Integrated network pharmacology and cellular assay reveal the biological mechanisms of Limonium sinense (Girard) Kuntze against Breast cancer.

BACKGROUND: Limonium Sinense (Girard) Kuntze (L. sinense) has been widely used for the treatment of anaemia, bleeding, cancer, and other disorders in Chinese folk medicine. The aim of this study is to predict the therapeutic effects of L. sinense and investigate the potential mechanisms using integrated network pharmacology methods and in vitro cellular experiments. METHODS: The active ingredients of L. sinense were collected from published literature, and the potential targets related to L. sinense were obtained from public databases. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and DisGeNET enrichment analyses were performed to explore the underlying mechanisms. Molecular docking, cellular experiments, RNA-sequencing (RNA-seq) and Gene Expression Omnibus (GEO) datasets were employed to further evaluate the findings. RESULTS: A total of 15 active ingredients of L. sinense and their corresponding 389 targets were obtained. KEGG enrichment analysis revealed that the biological effects of L. sinense were primarily associated with "Pathways in cancer". DisGeNET enrichment analysis highlighted the potential role of L. sinense in the treatment of breast cancer. Apigenin within L. sinense showed promising potential against cancer. Cellular experiments demonstrated that the L. sinense ethanol extract (LSE) exhibited a significant growth inhibitory effect on multiple breast cancer cell lines in both 2D and 3D cultures. RNA-seq analysis revealed a potential impact of LSE on breast cancer. Additionally, analysis of GEO datasets verified the significant enrichment of breast cancer and several cancer-related pathways upon treatment with Apigenin in human breast cancer cells. CONCLUSION: This study predicts the biological activities of L. sinense and demonstrates the inhibitory effect of LSE on breast cancer cells, highlighting the potential application of L. sinense in cancer treatment.

The Stabilization of S100A9 Structure by Calcium Inhibits the Formation of Amyloid Fibrils.

The calcium-binding protein S100A9 is recognized as an important component of the brain neuroinflammatory response to the onset and development of neurodegenerative disease. S100A9 is intrinsically amyloidogenic and in vivo co-aggregates with amyloid-ß peptide and α-synuclein in Alzheimer's and Parkinson's diseases, respectively. It is widely accepted that calcium dyshomeostasis plays an important role in the onset and development of these diseases, and studies have shown that elevated levels of calcium limit the potential for S100A9 to adopt a fibrillar structure. The exact mechanism by which calcium exerts its influence on the aggregation process remains unclear. Here we demonstrate that despite S100A9 exhibiting α-helical secondary structure in the absence of calcium, the protein exhibits significant plasticity with interconversion between different conformational states occurring on the micro- to milli-second timescale. This plasticity allows the population of conformational states that favour the onset of fibril formation. Magic-angle spinning solid-state NMR studies of the resulting S100A9 fibrils reveal that the S100A9 adopts a single structurally well-defined rigid fibrillar core surrounded by a shell of approximately 15-20 mobile residues, a structure that persists even when fibrils are produced in the presence of calcium ions. These studies highlight how the dysregulation of metal ion concentrations can influence the conformational equilibria of this important neuroinflammatory protein to influence the rate and nature of the amyloid deposits formed.

Impact on S. aureus and E. coli Membranes of Treatment with Chlorhexidine and Alcohol Solutions: Insights from Molecular Simulations and Nuclear Magnetic Resonance.

Membranes form the first line of defence of bacteria against potentially harmful molecules in the surrounding environment. Understanding the protective properties of these membranes represents an important step towards development of targeted anti-bacterial agents such as sanitizers. Use of propanol, isopropanol and chlorhexidine can significantly decrease the threat imposed by bacteria in the face of growing anti-bacterial resistance via mechanisms that include membrane disruption. Here we have employed molecular dynamics simulations and nuclear magnetic resonance to explore the impact of chlorhexidine and alcohol on the S. aureus cell membrane, as well as the E. coli inner and outer membranes. We identify how sanitizer components partition into these bacterial membranes, and show that chlorhexidine is instrumental in this process.

Lipophilicity Modulations by Fluorination Correlate with Membrane Partitioning.

