Epilepsies of presumed genetic etiology show enrichment of rare variants that occur in the general population.

Previous studies suggested that severe epilepsies, e.g., developmental and epileptic encephalopathies (DEEs), are mainly caused by ultra-rare de novo genetic variants. For milder disease, rare genetic variants could contribute to the phenotype. To determine the importance of rare variants for different epilepsy types, we analyzed a whole-exome sequencing cohort of 9,170 epilepsy-affected individuals and 8,436 control individuals. Here, we separately analyzed three different groups of epilepsies: severe DEEs, genetic generalized epilepsy (GGE), and non-acquired focal epilepsy (NAFE). We required qualifying rare variants (QRVs) to occur in control individuals with an allele count ≥ 1 and a minor allele frequency ≤ 1:1,000, to be predicted as deleterious (CADD ≥ 20), and to have an odds ratio in individuals with epilepsy ≥ 2. We identified genes enriched with QRVs primarily in NAFE (n = 72), followed by GGE (n = 32) and DEE (n = 21). This suggests that rare variants may play a more important role for causality of NAFE than for DEE. Moreover, we found that genes harboring QRVs, e.g., HSGP2, FLNA, or TNC, encode proteins that are involved in structuring the brain extracellular matrix. The present study confirms an involvement of rare variants for NAFE that occur also in the general population, while in DEE and GGE, the contribution of such variants appears more limited.

Pasa: leveraging population pangenome graph to scaffold prokaryote genome assemblies.

Whole genome sequencing has increasingly become the essential method for studying the genetic mechanisms of antimicrobial resistance and for surveillance of drug-resistant bacterial pathogens. The majority of bacterial genomes sequenced to date have been sequenced with Illumina sequencing technology, owing to its high-throughput, excellent sequence accuracy, and low cost. However, because of the short-read nature of the technology, these assemblies are fragmented into large numbers of contigs, hindering the obtaining of full information of the genome. We develop Pasa, a graph-based algorithm that utilizes the pangenome graph and the assembly graph information to improve scaffolding quality. By leveraging the population information of the bacteria species, Pasa is able to utilize the linkage information of the gene families of the species to resolve the contig graph of the assembly. We show that our method outperforms the current state of the arts in terms of accuracy, and at the same time, is computationally efficient to be applied to a large number of existing draft assemblies.

Dominant CST3 variants cause adult onset leukodystrophy without amyloid angiopathy.

Leukodystrophies are rare genetic white matter disorders that have been regarded as mainly occurring in childhood. This perception has been altered in recent years, as a growing number of leukodystrophies have been described as having an onset in adulthood. Still, many adult patients presenting with white matter changes remain without a specific molecular diagnosis. We describe a novel adult onset leukodystrophy in 16 patients from eight families carrying one of four different stop-gain or frameshift dominant variants in the CST3 gene. Clinical and radiological features differ markedly from the previously described Icelandic cerebral amyloid angiopathy found in patients carrying p.Leu68Asn substitution in CST3. The clinical phenotype consists of recurrent episodes of hemiplegic migraine associated with transient unilateral focal deficits and slowly progressing motor symptoms and cognitive decline in mid to older adult ages. In addition, in some cases acute onset clinical deterioration led to a prolonged episode with reduced consciousness and even early death. Radiologically, pathognomonic changes are found at typical predilection sites involving the deep cerebral white matter sparing a periventricular and directly subcortical rim, the middle blade of corpus callosum, posterior limb of the internal capsule, middle cerebellar peduncles, cerebral peduncles and specifically the globus pallidus. Histopathologic characterization in two autopsy cases did not reveal angiopathy, but instead micro- to macrocystic degeneration of the white matter. Astrocytes were activated at early stages and later displayed severe degeneration and loss. In addition, despite the loss of myelin, elevated numbers of partly apoptotic oligodendrocytes were observed. A structural comparison of the variants in CST3 suggests that specific truncations of cystatin C result in an abnormal function, possibly by rendering the protein more prone to aggregation. Future studies are required to confirm the assumed effect on the protein and to determine pathophysiologic downstream events at the cellular level.

AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance.

We have developed AMRViz, a toolkit for analyzing, visualizing, and managing bacterial genomics samples. The toolkit is bundled with the current best practice analysis pipeline allowing researchers to perform comprehensive analysis of a collection of samples directly from raw sequencing data with a single command line. The analysis results in a report showing the genome structure, genome annotations, antibiotic resistance and virulence profile for each sample. The pan-genome of all samples of the collection is analyzed to identify core- and accessory-genes. Phylogenies of the whole genome as well as all gene clusters are also generated. The toolkit provides a web-based visualization dashboard allowing researchers to interactively examine various aspects of the analysis results. Availability: AMRViz is implemented in Python and NodeJS, and is publicly available under open source MIT license at https://github.com/amromics/amrviz .

AMRomics: a scalable workflow to analyze large microbial genome collections.

Whole genome analysis for microbial genomics is critical to studying and monitoring antimicrobial resistance strains. The exponential growth of microbial sequencing data necessitates a fast and scalable computational pipeline to generate the desired outputs in a timely and cost-effective manner. Recent methods have been implemented to integrate individual genomes into large collections of specific bacterial populations and are widely employed for systematic genomic surveillance. However, they do not scale well when the population expands and turnaround time remains the main issue for this type of analysis. Here, we introduce AMRomics, an optimized microbial genomics pipeline that can work efficiently with big datasets. We use different bacterial data collections to compare AMRomics against competitive tools and show that our pipeline can generate similar results of interest but with better performance. The software is open source and is publicly available at https://github.com/amromics/amromics under an MIT license.

GABRA1-Related Disorders: From Genetic to Functional Pathways.

OBJECTIVE: Variants in GABRA1 have been associated with a broad epilepsy spectrum, ranging from genetic generalized epilepsies to developmental and epileptic encephalopathies. However, our understanding of what determines the phenotype severity and best treatment options remains inadequate. We therefore aimed to analyze the electroclinical features and the functional effects of GABRA1 variants to establish genotype-phenotype correlations. METHODS: Genetic and electroclinical data of 27 individuals (22 unrelated and 2 families) harboring 20 different GABRA1 variants were collected and accompanied by functional analysis of 19 variants. RESULTS: Individuals in this cohort could be assigned into different clinical subgroups based on the functional effect of their variant and its structural position within the GABRA1 subunit. A homogenous phenotype with mild cognitive impairment and infantile onset epilepsy (focal seizures, fever sensitivity, and electroencephalographic posterior epileptiform discharges) was described for variants in the extracellular domain and the small transmembrane loops. These variants displayed loss-of-function (LoF) effects, and the patients generally had a favorable outcome. A more severe phenotype was associated with variants in the pore-forming transmembrane helices. These variants displayed either gain-of-function (GoF) or LoF effects. GoF variants were associated with severe early onset neurodevelopmental disorders, including early infantile developmental and epileptic encephalopathy. INTERPRETATION: Our data expand the genetic and phenotypic spectrum of GABRA1 epilepsies and permit delineation of specific subphenotypes for LoF and GoF variants, through the heterogeneity of phenotypes and variants. Generally, variants in the transmembrane helices cause more severe phenotypes, in particular GoF variants. These findings establish the basis for a better understanding of the pathomechanism and a precision medicine approach in GABRA1-related disorders. Further studies in larger populations are needed to provide a conclusive genotype-phenotype correlation. ANN NEUROL 2023.

Replacement of Toxic Hydrazines in Satellite Propulsion with Greener Dinitramide-Based Energetic Ionic Liquid Candidates.

