Effect of gate voltage on spin transport along α\alpha-helical protein

Recently, the chiral-induced spin selectivity in molecular systems has attracted extensive interest among the scientific communities. Here, we investigate the effect of the gate voltage on spin-selective electron transport through the $\alpha$-helical peptide/protein molecule contacted by two nonmagnetic electrodes. Based on an effective model Hamiltonian and the Landauer-B\"uttiker formula, we calculate the conductance and the spin polarization under an external electric field which is perpendicular to the helix axis of the $\alpha$-helical peptide/protein molecule. Our results indicate that both the magnitude and the direction of the gate field have a significant effect on the conductance and the spin polarization. The spin filtration efficiency can be improved by properly tuning the gate voltage, especially in the case of strong dephasing regime. And the spin polarization increases monotonically with the molecular length without the gate voltage, which is consistent with the recent experiment, and presents oscillating behavior in the presence of the gate voltage. In addition, the spin selectivity is robust against the dephasing, the on-site energy disorder, and the space angle disorder under the gate voltage. Our results could motivate further experimental and theoretical works on the chiral-based spin selectivity in molecular systems.Comment: 8 pages, 7 figure

Altered circulating GDF-15 level predicts sex hormone imbalance in males with major depressive disorder

Background: It has been hypothesized that higher growth differentiation factor 15 (GDF15) level and lower testosterone/ estradiol (T/E) ratio are associated with major depressive disorder (MDD), yet the underlying effect of serum GDF15 on hinting the T/E ratio imbalance is not fully understood. We observed the correlation between serum T/E ratio and circulating GDF15 in male depressed cohort. // Methods: The sample consisted of participants (aged 18 ~ 65 years) from the Renmin Hospital of Wuhan University with MDD (n = 412) defined according to a Structured Clinical Interview for DSM-V (SCID), and male healthy controls (n = 137). Serum levels of testosterone, estradiol, and depression risk biomarkers (thyroid hormone, lipids, hs-CRP, Tenascin-C [TNC], GDF15, KLF4, Gas6, and sgp130) were measured. The associations among log-transformed T/E ratio and these biomarkers were analyzed using univariate correlation analysis, category analyses, and linear regression adjusting for standard risk factors. // Results: Of the sample, 36.89% had lower T/E ratio ( 20:1). After multivariable adjustment, T/E ratio was negatively associated with GDF15 (-0.095 [95% CI -0.170 ~ -0.023] standard deviation [SD] change per SD increase in lg[T/E], P = 0.015) and inversely related to TNC (-0.085 [95% CI -0.167 ~ 0.003] standard deviation [SD] change per SD increase in lg[T/E], P = 0.048). Serum T/E ratio was negatively associated with GDF15 level in both FT3, TSH and HDL strata, whereas this association was not observed in TNC. In T/E ratio strata analyses, there is a significant and negative correlation among T/E ratio and GDF15 in depressive patients with sex hormone imbalance, yet this relationship was not investigated in patients with sex hormone balance. // Conclusion: In our community-based observation, circulating GDF-15 level was greatly and inversely associated with serum T/E ratio, indicating that higher GDF-15 alerts sex hormone imbalance in patients with MDD

Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy

BACKGROUND: Understanding how amino acid substitutions affect protein functions is critical for the study of proteins and their implications in diseases. Although methods have been developed for predicting potential effects of amino acid substitutions using sequence, three-dimensional structural, and evolutionary properties of proteins, the applications are limited by the complication of the features and the availability of protein structural information. Another limitation is that the prediction results are hard to be interpreted with physicochemical principles and biological knowledge. RESULTS: To overcome these limitations, we proposed a novel feature set using physicochemical properties of amino acids, evolutionary profiles of proteins, and protein sequence information. We applied the support vector machine and the random forest with the feature set to experimental amino acid substitutions occurring in the E. coli lac repressor and the bacteriophage T4 lysozyme, as well as to annotated amino acid substitutions occurring in a wide range of human proteins. The results showed that the proposed feature set was superior to the existing ones. To explore physicochemical principles behind amino acid substitutions, we designed a simulated annealing bump hunting strategy to automatically extract interpretable rules for amino acid substitutions. We applied the strategy to annotated human amino acid substitutions and successfully extracted several rules which were either consistent with current biological knowledge or providing new insights for the understanding of amino acid substitutions. When applied to unclassified data, these rules could cover a large portion of samples, and most of the covered samples showed good agreement with predictions made by either the support vector machine or the random forest. CONCLUSION: The prediction methods using the proposed feature set can achieve larger AUC (the area under the ROC curve), smaller BER (the balanced error rate), and larger MCC (the Matthews' correlation coefficient) than those using the published feature sets, suggesting that our feature set is superior to the existing ones. The rules extracted by the simulated annealing bump hunting strategy have comparable coverage and accuracy but much better interpretability as those extracted by the patient rule induction method (PRIM), revealing that the strategy is more effective in inducing interpretable rules

