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Short tandem repeats (STRs) and variable number tandem repeats (VNTRs) are important sources of natural and disease-causing variation, yet they have been problematic to resolve in reference genomes and genotype with short-read technology. We created a framework tomodel the evolution and instability of STRs and VNTRs in apes. We phased and assembled 3 ape genomes (chimpanzee, gorilla, and orangutan) using long-read and 10x Genomics linkedread sequence data for 21,442 human tandem repeats discovered in 6 haplotype-resolved assemblies of Yoruban, Chinese, and Puerto Rican origin. We define a set of 1,584 STRs/VNTRs expanded specifically in humans, including large tandem repeats affecting coding and noncoding portions of genes (e.g., MUC3A, CACNA1C). We show that short interspersed nuclear element–VNTR–Alu (SVA) retrotransposition is the main mechanism for distributing GC-rich human-specific tandem repeat expansions throughout the genome but with a bias against genes. In contrast, we observe that VNTRs not originating from retrotransposons have a propensity to cluster near genes, especially in the subtelomere. Using tissuespecific expression from human and chimpanzee brains, we identify genes where transcript isoform usage differs significantly, likely caused by cryptic splicing variation within VNTRs. Using single-cell expression from cerebral organoids, we observe a strong effect for genes associated with transcription profiles analogous to intermediate progenitor cells. Finally, we compare the sequence composition of some of the largest human-specific repeat expansions and identify 52 STRs/VNTRs with at least 40 uninterrupted pure tracts as candidates for genetically unstable regions associated with disease.

TWIK-related acid-sensitive potassium (TASK) channels—members of the two pore domain potassium (K 2P ) channel family—are found in neurons 1 , cardiomyocytes 2 – 4 and vascular smooth muscle cells 5 , where they are involved in the regulation of heart rate 6 , pulmonary artery tone 5 , 7 , sleep/wake cycles 8 and responses to volatile anaesthetics 8 – 11 . K 2P channels regulate the resting membrane potential, providing background K + currents controlled by numerous physiological stimuli 12 – 15 . Unlike other K 2P channels, TASK channels are able to bind inhibitors with high affinity, exceptional selectivity and very slow compound washout rates. As such, these channels are attractive drug targets, and TASK-1 inhibitors are currently in clinical trials for obstructive sleep apnoea and atrial fibrillation 16 . In general, potassium channels have an intramembrane vestibule with a selectivity filter situated above and a gate with four parallel helices located below; however, the K 2P channels studied so far all lack a lower gate. Here we present the X-ray crystal structure of TASK-1, and show that it contains a lower gate—which we designate as an ‘X-gate’—created by interaction of the two crossed C-terminal M4 transmembrane helices at the vestibule entrance. This structure is formed by six residues ( 243 VLRFMT 248 ) that are essential for responses to volatile anaesthetics 10 , neurotransmitters 13 and G-protein-coupled receptors 13 . Mutations within the X-gate and the surrounding regions markedly affect both the channel-open probability and the activation of the channel by anaesthetics. Structures of TASK-1 bound to two high-affinity inhibitors show that both compounds bind below the selectivity filter and are trapped in the vestibule by the X-gate, which explains their exceptionally low washout rates. The presence of the X-gate in TASK channels explains many aspects of their physiological and pharmacological behaviour, which will be beneficial for the future development and optimization of TASK modulators for the treatment of heart, lung and sleep disorders. The X-ray crystal structure of the potassium channel TASK-1 reveals the presence of an X-gate, which traps small-molecule inhibitors in the intramembrane vestibule and explains their low washout rates from the channel.

Findings of retrospective studies suggest that sorafenib maintenance post-transplantation might reduce relapse in patients with FLT3 internal tandem duplication (FLT3-ITD) acute myeloid leukaemia undergoing allogeneic haematopoietic stem-cell transplantation. We investigated the efficacy and tolerability of sorafenib maintenance post-transplantation in this population. We did an open-label, randomised phase 3 trial at seven hospitals in China. Eligible patients (aged 18–60 years) had FLT3-ITD acute myeloid leukaemia, were undergoing allogeneic haematopoietic stem-cell transplantation, had an Eastern Cooperative Oncology Group performance status of 0–2, had composite complete remission before and after transplantation, and had haematopoietic recovery within 60 days post-transplantation. Patients were randomly assigned (1:1) to sorafenib maintenance (400 mg orally twice daily) or non-maintenance (control) at 30–60 days post-transplantation. Randomisation was done with permuted blocks (block size four) and implemented through an interactive web-based randomisation system. The primary endpoint was the 1-year cumulative incidence of relapse in the intention-to-treat population. This trial is registered with ClinicalTrials.gov, NCT02474290; the trial is complete. Between June 20, 2015, and July 21, 2018, 202 patients were enrolled and randomly assigned to sorafenib maintenance (n=100) or control (n=102). Median follow-up post-transplantation was 21·3 months (IQR 15·0–37·0). The 1-year cumulative incidence of relapse was 7·0% (95% CI 3·1–13·1) in the sorafenib group and 24·5% (16·6–33·2) in the control group (hazard ratio 0·25, 95% CI 0·11–0·57; p=0·0010). Within 210 days post-transplantation, the most common grade 3 and 4 adverse events were infections (25 [25%] of 100 patients in the sorafenib group vs 24 [24%] of 102 in the control group), acute graft-versus-host-disease (GVHD; 23 [23%] of 100 vs 21 [21%] of 102), chronic GVHD (18 [18%] of 99 vs 17 [17%] of 99), and haematological toxicity (15 [15%] of 100 vs seven [7%] of 102). There were no treatment-related deaths. Sorafenib maintenance post-transplantation can reduce relapse and is well tolerated in patients with FLT3-ITD acute myeloid leukaemia undergoing allogeneic haematopoietic stem-cell transplantation. This strategy could be a suitable therapeutic option for patients with FLT3-ITD acute myeloid leukaemia. None.