Satellite propulsion uses liquid mono or bi-propellants composed of a hydrazine in combination with a strong oxidant. However, hydrazines are highly toxic. As a result, many research efforts for more environmentally compatible propellants have been made over the past decade. In this study we evidence green formulations that retain high propulsive performances. They are based on the dinitramide anion. From an initial library of 37 ammonium dinitramides 3 best candidates were selected after evaluation of their potential syntheses, calculated theoretical performances, experimental synthesis optimizations and decomposition temperatures. These three salts were then formulated to obtain acceptable sensitivities and melting points, which eventually led to only one formulation being retained: a 40 : 60 mixture of dimethylammonium dinitramide and ammonium dinitramide phlegmatized by 10 % of glycerol.

Thy-1 restricts steatosis and liver fibrosis in steatotic liver disease.

BACKGROUND AND AIMS: Steatotic liver disease (SLD) is generally considered to represent a hepatic manifestation of metabolic syndrome and includes a disease spectrum comprising isolated steatosis, metabolic dysfunction-associated steatohepatitis, liver fibrosis and ultimately cirrhosis. A better understanding of the detailed underlying pathogenic mechanisms of this transition is crucial for the design of new and efficient therapeutic interventions. Thymocyte differentiation antigen (Thy-1, also known as CD90) expression on fibroblasts controls central functions relevant to fibrogenesis, including proliferation, apoptosis, cytokine responsiveness, and myofibroblast differentiation. METHODS: The impact of Thy-1 on the development of SLD and progression to fibrosis was investigated in high-fat diet (HFD)-induced SLD wild-type and Thy-1-deficient mice. In addition, the serum soluble Thy-1 (sThy-1) concentration was analysed in patients with metabolic dysfunction-associated SLD stratified according to steatosis, inflammation, or liver fibrosis using noninvasive markers. RESULTS: We demonstrated that Thy-1 attenuates the development of fatty liver and the expression of profibrogenic genes in the livers of HFD-induced SLD mice. Mechanistically, Thy-1 directly inhibits the profibrotic activation of nonparenchymal liver cells. In addition, Thy-1 prevents palmitic acid-mediated amplification of the inflammatory response of myeloid cells, which might indirectly contribute to the pronounced development of liver fibrosis in Thy-1-deficient mice. Serum analysis of patients with metabolically associated steatotic liver disease syndrome revealed that sThy-1 expression is correlated with liver fibrosis status, as assessed by liver stiffness, the Fib4 score, and the NAFLD fibrosis score. CONCLUSION: Our data strongly suggest that Thy-1 may function as a fibrosis-protective factor in mouse and human SLD.

Sodium sulfide-promoted regiodefined redox condensation of o-nitroanilines with aryl ketones to benzo[a]phenazines and quinoxalines.

Inexpensive sodium sulfide trihydrate was found to promote unprecedented 6e-regio-predefined redox condensation of o-nitroanilines with α-tetralones to benzo[a]phenazines. The method was also successfully extended to acetophenones and higher homologs as reducing partners to provide 2-phenylquinoxalines. Compared to traditional approaches toward benzo[a]phenazine and quinoxaline cores starting with o-phenylenediamines, the present strategy could afford these heterocycles with well-defined regiochemistry based on the structure of starting o-nitroanilines.

Regional activity and effective connectivity within the frontoparietal network during precision walking with visual cueing: an fNIRS study.

Precision walking (PW) incorporates precise step adjustments into regular walking patterns to navigate challenging surroundings. However, the brain processes involved in PW control, which encompass cortical regions and interregional interactions, are not fully understood. This study aimed to investigate the changes in regional activity and effective connectivity within the frontoparietal network associated with PW. Functional near-infrared spectroscopy data were recorded from adult subjects during treadmill walking tasks, including normal walking (NOR) and PW with visual cues, wherein the intercue distance was either fixed (FIX) or randomly varied (VAR) across steps. The superior parietal lobule (SPL), dorsal premotor area (PMd), supplementary motor area (SMA), and dorsolateral prefrontal cortex (dlPFC) were specifically targeted. The results revealed higher activities in SMA and left PMd, as well as left-to-right SPL connectivity, in VAR than in FIX. Activities in SMA and right dlPFC, along with dlPFC-to-SPL connectivity, were higher in VAR than in NOR. Overall, these findings provide insights into the roles of different brain regions and connectivity patterns within the frontoparietal network in facilitating gait control during PW, providing a useful baseline for further investigations into brain networks involved in locomotion.