Floquet Weyl semimetal phases in light-irradiated higher-order topological Dirac semimetals

Floquet engineering, the concept of tailoring a system by a periodic drive, is increasingly exploited to design and manipulate topological phases of matter. In this work, we study periodically driven higher-order topological Dirac semimetals associated with a $k$-dependent quantized quadrupole moment by applying circularly polarized light. The undriven Dirac semimetals feature gapless higher-order hinge Fermi arc states which are the consequence of the higher-order topology of the Dirac nodes. Floquet Weyl semimetal phases with hybrid-order topology, characterized by both a $k$-dependent quantized quadrupole moment and a $k$-dependent Chern number, emerge when illumining circularly polarized light. Such Floquet Weyl semimetals support both hinge Fermi arc states and topological surface Fermi arc states. In addition, Floquet Weyl semimetals with tilted Weyl cones in higher-order topological Dirac semimetals are also discussed. Considering numerous higher-order topological Dirac semimetal materials were recently proposed, our findings can be testable soon.Comment: Accepted for publication as a Letter in Phys. Rev.

miR-638 is a new biomarker for outcome prediction of non-small cell lung cancer patients receiving chemotherapy.

MicroRNAs (miRNAs), a class of small non-coding RNAs, mediate gene expression by either cleaving target mRNAs or inhibiting their translation. They have key roles in the tumorigenesis of several cancers, including non-small cell lung cancer (NSCLC). The aim of this study was to investigate the clinical significance of miR-638 in the evaluation of NSCLC patient prognosis in response to chemotherapy. First, we detected miR-638 expression levels in vitro in the culture supernatants of the NSCLC cell line SPC-A1 treated with cisplatin, as well as the apoptosis rates of SPC-A1. Second, serum miR-638 expression levels were detected in vivo by using nude mice xenograft models bearing SPC-A1 with and without cisplatin treatment. In the clinic, the serum miR-638 levels of 200 cases of NSCLC patients before and after chemotherapy were determined by quantitative real-time PCR, and the associations of clinicopathological features with miR-638 expression patterns after chemotherapy were analyzed. Our data helped in demonstrating that cisplatin induced apoptosis of the SPC-A1 cells in a dose- and time-dependent manner accompanied by increased miR-638 expression levels in the culture supernatants. In vivo data further revealed that cisplatin induced miR-638 upregulation in the serum derived from mice xenograft models, and in NSCLC patient sera, miR-638 expression patterns after chemotherapy significantly correlated with lymph node metastasis. Moreover, survival analyses revealed that patients who had increased miR-638 levels after chemotherapy showed significantly longer survival time than those who had decreased miR-638 levels. Our findings suggest that serum miR-638 levels are associated with the survival of NSCLC patients and may be considered a potential independent predictor for NSCLC prognosis

A review of the interaction of medicinal plants and arbuscular mycorrhizal fungi in the rhizosphere

Medicinal plants are well known to have the advantages of high concentration of medicinal ingredients having clinical importance, curative value, small toxic and side effects. Important compounds viz., paclitaxel, camptothecin, and vincristine have been developed from medicinal plants as first-line of clinical drugs, leading to their consistently increasing demand globally. However, the destruction of natural environment due to excessive mining threatened such resources jeopardizing the successful growing of medicinal plants. A group of beneficial arbuscular mycorrhizal (AM) fungi is known to exist in the rhizosphere of medicinal plants, which can establish a reciprocal symbiosis with their roots, namely arbuscular mycorrhizas. These AM fungi are pivotal in the habitat adaptation of medicinal plants. Studies have demonstrated that AM fungi aided in growth promotion and nutrient absorption of medicinal plants, thereby, accelerating the accumulation of medicinal ingredients and aiding resistance against abiotic stresses such as drought, low temperature, and salinity. An AM-like fungus Piriformospora indica is known to be cultured in vitro without roots, later showed analogous effects of AM fungi on medicinal plants. These fungi provide new mechanistic pathways towards the artificial cultivation of medicinal plants loaded with ingredients in huge demand in international market. This review provides an overview of the diversity of AM fungi inhabiting the rhizosphere of medicinal plants, and analyzes the functioning of AM fungi and P. indica, coupled with future lines of research

Stavudine exposure results in developmental abnormalities by causing DNA damage, inhibiting cell proliferation and inducing apoptosis in mouse embryos

