Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes

Explosive growth in the study of microbial epigenetics has revealed a diversity of chemical structures and biological functions of DNA modifications in restriction-modification (R-M) and basic genetic processes. Here, we describe the discovery of shared consensus sequences for two seemingly unrelated DNA modification systems, [superscript 6m]A methylation and phosphorothioation (PT), in which sulfur replaces a nonbridging oxygen in the DNA backbone. Mass spectrometric analysis of DNA from Escherichia coli B7A and Salmonella enterica serovar Cerro 87, strains possessing PT-based R-M genes, revealed d(G[subscript PS] [superscript 6m]A) dinucleotides in the G[subscript PS] [superscript 6m]AAC consensus representing ∼5% of the 1,100 to 1,300 PT-modified d(G[subscript PS] A) motifs per genome, with [superscript 6m]A arising from a yet-to-be-identified methyltransferase. To further explore PT and 6m A in another consensus sequence, G[subscript PS] [superscript 6m]ATC, we engineered a strain of E. coli HST04 to express Dnd genes from Hahella chejuensis KCTC2396 (PT in G[subscript PS] ATC) and Dam methyltransferase from E. coli DH10B ( [superscript 6m] A in G [superscript 6m] ATC). Based on this model, in vitro studies revealed reduced Dam activity in G PS ATC-containing oligonucleotides whereas single-molecule real-time sequencing of HST04 DNA revealed [superscript 6m] A in all 2,058 G[subscript PS] ATC sites (5% of 37,698 total GATC sites). This model system also revealed temperature-sensitive restriction by DndFGH in KCTC2396 and B7A, which was exploited to discover that [superscript 6m] A can substitute for PT to confer resistance to restriction by the DndFGH system. These results point to complex but unappreciated interactions between DNA modification systems and raise the possibility of coevolution of interacting systems to facilitate the function of each

Rapid detection of bacterial infections using nanotechnology-based point-of-care sensor with Raman spectroscopy

Background: Mass gathering is a risk factor for infectious diseases transmission. Therefore, rapid detection of infections is highly desirable. The current gold standard approach to detect bacterial infections in clinical samples (biological fluids) requires three days of bacterial culture to obtain the diagnosis and antibiotic sensitivity results1. This approach, although very accurate results in considerable delay in initiating proper treatment which increases the transmission of infection, mainly hospital-acquired infections. Therefore, rapid detection of infection would lead to rapid clinical interventions, which mitigate the spread of infection and support antibiotic stewardship consequently reducing the burden of hospital-acquired infections. The goal of this research is to develop a highly innovative sensor (point-of-care device) for rapid detection of bacterial infections in biological fluids. This project will also focus on identifying unique SERS spectra of bacterial infections commonly associated with mass gathering and early detection of antibiotic resistant bacteria. Methods: The proposed biosensor is a culture-free diagnostic method utilizing nanotechnology-based fabricated silver nanorod arrays (AgNR) as a substrate for the Surface Enhanced Raman Spectroscopy. Results: We reported the proof-of-concept study using this novel SERS-based diagnostic where we showed that rapid detection of bacterial biomarkers in sputum and exhaled breath condensates (EBC) from patients with cystic fibrosis2,3. We further identified unique SERS spectra of various bacterial siderophores and small molecule metabolites. Conclusion: This method is highly sensitive, fast, cheap, and can be implemented at the bedside using a portable (hand-held) Raman spectroscope.qscienc

Comparative studies of the anti-thrombotic effects of saffron and HongHua based on network pharmacology

Purpose: To investigate the comparative anti-thrombotic effects of saffron and Honghua, and also to explore possible mechanisms in thrombosis based on network pharmacology. Methods: A network pharmacology model was used for bioactive components, targets and pathways for saffron and HongHua via Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), PharmMapper, Genecard, Uniprot and KEGG databases. In animal experiments, 72 rats were randomly divided into 9 groups: normal control group (NC), model control group (MC), crocetin groups (80, 40, 20 mg/kg), hydroxysafflor yellow A(HSYA) groups (80, 40, 20 mg/kg), and aspirin group (40 mg/kg). Using in vitro thrombosis models and an acute blood stasis model in vivo, the anti-thrombotic effects of these treatments on clotting time, hemorheology parameters, Thromboxane B2 (TXB2), plasmin activator inhibitor (PAI), protein C (PC), protein S (PS), and thrombinantithrombin complex (TAT) were determined and comparisons made for saffron and HongHua. Results: Five potential compounds, 16 anti-thrombotic targets and 27 pathways were predicted for saffron, while 22 compounds, 37 disease targets and 35 pathways were found for HongHua (p < 0.05). Pharmacological experiments revealed that crocetin and HSYA had significant effects on thrombus length, thrombus wet/dry mass, whole blood viscosity (WBV), erythrocyte aggregation index (EAI), clotting time and D-dimer for the high and middle groups. Unlike HSYA, crocetin also had significant and dose-dependent effects on PAI, prothrombin fragment 1+2 (F1+2) and PS and had highly significant effects on TXB2 and TAT. Conclusion: This research provides a systematic, comprehensive and comparative analysis of component, target and anti-thrombotic pathways of saffron and HongHua based on network pharmacology, and also shows that saffron has more significant anti-thrombotic effect than HongHua. Keywords: Saffron; HongHua; Network pharmacology; Anti-thrombosis; Network mode

