Characterizing interaction of multiple nanocavity confined plasmids in presence of large DNA model nucleoid.

Bacteria have numerous large dsDNA molecules that freely interact within the cell, including multiple plasmids, primary and secondary chromosomes. The cell membrane maintains a micron-scale confinement, ensuring that the dsDNA species are proximal at all times and interact strongly in a manner influenced by the cell morphology (e.g. whether cell geometry is spherical or anisotropic). These interactions lead to non-uniform spatial organization and complex dynamics, including segregation of plasmid DNA to polar and membrane proximal regions. However, exactly how this organization arises, how it depends on cell morphology and number of interacting dsDNA species are under debate. Here, using an in vitro nanofluidic model, featuring a cavity that can be opened and closed in situ, we address how plasmid copy number and confinement geometry alter plasmid spatial distribution and dynamics. We find that increasing the plasmid number alters the plasmid spatial distribution and shortens the plasmid polar dwell time; sharper cavity end curvature leads to longer plasmid dwell times.

Mixing and demixing arising from compression of two semiflexible polymer chains in nanochannels.

We use molecular dynamics simulation to probe the non-equilibrium physics of two nanochannel-confined semiflexible polymers in a homogeneous flow field. We find that for sufficiently stiff chains the internal organization of the two chains takes the form of interwoven folds and circular coils. This organization can lead to mixing or demixing depending on chain stiffness and flow speed. At low and intermediate flow, the two chains adopt a folded configuration, which favours mixing. At high flow, the two chains adopt a predominantly coiled configuration. The coiled configuration results in demixing when the chains are compressed from an initially demixed condition and mixing when the chains are compressed from an initially mixed condition. We find that the mixing/demixing behaviour is governed by the ratio of the number of folded segments of one chain relative to the other at low flow and by the degree of coiling in both chains at high flow. For decreasing stiffness, the chains start to aggregate locally instead of mixing smoothly at low and intermediate flow. In the limit of completely flexible chains, the two chains either completely segregate at low flow, or adopt a locally demixed configuration consisting of large aggregates of one chain relative to the other that undergo complex stochastic dynamics, diffusing, disintegrating, and reforming at intermediate flow. The transition from complete segregation to the aggregate-dominated configuration occurs when the linear intra-chain ordering breaks down.

A tunable perfect absorber based on a black phosphorus/bowtie shaped cavity hybrid metasurface.

The practical application of black phosphorus (BP) is limited by its low absorption characteristics. In this work, we propose a perfect absorber based on a BP and bowtie shaped cavity, which has high tunability and excellent optical performance. This absorber effectively increases the light-matter interaction and achieves perfect absorption by using a monolayer BP and a reflector to form a Fabry-Perot cavity. We study the influence of structural parameters on the absorption spectrum and realize the adjustment of frequency and absorption in a certain range. Applying an external electric field on the surface of BP by electrostatic gating, we can change its carrier concentration to control its optical properties. In addition, we can flexibly tune the absorption and Q-factor by varying the polarization direction of incident light. This absorber has promising applications in optical switches, sensing, and slow light, which provides a new perspective for the practical application of BP and a foundation for future research, offering possibilities for more applications.

Targeting DNA-PK overcomes acquired resistance to third-generation EGFR-TKI osimertinib in non-small-cell lung cancer.

The third-generation of epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs), represented by osimertinib, has achieved remarkable clinical outcomes in the treatment of non-small-cell lung cancer (NSCLC) with EGFR mutation. However, resistance eventually emerges in most patients and the underlying molecular mechanisms remain to be fully understood. In this study, we generated an osimertinib-acquired resistant lung cancer model from a NSCLC cell line H1975 harboring EGFR L858R and T790M mutations. We found that the capacity of DNA damage repair was compromised in the osimertinib resistant cells, evidenced by increased levels of γH2AX and higher intensity of the comet tail after withdrawal from cisplatin. Pharmacological inhibiting the activity or genetic knockdown the expression of DNA-PK, a key kinase in DNA damage response (DDR), sensitized the resistant cells to osimertinib. Combination of osimertinib with the DNA-PK inhibitor, PI-103, or NU7441, synergistically suppressed the proliferation of the resistant cells. Mechanistically, we revealed that DNA-PK inhibitor in combination with osimertinib resulted in prolonged DNA damage and cell cycle arrest. These findings shed new light on the mechanisms of osimertinib resistance in the aspect of DNA repair, and provide a rationale for targeting DNA-PK as a therapeutic strategy to overcome osimertinib-acquired resistance in NSCLC.

