Slack Channels Research Articles

Slack potassium channels in spinal dorsal horn neurons control neuropathic pain and acute itch.

The sodium-activated potassium channel Slack (KNa1.1, Kcnt1) plays a critical role in tuning neuronal excitability. Previous studies have revealed that Slack is expressed in neurons of the superficial dorsal horn of the spinal cord. However, the precise role of Slack in spinal dorsal horn neurons is unclear. In this study, we used mice in which Slack is conditionally ablated in spinal dorsal horn neurons (Lbx1-Slack-/- mice) and analyzed their behaviors in various models of pain and itch. Lbx1-Slack-/- mice exhibited increased neuropathic pain behavior after peripheral nerve injury but normal responses in a model of inflammatory pain. Unexpectedly, Lbx1-Slack-/- mice demonstrated increased scratching after intradermal injection of chloroquine, LY344864, and histamine. Moreover, neuromedin B receptors are coexpressed with Slack in the dorsal horn, and scratching after intrathecal delivery of neuromedin B was increased in Lbx1-Slack-/- mice. Our study provides in vivo evidence that Slack expressed in spinal dorsal horn neurons inhibits nerve injury-induced allodynia and acute itch induced by various pruritogens.

Carvedilol inhibits neuronal hyperexcitability caused by epilepsy-associated KCNT1 mutations.

KCNT1 encodes a sodium-activated potassium channel (Slack channel), and its mutation can cause several forms of epilepsy. Traditional antiepileptic medications have limited efficacy in treating patients with KCNT1 mutations. Here, we describe one heterozygous KCNT1 mutation, M267T, in a patient with EIMFS. The pathological channel properties of this mutation and its effect on neuronal excitability were investigated. Additionally, this study aimed to develop a medication for effective prevention of KCNT1 mutation-induced seizures. Wild-type or mutant KCNT1 plasmids were expressed heterologously in Xenopus laevis oocytes, and channel property assessment and drug screening were performed based on two-electrode voltage-clamp recordings. The single-channel properties were investigated using the excised inside-out patches from HEK293T cells. Through in utero electroporation, WT and M267T Slack channels were expressed in the hippocampal CA1 pyramidal neurons in male mice, followed by the examination of the electrical properties using the whole-cell current-clamp technique. The kainic acid-induced epilepsy model in male mice was used to evalute the antiseizure effects of carvedilol. The KCNT1 M267T mutation enhanced Slack channel function by increasing single-channel open probability. Through screening 16 FDA-approved ion channel blockers, we found that carvedilol effectively reversed the mutation-induced gain-of-function channel properties. Notably, the KCNT1 M267T mutation in the mouse hippocampal CA1 pyramidal neurons affected afterhyperpolarization properties and induced neuronal hyperexcitability, which was inhibited by carvedilol. Additionally, carvedilol exhibited antiseizure effects in the kainic acid-induced epilepsy model. Our findings suggest carvedilol as a new potential candidate for treatment of epilepsies.

Slack Channels as Key Regulators of Neuronal Excitability: Implications for Neural Function and the Link to Epilepsy Pathogenesis

The Slack channel encoded by the KCNT1 gene is a sodium-activated potassium channel. By regulating the flow of potassium ions, the Slack channel affects the membrane potential and discharge activity of neurons, thus participating in regulating neuronal excitability. Therefore, it plays a crucial role in maintaining the normal function of the nervous system. Consequently, abnormal Slack channel function is closely linked to various neurological diseases, such as epilepsy. Currently, quinidine-based medication therapy and neuroregulatory therapy are key components of the treatment of epilepsy resulting from Slack channel dysfunction. This article aims to outline the fundamental features of the Slack channel while providing a thorough analysis of the main distinctions and possible connections between Slick and Slack channels. Furthermore, this study focuses on the function of controlling the neuronal excitability of Slack channels while delving deeper into the potential correlation between Slack channels and epilepsy and their treatment strategies.

