Query: OCTOPUS

title: Octopus Arm Inspired Tapered Soft Actuators with Suckers for Improved Grasping.
abstract: Octopuses can employ their tapered arms to catch prey of all shapes and sizes due to their dexterity, flexibility, and gripping power. Intrigued by variability in arm taper angle between different octopus species, we explored the utility of designing soft actuators exhibiting a distinctive conical geometry, compared with more traditional cylindrical forms. We find that these octopus inspired conical shaped actuators exhibit a wide range of bending curvatures that can be tuned by simply altering their taper angle and they also demonstrate greater flexibility compared with their cylindrical counterparts. The taper angle and bending curvature are inversely related, whereas taper angle and applied bending force are directly related. To further expand the functionality of our soft actuators, we incorporated vacuum actuated suckers into the actuators for the production of a fully integrated octopus arm inspired gripper. Notably, our results reveal that because of their enhanced flexibility, these tapered actuators with suckers have better gripping power than their cylindrical shaped counterparts and require significantly larger forces to be detached from both flat and curved surfaces. Finally, we show that by choosing appropriate taper angles, our tapered actuators with suckers can grip, move, and place a remarkably wide range of objects with flat, nonplanar, smooth, or rough surfaces, as well as retrieve objects through narrow openings. The results from this study not only provide new design insights into the creation of next generation soft actuators for gripping a wide range of morphologically diverse objects but also contribute to our understanding of the functional significance of arm taper angle variability across octopus species.

title: What is in an octopus's mind?
abstract: It is difficult to imagine what an animal as different from us as the octopus 'thinks' but we can make some progress. In the Umwelt or perceptual world of an octopus, what the lateralized monocular eyes perceive is not color but the plane of polarization of light. Information is processed by a bilateral brain but manipulation is done by a radially symmetrical set of eight arms. Octopuses do not self monitor by vision. Their skin pattern system, used for excellent camouflage, is open loop. The output of the motor system of the eight arms is organized at several levels brain, intrabrachial commissure and local brachial ganglia. Octopuses may be motivated by a combination of fear and exploration. Several actions a head bob for motion parallax, a 'Passing Cloud' skin display to startle prey, and particularly exploration by their arms demonstrate the presence of a controlling mind, motivated to gather information. Yet most octopuses are solitary and many are cannibalistic, so they must always be on guard, even against conspecifics. The actions of octopuses can be domain general, with flexible problem solving strategies, enabling them to survive "by their wits" in a challenging and variable environment.

title: The survey and reference assisted assembly of the Octopus vulgaris genome
abstract: The common octopus, Octopus vulgaris, is an active marine predator known for the richness and plasticity of its behavioral repertoire, and remarkable learning and memory capabilities. Octopus and other coleoid cephalopods, cuttlefish and squid, possess the largest nervous system among invertebrates, both for cell counts and body to brain size. O. vulgaris has been at the center of a long tradition of research into diverse aspects of its biology. To leverage research in this iconic species, we generated 270 Gb of genomic sequencing data, complementing those available for the only other sequenced congeneric octopus, Octopus bimaculoides. We show that both genomes are similar in size, but display different levels of heterozygosity and repeats. Our data give a first quantitative glimpse into the rate of coding and non coding regions and support the view that hundreds of novel genes may have arisen independently despite the close phylogenetic distance. We furthermore describe a reference guided assembly and an open genomic resource (CephRes gdatabase) opening new avenues in the study of genomic novelties in cephalopods and their biology. Type(s)species comparison design sequence analysis objective sequence assembly objectiveMeasurement Type(s)whole genome sequencing assayTechnology Type(s)DNA sequencingFactor Type(s) Sample Characteristic(s)Octopus vulgaris testis ocean biomeMachine accessible metadata file describing the reported data (ISA Tab format)

title: Other Minds The Octopus the Sea and the Deep Origins of Consciousness
abstract: This qualitative case study featured an interpretive approach to understanding the culture of a fire station utilizing participant observation and semi structured interviews. The goal of this study is to investigate the layer(s) of Complexity Leadership that are enacted and valued by organizational members to create an adaptive and collaborative work environment. It also aims to understand the role of organizational culture (Pacanowsky O'Donnell Trujillo, 1982) in creating the collective identity of the fire station. In addition, the study navigates the tension between this collective identity, individual specialization and fixed place in the hierarchy when dealing with unpredictability. The results suggest that firefighters construct their culture through the negotiation of three main elements, which are organizational structure, social structure and episodic unpredictability. The interactive sense making of these elements lays the ground for the collective identity through constructing a shared cognitive understanding of organizational reality, active relationships and emotional investment (Melucci, 1995) This helps firefighters navigate uncertainty and unpredictability at a micro level by self organization and formulation around specialization. In addition, the findings indicate that firefighters create an adaptive outcome at a macro level through the utilization of Administrative leadership (Uhl Bien, Marion, McKelvey, 2007) that enforces order yet practices Enabling Leadership to empower leaders. This empowerment allows the balance between order and presented social and professional chaos to maintain the level of complexity needed to deal with complex and unpredictable problems.