Stavudine is an anti-AIDS drug widely used to prevent HIV transmission from pregnant mothers to the fetuses in underdeveloped countries for its low price. However, there is still a controversy on whether stavudine affects embryo development. In the current study, embryotoxicity of stavudine was evaluated using cultured mouse embryos with the concentrations: 5, 10, 15 μM and vehicle control. The data indicated that the effect of stavudine was dose-dependent at early neurogenesis. Stavudine exposure reduced somite numbers, yolk sac diameter, crown-rump length, and increased the rate of embryonic degeneration compared with the control. We chose the lowest but clearly toxic concentration: 5 μM to investigate the molecular mechanisms of the damage. At the molecular level, stavudine produced DNA damage, increased the levels of the phospho-CHK1 and cleaved-caspase-3, and decreased the expression level of proliferating cell nuclear antigen. These changes indicated that stavudine caused a coordinated DNA damage response, inhibited cell proliferation, and induced apoptosis in the embryos. Collectively these results suggest that stavudine exposure disturbs the embryonic development, and its use in pregnant mothers should be re-examined

Nanoparticles (NPs)-mediated lncMALAT1 silencing to reverse cisplatin resistance for effective hepatocellular carcinoma therapy

Platinum-based chemotherapy has been widely used for clinical cancer treatment, but drug resistance is the main barrier to induce the poor prognosis of cancer patients. Long non-coding RNAs (lncRNAs) have been recognized as a type of new cancer therapeutic targets due to their important role in regulating cancer progression such as drug resistance. However, it is still challenged to effectively intervene the expression of lncRNAs as they are usually located at various subcellular organelles (e.g., nucleus, mitochondrion, and endoplasmic reticulum). We herein developed an endosomal pH-responsive nanoparticle (NP) platform for small interfering RNA (siRNA) and cisplatin prodrug co-delivery and effective cisplatin-resistant hepatocellular carcinoma (HCC) therapy. This co-delivery nanoplatform is comprised of a hydrophilic polyethylene glycol (PEG) shell and a hydrophobic poly (2-(diisopropylamino)ethyl methacrylate) (PDPA) core, in which cisplatin prodrug and electrostatic complexes of nucleus-targeting amphiphilic peptide (NTPA) and siRNA are encapsulated. After intravenous injection and then uptake by tumor cells, the endosomal pH could trigger the dissociation of nanoplatform and enhance the endosomal escape of loaded cisplatin prodrug and NTPA/siRNA complexes via the “proton sponge” effect. Subsequently, the NTPA/siRNA complexes could specifically transport siRNA into the nucleus and efficiently reverse cisplatin resistance via silencing the expression of lncRNA metastasis-associated lung adenocarcinoma transcript 1 (lncMALAT1) mainly localized in the nucleus, ultimately inhibiting the growth of cisplatin-resistant HCC tumor

Tilianin improves cognition in a vascular dementia rodent model by targeting miR-193b-3p/CaM- and miR-152-3p/CaMKIIα-mediated inflammatory and apoptotic pathways

IntroductionAlthough vascular dementia (VaD) is the second most prevalent form of dementia, there is currently a lack of effective treatments. Tilianin, isolated from the traditional drug Dracocephalum moldavica L., may protect against ischemic injury by inhibiting oxidative stress and inflammation via the CaMKII-related pathways but with weak affinity with the CaMKII molecule. microRNAs (miRNAs), functioning in post-transcriptional regulation of gene expression, may play a role in the pathological process of VaD via cognitive impairment, neuroinflammatory response, and neuronal dysfunction. This study aimed to investigate the role of tilianin in VaD therapy and the underlying mechanism through which tilianin regulates CaMKII signaling pathways based on miRNA-associated transcriptional action.MethodsRats with 2-vessel occlusion (2VO), a standard model of VaD, were treated with tilianin, vehicle control, and target overexpression or downregulation. High-throughput sequencing, qRT-PCR, and western blot analyses were utilized to identify the downstream target genes and signaling pathways of tilianin involved in VaD.ResultsOur results showed that tilianin ameliorated cognitive deficits, neurodegeneration, and microglial and astrocytic activation in rats with 2VO. Subsequent high-throughput sequencing and qRT-PCR analyses revealed that tilianin increased the downregulated miR-193b-3p and miR-152-3p levels in the cortex and hippocampus of 2VO rats. Mechanistically, miR-193b-3p targeting CaM and miR-152-3p targeting CaMKIIα were identified to play a role in VaD-associated pathology, inhibiting the p38 MAPK/NF--κB p65 pathway and decreasing TNF-α and IL-6 levels. Further gain- and loss-of-function experiments for these key genes showed that tilianin-exerted cognitive improvement by activating the p38 MAPK/NF--κB p65 and Bcl-2/Bax/caspase-3/PARP pathways in the brain of 2VO rats was abolished by miR-193b-3p and miR-152-3p inhibition. Moreover, CaM and CaMKIIα overexpression eliminated the elevated effects of miR-193b-3p and miR-152-3p on tilianin’s protection against ischemic injury through increased inflammatory reactions and apoptotic signaling.DiscussionTogether, these findings indicate that tilianin improves cognition by regulating the miR-193b-3p/CaM- and miR-152-3p/CaMKIIα-mediated inflammatory and apoptotic pathways, suggesting a potential small-molecule regulator of miRNA associated with inflammatory signaling for VaD treatment