Bioactive compounds generally need to cross membranes to arrive at their site of action. The octanol-water partition coefficient (lipophilicity, logPOW ) has proven to be an excellent proxy for membrane permeability. In modern drug discovery, logPOW and bioactivity are optimized simultaneously, for which fluorination is one of the relevant strategies. The question arises as to which extent the often subtle logP modifications resulting from different aliphatic fluorine-motif introductions also lead to concomitant membrane permeability changes, given the difference in molecular environment between octanol and (anisotropic) membranes. It was found that for a given compound class, there is excellent correlation between logPOW values with the corresponding membrane molar partitioning coefficients (logKp ); a study enabled by novel solid-state 19 F NMR MAS methodology using lipid vesicles. Our results show that the factors that cause modulation of octanol-water partition coefficients similarly affect membrane permeability.

Integrated analysis reveals effects of bioactive ingredients from Limonium Sinense (Girard) Kuntze on hypoxia-inducible factor (HIF) activation.

Limonium Sinense (Girard) Kuntze is a traditional Chinese medicinal herb, showing blood replenishment, anti-tumour, anti-hepatitis, and immunomodulation activities amongst others. However, the mechanism of its pharmacological activities remains largely unknown. Here, we investigated the effects of bioactive ingredients from Limonium Sinense using an integrated approach. Water extracts from Limonium Sinense (LSW) showed a strong growth inhibitory effect on multiple cells in both 2D and 3D cultures. Global transcriptomic profiling and further connectivity map (CMap) analysis identified several similarly acting therapeutic candidates, including Tubulin inhibitors and hypoxia-inducible factor (HIF) modulators. The effect of LSW on the cell cycle was verified with flow cytometry showing a G2/M phase arrest. Integrated analysis suggested a role for gallic acid in mediating HIF activation. Taken together, this study provides novel insights into the bioactive ingredients in Limonium Sinense, highlighting the rich natural resource and therapeutic values of herbal plants.

Phylogenetic diversity of two common Trypanosoma cruzi lineages in the Southwestern United States.

Trypanosoma cruzi is the causative agent of Chagas disease, a devastating parasitic disease endemic to Central and South America, Mexico, and the USA. We characterized the genetic diversity of Trypanosoma cruzi circulating in five triatomine species (Triatoma gerstaeckeri, T. lecticularia, T.indictiva, T. sanguisuga and T. recurva) collected in Texas and Southern Arizona using multilocus sequence typing (MLST) with four single-copy loci (cytochrome oxidase subunit II- NADH dehydrogensase subunit 1 region (COII-ND1), mismatch-repair class 2 (MSH2), dihydrofolate reductase-thymidylate synthase (DHFR-TS) and a nuclear gene with ID TcCLB.506529.310). All T. cruzi variants fall in two main genetic lineages: 75% of the samples corresponded to T. cruzi Discrete Typing Unit (DTU) I (TcI), and 25% to a North American specific lineage previously labelled TcIV-USA. Phylogenetic and sequence divergence analyses of our new data plus all previously published sequence data from those four loci collected in the USA, show that TcIV-USA is significantly different from any other previously defined T. cruzi DTUs. The significant level of genetic divergence between TcIV-USA and other T. cruzi DTUs should lead to an increased focus on understanding the epidemiological importance of this DTU, as well as its geographical range and pathogenicity in humans and domestic animals. Our findings further corroborate the fact that there is a high genetic diversity of the parasite in North America and emphasize the need for appropriate surveillance and vector control programs for Chagas disease in southern USA and Mexico.

Inter-Individual Differences in the Responses to Pain Neuroscience Education in Adults With Chronic Musculoskeletal Pain: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.

Pain neuroscience education (PNE) is an approach used in the management of chronic musculoskeletal pain. Previous reviews on PNE and other pain interventions, have focused on mean treatment effects, but in the context of "precision medicine," any inter-individual differences in treatment response are also important to quantify. If inter-individual differences are present, and predictors identified, PNE could be tailored to certain people for optimizing effectiveness. Such heterogeneity can be quantified using recently formulated approaches for comparing the response variance between the treatment and control groups. Therefore, we conducted a systematic review and meta-analysis on the extracted standard deviations of baseline-to-follow up change to quantify the inter-individual variation in pain, disability and psychosocial outcomes in response to PNE. Electronic databases were searched between January 1, 2002 and June 14, 2018. The review included 5 randomized controlled trials (n = 428) in which disability outcomes were reported. Using a random effects meta-analysis, the pooled SD (95% confidence interval) for control group-adjusted response heterogeneity to PNE was 7.36 units /100 (95% confidence interval = -3.93 to 11.12). The 95% prediction interval for this response heterogeneity SD was wide (-10.20 to 14.57 units /100). The control group-adjusted proportion of "responders" in the population who would be estimated to exceed a clinically important change of 10/100 ranged from 18 to 45%. Therefore, when baseline-to-follow up random variability in disability is taken into account (informed by the control arm), there is currently insufficient evidence for the notion of clinically important inter-individual differences in disability responses to PNE in people with chronic musculoskeletal pain. The protocol was published on PROSPERO (CRD42017068436). PERSPECTIVE: We bring a novel method to pain science for calculating inter-individual differences in response to a treatment. This is conductedwithin the context of a systematic review and meta-analysis on PNE. We highlight how using erroneous methods for calculating inter-individual differences can drastically change conclusions when compared to appropriate methods.