Correction: Probing the organization and dynamics of two DNA chains trapped in a nanofluidic cavity.

Correction for 'Probing the organization and dynamics of two DNA chains trapped in a nanofluidic cavity' by Xavier Capaldi et al., Soft Matter, 2018, 14, 8455-8465.

Comparison Study of ASCO and TOAST Classification System in Chinese Minor Stroke Patients.

BACKGROUND: Precise subtype classification based on underlying pathophysiology is important to prevent recurrent attack in minor stroke patients. A newly developed Atherosclerosis, Small vessel disease, Cardiac source, Others (ASCO) phenotypic classification system aims to characterize patients using different grades of evidence for stroke subtypes. However, this system has not been specifically applied to minor stroke population. In our study, the impact of using the newer ASCO criteria on minor stroke etiologies was investigated, and compared with that of Trial of ORG 10172 in Acute Stroke Treatment (TOAST) classification. METHODS: Consecutive patients with minor ischemic stroke (NIHSS ≤3) were assessed and subtyped by the ASCO and TOAST systems. Stroke etiologies were presented and compared. The McNemar test and k statistic were used to analyze the difference and concordance between the 2 algorithms, respectively. RESULTS: A total of 604 first-ever minor stroke patients were analyzed in the present study. Using TOAST classification, large artery atherosclerosis was the most frequent subtype (281, 46.5%), followed by small artery occlusion category (165, 27.3%). When ASCO was applied, 37 different profiles of stroke etiologies were identified. Using grade 1 of evidence, atherosclerosis (A1) was the most frequent subtype (308, 51.0%), followed by small vessel disease (S1, 178, 29.5%). Under consideration of grades 1 and 2, 239 (39.6%) patients were classified into more than 1 category. The ASCO system revealed determined etiologies in 104 of the 137 patients classified to cause undetermined subtype by TOAST classification. Good to very good accordance was observed between ASCO grade 1 and TOAST schemes across etiologic subtypes (κ = 0.719-0.832) except cause undetermined category (κ = 0.470). CONCLUSION: Application of ASCO decreased the proportion of patients assigned to cause undermined category compared to TOAST system. Comprehensive characteristics of ASCO system might be helpful in the personalized therapy or secondary prevention for individual patients in the future.

Probing the organization and dynamics of two DNA chains trapped in a nanofluidic cavity.

Here we present a pneumatically-actuated nanofluidic platform that has the capability of dynamically controlling the confinement environment of macromolecules in solution. Using a principle familiar from classic devices based on soft-lithography, the system uses pneumatic pressure to deflect a thin nitride lid into a nanoslit, confining molecules in an array of cavities embedded in the slit. We use this system to quantify the interactions of multiple confined DNA chains, a key problem in polymer physics with important implications for nanofluidic device performance and DNA partitioning/organization in bacteria and the eukaryotes. In particular, we focus on the problem of two-chain confinement, using differential staining of the chains to independently assess the chain conformation, determine the degree of partitioning/mixing in the cavities and assess coupled diffusion of the chain center-of-mass positions. We find that confinement of more than one chain in the cavity can have a drastic impact on the polymer dynamics and conformation.

Theoretical analysis and applications in inverse T-shape structure.

An inverse T-shape structure, consisting of a bus waveguide coupled with two perpendicular rectangular cavities, has been investigated numerically and theoretically. The position of the transparency window can be manipulated by adjusting the lateral displacement between the two perpendicular cavities. The effects of changing different structural parameters on the transmission features are investigated in detail. The results indicate that the length of two cavities play important roles in optimizing optical response. Finally, two simple applications based on the inverse T-shape structure are briefly discussed. The findings demonstrate that the first- and second-order modes can be separated without interference, and the sensitivity of the inverse T-shape is as high as 1750 nm per refractive index unit (RIU); the corresponding figure of merit (FOM) reaches up to 77.1 RIU-1, which is higher than in previous reports. The plasmonic configuration possesses the advantages of easy fabrication, compactness, and higher sensitivity as well as higher FOM, which will greatly benefit the compact plasmonic filter and high-sensitivity nanosensor in highly integrated optical devices.