Thermal Stability of Neodymium Aluminates High- κ

Thin films of neodymium aluminate (NdAlOx) have been deposited by liquid injection metalorganic chemical vapor deposition (MOCVD) using the bimetallic alkoxide precursor [NdAl(OPri)6(PriOH)]2. The effects of high-temperature postdeposition annealing on NdAlOx thin films are reported. The as-deposited thin films are amorphous in nature. X-ray diffraction (XRD) and medium energy ion scattering (MEIS) show, respectively, no crystallization or interdiffusion of metal ions into the substrate after annealing at 950°C. The capacitance-voltage (C-V) and current-voltage (I-V) characteristics of the thin films exhibited good electrical integrity following annealing. The dielectric permittivity (κ) of the annealed NdAlOx was 12, and a density of interface states at flatband (Dit) of 4.01×1011  cm−2 eV−1 was measured. The deposited NdAlOx thin films are shown to be able to endure high-temperature stress and capable of maintaining excellent dielectric properties

Plasma-catalytic synthesis of ammonia over Ru/BaTiO3-based bimetallic catalysts: Synergistic effect from dual-metal active sites

Plasma-catalytic synthesis of ammonia (NH3) was carried out using BaTiO3 supported Ru-M bimetallic catalysts (Ru-M/BaTiO3, M = Fe, Co and Ni) in a dielectric barrier discharge (DBD) reactor. The NH3 synthesis performance followed the order of Ru-Ni/BaTiO3 > Ru/BaTiO3 > Ru-Co/BaTiO3 > Ru-Fe/BaTiO3, with the highest NH3 concentration (3895 ppm) and energy yield (0.39 g kWh−1) achieved over Ru-Ni/BaTiO3 at 25 W and 10 W, respectively. To gain insights into the physio-chemical properties of the Ru-M/BaTiO3 catalysts, comprehensive catalyst characterizations were performed, including X-ray diffraction, N2 physisorption measurements, X-ray photoelectron spectroscopy (XPS), high-resolution transmission electron microscopy (HRTEM), energy dispersive spectroscopy (EDS), and temperature-programmed desorption of CO2 and N2 (CO2 and N2-TPD). The results indicated that the loading of Ni enhanced the basicity and N2 adsorption capacity of the catalyst, as well as the density of oxygen vacancy (OV) on the BaTiO3 surface, which facilitated the adsorption and activation of N2 on catalyst surface. These effects led to the enhanced NH3 synthesis, as excited N2 could be adsorbed on Ru-Ni/BaTiO3 from plasma region and stepwise hydrogenated to form NHx species and ultimately NH3

A scalable implementation of the recursive least-squares algorithm for training spiking neural networks

Training spiking recurrent neural networks on neuronal recordings or behavioral tasks has become a popular way to study computations performed by the nervous system. As the size and complexity of neural recordings increase, there is a need for efficient algorithms that can train models in a short period of time using minimal resources. We present optimized CPU and GPU implementations of the recursive least-squares algorithm in spiking neural networks. The GPU implementation can train networks of one million neurons, with 100 million plastic synapses and a billion static synapses, about 1,000 times faster than an unoptimized reference CPU implementation. We demonstrate the code's utility by training a network, in less than an hour, to reproduce the activity of > 66, 000 recorded neurons of a mouse performing a decision-making task. The fast implementation enables a more interactive in-silico study of the dynamics and connectivity underlying multi-area computations. It also admits the possibility to train models as in-vivo experiments are being conducted, thus closing the loop between modeling and experiments

Reactive Oxygen Species Released from Hypoxic Hepatocytes Regulates MMP-2 Expression in Hepatic Stellate Cells