Strategies for 1 H-Detected Dynamic Nuclear Polarization Magic-Angle Spinning NMR Spectroscopy.

Combining dynamic nuclear polarization with proton detection significantly enhances the sensitivity of magic-angle spinning NMR spectroscopy. Herein, the feasibility of proton-detected experiments with slow (10 kHz) magic angle spinning was demonstrated. The improvement in sensitivity permits the acquisition of indirectly detected 14 N NMR spectra allowing biomolecular structures to be characterized without recourse to isotope labelling. This provides a new tool for the structural characterization of environmental and medical samples, in which isotope labelling is frequently intractable.

The impacts of ocean acidification on marine trace gases and the implications for atmospheric chemistry and climate.

Surface ocean biogeochemistry and photochemistry regulate ocean-atmosphere fluxes of trace gases critical for Earth's atmospheric chemistry and climate. The oceanic processes governing these fluxes are often sensitive to the changes in ocean pH (or pCO2) accompanying ocean acidification (OA), with potential for future climate feedbacks. Here, we review current understanding (from observational, experimental and model studies) on the impact of OA on marine sources of key climate-active trace gases, including dimethyl sulfide (DMS), nitrous oxide (N2O), ammonia and halocarbons. We focus on DMS, for which available information is considerably greater than for other trace gases. We highlight OA-sensitive regions such as polar oceans and upwelling systems, and discuss the combined effect of multiple climate stressors (ocean warming and deoxygenation) on trace gas fluxes. To unravel the biological mechanisms responsible for trace gas production, and to detect adaptation, we propose combining process rate measurements of trace gases with longer term experiments using both model organisms in the laboratory and natural planktonic communities in the field. Future ocean observations of trace gases should be routinely accompanied by measurements of two components of the carbonate system to improve our understanding of how in situ carbonate chemistry influences trace gas production. Together, this will lead to improvements in current process model capabilities and more reliable predictions of future global marine trace gas fluxes.

Magnetically aligned membrane mimetics enabling comparable chiroptical and magnetic resonance spectroscopy studies.

Lipidic bicelles have been widely used for the analysis of integral membrane proteins where their spontaneous alignment in an magnetic field has been exploited for oriented sample solid-state NMR studies. Many of their physical properties however make them well suited to the analysis of membrane proteins by circular dichroism (CD) and synchrotron radiation circular dichroism (SRCD). In this paper we have identified bicelle compositions that permit comparable studies of integral membrane proteins by solid-state NMR, CD, and SRCD; complementary methods that can provide insights into protein structure and the interactions with drugs and other small molecules. Furthermore we have been able to identify bicelle compositions that allow the magnetic alignment of the bicelles at fields routinely available in magnetic CD instruments. This potentially provides a route to the preparation of samples for oriented CD that mitigates many of the issues associated with the preparation of mechanically aligned samples, although we demonstrate that the dynamics present within the system can complicate the analysis of such spectra.

Optimization and validation of a deep learning CuZr atomistic potential: Robust applications for crystalline and amorphous phases with near-DFT accuracy.

