scholarly journals From skylight input to behavioural output: a computational model of the insect polarised light compass

2018 ◽  
Author(s):  
Evripidis Gkanias ◽  
Benjamin Risse ◽  
Michael Mangan ◽  
Barbara Webb
Keyword(s):  
Path Integration ◽  
Sensor Array ◽  
Neural Model ◽  
Biological Data ◽  
Insect Brain ◽  
Uneven Terrain ◽  
Starting Point ◽  
Celestial Compass ◽  
Insect Eye ◽  
New Hypothesis

AbstractMany insects navigate by integrating the distances and directions travelled on an outward path, allowing direct return to the starting point. Fundamental to the reliability of this process is the use of a neural compass based on external celestial cues. Here we examine how such compass information could be reliably computed by the insect brain, given realistic constraints on the sky polarisation pattern and the insect eye sensor array. By processing the degree of polarisation in different directions for different parts of the sky, our model can directly estimate the solar azimuth and also infer the confidence of the estimate. We introduce a method to correct for tilting of the sensor array, as might be caused by travel over uneven terrain. We also show that the confidence can be used to approximate the change in sun position over time, allowing the compass to remain fixed with respect to ‘true north’ during long excursions. We demonstrate that the compass is robust to disturbances and can be effectively used as input to an existing neural model of insect path integration. We discuss the plausibility of our model to be mapped to known neural circuits, and to be implemented for robot navigation.Author summaryWe propose a new hypothesis for how insects process polarised skylight to extract global orientation information that can be used for accurate path integration. Our model solves the problem of solar/anti-solar meridian ambiguity by using a biologically constrained sensor array, and includes methods to deal with tilt and time, providing a complete insect celestial compass output. We analyse the performance of the model using a realistic sky simulation and various forms of disturbances, and compare the results to both engineering approaches and biological data.

scholarly journals Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yi Chen ◽  
Fons. J. Verbeek ◽  
Katherine Wolstencroft
Keyword(s):  
Gene Ontology ◽  
Enrichment Analysis ◽  
Biological Data ◽  
Hallmarks Of Cancer ◽  
High Throughput Analysis ◽  
Knowledge Resources ◽  
Gene Set ◽  
Cancer Hallmarks ◽  
Starting Point ◽  
High Level

Abstract Background The hallmarks of cancer provide a highly cited and well-used conceptual framework for describing the processes involved in cancer cell development and tumourigenesis. However, methods for translating these high-level concepts into data-level associations between hallmarks and genes (for high throughput analysis), vary widely between studies. The examination of different strategies to associate and map cancer hallmarks reveals significant differences, but also consensus. Results Here we present the results of a comparative analysis of cancer hallmark mapping strategies, based on Gene Ontology and biological pathway annotation, from different studies. By analysing the semantic similarity between annotations, and the resulting gene set overlap, we identify emerging consensus knowledge. In addition, we analyse the differences between hallmark and gene set associations using Weighted Gene Co-expression Network Analysis and enrichment analysis. Conclusions Reaching a community-wide consensus on how to identify cancer hallmark activity from research data would enable more systematic data integration and comparison between studies. These results highlight the current state of the consensus and offer a starting point for further convergence. In addition, we show how a lack of consensus can lead to large differences in the biological interpretation of downstream analyses and discuss the challenges of annotating changing and accumulating biological data, using intermediate knowledge resources that are also changing over time.

Inflammation and Pruning May Inform Risk to Psychiatric Disorders. Lessons From Large Genetic Data

2017 ◽  
Vol 41 (S1) ◽  
pp. S56-S56
Author(s):  
C. Crisafulli
Keyword(s):  
Psychiatric Disorders ◽  
Molecular Mechanics ◽  
Association Studies ◽  
Molecular Pathway ◽  
Starting Point ◽  
Single Effect ◽  
Competing Interest ◽  
The Brain ◽  
New Hypothesis