This study investigated the concentration of the pesticide residues found in Fragaria and Myrica rubra sold in the city of Hangzhou, People's Republic of China. From an analysis of 151 (77 Fragaria and 74 M. rubra) samples using gas chromatography–tandem mass spectrometry (GC-MS/MS) and liquid chromatography–tandem mass spectrometry (LC-MS/MS), 41 pesticide residues were found to be present. Of the 41 residues, 14 were found using GC-MS/MS and 27 were found using LC-MS/MS. Of the 151 samples, 10 (13.0%) of the 77 Fragaria samples and 5 (6.8%) of the 74 M. rubra samples were found to contain a specific pesticide residue, and only 4 Fragaria samples and 2 M. rubra samples were found to be without pesticide residue. In addition, 18 of the 41 pesticides were not detected in either Fragaria or M. rubra samples. Of the 41 residues, 10 were detected in Fragaria samples and 20 were detected in M. rubra samples. In Fragaria, procymidone was the most commonly detected residue, with a detection rate of 88.3%, followed by prochloraz, with a detection rate of 53.2%. In M. rubra, prochloraz was the most commonly detected residue, with a detection rate of 71.6%, followed by carbendazim, with a detection rate of 68.9%. The pesticide residues in some samples exceeded the maximum residue limit set in China. The limit of dimethomorph was exceeded in three of the Fragaria samples, and that of dichlorvos was exceeded in two of the M. rubra samples. •The study detected the concentration of the pesticide residues in Fragaria and Myrica rubra.•A total of 41 pesticide residues were investigated.•The QUECHERS method was used.

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has become an indispensable analytical technique in clinical and forensic toxicology for detection and identification of potentially toxic or harmful compounds. Particularly, non-target LC-MS/MS assays enable extensive and universal screening requested in systematic toxicological analysis. An integral part of the identification process is the generation of information-rich product ion spectra which can be searched against libraries of reference mass spectra. Usually, ‘data-dependent acquisition’ (DDA) strategies are applied for automated data acquisition. In this study, the ‘data-independent acquisition’ (DIA) method ‘Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra’ (SWATH) was combined with LC-MS/MS on a quadrupole-quadrupole-time-of-flight (QqTOF) instrument for acquiring informative high-resolution tandem mass spectra. SWATH performs data-independent fragmentation of all precursor ions entering the mass spectrometer in 21 m/z isolation windows. The whole m/z range of interest is covered by continuous stepping of the isolation window. This allows numerous repeat analyses of each window during the elution of a single chromatographic peak and results in a complete fragment ion map of the sample. Compounds and samples typically encountered in forensic casework were used to assess performance characteristics of LC-MS/MS with SWATH. Our experiments clearly revealed that SWATH is a sensitive and specific identification technique. SWATH is capable of identifying more compounds at lower concentration levels than DDA does. The dynamic range of SWATH was estimated to be three orders of magnitude. Furthermore, the >600,000 SWATH spectra matched led to only 408 incorrect calls (false positive rate = 0.06 %). Deconvolution of generated ion maps was found to be essential for unravelling the full identification power of LC-MS/MS with SWATH. With the available software, however, only semi-automated deconvolution was enabled, which rendered data interpretation a laborious and time-consuming process. Graphical Abstract High-resolution LC-MS/MS with SWATH represents a sensitive and specific compound identification tool that has vast potential to become a leading technique in systematic toxicological analysis. SWATH solves the problem of unused precursor ions often encountered with data-dependent acquisition methods by acquiring complete fragment ion maps of a sample

