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Proteomic Responses to Ocean Acidification in the Brain of Juvenile Coral Reef Fish
Get PDFElevated CO₂ levels predicted to occur by the end of the century can affect the physiology and behavior of marine fishes. For one important survival mechanism, the response to chemical alarm cues from conspecifics, substantial among-individual variation in the extent of behavioral impairment when exposed to elevated CO₂ has been observed in previous studies. Whole brain transcriptomic data has further emphasized the importance of parental phenotypic variation in the response of juvenile fish to elevated CO₂. In this study, we investigate the genome-wide proteomic responses of this variation in the brain of 5-week old spiny damselfish, Acanthochromis polyacanthus. We compared the accumulation of proteins in the brains of juvenile A. polyacanthus from two different parental behavioral phenotypes (sensitive and tolerant) that had been experimentally exposed to short-term, long-term and inter-generational elevated CO₂. Our results show differential accumulation of key proteins related to stress response and epigenetic markers with elevated CO₂ exposure. Proteins related to neurological development and glucose metabolism were also differentially accumulated particularly in the long-term developmental treatment, which might be critical for juvenile development. By contrast, exposure to elevated CO₂ in the parental generation resulted in only three differentially accumulated proteins in the offspring, revealing potential for inter -generational acclimation. Lastly, we found a distinct proteomic pattern in juveniles due to the behavioral sensitivity of parents to elevated CO₂, even though the behavior of the juvenile fish was impaired regardless of parental phenotype. Our data shows that developing juveniles are affected in their brain protein accumulation by elevated CO₂, but the effect varies with the length of exposure as well as due to variation of parental phenotypes in the population.journal articl
Firing rate-dependent phase responses of Purkinje cells support transient oscillations
Get PDFBoth spike rate and timing can transmit information in the brain. Phase response curves (PRCs) quantify how a neuron transforms input to output by spike timing. PRCs exhibit strong firing-rate adaptation, but its mechanism and relevance for network output are poorly understood. Using our Purkinje cell (PC) model, we demonstrate that the rate adaptation is caused by rate-dependent subthreshold membrane potentials efficiently regulating the activation of Na(+) channels. Then, we use a realistic PC network model to examine how rate-dependent responses synchronize spikes in the scenario of reciprocal inhibition-caused high-frequency oscillations. The changes in PRC cause oscillations and spike correlations only at high firing rates. The causal role of the PRC is confirmed using a simpler coupled oscillator network model. This mechanism enables transient oscillations between fast-spiking neurons that thereby form PC assemblies. Our work demonstrates that rate adaptation of PRCs can spatio-temporally organize the PC input to cerebellar nuclei.journal articl
Dynamic Pd(II) /Cu(I) Multimetallic Assemblies as Molecular Models to Study Metal-Metal Cooperation in Sonogashira Coupling
Get PDFCooperation between two different metals plays a crucial role in many synergistic catalytic reactions, such as the Sonogashira C-C cross-coupling reaction, where an interaction between the Pd and Cu centers is proposed in the transmetalation step. Although several heterobimetallic Pd/Cu complexes were proposed as structural models of the active species in Sonogashira coupling, the detailed understanding of the metal-metal cooperation in transmetalation is still lacking in current systems. In this work, we report a stepwise and systematic approach to building heteromultimetallic Pd/Cu assemblies as a tool to study metal-metal cooperativity. We obtained fully characterized Pd/Cu multimetallic assemblies that show reactivity in alkyne activation, formation of catalytically relevant aryl/acetylide species, and C-C elimination, serving as functional models for Sonogashira reaction intermediates. The combined experimental and DFT studies highlight the importance of ligand-controlled coordination geometry, metal-metal distances and dynamics of the multimetallic assembly for transmetalation step.journal articl
Microtubule and Actin Differentially Regulate Synaptic Vesicle Cycling to Maintain High-Frequency Neurotransmission
Get PDFCytoskeletal filaments such as microtubules (MTs) and filamentous actin (F-actin) dynamically support cell structure and functions. In central presynaptic terminals, F-actin is expressed along the release edge and reportedly plays diverse functional roles, but whether axonal MTs extend deep into terminals and play any physiological role remains controversial. At the calyx of Held in rats of either sex, confocal and high-resolution microscopy revealed that MTs enter deep into presynaptic terminal swellings and partially colocalize with a subset of synaptic vesicles (SVs). Electrophysiological analysis demonstrated that depolymerization of MTs specifically prolonged the slow-recovery time component of EPSCs from short-term depression induced by a train of high-frequency stimulation, whereas depolymerization of F-actin specifically prolonged the fast-recovery component. In simultaneous presynaptic and postsynaptic action potential recordings, depolymerization of MTs or F-actin significantly impaired the fidelity of high-frequency neurotransmission. We conclude that MTs and F-actin differentially contribute to slow and fast SV replenishment, thereby maintaining high-frequency neurotransmission.journal articl
The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins
Get PDFSnakebite envenoming is a serious and neglected tropical disease that kills ~100,000 people annually. High-quality, genome-enabled comprehensive characterization of toxin genes will facilitate development of effective humanized recombinant antivenom. We report a de novo near-chromosomal genome assembly of Naja naja, the Indian cobra, a highly venomous, medically important snake. Our assembly has a scaffold N50 of 223.35 Mb, with 19 scaffolds containing 95% of the genome. Of the 23,248 predicted protein-coding genes, 12,346 venom-gland-expressed genes constitute the 'venom-ome' and this included 139 genes from 33 toxin families. Among the 139 toxin genes were 19 'venom-ome-specific toxins' (VSTs) that showed venom-gland-specific expression, and these probably encode the minimal core venom effector proteins. Synthetic venom reconstituted through recombinant VST expression will aid in the rapid development of safe and effective synthetic antivenom. Additionally, our genome could serve as a reference for snake genomes, support evolutionary studies and enable venom-driven drug discovery.journal articl