title: A Conserved Role for Serotonergic Neurotransmission in Mediating Social Behavior in Octopus
abstract: Human and octopus lineages are separated by over 500 million years of evolution [1, 2] and show divergent anatomical patterns of brain organization [3, 4] Despite these differences, growing evidence suggests that ancient neurotransmitter systems are shared across vertebrate and invertebrate species and in many cases enable overlapping functions  Sociality is widespread across the animal kingdom, with numerous examples in both invertebrate (e.g. bees, ants, termites, and shrimps) and vertebrate (e.g. fishes, birds, rodents, and primates) lineages [6] Serotonin is an evolutionarily ancient molecule [7] that has been implicated in regulating both invertebrate [8] and vertebrate [9] social behaviors, raising the possibility that this neurotransmitter's prosocial functions may be conserved across evolution. Members of the order Octopoda are predominantly asocial and solitary  Although at this time it is unknown whether serotonergic signaling systems are functionally conserved in octopuses, ethological studies indicate that agonistic behaviors are suspended during mating [11 13] suggesting that neural mechanisms subserving social behaviors exist in octopuses but are suppressed outside the reproductive period. Here we provide evidence that, as in humans, the phenethylamine 3,4 methylendioxymethamphetamine (MDMA) enhances acute prosocial behaviors in Octopus bimaculoides. This finding is paralleled by the evolutionary conservation of the serotonin transporter (SERT, encoded by the Slc6A4 gene) binding site of MDMA in the O. bimaculoides genome. Taken together, these data provide evidence that the neural mechanisms subserving social behaviors exist in O. bimaculoides and indicate that the role of serotonergic neurotransmission in regulating social behaviors is evolutionarily conserved.

title: The octopus genome and the evolution of cephalopod neural and morphological novelties
abstract: Coleoid cephalopods (octopus, squid and cuttlefish) are active, resourceful predators with a rich behavioural repertoire. They have the largest nervous systems among the invertebrates and present other striking morphological innovations including camera like eyes, prehensile arms, a highly derived early embryogenesis and a remarkably sophisticated adaptive colouration system. To investigate the molecular bases of cephalopod brain and body innovations, we sequenced the genome and multiple transcriptomes of the California two spot octopus, Octopus bimaculoides. We found no evidence for hypothesized whole genome duplications in the octopus lineage. The core developmental and neuronal gene repertoire of the octopus is broadly similar to that found across invertebrate bilaterians, except for massive expansions in two gene families previously thought to be uniquely enlarged in vertebrates: the protocadherins, which regulate neuronal development, and the C2H2 superfamily of zinc finger transcription factors. Extensive messenger RNA editing generates transcript and protein diversity in genes involved in neural excitability, as previously described, as well as in genes participating in a broad range of other cellular functions. We identified hundreds of cephalopod specific genes, many of which showed elevated expression levels in such specialized structures as the skin, the suckers and the nervous system. Finally, we found evidence for large scale genomic rearrangements that are closely associated with transposable element expansions. Our analysis suggests that substantial expansion of a handful of gene families, along with extensive remodelling of genome linkage and repetitive content, played a critical role in the evolution of cephalopod morphological innovations, including their large and complex nervous systems.

title: Octopus toolkit: a workflow to automate mining of public epigenomic and transcriptomic next generation sequencing data
abstract: Octopus toolkit is a stand alone application for retrieving and processing large sets of next generation sequencing (NGS) data with a single step. Octopus toolkit is an automated set up and analysis pipeline utilizing the Aspera, SRA Toolkit, FastQC, Trimmomatic, HISAT2, STAR, Samtools, and HOMER applications. All the applications are installed on the user's computer when the program starts. Upon the installation, it can automatically retrieve original files of various epigenomic and transcriptomic data sets, including ChIP seq, ATAC seq, DNase seq, MeDIP seq, MNase seq and RNA seq, from the gene expression omnibus data repository. The downloaded files can then be sequentially processed to generate BAM and BigWig files, which are used for advanced analyses and visualization. Currently, it can process NGS data from popular model genomes such as, human (Homo sapiens) mouse (Mus musculus) dog (Canis lupus familiaris) plant (Arabidopsis thaliana) zebrafish (Danio rerio) fruit fly (Drosophila melanogaster) worm (Caenorhabditis elegans) and budding yeast (Saccharomyces cerevisiae) genomes. With the processed files from Octopus toolkit, the meta analysis of various data sets, motif searches for DNA binding proteins, and the identification of differentially expressed genes and/or protein binding sites can be easily conducted with few commands by users. Overall, Octopus toolkit facilitates the systematic and integrative analysis of available epigenomic and transcriptomic NGS big data.