BackgroundIt's known that psychiatric disorders are caused to either environmental and genetics factors. Through the years several hypotheses were tested and many genes were screened for association, resulting in a huge amount of data available for the scientific community. Despite that, the molecular mechanics behind psychiatric disorders remains largely unknown. Traditional association studies may be not enough to pinpoint the molecular underpinnings of psychiatric disorder. We tried to applying a methodology that investigates molecular-pathway-analysis that takes into account several genes per time, clustered in consistent molecular groups and may successfully capture the signal of a number of genetic variations with a small single effect on the disease. This approach might reveal more of the molecular basis of psychiatric disorders.Methodsi)We collected data on studies available in literature for the studied disorder (e.g. Schizophrenia, Bipolar Disorder);ii)We extracted a pool of genes that are likely involved with the disease;iii)We used these genes as starting point to map molecular cascades function-linked. The molecular cascades are then analyzed and pathways and sub-pathways, possibly involved with them, are identified and tested for association.Results/discussionWe obtained interesting results. In particular, signals of enrichment (association) were obtained multiple times on the molecular pathway associated with the pruning activity and inflammation. Molecular mechanics related to neuronal pruning were focused as a major and new hypothesis for the pathophysiology of psychiatric disorders and the role of inflammatory events has been extensively investigated in psychiatry. intersting, inflammatory mechanics in the brain may also play a role in neuronal pruning during the early development of CNS.Disclosure of interestThe author has not supplied his declaration of competing interest.

Analysis and Integration of Biological Data

2010 ◽  
pp. 287-314
Author(s):  
Diego Milone ◽  
Georgina Stegmayer ◽  
Matías Gerard ◽  
Laura Kamenetzky ◽  
Mariana López ◽  
...  
Keyword(s):  
Data Integration ◽  
New Technologies ◽  
Biological Significance ◽  
Neural Model ◽  
Biological Data ◽  
Data Sets ◽  
Clustering Methods ◽  
Gene Expressions ◽  
Internal Coherence ◽  
Biological Data Integration

The volume of information derived from post genomic technologies is rapidly increasing. Due to the amount of involved data, novel computational methods are needed for the analysis and knowledge discovery into the massive data sets produced by these new technologies. Furthermore, data integration is also gaining attention for merging signals from different sources in order to discover unknown relations. This chapter presents a pipeline for biological data integration and discovery of a priori unknown relationships between gene expressions and metabolite accumulations. In this pipeline, two standard clustering methods are compared against a novel neural network approach. The neural model provides a simple visualization interface for identification of coordinated patterns variations, independently of the number of produced clusters. Several quality measurements have been defined for the evaluation of the clustering results obtained on a case study involving transcriptomic and metabolomic profiles from tomato fruits. Moreover, a method is proposed for the evaluation of the biological significance of the clusters found. The neural model has shown a high performance in most of the quality measures, with internal coherence in all the identified clusters and better visualization capabilities.

Leaky integration during blindfolded walking along veering paths

2012 ◽  
Vol 25 (0) ◽  
pp. 139
Author(s):  
Markus Lappe ◽  
Claudia Fontaine ◽  
Harald Frenz
Keyword(s):  
Path Integration ◽  
Path Length ◽  
Distance Estimation ◽  
Forward Direction ◽  
Travel Distance ◽  
Integration Model ◽  
Starting Point ◽  
End Distance ◽  
Leaky Integration ◽  
The Right

We compare travel distance estimation from path integration during walking with path integration from visual flow. For visually simulated self-movement humans typically underestimate travel distance, which can be explained by leaky path integration. The amount of leak, i.e., the underestimation, is determined by the length of the path. For visually simulated movements along curved paths that veer left and right around a central forward direction estimates of the start-to-end distance decrease as the veering, i.e., the path length increases. Leaky path integration for visual travel distance estimation thus takes place along the actually traversed path even when a straight beeline distance is calculated. We studied whether the same leaky path integration occurs during real self-motion when vestibular and proprioceptive cues are available instead of vision. Sixteen subjects walked blindfolded from a starting point to targets 20, 30 or 40 m away, guided by an experimenter. They walked either along a straight line, or along paths that deviated first to the right and then to the left (or vice versa) before they reached the end point. This increased the path length by 5, 10, 20 or 30%. Subjects then gave a verbal estimate of their beeline distance from the starting point. Like in the visually simulated case, distance estimates for the same start-to-end distance of 40 m dropped as the path length increased, consistent with the prediction of the leaky integration model. We conclude that travel distance estimation is similar for visual and for vestibular/proprioceptive cues.