We show that a deep-learning neural network potential (DP) based on density functional theory (DFT) calculations can well describe Cu-Zr materials, an example of a binary alloy system, that can coexist in as ordered intermetallic and as an amorphous phase. The complex phase diagram for Cu-Zr makes it a challenging system for traditional atomistic force-fields that cannot accurately describe the different properties and phases. Instead, we show that a DP approach using a large database with ∼300k configurations can render results generally on par with DFT. The training set includes configurations of pristine and bulk elementary metals and intermetallic structures in the liquid and solid phases in addition to slab and amorphous configurations. The DP model was validated by comparing bulk properties such as lattice constants, elastic constants, bulk moduli, phonon spectra, and surface energies to DFT values for identical structures. Furthermore, we contrast the DP results with values obtained using well-established two embedded atom method potentials. Overall, our DP potential provides near DFT accuracy for the different Cu-Zr phases but with a fraction of its computational cost, thus enabling accurate computations of realistic atomistic models, especially for the amorphous phase.

Issues in the determination of 'responders' and 'non-responders' in physiological research.

NEW FINDINGS: What is the topic for this review? We discuss the dichotomization of continuous-level physiological measurements into 'responders' and 'non-responders' when interventions/treatments are examined in robust parallel-group studies. What advances does it highlight? Sample responder counts are biased by pre-to-post within-subject variability. Sample differences in counts may be explained wholly by differences in mean response, even without individual response heterogeneity and even if test-retest measurement error informs the choice of response threshold. A less biased and more informative approach uses the SD of individual responses to estimate the chance a new person from the population of interest will be a responder. ABSTRACT: As a follow-up to our 2015 review, we cover more issues on the topic of 'response heterogeneity', which we define as clinically important individual differences in the physiological responses to the same treatment/intervention that cannot be attributed to random within-subject variability. We highlight various pitfalls with the common practice of counting the number of 'responders', 'non-responders' and 'adverse responders' in samples that have been given certain treatments or interventions for research purposes. We focus on the classical parallel-group randomized controlled trial and assume typical good practice in trial design. We show that sample responder counts are biased because individuals differ in terms of pre-to-post within-subject random variability in the study outcome(s) and not necessarily treatment response. Ironically, sample differences in responder counts may be explained wholly by sample differences in mean response, even if there is no response heterogeneity at all. Sample comparisons of responder counts also have relatively low statistical precision. These problems do not depend on how the response threshold has been selected, e.g. on the basis of a measurement error statistic, and are not rectified fully by the use of confidence intervals for individual responses in the sample. The dichotomization of individual responses in a research sample is fraught with pitfalls. Less biased approaches for estimating the proportion of responders in a population of interest are now available. Importantly, these approaches are based on the SD for true individual responses, directly incorporating information from the control group.

Quantitative analysis of 14N quadrupolar coupling using 1H detected 14N solid-state NMR.

Magic-angle spinning solid-state NMR is increasingly utilized to study the naturally abundant, spin-1 nucleus 14N, providing insights into the structure and dynamics of biological and organic molecules. In particular, the characterisation of 14N sites using indirect detection has proven useful for complex molecules, where the 'spy' nucleus provides enhanced sensitivity and resolution. Here we exploit the sensitivity of proton detection, to indirectly characterise 14N sites using a moderate rf field to generate coherence between the 1H and 14N at moderate and fast-magic-angle spinning frequencies. Efficient numerical simulations have been developed that have allowed us to quantitatively analyse the resulting 14N lineshapes to determine both the size and asymmetry of the quadrupolar interaction. Exploiting only naturally occurring abundant isotopes will aid the analysis of materials with the need to resort to isotope labelling, whilst providing additional insights into the structure and dynamics that the characterisation of the quadrupolar interaction affords.

14N overtone NMR under MAS: Signal enhancement using cross-polarization methods.

Polarization transfer methods are widely adopted for the purpose of correlating different nuclear species as well as to achieve signal enhancement. Polarization transfer from 1H to the 14N overtone transition (Δm = 2) can be achieved using cross polarization methods under magic-angle spinning conditions, where spin locks of the order of several milliseconds can be obtained on common bio-solids (α-glycine and N-acetylvaline). Signal enhancement factors up to 4.4 per scan, can be achieved under favorable conditions, despite MHz-sized quadrupolar interaction. Moreover, we present a detailed theoretical treatment and accurate numerical simulations which are in excellent agreement the unusual experimental matching conditions observed for cross-polarization to 14N overtone.

Structural basis of membrane disruption and cellular toxicity by α-synuclein oligomers.