Developing a High Velocity Dataset Quality Checking Pipeline

ObjectiveThe volume and frequency of refreshed data within the [organisation] has increased significantly since the beginning of the COVID-19 pandemic. Therefore, a more efficient data quality (DQ) checking process was necessary. Approach Having previously developed an automated DQ checking tool, the focus was on re-engineering the process of DQ task allocation and communication of results. Results 5 analysts were trained in DQ checking. A JIRA workflow tracks the management of data loading. When a dataset is ready for DQ, the Data Manager allocates a ticket to the DQ Lead who then allocates it onto one of the 5 analysts. Via a DQ Slack channel, the analyst is informed and acknowledges receipt of the task. On completion of DQ, the analyst updates the ticket and transfers it to the appropriate workflow stage. Passed DQ tickets are transferred to the Data Manager for data release, whereas failed ones are placed “On Hold”. The DQ Lead triages the issues and liaises with relevant parties for resolution, which may require data amendments. On receipt of amended data, the DQ ticket is transferred back to the queue and the analyst is notified to re-check the data. ConclusionsThe team now complete a high volume of DQ checks efficiently. In 2023, 405 datasets, containing 1716 tables, were quality checked, with the initial DQ taking, on average, 2.6 days. Implications The improved speed of DQ checking ensures projects access the latest available data whilst maintaining the expected DQ levels, integrity and reputation of the TRE.

Dissemination of agricultural knowledge using a collaborative multidisciplinary co-creation platform: a case study

ABSTRACT This work defines a framework for agricultural learning based on university-led collaborative co-creation vehicles such as multidisciplinary innovation platforms. This work compares the scope of dissemination and learning strategies of European research projects with the use of an innovation and co-creation training platform boasting an attractive central theme that integrates different online activities, social media, webinars, podcasts, slack channel, online courses and, after COVID-19, face-to-face field days. The materials to be disseminated are created and transmitted by farmers, technicians, researchers, … The farmer is linked to a platform of a current topic, which involves coordination from the university, with no commercial aspects and free for users. The platform, after 3 years in operation, has more than 90,000 annual views from 10 countries. Comparing with the best answer in research project dissemination, the platform has 94%, 25% and 50% more users in LinkedIn, Facebook and Instagram, respectively. Users value the usefulness of the webinars and blog. With these results, we want to show agricultural communicators and dissemination agents of research projects, that there are more efficient ways of dissemination, not only social media or conferences focused only on project results.

Structure-Activity Relationship Studies in a Series of Xanthine Inhibitors of SLACK Potassium Channels.

Gain-of-function mutations in the KCNT1 gene, which encodes the sodium-activated potassium channel known as SLACK, are associated with the rare but devastating developmental and epileptic encephalopathy known as epilepsy of infancy with migrating focal seizures (EIMFS). The design of small molecule inhibitors of SLACK channels represents a potential therapeutic approach to the treatment of EIMFS, other childhood epilepsies, and developmental disorders. Herein, we describe a hit optimization effort centered on a xanthine SLACK inhibitor (8) discovered via a high-throughput screen. Across three distinct regions of the chemotype, we synthesized 58 new analogs and tested each one in a whole-cell automated patch-clamp assay to develop structure-activity relationships for inhibition of SLACK channels. We further evaluated selected analogs for their selectivity versus a variety of other ion channels and for their activity versus clinically relevant SLACK mutants. Selectivity within the series was quite good, including versus hERG. Analog 80 (VU0948578) was a potent inhibitor of WT, A934T, and G288S SLACK, with IC50 values between 0.59 and 0.71 µM across these variants. VU0948578 represents a useful in vitro tool compound from a chemotype that is distinct from previously reported small molecule inhibitors of SLACK channels.

Disease-causing Slack potassium channel mutations produce opposite effects on excitability of excitatory and inhibitory neurons

The KCNT1 gene encodes the sodium-activated potassium channel Slack (KCNT1, KNa1.1), a regulator of neuronal excitability. Gain-of-function mutations in humans cause cortical network hyperexcitability, seizures, and severe intellectual disability. Using a mouse model expressing the Slack-R455H mutation, we find that Na+-dependent K+ (KNa) and voltage-dependent sodium (NaV) currents are increased in both excitatory and inhibitory cortical neurons. These increased currents, however, enhance the firing of excitability neurons but suppress that of inhibitory neurons. We further show that the expression of NaV channel subunits, particularly that of NaV1.6, is upregulated and that the length of the axon initial segment and of axonal NaV immunostaining is increased in both neuron types. Our study on the coordinate regulation of KNa currents and the expression of NaV channels may provide an avenue for understanding and treating epilepsies and other neurological disorders.