scholarly journals Wikidata as a semantic framework for the Gene Wiki initiative

2015 ◽  
Author(s):  
Sebastian Burgstaller-Muehlbacher ◽  
Andra Waagmeester ◽  
Elvira Mitraka ◽  
Julia Turner ◽  
Tim E. Putman ◽  
...  
Keyword(s):  
English Language ◽  
Biological Data ◽  
Use Case ◽  
Data Resource ◽  
Semantic Framework ◽  
Language Version ◽  
Human Genes ◽  
Starting Point ◽  
Human Proteins ◽  
Human And Mouse

Open biological data is distributed over many resources making it challenging to integrate, to update and to disseminate quickly. Wikidata is a growing, open community database which can serve this purpose and also provides tight integration with Wikipedia. In order to improve the state of biological data, facilitate data management and dissemination, we imported all human and mouse genes, and all human and mouse proteins into Wikidata. In total, 59,530 human genes and 73,130 mouse genes have been imported from NCBI and 27,662 human proteins and 16,728 mouse proteins have been imported from the Swissprot subset of UniProt. As Wikidata is open and can be edited by anybody, our corpus of imported data serves as the starting point for integration of further data by scientists, the Wikidata community and citizen scientists alike. The first use case for this data is to populate Wikipedia Gene Wiki infoboxes directly from Wikidata with the data integrated above. This enables immediate updates of the Gene Wiki infoboxes as soon as the data in Wikidata is modified. Although Gene Wiki pages are currently only on the English language version of Wikipedia, the multilingual nature of Wikidata allows for a usage of the data we imported in all 280 different language Wikipedias. Apart from the Gene Wiki infobox use case, a powerful SPARQL endpoint and up to date exporting functionality (e.g. JSON, XML) enable very convenient further use of the data by scientists. In summary, we created a fully open and extensible data resource for human and mouse molecular biology and biochemistry data. This resource enriches all the Wikipedias with structured information and serves as a new linking hub for the biological semantic web.

Insect Navigation: Neural Basis to Behavior

2018 ◽  
Author(s):  
Stanley Heinze
Keyword(s):  
Path Integration ◽  
Sensory Information ◽  
Central Complex ◽  
Insect Brain ◽  
Head Direction ◽  
Neural Basis ◽  
Long Distance ◽  
Insect Navigation ◽  
Straight Line ◽  
Wide Range

Navigation is the ability of animals to move through their environment in a planned manner. Different from directed but reflex-driven movements, it involves the comparison of the animal’s current heading with its intended heading (i.e., the goal direction). When the two angles don’t match, a compensatory steering movement must be initiated. This basic scenario can be described as an elementary navigational decision. Many elementary decisions chained together in specific ways form a coherent navigational strategy. With respect to navigational goals, there are four main forms of navigation: explorative navigation (exploring the environment for food, mates, shelter, etc.); homing (returning to a nest); straight-line orientation (getting away from a central place in a straight line); and long-distance migration (seasonal long-range movements to a location such as an overwintering place). The homing behavior of ants and bees has been examined in the most detail. These insects use several strategies to return to their nest after foraging, including path integration, route following, and, potentially, even exploit internal maps. Independent of the strategy used, insects can use global sensory information (e.g., skylight cues), local cues (e.g., visual panorama), and idiothetic (i.e., internal, self-generated) cues to obtain information about their current and intended headings. How are these processes controlled by the insect brain? While many unanswered questions remain, much progress has been made in recent years in understanding the neural basis of insect navigation. Neural pathways encoding polarized light information (a global navigational cue) target a brain region called the central complex, which is also involved in movement control and steering. Being thus placed at the interface of sensory information processing and motor control, this region has received much attention recently and emerged as the navigational “heart” of the insect brain. It houses an ordered array of head-direction cells that use a wide range of sensory information to encode the current heading of the animal. At the same time, it receives information about the movement speed of the animal and thus is suited to compute the home vector for path integration. With the help of neurons following highly stereotypical projection patterns, the central complex theoretically can perform the comparison of current and intended heading that underlies most navigation processes. Examining the detailed neural circuits responsible for head-direction coding, intended heading representation, and steering initiation in this brain area will likely lead to a solid understanding of the neural basis of insect navigation in the years to come.