title: In vitro and in vivo anti diabetic and anti hyperlipidemic effects of protein hydrolysates from Octopus vulgaris in alloxanic rats.
abstract: This study aims to examine the effects of non hydrolyzed octopus (Octopus vulgaris) muscle proteins (NHOPs) and their hydrolysates (OPHs) on alloxan induced diabetes in Wistar rats (AIDR) Animals were allocated into seven groups of six rats each: control group (C) diabetic group (D) and diabetic rats treated with acarbose (D Acar) non hydrolyzed octopus proteins (D NHOPs) and octopus proteins hydrolysates (D OPHs) groups. The diabetic rats presented a significant increase in glycemic status such as a amylase activity (in plasma, pancreas and intestine) hepatic glycogen, blood glucose and glycated hemoglobin (HbA1c) levels, as well as a significant decrease in the levels of plasma insulin and total hemoglobin compared to control group. In addition, plasma and liver contents in total cholesterol, triglycerides and LDL cholesterol significantly increased in AIDR compared to control group. However, the daily administration of OPHs for 30 days improved the glucose tolerance test, the glycemic status of diabetic rats and corrected the lipid profiles. Further, a significant increase in the activities of alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase and gamma glutamyl transpeptidase as well as in the level of plasma bilirubin on diabetic status was observed, indicating considerable hepatocellular injury. OPHs treatment was found to attenuate the increased activities of the plasma enzymes produced by diabetes and caused a subsequent recovery towards normalization compared to the control group. By contrast, the NHOPs treatment was found to increase the glucose metabolic disorders in AIDR. These beneficial effects of OPHs were confirmed by histological findings in the hepatic and pancreatic tissues of diabetic treated rats. Indeed, they avoid lipid accumulation in the hepatocytes and protect the pancreatic b cells from degeneration. Our results thus suggest that OPHs may be helpful in the preventing from diabetic complications by reversing hepatotoxicity.

title: The genome of common long arm octopus Octopus minor
abstract: The common long arm octopus (Octopus minor) is found in mudflats of subtidal zones and faces numerous environmental challenges. The ability to adapt its morphology and behavioral repertoire to diverse environmental conditions makes the species a promising model for understanding genomic adaptation and evolution in cephalopods.  The final genome assembly of O. minor is 5.09 Gb, with a contig N50 size of 197 kb and longest size of 3.027 Mb, from a total of 419 Gb raw reads generated using the Pacific Biosciences RS II platform. We identified 30,010 genes; 44.43% of the genome is composed of repeat elements. The genome wide phylogenetic tree indicated the divergence time between O. minor and Octopus bimaculoides was estimated to be 43 million years ago based on single copy orthologous genes. In total, 178 gene families are expanded in O. minor in the 14 bilaterian species.  We found that the O. minor genome was larger than that of closely related O. bimaculoides, and this difference could be explained by enlarged introns and recently diversified transposable elements. The high quality O. minor genome assembly provides a valuable resource for understanding octopus genome evolution and the molecular basis of adaptations to mudflats.

title: An integrative taxonomic approach reveals Octopus insularis as the dominant species in the Veracruz Reef System (southwestern Gulf of Mexico)
abstract: The common octopus of the Veracruz Reef System (VRS, southwestern Gulf of Mexico) has historically been considered as Octopus vulgaris, and yet, to date, no study including both morphological and genetic data has tested that assumption. To assess this matter, 52 octopuses were sampled in different reefs within the VRS to determine the taxonomic identity of this commercially valuable species using an integrative taxonomic approach through both morphological and genetic analyses. Morphological and genetic data confirmed that the common octopus of the VRS is not O. vulgaris and determined that it is, in fact, the recently described O. insularis. Morphological measurements, counts, indices, and other characteristics such as specific colour patterns, closely matched what had been reported for O. insularis in Brazil. In addition, sequences from cytochrome oxidase I (COI) and 16S ribosomal RNA (r16S) mitochondrial genes confirmed that the common octopus from the VRS is in the same highly supported clade as O. insularis from Brazil. Genetic distances of both mitochondrial genes as well as of cytochrome oxidase subunit III (COIII) and novel nuclear rhodopsin sequences for the species, also confirmed this finding (0 0.8% We discuss our findings in the light of the recent reports of octopus species misidentifications involving the members of the 'O. vulgaris species complex' and underscore the need for more morphological studies regarding this group to properly address the management of these commercially valuable and similar taxa.