Cephalopod genomics: a plan of strategies and organization

The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, "Paths to Cephalopod Genomics-Strategies, Choices, Organization," held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described in this white paper

Cephalopod genomics : a plan of strategies and organization

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Standards in Genomic Sciences 7 (2012): 175-188, doi:10.4056/sigs.3136559.The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, “Paths to Cephalopod Genomics- Strategies, Choices, Organization,” held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod molluscs. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described in this White Paper.The Catalysis Group Meeting was supported by the National Science Foundation through the National Evolutionary Synthesis Center (NESCent) under grant number NSF #EF-0905606

Cephalopod-omics: emerging fields and technologies in cephalopod biology

14 pages, 1 figure.-- This is an Open Access article distributed under the terms of the Creative Commons Attribution LicenseFew animal groups can claim the level of wonder that cephalopods instill in the minds of researchers and the general public. Much of cephalopod biology, however, remains unexplored: the largest invertebrate brain, difficult husbandry conditions, and complex (meta-)genomes, among many other things, have hindered progress in addressing key questions. However, recent technological advancements in sequencing, imaging, and genetic manipulation have opened new avenues for exploring the biology of these extraordinary animals. The cephalopod molecular biology community is thus experiencing a large influx of researchers, emerging from different fields, accelerating the pace of research in this clade. In the first post-pandemic event at the Cephalopod International Advisory Council (CIAC) conference in April 2022, over 40 participants from all over the world met and discussed key challenges and perspectives for current cephalopod molecular biology and evolution. Our particular focus was on the fields of comparative and regulatory genomics, gene manipulation, single-cell transcriptomics, metagenomics, and microbial interactions. This article is a result of this joint effort, summarizing the latest insights from these emerging fields, their bottlenecks, and potential solutions. The article highlights the interdisciplinary nature of the cephalopod-omics community and provides an emphasis on continuous consolidation of efforts and collaboration in this rapidly evolving fieldPeer reviewe

Calcium imaging data from: Functional organization of visual responses in the octopus optic lobe

Cephalopods are highly visual animals with camera-type eyes, large brains, and a rich repertoire of visually guided behaviors. However, the cephalopod brain evolved independently from that of other highly visual species, such as vertebrates, and therefore the neural circuits that process sensory information are profoundly different. It is largely unknown how their powerful but unique visual system functions, since there have been no direct neural measurements of visual responses in the cephalopod brain. In this study, we used two-photon calcium imaging to record visually evoked responses in the primary visual processing center of the octopus central brain, the optic lobe, to determine how basic features of the visual scene are represented and organized. We found spatially localized receptive fields for light (ON) and dark (OFF) stimuli, which were retinotopically organized across the optic lobe, demonstrating a hallmark of visual system organization shared across many species. Examination of these responses revealed transformations of the visual representation across the layers of the optic lobe, including the emergence of the OFF pathway and increased size selectivity. We also identified asymmetries in the spatial processing of ON and OFF stimuli, which suggest unique circuit mechanisms for form processing that may have evolved to suit the specific demands of processing an underwater visual scene. This study provides insight into the neural processing and functional organization of the octopus visual system, highlighting both shared and unique aspects, and lays a foundation for future studies of the neural circuits that mediate visual processing and behavior in cephalopods.Data files are in Matlab .mat format, which is based on HDF5 and is readable across languages.Funding provided by: National Institute of Neurological Disorders and StrokeCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000065Award Number: 1R01NS118466-01Funding provided by: Office of Naval ResearchCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000006Award Number: N00014-21-1-2426Calcium imaging was performed with a two-photon microscope (Neurolabware Inc.), using a 16X Nikon CFI75 LWD objective, via the Scanbox software package for Matlab (MATHWORKS). Data were acquired at a 10Hz framerate, with an 800x800μm (796x796 pixel) field of view. Recordings were taken at 90 to 170μm depths from the dorsal surface of the optic lobe. Custom generated visual stimuli, rendered using the PsychToolbox package for Matlab72, were displayed with a pico LCD projector (AAXA Technologies) onto the diffusing glass on the side of the recording chamber. To avoid light from the stimulus entering the two-photon detection pathway, the projected light was passed through a 450/50 bandpass filter (Chroma Technology Corporation), avoiding overlap with the emission spectrum of the Cal-520 calcium dye and the bandpass 525/50 emission filter of the microscope. The stimulus bandpass filter also restricted the stimulus light to be within the known absorption spectrum of cephalopod photopigments26. Stimuli were gamma-corrected in software and presented at 60FPS. Full RF mapping was performed using a sparse noise stimulus, consisting of white and black spots (radius = 3, 6, 12 deg; density = 10%) on a gray (50% luminance) background, along with full-field white or black on 2% of frames. Each stimulus frame was presented for 1sec in a randomized order for a total duration of 10min. Data analysis was performed using custom software in MATLAB. We applied a rigid alignment of imaging data using the sbxalign function in Scanbox (Neurolabware, Inc.). In order to detect large movements that were not corrected by the alignment algorithm, for each frame we calculated the pixel-wise correlation coefficient to the mean image. Frames with less that 90% correlation were discarded from further analyses. We calculated the fluorescence activity (dF/F0) at each pixel as the standard (F(t) - F0) / F0, where F(t) is the fluorescence intensity of the pixel on each frame and F0 is the median fluorescence intensity of the pixel across the recording. To analyze local responses, we defined "units" as a 20μmx20μm wide square window, centered on local peaks within the mean fluorescence that were above the background fluorescence, to ensure that only areas with sufficient dye loading were analyzed. dF/F0 for each unit was calculated as the mean dF/F0 across pixels within the unit. Units were manually assigned to anatomical layers (OGL, IGL, Plex, and Med) based on location within the mean fluorescence image from the recording session