A chromosome-level genome assembly for the dugong (Dugong dugon).

The dugong (Dugong dugon) is a marine mammal widely distributed throughout the Indo-Pacific and the Red Sea, with a Vulnerable conservation status, and little is known about many of the more peripheral populations, some of which are thought to be close to extinction. We present a de novo high-quality genome assembly for the dugong from an individual belonging to the well-monitored Moreton Bay population in Queensland, Australia. Our assembly uses long-read PacBio HiFi sequencing and Omni-C data following the Vertebrate Genome Project pipeline to reach chromosome-level contiguity (24 chromosome-level scaffolds; 3.16 Gbp) and high completeness (97.9% complete BUSCOs). We observed relatively high genome-wide heterozygosity, which likely reflects historical population abundance before the last interglacial period, approximately 125,000 yr ago. Demographic inference suggests that dugong populations began declining as sea levels fell after the last interglacial period, likely a result of population fragmentation and habitat loss due to the exposure of seagrass meadows. We find no evidence for ongoing recent inbreeding in this individual. However, runs of homozygosity indicate some past inbreeding. Our draft genome assembly will enable range-wide assessments of genetic diversity and adaptation, facilitate effective management of dugong populations, and allow comparative genomics analyses including with other sirenians, the oldest marine mammal lineage.

Alignment of ND3 molecules in dc-electric fields.

The control of movement and orientation of gas-phase molecules has become the focus of many research areas in molecular physics. Here, ND3 molecules are polarized in a segmented, curved electrostatic guide and adiabatically aligned inside a rotatable mass spectrometer (MS). Alignment is probed by photoionization using a linearly polarized laser. Rotation of the polarization at fixed MS orientation has the same effect as the rotation of the MS at fixed polarization, proving that the molecular alignment adiabatically follows the MS axis. Polarization-dependent ion signals reveal state-specific populations and allow for a quantification of the aligned sample in the space-fixed reference frame.

How does fetal inflammatory response syndrome change fetal response to hypoxia? An experimental study in a fetal sheep model.

INTRODUCTION: Fetal inflammatory response syndrome associated with acidosis during labor is a high-risk situation for the fetus. This study evaluated hemodynamic, gasometric, and heart rate variability changes during acute fetal inflammatory response syndrome associated with hypoxia, compared with isolated hypoxia. MATERIAL AND METHODS: Acute fetal inflammatory response syndrome was obtained via an intravenously injection of lipopolysaccharide derived from Escherichia coli. Hypoxia was induced by repeated umbilical cord occlusions during three phases: mild, moderate, and severe umbilical cord occlusions. Two groups were created with chronically instrumented near-term fetal sheep: one group with isolated hypoxia, the other with hypoxia and fetal inflammatory response syndrome. Hemodynamic, gas parameters, and fetal heart rate variability were compared between the groups. RESULTS: The hypoxia and fetal inflammatory response syndrome group had a higher mortality rate (n = 4/9) compared with the hypoxia group (n = 0/9). Gasometric state was altered earlier in case of lipopolysaccharide injection (pH = 7.22 (7.12-7.24) vs 7.28 (7.23-7.34) p = 0.01; lactate = 10.3 mmol/L (9.4-11.0) vs 6.0 mmol/L (4.1-8.2) p < 0.001 after mild occlusions). After mild occlusions, the hypoxia and fetal inflammatory response syndrome group had higher values on seven heart rate variability parameters compared with the hypoxia group. After moderate occlusions, two parameters remained significantly higher. CONCLUSIONS: During fetal inflammatory response syndrome, fetal adaptation to hypoxia is impaired. In case of fetal infection, acidosis during labor is likely to become severe more rapidly, requiring closer fetal monitoring during labor.