Increase of circulating miR-223 and insulin-like growth factor-1 is associated with the pathogenesis of acute ischemic stroke in patients.

BACKGROUND: The relationship between circulating microRNA-223 and pathogenesis of acute ischemic stroke is unknown. Here we investigated the roles and possible targets of circulating microRNA-223 in human ischemic stroke within the first 72 hours. METHODS: Blood samples were collected from patients within 72 hours after cerebral ischemia (n = 79) and compared with healthy control samples (n = 75). The level of possible downstream factors of microRNA-223 including insulin-like growth factor-1, insulin-like growth factor-1 receptor and interleukin-6 was examined by ELISA assay. The relationship between the microRNA-223 level and NIHSS scores, TOAST subtypes, and infarct volume was analyzed respectively. In addition, twelve adult male CD-1 mice underwent middle cerebral artery occlusion using the suture technique. Circulating blood and brain tissue in the ischemic ipsilateral hemisphere were collected at 24 hours after middle cerebral artery occlusion. microRNA-223 was detected by real-time polymerase chain reactions. RESULTS: microRNA-223 levels in the circulating blood of acute ischemic stroke patients were greatly increased compared to the control (p < 0.05). microRNA-223, which were negatively correlated with NIHSS scores (r = -0.531, p < 0.01) and infarct volume (r = -0.265, p = 0.039), was significantly up-regulated in large artery and small artery strokes. The plasma level of insulin-like growth factor-1 was positively associated with that of microRNA-223 (r = 0.205, p = 0.022). Moreover, microRNA-223 in blood and brain were positively correlated (r = 0.834, p < 0.05), and they were up-regulated significantly in mice that underwent middle cerebral artery occlusion (p < 0.05). CONCLUSIONS: Our results suggest that microRNA-223 is associated with acute ischemic stroke and possibly plays a role in stroke through up-regulating growth factor such as insulin-like growth factor-1 gene.

[A novel dipeptidyl peptidase IV inhibitors developed through scaffold hopping and drug splicing strategy].

Though all the marketed drugs of dipeptidyl peptidase IV inhibitors are structurally different, their inherent correlation is worthy of further investigation. Herein we rapidly discovered a novel DPP-IV inhibitor 8g (IC50 = 4.9 nmol.L-1) which exhibits as good activity and selectivity as the market drugs through scaffold hopping and drug splicing strategies based on alogliptin and linagliptin. This study demonstrated that the employment of classic medicinal chemistry strategy to the marketed drugs with specific target is an efficient approach to discover novel bioactive molecules.

Transient physics in the compression and mixing dynamics of two nanochannel-confined polymer chains.

We use molecular dynamics (MD) simulation and nanofluidic experiments to probe the non-equilibrium transient physics of two nanochannel-confined polymers driven against a permeable barrier in a flow field. For chains with a persistence length P smaller than the channel diameter D, both simulation and experiment with dsDNA reveal nonuniform mixing of the two chains, with one chain dominating locally in what we term "aggregates." Aggregates undergo stochastic dynamics, persisting for a limited time, then disappearing and reforming. Whereas aggregate-prone mixing occurs immediately at sufficiently high flow speeds, chains stay segregated at intermediate flow for some time, often attempting to mix multiple times, before suddenly successfully mixing. Observation of successful mixing nucleation events in nanofluidic experiments reveal that they arise through a peculiar "back-propagation" mechanism whereby the upstream chain, closest to the barrier, penetrates and passes through the downstream chain (farthest from the barrier) moving against the flow direction. Simulations suggest that the observed back-propagation nucleation mechanism is favored at intermediate flow speeds and arises from a special configuration where the upstream chain exhibits one or more folds facing the downstream chain, while the downstream chain has an unfolded chain end facing upstream.

Development and validation of a predictive model for severe white matter hyperintensity with obesity.