Measurement of the integrated luminosity of the Phase 2 data of the Belle II experiment
Get PDFFrom April to July 2018, a data sample at the peak energy of the resonance was collected with the Belle II detector at the SuperKEKB electron-positron collider. This is the first data sample of the Belle II experiment. Using Bhabha and digamma events, we measure the integrated luminosity of the data sample to be (, where the first uncertainty is statistical and the second is systematic. This work provides a basis for future luminosity measurements at Belle II.journal articl
Intracellular Nanomaterial Delivery via Spiral Hydroporation
Get PDFIn recent nanobiotechnology developments, a wide variety of functional nanomaterials and engineered biomolecules have been created, and these have numerous applications in cell biology. For these nanomaterials to fulfill their promises completely, they must be able to reach their biological targets at the subcellular level and with a high level of specificity. Traditionally, either nanocarrier- or membrane disruption-based method has been used to deliver nanomaterials inside cells; however, these methods are suboptimal due to their toxicity, inconsistent delivery, and low throughput, and they are also labor intensive and time-consuming, highlighting the need for development of a next-generation, intracellular delivery system. This study reports on the development of an intracellular nanomaterial delivery platform, based on unexpected cell-deformation phenomena via spiral vortex and vortex breakdown exerted in the cross- and T-junctions at moderate Reynolds numbers. These vortex-induced cell deformation and sequential restoration processes open cell membranes transiently, allowing effective and robust intracellular delivery of nanomaterials in a single step without the aid of carriers or external apparatus. By using the platform described here (termed spiral hydroporator), we demonstrate the delivery of different nanomaterials, including gold nanoparticles (200 nm diameter), functional mesoporous silica nanoparticles (150 nm diameter), dextran (hydrodynamic diameters between 2–55 nm), and mRNA, into different cell types. We demonstrate here that the system is highly efficient (up to 96.5%) with high throughput (up to 1 × 106 cells/min) and rapid delivery (∼1 min) while maintaining high levels of cell viability (up to 94%).journal articl
From Far-Field to Near-Field Micro- and Nanoparticle Optical Trapping
Get PDFOptical tweezers are a very well-established technique that have developed into a standard tool for trapping and manipulating micron and submicron particles with great success in the last decades. Although the nature of light enforces restrictions on the minimum particle size that can be efficiently trapped due to Abbe’s diffraction limit, scientists have managed to overcome this problem by engineering new devices that exploit near-field effects. Nowadays, metallic nanostructures can be fabricated which, under laser illumination, produce a secondary plasmonic field that does not suffer from the diffraction limit. This advance offers a great improvement in nanoparticle trapping, as it relaxes the trapping requirements compared to conventional optical tweezers although problems may arise due to thermal heating of the metallic nanostructures. This could hinder efficient trapping and damage the trapped object. In this work, we review the fundamentals of conventional optical tweezers, the so-called plasmonic tweezers, and related phenomena. Starting from the conception of the idea by Arthur Ashkin until recent improvements and applications, we present the principles of these techniques along with their limitations. Emphasis in this review is on the successive improvements of the techniques and the innovative aspects that have been devised to overcome some of the main challenges.journal articl
Novel genomic resources for shelled pteropods: a draft genome and target capture probes for Limacina bulimoides, tested for cross-species relevance
Get PDFBACKGROUND: Pteropods are planktonic gastropods that are considered as bio-indicators to monitor impacts of ocean acidification on marine ecosystems. In order to gain insight into their adaptive potential to future environmental changes, it is critical to use adequate molecular tools to delimit species and population boundaries and to assess their genetic connectivity. We developed a set of target capture probes to investigate genetic variation across their large-sized genome using a population genomics approach. Target capture is less limited by DNA amount and quality than other genome-reduced representation protocols, and has the potential for application on closely related species based on probes designed from one species.
RESULTS: We generated the first draft genome of a pteropod, Limacina bulimoides, resulting in a fragmented assembly of 2.9 Gbp. Using this assembly and a transcriptome as a reference, we designed a set of 2899 genome-wide target capture probes for L. bulimoides. The set of probes includes 2812 single copy nuclear targets, the 28S rDNA sequence, ten mitochondrial genes, 35 candidate biomineralisation genes, and 41 non-coding regions. The capture reaction performed with these probes was highly efficient with 97% of the targets recovered on the focal species. A total of 137,938 single nucleotide polymorphism markers were obtained from the captured sequences across a test panel of nine individuals. The probes set was also tested on four related species: L. trochiformis, L. lesueurii, L. helicina, and Heliconoides inflatus, showing an exponential decrease in capture efficiency with increased genetic distance from the focal species. Sixty-two targets were sufficiently conserved to be recovered consistently across all five species.
CONCLUSION: The target capture protocol used in this study was effective in capturing genome-wide variation in the focal species L. bulimoides, suitable for population genomic analyses, while providing insights into conserved genomic regions in related species. The present study provides new genomic resources for pteropods and supports the use of target capture-based protocols to efficiently characterise genomic variation in small non-model organisms with large genomes.journal articl