The gain-of-function mutants of the Slo1 and Slack channels cause epilepsy through different neural circuits

The gain-of-function mutants of the Slo1 and Slack channels cause epilepsy through different neural circuits

Exploration of support for Black, Indigenous, and people of color students in genetic counseling programs.

Students in higher education who identify as Black, Indigenous, and people of color (BIPOC) experience racism, discrimination, and microaggressions through tokenization, hypervisibility, invisibility, and marginalization. The experiences of BIPOC genetic counseling students with curriculum, clinical training, and sense of belonging also differ. Therefore, there is a large need for understanding how support is defined by BIPOC genetic counseling students, and then how to integrate specific aspects of training into a practical framework for programs to address racism and the resulting emotional implications. This study aimed to define current practices of support and identify gaps in genetic counseling programs as described by BIPOC students. BIPOC genetic counseling students (N = 40) were recruited through Listserv, social media, and Slack channels to complete an online survey eliciting demographic data, perspectives on support, and available support resources. The online survey consisted of 22 open- and closed-ended questions. Data were collected over a 5-week period. Open-ended responses were coded by thematic analysis and audited. The top three supports were as follows: (1) presence of other BIPOC students; (2) presence of BIPOC faculty; and (3) financial funding. Participants' individual definitions of support indicated that each student defined support in a unique way. Most participants defined understanding and empathy stemming from peers, supervisors, and faculty within the program setting as important aspects of overall support. The majority of participants felt somewhat or strongly supported in areas of training. The area with the least support was within rotation/fieldwork experiences. Programs should consider social- and program-level support combined with emotional support. Individualized support for every student is needed while avoiding assumptions about their identity and support needs. Training programs may consider a balance of efforts to prioritize recruiting more BIPOC faculty and students and providing the outlined support and funding resources for their students.

Interaction Between HCN and Slack Channels Regulates mPFC Pyramidal Cell Excitability in Working Memory Circuits.

The ability of monkeys and rats to carry out spatial working memory tasks has been shown to depend on the persistent firing of pyramidal cells in the prefrontal cortex (PFC), arising from recurrent excitatory connections on dendritic spines. These spines express hyperpolarization-activated cyclic nucleotide-gated (HCN) channels whose open state is increased by cAMP signaling, and which markedly alter PFC network connectivity and neuronal firing. In traditional neural circuits, activation of these non-selective cation channels leads to neuronal depolarization and increased firing rate. Paradoxically, cAMP activation of HCN channels in PFC pyramidal cells reduces working memory-related neuronal firing. This suggests that activation of HCN channels may hyperpolarize rather than depolarize these neurons. The current study tested the hypothesis that Na+ influx through HCN channels activates Slack Na+-activated K+ (KNa) channels to hyperpolarize the membrane. We have found that HCN and Slack KNa channels co-immunoprecipitate in cortical extracts and that, by immunoelectron microscopy, they colocalize at postsynaptic spines of PFC pyramidal neurons. A specific blocker of HCN channels, ZD7288, reduces KNa current in pyramidal cells that express both HCN and Slack channels, but has no effect on KNa currents in an HEK cell line expressing Slack without HCN channels, indicating that blockade of HCN channels in neurons reduces K+ current indirectly by lowering Na+ influx. Activation of HCN channels by cAMP in a cell line expressing a Ca2+ reporter results in elevation of cytoplasmic Ca2+, but the effect of cAMP is reversed if the HCN channels are co-expressed with Slack channels. Finally, we used a novel pharmacological blocker of Slack channels to show that inhibition of Slack in rat PFC improves working memory performance, an effect previously demonstrated for blockers of HCN channels. Our results suggest that the regulation of working memory by HCN channels in PFC pyramidal neurons is mediated by an HCN-Slack channel complex that links activation HCN channels to suppression of neuronal excitability.

A community-endorsed open-source lexicon for contrast agent-based perfusion MRI: A consensus guidelines report from the ISMRM Open Science Initiative for Perfusion Imaging (OSIPI).