Metallodrugs as Anticancer Chemotherapeutics and Diagnostic Agents: A Critical Patent Review (2010-2020)

2021 ◽  
Vol 16 ◽  
Author(s):  
Eirini Fotopoulou ◽  
Ioannis Titilas ◽  
Luca Ronconi
Keyword(s):  
Tumor Imaging ◽  
Clinical Status ◽  
Biological Data ◽  
Specific Tumor ◽  
Patent Review ◽  
Starting Point ◽  
Diagnostic Agents ◽  
Potential Applications ◽  
Novel Drug ◽  
Imaging Properties

Background: The development of metallodrugs with potential applications in cancer treatment and diagnosis has been a hot topic since the approval and subsequent marketing of the anticancer drug cisplatin in 1978. Since then, thousands of metal-based derivatives have been reported and evaluated for their chemotherapeutic or tumor imaging properties, but only a very limited number gained clinical status. Nonetheless, research in the field has been increasing exponentially over the years, especially in a view to exploiting novel drug designing approaches and strategies aimed at improving pharmacological outcomes and, at the same time, reducing side-effects. Objective: This review article reports on the patents filed during the last decade and strictly focusing on the development of metal-based anticancer and diagnostic agents. The goal is to identify the latest trends and designing strategies in the field, which would represent a valuable starting point to researchers interested in the development of metallodrugs. Methods: The most relevant patents filed in the 2010-2020 timeframe have been retrieved from various databases using dedicated search engines (such as SciFinder, Google Patents, PatentPak, Espacenet, Global Dossier, PatentScope), sorted by type of metallodrug and screened to include those reporting a substantial amount of biological data. Results : The majority of patents here reviewed are concerned with metallodrugs (mostly platinum-based) showing interesting pharmacological properties but no specific tumor-targeting features. Nonetheless, some promising trends in the development of novel drug delivery strategies and/or metallodrugs with potential applications in targeted chemotherapy are envisaged. Conclusion: In this review, the latest trends in the development of metallodrugs from recent patents are summarized and critically discussed. Such trends would be of interest not only to the scientific community but also to lay audiences aiming to broaden their knowledge of the field and industrial stakeholders potentially interested in the exploitation and commercialization of this class of pharmaceuticals.

Multiple orientation cues in an Australian trunk-trail-forming ant, Iridomyrmex purpureus

2016 ◽  
Vol 64 (3) ◽  
pp. 227 ◽  
Author(s):  
Ashley Card ◽  
Caitlin McDermott ◽  
Ajay Narendra
Keyword(s):  
Path Integration ◽  
Trail Following ◽  
Visual Landmarks ◽  
Directional Information ◽  
Nest Location ◽  
Visual Landmark ◽  
Pheromone Trails ◽  
Orientation Cues ◽  
Celestial Compass ◽  
Path Integrator

Ants use multiple cues for navigating to a food source or nest location. Directional information is derived from pheromone trails or visual landmarks or celestial objects. Some ants use the celestial compass information along with an ‘odometer’ to determine the shortest distance home, a strategy known as path integration. Some trail-following ants utilise visual landmark information whereas few of the solitary-foraging ants rely on both path integration and visual landmark information. However, it is unknown to what degree trail-following ants use path integration and we investigated this in a trunk-trail-following ant, Iridomyrmex purpureus. Trunk-trail ants connect their nests to food sites with pheromone trails that contain long-lasting orientation information. We determined the use of visual landmarks and the ability to path integrate in a trunk-trail forming ant. We found that experienced animals switch to relying on visual landmark information, and naïve individuals rely on odour trails. Ants displaced to unfamiliar locations relied on path integration, but, surprisingly, they did not travel the entire homebound distance. We found that as the homebound distance increased, the distance ants travelled relying on the path integrator reduced.

scholarly journals Identification of 6-(piperazin-1-yl)-1,3,5-triazine as a chemical scaffold with broad anti-schistosomal activities

2020 ◽  
Vol 5 ◽  
pp. 169
Author(s):  
Gilda Padalino ◽  
Iain W. Chalmers ◽  
Andrea Brancale ◽  
Karl F. Hoffmann
Keyword(s):  
Virtual Screening ◽  
Small Molecules ◽  
Adult Worm ◽  
In Silico ◽  
Egg Production ◽  
Homology Modelling ◽  
Homology Model ◽  
Biological Data ◽  
Significant Activity ◽  
Starting Point