The Tandem of pore domain in a Weak Inward Rectifying K + channel 2 (TWIK-2; KCNK6 ) is a member of the Two-Pore Domain K + (K 2P ) channel family, which is associated with pulmonary hypertension, lung injury, and inflammation. Despite its physiological relevance, the structure, regulatory mechanisms, and selective modulators of TWIK-2 remain largely unknown. Here, we present a 3.7 Å single particle cryo-electron microscopy structure of human TWIK-2 and highlight its conserved and distinctive features. Using automated whole-cell patch clamp recordings, we demonstrate that gating in TWIK-2 is voltage-dependent and insensitive to changes in the extracellular pH. We identify key residues that influence TWIK-2 activity by employing site-directed mutagenesis and provide insights into the possible lipid-mediated mechanism of TWIK-2 regulation. Additionally, we demonstrate the application of high-throughput automated whole-cell patch clamp platforms to screen small molecule modulators of TWIK-2. Our work serves as a foundation for designing high-throughput small molecule screening campaigns to identify specific high-affinity TWIK-2 modulators, including promising- anti-inflammatory therapeutics. TWIK-2 is an endolysosomal potassium channel implicated in inflammatory responses. Here, authors present a cryo-EM structure of human TWIK-2 and establish a high-throughput automated patch-clamp electrophysiology assay to investigate modulation of TWIK-2.

TREK-2 (KCNK10/K2P10), a two-pore domain potassium (K2P) channel, is gated by multiple stimuli such as stretch, fatty acids, and pH and by several drugs. However, the mechanisms that control channel gating are unclear. Here we present crystal structures of the human TREK-2 channel (up to 3.4 angstrom resolution) in two conformations and in complex with norfluoxetine, the active metabolite of fluoxetine (Prozac) and a state-dependent blocker of TREK channels. Norfluoxetine binds within intramembrane fenestrations found in only one of these two conformations. Channel activation by arachidonic acid and mechanical stretch involves conversion between these states through movement of the pore-lining helices. These results provide an explanation for TREK channel mechanosensitivity, regulation by diverse stimuli, and possible off-target effects of the serotonin reuptake inhibitor Prozac.

Controlling body temperature is a matter of life or death for most animals, and in mammals the complex thermoregulatory system is comprised of thermoreceptors, thermosensors, and effectors. The activity of thermoreceptors and thermoeffectors has been studied for many years, yet only recently have we begun to obtain a clear picture of the thermosensors and the molecular mechanisms involved in thermosensory reception. An important step in this direction was the discovery of the thermosensitive transient receptor potential (TRP) cationic channels, some of which are activated by increases in temperature and others by a drop in temperature, potentially converting the cells in which they are expressed into heat and cold receptors. More recently, the TWIK-related potassium (TREK) channels were seen to be strongly activated by increases in temperature. Hence, in this review we want to assess the hypothesis that both these groups of channels can collaborate, possibly along with other channels, to generate the wide range of thermal sensations that the nervous system is capable of handling.

In a family with pulmonary arterial hypertension, whole-exome sequencing led to identification of a mutation in the potassium-channel gene KCNK3 . Additional mutations resulting in loss of function of the channel were found in other families and in patients with idiopathic disease. Pulmonary arterial hypertension is a rare disease that is characterized by increased pulmonary-artery pressure in the absence of common causes of pulmonary hypertension, such as chronic heart, lung, or thromboembolic disease. 1 Before the advent of novel therapies, patients with idiopathic or familial pulmonary arterial hypertension had an estimated median survival of 2.8 years, with 1-year, 3-year, and 5-year survival rates of 68%, 48%, and 34%, respectively. 2 However, despite progress in treatment, pulmonary arterial hypertension remains a progressive, fatal disease. The clinical presentation can be nonspecific, and patients often receive a diagnosis late in their clinical course. The cause of pulmonary . . .

TASK2 (also known as KCNK5) channels generate pH-gated leak-type K + currents to control cellular electrical excitability 1 – 3 . TASK2 is involved in the regulation of breathing by chemosensory neurons of the retrotrapezoid nucleus in the brainstem 4 – 6 and pH homeostasis by kidney proximal tubule cells 7 , 8 . These roles depend on channel activation by intracellular and extracellular alkalization 3 , 8 , 9 , but the mechanistic basis for TASK2 gating by pH is unknown. Here we present cryo-electron microscopy structures of Mus musculus TASK2 in lipid nanodiscs in open and closed conformations. We identify two gates, distinct from previously observed K + channel gates, controlled by stimuli on either side of the membrane. Intracellular gating involves lysine protonation on inner helices and the formation of a protein seal between the cytoplasm and the channel. Extracellular gating involves arginine protonation on the channel surface and correlated conformational changes that displace the K + -selectivity filter to render it nonconductive. These results explain how internal and external protons control intracellular and selectivity filter gates to modulate TASK2 activity. The authors report on the structure of the K + channel TASK2 and how this channel opens in response to pH changes on either side of the cell membrane.