Essential oil and Waste Hydrosol of Ocimum Tenuiflorum L.: A Low-Cost Raw Material Source of Eugenol, Botanical Pesticides, and Therapeutic Potentiality.

In this study, essential oils and waste hydrosols of leaves of Ocimum tenuiflorum in four different geographical locations were extracted by hydrodistillation method and using gas chromatography/mass spectrometry (GC/MS) for chemical composition analysis. All four essential oil samples contained the main components (E)-ß-caryophyllene (27.8-49.0 %), trans-ß-elemene (20.3-37.1 %) and eugenol (9.0-44.0 %). Three of the four hydrosol samples had eugenol in absolute content (94.5-98.6 %), while the remaining hydrosol sample had two main components, elemicin (77.8 %) and eugenol (14.2 %). Essential oils and hydrosols demonstrated larvicidal activities against four important disease-transmitting mosquito species including Aedes aegypti, Aedes albopictus, Culex quinquefasciatus, and Culex fuscocephala with 24-h LC50 values in the range 15.42-56.01 µg/mL and 53.88-97.80 µg/mL for the essential oils and the hydrosols, respectively. Essential oils and hydrosols strongly inhibited the acetylcholinesterase (AChE) enzyme of electric eels with IC50 values in the range of 25.35-107.19 µg/mL. Microemulsion (ME) can be considered as a sustainable pesticide formulation over 300 days and has improved larvicidal activity compared to free essential oil. The O. tenuiflorum in Vietnam can be considered a low-cost source of eugenol, botanical pesticides that control disease-transmitting mosquitoes, as well as having therapeutic potential to be further investigated.

Three Undescribed Furanoditerpenoids from the Tinospora crispa that Inhibit NO Production.

Phytochemical study on the methanol extract of the stems of Tinospora crispa (L.) Hook.f. & Thomson led to the isolation of thirteen compounds including three undescribed cis-clerodane-type furanoditerpenoids (1-3) and ten known ones (4-13). Their chemical structures were determined by IR, HR-ESI-MS, 1D-, and 2D-NMR spectra. Compounds 2-6 and 8 inhibited moderately NO production in LPS activated RAW 264.7 cell with the IC50 values of 83.5, 57.6, 75.3, 78.1, and 74.7 µM, respectively.

Chemical Constituents, Biological Activities and Molecular Docking Studies of Root and Aerial Part Essential Oils from Erigeron sublyratus Roxb. ex DC. (Asteraceae).

In this study, the volatile components of Erigeron sublyratus essential oils and their anti-inflammatory and cytotoxic activities were investigated for the first time. Gas chromatography-mass spectrometry (GC-MS) analysis revealed that a total of 28 components were identified in the root and aerial part essential oils. Among them, cis-lachnophyllum ester (53.4-64.2%), followed by germacrene D (5.6-8.6%), trans-ß-ocimene (2.6-7.5%), ß-caryophyllene (4.7-6.8%), ß-myrcene (2.0-6.3%), and (E)-ß-famesene (4.8-5.0%) were principal components. The root essential oil significantly inhibited nitric oxide (NO) production on LPS-induced RAW264.7 cells (IC50 = 1.41 ± 0.10 µg/mL) as compared to standard, dexamethasone (IC50 = 5.43 ± 0.54 µg/mL). Besides, both root and aerial part essential oils exhibited cytotoxic activity against MCF-7, SK-LU-1, and HepG2 (IC50 from 1.11 ± 0.04 to 1.70 ± 0.05 µg/mL). Molecular docking simulation results show that (E)-ß-farnesene exhibits the strongest binding energy among the studied compounds with the VEGFR-2 enzyme (ΔG = -7.295 kcal/mol), while δ-cadinene demonstrates the strongest affinity (ΔG = -8.047 kcal/mol) towards the COX-2 enzyme. Furthermore, hydrophobic interactions were indicated to be the main contributors to the binding ability in the studied protein-ligand complex. These findings proposed that E. sublyratus can be exploited for its anti-inflammatory and anti-cytotoxicity potential.