Background: Schistosomiasis, caused by infection with blood fluke schistosomes, is a neglected tropical disease of considerable importance in resource-poor communities throughout the developing world. In the absence of an immunoprophylactic vaccine and due to over-reliance on a single chemotherapy (praziquantel), schistosomiasis control is at risk should drug insensitive schistosomes develop. In this context, application of in silico virtual screening on validated schistosome targets has proven successful in the identification of novel small molecules with anti-schistosomal activity.   Methods: Focusing on the Schistosoma mansoni histone methylation machinery, we herein have used RNA interference (RNAi), ELISA-mediated detection of H3K4 methylation, homology modelling and in silico virtual screening to identify a small collection of small molecules for anti-schistosomal testing. A combination of low to high-throughput whole organism assays were subsequently used to assess these compounds’ activities on miracidia to sporocyst transformation, schistosomula phenotype/motility metrics and adult worm motility/oviposition readouts. Results: RNAi-mediated knockdown of smp_138030/smmll-1 (encoding a histone methyltransferase, HMT) in adult worms (~60%) reduced parasite motility and egg production. Moreover, in silico docking of compounds into Smp_138030/SmMLL-1’s homology model highlighted competitive substrate pocket inhibitors, some of which demonstrated significant activity on miracidia, schistosomula and adult worm lifecycle stages together with variable effects on HepG2 cells. Particularly, the effect of compounds containing a 6-(piperazin-1-yl)-1,3,5-triazine core on adult schistosomes recapitulated the results of the smp_138030/smmll-1 RNAi screens. Conclusions: The biological data and the structure-activity relationship presented in this study define the 6-(piperazin-1-yl)-1,3,5-triazine core as a promising starting point in ongoing efforts to develop new urgently needed schistosomicides.

scholarly journals Identification of 6-(piperazin-1-yl)-1,3,5-triazine as a chemical scaffold with broad anti-schistosomal activities

2020 ◽  
Vol 5 ◽  
pp. 169
Author(s):  
Gilda Padalino ◽  
Iain W. Chalmers ◽  
Andrea Brancale ◽  
Karl F. Hoffmann
Keyword(s):  
Virtual Screening ◽  
Small Molecules ◽  
Adult Worm ◽  
In Silico ◽  
Egg Production ◽  
Homology Modelling ◽  
Homology Model ◽  
Biological Data ◽  
Significant Activity ◽  
Starting Point

Background: Schistosomiasis, caused by infection with blood fluke schistosomes, is a neglected tropical disease of considerable importance in resource-poor communities throughout the developing world. In the absence of an immunoprophylactic vaccine and due to over-reliance on a single chemotherapy (praziquantel), schistosomiasis control is at risk should drug insensitive schistosomes develop. In this context, application of in silico virtual screening on validated schistosome targets has proven successful in the identification of novel small molecules with anti-schistosomal activity.   Methods: Focusing on the Schistosoma mansoni histone methylation machinery, we herein have used RNA interference (RNAi), ELISA-mediated detection of H3K4 methylation, homology modelling and in silico virtual screening to identify a small collection of small molecules for anti-schistosomal testing. A combination of low to high-throughput whole organism assays were subsequently used to assess these compounds’ activities on miracidia to sporocyst transformation, schistosomula phenotype/motility metrics and adult worm motility/oviposition readouts. Results: RNAi-mediated knockdown of smp_138030/smmll-1 (encoding a histone methyltransferase, HMT) in adult worms (~60%) reduced parasite motility and egg production. Moreover, in silico docking of compounds into Smp_138030/SmMLL-1’s homology model highlighted competitive substrate pocket inhibitors, some of which demonstrated significant activity on miracidia, schistosomula and adult worm lifecycle stages together with variable effects on HepG2 cells. Particularly, the effect of compounds containing a 6-(piperazin-1-yl)-1,3,5-triazine core on adult schistosomes recapitulated the results of the smp_138030/smmll-1 RNAi screens. Conclusions: The biological data and the structure-activity relationship presented in this study define the 6-(piperazin-1-yl)-1,3,5-triazine core as a promising starting point in ongoing efforts to develop new urgently needed schistosomicides.

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