This manuscript describes the ISMRM OSIPI (Open Science Initiative for Perfusion Imaging) lexicon for dynamic contrast-enhanced and dynamic susceptibility-contrast MRI. The lexicon was developed by Taskforce 4.2 of OSIPI to provide standardized definitions of commonly used quantities, models, and analysis processes with the aim of reducing reporting variability. The taskforce was established in February 2020 and consists of medical physicists, engineers, clinicians, data and computer scientists, and DICOM (Digital Imaging and Communications in Medicine) standard experts. Members of the taskforce collaborated via a slack channel and quarterly virtual meetings. Members participated by defining lexicon items and reporting formats that were reviewed by at least two other members of the taskforce. Version 1.0.0 of the lexicon was subject to open review from the wider perfusion imaging community between January and March 2022, and endorsed by the Perfusion Study Group of the ISMRM in the summer of 2022. The initial scope of the lexicon was set by the taskforce and defined such that it contained a basic set of quantities, processes, and models to enable users to report an end-to-end analysis pipeline including kinetic model fitting. We also provide guidance on how to easily incorporate lexicon items and definitions into free-text descriptions (e.g., in manuscripts and other documentation) and introduce an XML-based pipeline encoding format to encode analyses using lexicon definitions in standardized and extensible machine-readable code. The lexicon is designed to be open-source and extendable, enabling ongoing expansion of its content. We hope that widespread adoption of lexicon terminology and reporting formats described herein will increase reproducibility within the field.

Slack K+ channels limit kainic acid-induced seizure severity in mice by modulating neuronal excitability and firing

Mutations of the Na+-activated K+ channel Slack (KCNT1) are associated with terrible epilepsy syndromes that already begin in infancy. Here we report increased severity of acute kainic acid-induced seizures in adult and juvenile Slack knockout mice (Slack−/−) in vivo. Fittingly, we find exacerbation of cell death following kainic acid exposure in organotypic hippocampal slices as well as dissociated hippocampal cultures from Slack−/− in vitro. Furthermore, in cultured Slack−/− neurons, kainic acid-triggered Ca2+ influx and K+ efflux as well as depolarization-induced tetrodotoxin-sensitive inward currents are higher compared to the respective controls. This apparent changes in ion homeostasis could possibly explain altered action potential kinetics of Slack−/− neurons: steeper rise slope, decreased threshold, and duration of afterhyperpolarization, which ultimately lead to higher action potential frequencies during kainic acid application or injection of depolarizing currents. Based on our data, we propose Slack as crucial gatekeeper of neuronal excitability to acutely limit seizure severity.

Design, synthesis, and biological evaluation of a novel series of 1,2,4-oxadiazole inhibitors of SLACK potassium channels: Identification of in vitro tool VU0935685

Malignant migrating partial seizure of infancy (MMPSI) is a devastating and pharmacoresistant form of infantile epilepsy. MMPSI has been linked to multiple gain-of-function (GOF) mutations in the KCNT1 gene, which encodes for a potassium channel often referred to as SLACK. SLACK channels are sodium-activated potassium channels distributed throughout the central nervous system (CNS) and the periphery. The investigation described here aims to discover SLACK channel inhibitor tool compounds and profile their pharmacokinetic and pharmacodynamic properties. A SLACK channel inhibitor VU0531245 (VU245) was identified via a high-throughput screen (HTS) campaign. Structure-activity relationship (SAR) studies were conducted in five distinct regions of the hit VU245. VU245 analogs were evaluated for their ability to affect SLACK channel activity using a thallium flux assay in HEK-293 cells stably expressing wild-type (WT) human SLACK. Selected analogs were tested for metabolic stability in mouse liver microsomes and plasma-protein binding in mouse plasma. The same set of analogs was tested via thallium flux for activity versus human A934T SLACK and other structurally related potassium channels, including SLICK and Maxi-K. In addition, potencies for selected VU245 analogs were obtained using whole-cell electrophysiology (EP) assays in CHO cells stably expressing WT human SLACK through an automated patch clamp system. Results revealed that this scaffold tolerates structural changes in some regions, with some analogs demonstrating improved SLACK inhibitory activity, good selectivity against the other channels tested, and modest improvements in metabolic clearance. Analog VU0935685 represents a new, structurally distinct small-molecule inhibitor of SLACK channels that can serve as an in vitro tool for studying this target.