Purpose: The purpose of the present study was to identify predictors of severe white matter hyperintensity (WMH) with obesity (SWO), and to build a prediction model for screening obese people with severe WMH without Nuclear Magnetic Resonance Imaging (MRI) examination. Patients subjects and methods: From September 2020 to October 2021, 650 patients with WMH were recruited consecutively. The subjects were divided into two groups, SWO group and non-SWO group. Univariate and Logistic regression analysis were was applied to explore the potential predictors of SWO. The Youden index method was adopted to determine the best cut-off value in the establishment of the prediction model of SWO. Each parameter had two options, low and high. The score table of the prediction model and nomogram based on the logistic regression were constructed. Of the 650 subjects, 487 subjects (75%) were randomly assigned to the training group and 163 subjects (25%) to the validation group. By resampling the area under the curve (AUC) of the subject's operating characteristics and calibration curves 1,000 times, nomogram performance was verified. A decision curve analysis (DCA) was used to evaluate the nomogram's clinical usefulness. By resampling the area under the curve (AUC) of the subject's operating characteristics and calibration curves 1,000 times, nomogram performance was verified. A decision curve analysis (DCA) was used to evaluate the nomogram's clinical usefulness. Results: Logistic regression demonstrated that hypertension, uric acid (UA), complement 3 (C3) and Interleukin 8 (IL-8) were independent risk factors for SWO. Hypertension, UA, C3, IL-8, folic acid (FA), fasting C-peptide (FCP) and eosinophil could be used to predict the occurrence of SWO in the prediction models, with a good diagnostic performance, Areas Under Curves (AUC) of Total score was 0.823 (95% CI: 0.760-0.885, p < 0.001), sensitivity of 60.0%, specificity of 91.4%. In the development group, the nomogram's AUC (C statistic) was 0.829 (95% CI: 0.760-0.899), while in the validation group, it was 0.835 (95% CI: 0.696, 0.975). In both the development and validation groups, the calibration curves following 1,000 bootstraps showed a satisfactory fit between the observed and predicted probabilities. DCA showed that the nomogram had great clinical utility. Conclusion: Hypertension, UA, C3, IL-8, FA, FCP and eosinophil models had the potential to predict the incidence of SWO. When the total score of the model exceeded 9 points, the risk of SWO would increase significantly, and the nomogram enabled visualization of the patient's WMH risk. The application prospect of our models mainly lied in the convenient screening of SWO without MRI examination in order to detect SWO and control the WMH hazards early.

One-Step Synthesis of Chitosan Hydrogel as Electrochemical Chemosensor for Hydrogen Sulfide Detection in Pregnancy-Induced Hypertension Syndrome Serum Sample.

Oxidative stress caused by pregnancy-induced hypertension syndrome significantly affects the health of pregnant women. Hydrogen sulfide is a typical gaseous signal molecule against oxidative stress, and it is of profound significance to develop a detection method. In this study, a stimuli-responsive hydrogel was constructed based on the coordination and bonding principle of metal ions and chitosan (CS) to realize the quantitative detection of hydrogen sulfide (H2S). The chain of CS contains a large number of amino groups and hydroxyl groups, which can form the coordination structure with Cu2+, triggering CS to form a stable hydrogel. The hydrogel can be formed within about 5 s, which has the characteristics of rapid preparation. In the presence of target H2S, the cross-linking agent Cu2+ in the hydrogel can compete out, resulting in the collapse of the hydrogel and the release of the electrochemical probe. By detecting the concentration of the released electrochemical probe, the quantitative detection of H2S can be achieved. The prepared hydrogel has a good linear relationship with the concentration of H2S from 1 µM to 60 µm. At the same time, the hydrogel has good specificity and stability, and it can be applied to the detection of H2S in serum samples.

Discovery of potent dipeptidyl peptidase IV inhibitors through pharmacophore hybridization and hit-to-lead optimization.

A novel dipeptidyl peptidase IV inhibitor hit (5, IC50=0.86 µM) was structurally derived from our recently disclosed preclinical candidate 4 by replacing the cyanobenzyl with a butynyl based on pharmacophore hybridization. A hit-to-lead optimization effort was then initiated to improve its potency. Most N-substituted analogs exhibited good in vitro activity, and compound 18o (IC50=1.55 nM) was identified to be a potent dipeptidyl peptidase IV inhibitor with a significantly improved pharmacokinetic properties (bioavailablity: 41% vs 82.9%; T1/2: 2h vs 4.9h).