Oligomeric species populated during the aggregation process of α-synuclein have been linked to neuronal impairment in Parkinson's disease and related neurodegenerative disorders. By using solution and solid-state nuclear magnetic resonance techniques in conjunction with other structural methods, we identified the fundamental characteristics that enable toxic α-synuclein oligomers to perturb biological membranes and disrupt cellular function; these include a highly lipophilic element that promotes strong membrane interactions and a structured region that inserts into lipid bilayers and disrupts their integrity. In support of these conclusions, mutations that target the region that promotes strong membrane interactions by α-synuclein oligomers suppressed their toxicity in neuroblastoma cells and primary cortical neurons.

Relevance of CARC and CRAC Cholesterol-Recognition Motifs in the Nicotinic Acetylcholine Receptor and Other Membrane-Bound Receptors.

Cholesterol is a ubiquitous neutral lipid, which finely tunes the activity of a wide range of membrane proteins, including neurotransmitter and hormone receptors and ion channels. Given the scarcity of available X-ray crystallographic structures and the even fewer in which cholesterol sites have been directly visualized, application of in silico computational methods remains a valid alternative for the detection and thermodynamic characterization of cholesterol-specific sites in functionally important membrane proteins. The membrane-embedded segments of the paradigm neurotransmitter receptor for acetylcholine display a series of cholesterol consensus domains (which we have coined "CARC"). The CARC motif exhibits a preference for the outer membrane leaflet and its mirror motif, CRAC, for the inner one. Some membrane proteins possess the double CARC-CRAC sequences within the same transmembrane domain. In addition to in silico molecular modeling, the affinity, concentration dependence, and specificity of the cholesterol-recognition motif-protein interaction have recently found experimental validation in other biophysical approaches like monolayer techniques and nuclear magnetic resonance spectroscopy. From the combined studies, it becomes apparent that the CARC motif is now more firmly established as a high-affinity cholesterol-binding domain for membrane-bound receptors and remarkably conserved along phylogenetic evolution.

Salt Gradient Modulation of MicroRNA Translocation through a Biological Nanopore.

In resistive pulse sensing of microRNA biomarkers, selectivity is achieved with polynucleotide-extended DNA probes, with the unzipping of a miRNA-DNA duplex in the nanopore recorded as a resistive current pulse. As the assay sensitivity is determined by the pulse frequency, we investigated the effect of cis/trans electrolyte concentration gradients applied over α-hemolysin nanopores. KCl gradients were found to exponentially increase the pulse frequency, while reducing the preference for 3'-first pore entry of the duplex and accelerating duplex unzipping, all manifestations of an enhanced electrophoretic force. Unlike silicon nitride pores, a counteracting contribution from electro-osmotic flow along the pore wall was not apparent. Significantly, a gradient of 0.5/4 M KCl increased the pulse frequency ∼60-fold with respect to symmetrical 1 M KCl, while the duplex dwell time in the nanopore remained acceptable for pulse detection and could be extended by LiCl addition. Steeper gradients caused lipid bilayer destabilization and pore instability, limiting the total number of recorded pulses. The 8-fold KCl gradient enabled a linear relationship between pulse frequency and miRNA concentration for the range of 0.1-100 nM. This work highlights differences between biological and solid-state nanopore sensing and provides strategies for subnanomolar miRNA quantification with bilayer-embedded porins.

Lipid Driven Nanodomains in Giant Lipid Vesicles are Fluid and Disordered.

It is a fundamental question in cell biology and biophysics whether sphingomyelin (SM)- and cholesterol (Chol)- driven nanodomains exist in living cells and in model membranes. Biophysical studies on model membranes revealed SM and Chol driven micrometer-sized liquid-ordered domains. Although the existence of such microdomains has not been proven for the plasma membrane, such lipid mixtures have been often used as a model system for 'rafts'. On the other hand, recent super resolution and single molecule results indicate that the plasma membrane might organize into nanocompartments. However, due to the limited resolution of those techniques their unambiguous characterization is still missing. In this work, a novel combination of Förster resonance energy transfer and Monte Carlo simulations (MC-FRET) identifies directly 10 nm large nanodomains in liquid-disordered model membranes composed of lipid mixtures containing SM and Chol. Combining MC-FRET with solid-state wide-line and high resolution magic angle spinning NMR as well as with fluorescence correlation spectroscopy we demonstrate that these nanodomains containing hundreds of lipid molecules are fluid and disordered. In terms of their size, fluidity, order and lifetime these nanodomains may represent a relevant model system for cellular membranes and are closely related to nanocompartments suggested to exist in cellular membranes.