Analytical performances of lipophilic diamides based alkaline earth ion‐selective electrodes

Based on complex chemical considerations, lipophilic diamide derivatives have been designed and synthesized as ionophores for liquid membrane electrodes. The structure‐selectivity studies revealed that the majority of the ligands exhibit calcium ion selectivity, except the compound bis‐N,N‐dicyclohexyl‐malonamide. The latter has an almost equal selectivity for Ca2+ and Mg2+ and sufficiently rejects sodium ions, thus it lends itself to water hardness measurements. Copyright © 1993 VCH Publishers, Inc

Novel bis (crown ether)-based potassium sensor for biological applications

Based on structure-selectivity studies on bis-benzo-crown ether derivatives, 2,2′-bis[3,4-(15-crown-5)-2-nitrophenylcarbamoxymethyl]tetradecane (BME-44) was designed and synthesized. The performance characteristics of this new, highly lipophilic ionophore of the group of bis-nitrobenzo-15-crown-5 derivatives with urethane linkage when used in liquid membrane electrodes are evaluated with special regard to the requirements of biological and clinical applications. Potentiometric steady-state and flow-through dynamic data are presented to prove the sensor capabilities for clinical and physiological potassium determinations. © 1990 Springer-Verlag

Membrane Technology and Dynamic Response of Ion-Selective Liquid-Membrane Electrodes

In order to study the parameters affecting the dynamic response behavior of neutral-carrier-based liquid-membrane electrodes, the potential response vs time curves of Na+-, Ca2+-, and Mg2+-selective electrodes with different membrane compositions were recorded. The effects of the lipophllicity of lonophores and plasticizers, of the presence of incorporated mobile anionic sites and of modifications of the membrane matrix were Investigated. The experimental potential-time curves were compared to fitted functions on the basis of theoretical models. © 1991, American Chemical Society. All rights reserved

Responses of H\u3csup\u3e+\u3c/sup\u3e selective solvent polymeric membrane electrodes fabricated from modified PVC membranes

Potentiometric responses of a novel class of pH sensitive ionophores, namely several phenoxazine derivatives, were tested in different modified PVC matrices. The ionophores were compounded into liquid membranes as usual or were covalently coupled to the polymeric matrix. The general analytical performance of the membranes and other membrane characteristics (i.e., resistance and response time, as measures of membrane decomposition or structural changes) were followed in time. The transient responses of membranes with mobile ionophores in high molecular weight (HMW) and carboxylated PVC (PVC-COOH) were compared to those with immobilized ionophores. The response time of membranes with immobilized ionophores was found to be between those with mobile ionophores in HMW (fast response) and PVC-COOH (sluggish response). Accordingly, the rate of response was correlated primarily to the -COOH content of the membranes. © 1993