaryotic cell. During the course of evolution organellar targeting proteins encoded by the nuclear genome involved in fundamental biological processes including mRNA processing/splicing (Leukothea1) or protein processing (Lon1) mechanisms, attained dual-targeting properties. These features for multi sub-cellular localization provide a sophisticated network for plant signaling response to environmental or developmental cues.Η παρούσα διατριβή αποδεικνύει ότι το πυρηνικό γονίδιο AtLOn1 περιέχει δύο ενάρξεις της μετάφρασης στο ίδιο αναγνωστικό πλαίσιο κωδικοποιώντας για δύο ισόμορφα. Το πλασιδιακό ισόμορφο Lon1L που ξεκινά στην πρώτη Μεθειονίνη και το μιτοχονδριακό ισόμορφο Lon1S το οποίο ξεκινά στη Μεθειονίνη 46. In vivo μικροσκοπία φθορισμού του AtLon1 γονιδίου σε σύντηξη με το YFP έδειξε ότι συμβαίνει ολίσθηση του μηχανισμού σάρωσης του ριβοσώματος στην περιοχή του πρώτου AUG, οδηγώντας σε εναλλακτική έναρξη της μετάφρασης στο δεύτερο κωδικόνιο έναρξης. Επίσης παρουσιάζεται ρύθμιση και σε μεταγραφικό επίπεδο αφού υπάρχει και εναλλακτική έναρξη της μεταγραφής σε συνδυασμό με την ανάπτυξη ή περιβαλλοντικές συνθήκες. Το γονίδιο AtLon1 επιτυχώς συμπλήρωσε το φαινότυπο του μεταλλάγματος Pim1 στη ζύμη ανεξάρτητα του πεπτιδίου οδηγού. Ακόμη, το πεπτίδιο οδηγός του AtLon1 είναι αρκετα συντηρημένο και σε άλλους φυτικούς οργανισμούς. Οι πρωτεΐνες που περιέχουν το τμήμα PORR (Plant Organelle RNA Recognition) εμπλέκονται στο μάτισμα των πλαστιδιακών γονιδίων της ομάδας ΙΙ. Το γονίδιο Leukothea1 περιέχει το τμήμα PORR και είναι αναγκαίο την ανάπτυξη του εμβρύου. Το μετάλλαγμα leuko1-1 εμφανίζει λευκές κοτυληδόνες, ενώ η ολική έλλειψη της πρωτεΐνης οδηγεί στη θνησιμότητα του εμβρύου, όπως εμφανίζεται στο μετάλλαγμα leuko1-2. Η πρωτεΐνη Leuko1 έχει πεπτίδιο οδηγό για τον χλωροπλάστη, αλλά και σινιάλα εισόδου και εξόδου από τον πυρήνα, τα NLS και NES αντίστοιχα. Μικροσκοπική ανάλυση των κατασκευών του γονιδίου με YFP έδειξε ότι η πρωτεΐνη μπορεί να τοποθετείται στον πυρήνα, αλλά και στον χλωροπλάστη και μάλιστα διακινούμενη από τον πυρήνα στον χλωροπλάστη. Ο φαινότυπος του μεταλλάγματος leuko1-1 οφείλεται στην έλλειψη της πρωτεΐνης από τον πυρήνα. Για αυτό το λόγο, η αποκλειστική τοποθέτηση της πρωτεΐνης Leuko1 στον πυρήνα συμπλήρωσε το φαινότυπο του μεταλλάγματος leuko1-1. Η παρούσα διατριβή παρέχει πληροφορίες και αποτελέσματα που έχουν να κάνουν με τους μηχανισμούς τοποθέτησης και λειτουργίας των γονιδίων Lon1 και Leukothea αναφορικά της ανάπτυξης του φυτικού σώματος. Η πολλαπλή επανοτοποθέτηση των παραπάνω πρωτεϊνών παρέχει ένα εξελιγμένο δίκτυο σηματοδότησης μέσα στο φυτό έναnτι της ανάπτυξη ή και των περιβαλλοντικών συνθηκών που επικρατούν

Stomatal Complex Development and F-Actin Organization in Maize Leaf Epidermis Depend on Cellulose Synthesis

Cellulose microfibrils reinforce the cell wall for morphogenesis in plants. Herein, we provide evidence on a series of defects regarding stomatal complex development and F-actin organization in Zea mays leaf epidermis, due to inhibition of cellulose synthesis. Formative cell divisions of stomatal complex ontogenesis were delayed or inhibited, resulting in lack of subsidiary cells and frequently in unicellular stomata, with an atypical stomatal pore. Guard cells failed to acquire a dumbbell shape, becoming rounded, while subsidiary cells, whenever present, exhibited aberrant morphogenesis. F-actin organization was also affected, since the stomatal complex-specific arrays were scarcely observed. At late developmental stages, the overall F-actin network was diminished in all epidermal cells, although thick actin bundles persisted. Taken together, stomatal complex development strongly depends on cell wall mechanical properties. Moreover, F-actin organization exhibits a tight relationship with the cell wall

Mitochondria biogenesis via Lon1 selective proteolysis: Who dares to live for ever?

Quality control of proteins in eukaryotic organelles is predominantly maintained by members of the ATP-dependent proteases. Even though numerous biological analyses have shed light on the functional implications of such proteases, their involvement in developmental processes of multicellular organisms has not been determined. We recently identified two lon1 mutant alleles, both missing the carboxy terminal proteolytic domain, that show post-embryonic growth retardation resulting in delayed seedling establishment. In this addendum, we enlighten the role of Lon1 selective proteolysis in plant mitochondria biogenesis, a prerequisite for post-embryonic development and growth. In contrast to the weak lon1-2 allele, the polypeptide encoded by the strong lon1-1 allele carries the sensor- and substrate-discrimination domain allowing substrate recognition and binding. This type of molecular recognition hinders further degradation by the complementary Lon-independent proteolytic machineries resulting in an extra deleterious accumulation of protein aggregates into lon1-1 mitochondria. The most challenging and informative task will be to identify the recognition motifs on the Lon protein substrates and elucidate the molecular events that control plant mitochondrial differentiation

Updating Insights into the Catalytic Domain Properties of Plant Cellulose synthase (CesA) and Cellulose synthase-like (Csl) Proteins

The wall is the last frontier of a plant cell involved in modulating growth, development and defense against biotic stresses. Cellulose and additional polysaccharides of plant cell walls are the most abundant biopolymers on earth, having increased in economic value and thereby attracted significant interest in biotechnology. Cellulose biosynthesis constitutes a highly complicated process relying on the formation of cellulose synthase complexes. Cellulose synthase (CesA) and Cellulose synthase-like (Csl) genes encode enzymes that synthesize cellulose and most hemicellulosic polysaccharides. Arabidopsis and rice are invaluable genetic models and reliable representatives of land plants to comprehend cell wall synthesis. During the past two decades, enormous research progress has been made to understand the mechanisms of cellulose synthesis and construction of the plant cell wall. A plethora of cesa and csl mutants have been characterized, providing functional insights into individual protein isoforms. Recent structural studies have uncovered the mode of CesA assembly and the dynamics of cellulose production. Genetics and structural biology have generated new knowledge and have accelerated the pace of discovery in this field, ultimately opening perspectives towards cellulose synthesis manipulation. This review provides an overview of the major breakthroughs gathering previous and recent genetic and structural advancements, focusing on the function of CesA and Csl catalytic domain in plants