The Journey to a TDWG Mappings Task Group and its Plans for the Future

Some Biodiversity Information Standards (TDWG) standards have had mappings to other standards for years or even decades. However each standard is using its own approach to documenting those mappings, some are incomplete and often hard to find. There is no TDWG recommended approach for how mappings should be documented, like the Standards Documentation Standard (SDS) does for the standards themselves. During TDWG 2022 in Sofia, Bulgaria, the topic of mapping between standards was mentioned several times throughout the conference, which led to an impromptu discussion about standards mappings at the Unconference slot on the last conference day. Afterwards a dedicated Slack channel within the TDWG Slack workspace was added to continue the conversation (#mappings-between-standards). During further discussions, both within the Technical Architecture Group (TAG) of TDWG and during separate video conferences on the topic, it was decided to form a dedicated task group under the umbrella of the TAG. This task group is still in the process of formation. The goal of the group is to review the current state of mappings for TDWG standards, align approaches by the different standards to foster interoperability and give recommendations for current and future standards on how to specify mappings. Further work to define the strategy and scope for achieving these goals is needed, particularly to gain community input and acceptance. Consideration has been given to a range of possible types of mappings, which serve the different use cases and expectations for mappings such as machine actionability and improved documentation of the TDWG standards landscape to aid user understanding and implementation. In this talk we will show the work that has already been done, outline our planned steps and invite the community to give input on our process.

Nf-core/clipseq - a robust Nextflow pipeline for comprehensive CLIP data analysis.

Crosslinking and immunoprecipitation (CLIP) technologies have become a central component of the molecular biologists' toolkit to study protein-RNA interactions and thus to uncover core principles of RNA biology. There has been a proliferation of CLIP-based experimental protocols, as well as computational tools, especially for peak-calling. Consequently, there is an urgent need for a well-documented bioinformatic pipeline that enshrines the principles of robustness, reproducibility, scalability, portability and flexibility while embracing the diversity of experimental and computational CLIP tools. To address this, we present nf-core/clipseq - a robust Nextflow pipeline for quality control and analysis of CLIP sequencing data. It is part of the international nf-core community effort to develop and curate a best-practice, gold-standard set of pipelines for data analysis. The standards enabled by Nextflow and nf-core, including workflow management, version control, continuous integration and containerisation ensure that these key needs are met. Furthermore, multiple tools are implemented ( e.g. for peak-calling), alongside visualisation of quality control metrics to empower the user to make their own informed decisions based on their data. nf-core/clipseq remains under active development, with plans to incorporate newly released tools to ensure that pipeline remains up-to-date and relevant for the community. Engagement with users and developers is encouraged through the nf-core GitHub repository and Slack channel to promote collaboration. It is available at https://nf-co.re/clipseq.

Reproducible Speech Research With the Artificial Intelligence-Ready PERCEPT Corpora.

Publicly available speech corpora facilitate reproducible research by providing open-access data for participants who have consented/assented to data sharing among different research teams. Such corpora can also support clinical education, including perceptual training and training in the use of speech analysis tools. In this research note, we introduce the PERCEPT (Perceptual Error Rating for the Clinical Evaluation of Phonetic Targets) corpora, PERCEPT-R (Rhotics) and PERCEPT-GFTA (Goldman-Fristoe Test of Articulation), which together contain over 36 hr of speech audio (> 125,000 syllable, word, and phrase utterances) from children, adolescents, and young adults aged 6-24 years with speech sound disorder (primarily residual speech sound disorders impacting /ɹ/) and age-matched peers. We highlight PhonBank as the repository for the corpora and demonstrate use of the associated speech analysis software, Phon, to query PERCEPT-R. A worked example of research with PERCEPT-R, suitable for clinical education and research training, is included as an appendix. Support for end users and information/descriptive statistics for future releases of the PERCEPT corpora can be found in a dedicated Slack channel. Finally, we discuss the potential for PERCEPT corpora to support the training of artificial intelligence clinical speech technology appropriate for use with children with speech sound disorders, the development of which has historically been constrained by the limited representation of either children or individuals with speech impairments in publicly available training corpora. We demonstrate the use of PERCEPT corpora, PhonBank, and Phon for clinical training and research questions appropriate to child citation speech. Increased use of these tools has the potential to enhance reproducibility in the study of speech development and disorders.