Five New Furostanol Glycosides from the Fruits of Tribulus terrestris with NO Production Inhibitory Activity.

Eight furostanol glycosides including five undescribed compounds, named tribufurostanosides A-E (1-5), and three known ones (6-8) were isolated from the fruits of Tribulus terrestris L. Their chemical structures were determined by the IR, HR-ESI-MS, 1D-, and 2D-NMR spectra. Furostanols 1-8 significantly inhibited nitric oxide production in LPS activated RAW 264.7 cells with IC50 values ranging from 14.2 to 64.7 µM, compared to that of the positive control compound, dexamethazone (IC50 13.6 µM).

Configurable Crack Wall Conduction in a Complex Oxide.

Mobile defects in solid-state materials play a significant role in memristive switching and energy-efficient neuromorphic computation. Techniques for confining and manipulating point defects may have great promise for low-dimensional memories. Here, we report the spontaneous gathering of oxygen vacancies at strain-relaxed crack walls in SrTiO3 thin films grown on DyScO3 substrates as a result of flexoelectricity. We found that electronic conductance at the crack walls was enhanced compared to the crack-free region, by a factor of 104. A switchable asymmetric diode-like feature was also observed, and the mechanism is discussed, based on the electrical migration of oxygen vacancy donors in the background of Sr-deficient acceptors forming n+-n or n-n+ junctions. By tracing the temporal relaxations of surface potential and lattice expansion of a formed region, we determine the diffusivity of mobile defects in crack walls to be 1.4 × 10-16 cm2/s, which is consistent with oxygen vacancy kinetics.

Converting the Bulk Transition Metal Dichalcogenides Crystal into Stacked Monolayers via Ethylenediamine Intercalation.

We report the synthesis of ethylenediamine-intercalated NbSe2 and Li-ethylenediamine-intercalated MoSe2 single crystals with increased interlayer distances and their electronic structures measured by means of angle-resolved photoemission spectroscopy (ARPES). X-ray diffraction patterns and transmission electron microscopy images confirm the successful intercalation and an increase in the interlayer distance. ARPES measurement reveals that intercalated NbSe2 shows an electronic structure almost identical to that of monolayer NbSe2. Intercalated MoSe2 also returns the characteristic feature of the monolayer electronic structure, a direct band gap, which generates sizable photoluminescence even in the bulk form. Our results demonstrate that the properties and phenomena of the monolayer transition metal dichalcogenides can be achieved with large-scale bulk samples by blocking the interlayer interaction through intercalation.

Distance-controlled surface-enhanced Raman spectroscopy of nanoparticles.

Biological particles, e.g., viruses, lipid particles, and extracellular vesicles, are attracting significant research interest due to their role in biological processes and potential in practical applications, such as vaccines, diagnostics, and therapies. Their surface and interior contain many different molecules including lipids, nucleic acids, proteins, and carbohydrates. In this Letter, we show how distance-controlled surface-enhanced Raman spectroscopy (SERS) is a promising method to extract essential information from the spatial origin of the signal. This is a highly important parameter in the analysis of these biological particles. The principle of the method is demonstrated by using polystyrene (PS) beads as a biological particle model conjugated with gold nanospheres (AuNSs) functioning as distance-controlled SERS probes via biotin-streptavidin binding. By tuning the size of AuNSs, the Raman signal from the PS beads can be weakened while the signal from the biotin-streptavidin complex is enhanced.