Hypoxia is a common environmental stress factor and is associated with fibrogenesis. Matrix metalloproteinase-2 (MMP-2), produced by hepatic stellate cells (HSCs), plays an important role in liver fibrogenesis. However, inconsistent results have been reported on the impact of hypoxia on MMP-2 expression and activity in HSCs. We speculated that cell–cell interaction is involved in the regulation of MMP-2 expression and activity at low oxygen level in vivo. Therefore, in this report we investigated the mechanism by which hypoxic hepatocytes regulates MMP-2 expression in HSCs. Our results showed that the conditioned medium from hypoxia-treated rat hepatocytes strongly induced the expression of MMP-2 mRNA and protein in rat HSC-T6 cells. Reduced glutathione neutralized ROS released from hypoxic hepatocytes, leading to reduced MMP-2 expression in HSC-T6 cells. In addition, phospho-IκB-α protein level was increased in HSC-T6 cells treated with hypoxia conditioned medium, and NF-κB signaling inhibitor inhibited MMP-2 expression in HSC-T6 cells. Taken together, our data suggest that ROS is an important factor released by hypoxic hepatocytes to regulate MMP-2 expression in HSCs, and NF-κB signaling is crucially involved in ROS-induced MMP-2 expression in HSCs. Our findings suggest that strategies aimed at antagonizing the generation of ROS in hypoxic hepatocytes and inhibiting NF-κB signaling in HSCs may represent novel therapeutic options for liver fibrosis

Differentiation and classification of bacterial endotoxins based on surface enhanced Raman scattering and advanced machine learning

Bacterial endotoxin, a major component of the Gram-negative bacterial outer membrane leaflet, is a lipopolysaccharide shed from bacteria during their growth and infection and can be utilized as a biomarker for bacterial detection. Here, the surface enhanced Raman scattering (SERS) spectra of eleven bacterial endotoxins with an average detection amount of 8.75 pg per measurement have been obtained based on silver nanorod array substrates, and the characteristic SERS peaks have been identified. With appropriate spectral pre-processing procedures, different classical machine learning algorithms, including support vector machine, k-nearest neighbor, random forest, etc., and a modified deep learning algorithm, RamanNet, have been applied to differentiate and classify these endotoxins. It has been found that most conventional machine learning algorithms can attain a differentiation accuracy of >99%, while RamanNet can achieve 100% accuracy. Such an approach has the potential for precise classification of endotoxins and could be used for rapid medical diagnoses and therapeutic decisions for pathogenic infections

Accurate localization of linear probe Electrode arrays across multiple brains

Recently developed probes for extracellular electrophysiological recordings have large numbers of electrodes on long linear shanks. Linear electrode arrays, such as Neuropixels probes, have hundreds of recording electrodes distributed over linear shanks that span several millimeters. Because of the length of the probes, linear probe recordings in rodents usually cover multiple brain areas. Typical studies collate recordings across several recording sessions and animals. Neurons recorded in different sessions and animals thus have to be aligned to each other and to a standardized brain coordinate system. Here, we evaluate two typical workflows for localization of individual electrodes in standardized coordinates. These workflows rely on imaging brains with fluorescent probe tracks and warping 3D image stacks to standardized brain atlases. One workflow is based on tissue clearing and selective plane illumination microscopy (SPIM), whereas the other workflow is based on serial block-face two-photon (SBF2P) microscopy. In both cases electrophysiological features are then used to anchor particular electrodes along the reconstructed tracks to specific locations in the brain atlas and therefore to specific brain structures. We performed groundtruth experiments, in which motor cortex outputs are labeled with ChR2 and a fluorescence protein. Light-evoked electrical activity and fluorescence can be independently localized. Recordings from brain regions targeted by the motor cortex reveal better than 0.1-mm accuracy for electrode localization, independent of workflow used.204717/Z/16/Z - Wellcome Trust; Howard Hughes Medical Institute; 209558/Z/17/Z - Wellcome Trust; CIHR; R01 NS112312 - NINDS NIH HHS; Wellcome TrustPublished versio

Genomic heterogeneity of multiple synchronous lung cancer

Multiple synchronous lung cancers (MSLCs) present a clinical dilemma as to whether individual tumours represent intrapulmonary metastases or independent tumours. In this study we analyse genomic profiles of 15 lung adenocarcinomas and one regional lymph node metastasis from 6 patients with MSLC. All 15 lung tumours demonstrate distinct genomic profiles, suggesting all are independent primary tumours, which are consistent with comprehensive histopathological assessment in 5 of the 6 patients. Lung tumours of the same individuals are no more similar to each other than are lung adenocarcinomas of different patients from TCGA cohort matched for tumour size and smoking status. Several known cancer-associated genes have different mutations in different tumours from the same patients. These findings suggest that in the context of identical constitutional genetic background and environmental exposure, different lung cancers in the same individual may have distinct genomic profiles and can be driven by distinct molecular events