An Invitation to Discomfort in Pursuit of Diversity, Inclusion, and Excellence

An Invitation to Discomfort in Pursuit of Diversity, Inclusion, and Excellence

Identification of sodium- and chloride-sensitive sites in the Slack channel.

The Slack channel (KCNT1, Slo2.2) is a sodium and chloride-activated potassium channel that regulates heart rate and maintains the normal excitability of the nervous system. Despite intense interest in the sodium gating mechanism, a comprehensive investigation to identify the sodium-sensitive and chloride-sensitive sites has been missing. In the present study, we identified two potential sodium-binding sites in the C-terminal domain of the rat Slack channel by conducting electrophysical recordings and systematic mutagenesis of cytosolic acidic residues in the rat Slack channel C-terminus. In particular, by taking advantage of the M335A mutant, which results in the opening of the Slack channel in the absence of cytosolic sodium, we found that among the screened ninety-two negatively charged amino acids, E373 mutants could completely remove sodium sensitivity of the Slack channel. In contrast, several other mutants showed dramatic decreases in sodium sensitivity but did not abolish it altogether. Furthermore, Molecular Dynamics (MD) simulations performed at the hundreds of nanoseconds time scale revealed one or two sodium ions at the E373 position or an acidic pocket composed of several negatively charged residues. Moreover, the MD simulations predicted possible chloride interaction sites. By screening predicted positively charged residues, we identified R379 as a chloride interaction site. Thus, we conclude that the E373 site and the D863/E865 pocket are two potential sodium-sensitive sites, while R379 is a chloride interaction site in the Slack channel.Significance Statement:The research presented here identified two distinct sodium and one chloride interaction sites located in the intracellular C-terminal domain of the Slack (Slo2.2, KCNT1) channel. Identification of the sites responsible for the sodium and chloride activation of the Slack channel sets its gating property apart from other potassium channels in the BK channel family. This finding sets the stage for this channel's future functional and pharmacological studies.

SSCS PICO Chronicles: The Open Source Community is Growing Further and Supported by SSCS PICO [Society News

The previous year was another great success for the open source integrated circuit (IC) design ecosystem. It finished with two actions: the second IEEE Solid-State Circuits Society (SSCS) PICO open source IC design contest, known as <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">the Chipathon</i> , and the first Code-a-Chip travel grant award. The second Chipathon installment in 2022 attracted 55 teams across the globe, out of which volunteers selected 22 outstanding proposals. The finishing line was reached by 14 teams at the end of November (see the summaries in <xref ref-type="fig" rid="fig1" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Figure 1</xref> and <xref ref-type="table" rid="table1" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Table 1</xref> ), after months of global joint action, including weekly technical checkup meetings and conversations on the bustling IEEE-SSCS-DC-22 Slack channel.

Slack Potassium Channels Modulate TRPA1-Mediated Nociception in Sensory Neurons.

The transient receptor potential (TRP) ankyrin type 1 (TRPA1) channel is highly expressed in a subset of sensory neurons where it acts as an essential detector of painful stimuli. However, the mechanisms that control the activity of sensory neurons upon TRPA1 activation remain poorly understood. Here, using in situ hybridization and immunostaining, we found TRPA1 to be extensively co-localized with the potassium channel Slack (KNa1.1, Slo2.2, or Kcnt1) in sensory neurons. Mice lacking Slack globally (Slack−/−) or conditionally in sensory neurons (SNS-Slack−/−) demonstrated increased pain behavior after intraplantar injection of the TRPA1 activator allyl isothiocyanate. By contrast, pain behavior induced by the TRP vanilloid 1 (TRPV1) activator capsaicin was normal in Slack-deficient mice. Patch-clamp recordings in sensory neurons and in a HEK cell line transfected with TRPA1 and Slack revealed that Slack-dependent potassium currents (IKS) are modulated in a TRPA1-dependent manner. Taken together, our findings highlight Slack as a modulator of TRPA1-mediated, but not TRPV1-mediated, activation of sensory neurons.