Differences of circulating inflammatory markers between large- and small vessel disease in patients with acute ischemic stroke.

BACKGROUND: The difference of inflammatory response between the pathogenesis of cerebral large- and small vessel disease after stroke remains unclear. In present study, we aim to determine the association of circulating inflammatory markers with different stroke subtype. METHODS: 99 patients with non-cardioembolic stroke were divided into large artery atherosclerosis (LAA) and small-artery occlusion (SAO) according to TOAST classification. A panel of plasma inflammatory markers including leukocyte, lymphocyte, CRP, fibrinogen, D-dimer, CD40L, IFN-γ, IL-1α, IL-1ß, IL-6, IL-8, IL-17 and TNF-α were measured within 72 hours following cerebral ischemia. The relation of their levels in plasma with stroke subtype was further studied. All statistical data analysis was performed by SPSS 17.0 software. RESULTS: We found that only CRP were closely associated with stroke subtype (p<0.05). Compared to SAO subgroup, the plasma levels of CRP was higher in LAA subgroup (p<0.05). The predictive efficiency of CRP more than 3.2 for LAA was 85.7% sensitivity. The influencing factor of CRP includes IL-6, lymphocyte, fibrinogen and D-dimer. CONCLUSION: LAA had a stronger activation of inflammation than SAO in the pathogenesis, which was associated with the changes of CRP.

Cocktail blood biomarkers: prediction of clinical outcomes in patients with acute ischemic stroke.

BACKGROUND: Timely prediction of stroke outcomes is important for proper personalized treatment. In the present study, we aimed to develop cocktail blood biomarkers to increase prediction efficiency using a combination of hemostasis, inflammatory and repair-related biomarkers. METHODS: 105 patients suffering from acute ischemic stroke were divided into good outcome group and poor outcome group by modified Rankin Scale (mRS). Cytokines including CD40L, IFN-γ, IL-1α, IL-1ß, IL-6, IL-8, IL-17 and TNF-α, as well as hemostasis markers fibrinogen, fibrin degradation products (FDP), D-dimer, tissue plasminogen activator, and plasminogen activation inhibitor-1 in plasma were examined by ELISA. Repair-related biomarker microRNA-210 (miR-210) was measured by real-time PCR. The prediction efficiency was explored by receiver operator characteristic analysis. RESULTS: We demonstrated that FDP, IL-6 and miR-210 levels were closely associated with mRS in stroke patients. The prediction sensitivity of FDP, IL-6 and miR-210 for stroke outcome was 72.0, 86.7 and 82.5%, respectively. Using a combination of biomarkers including FDP, IL-6 and miR-210, the prognostic sensitivity of ischemic stroke increased to 95.2%. CONCLUSION: The combination of FDP, IL-6 and miR-210 has a high sensitivity for predicting stroke recovery, it serves as a potential cocktail blood biomarker. It provides a novel approach for stroke prognosis.

Idiopathic hypereosinophilic syndrome presenting as capsular warning syndrome: A case report and literature review.

RATIONALE: Few reports of idiopathic hypereosinophilic syndrome exist presenting as ischemic cerebrovascular disease, and the majority are watershed infarction. We report the first case of idiopathic hypereosinophilic syndrome that has clinical features of capsular warning syndrome lasting 6 weeks. PATIENT CONCERNS: A 26-year-old man complained of recurrent right limb weakness, accompanying slurred speech, and right facial paresthesia. DIAGNOSES: The patient was diagnosed with idiopathic hypereosinophilic syndrome (IHES). INTERVENTIONS: Adequate glucocorticoid and anticoagulant treatments were given. OUTCOMES: The patient's motor ability improved, and he was discharged 2 weeks later. Muscle strength in the right-side extremities had fully recovered at a 3-month follow-up after discharge. LESSONS: This case suggests that idiopathic hypereosinophilic syndrome should be considered as a cause of capsular warning syndrome, and the dose of glucocorticoid and the efficacy evaluation index needs to be reevaluated for the treatment of ischemic cerebrovascular disease associated with idiopathic hypereosinophilic syndrome.

An epitope encoded by uORF of RNF10 elicits a therapeutic anti-tumor immune response.

Tumor-specific antigens (TSAs) are crucial for tumor-specific immune response that reduces tumor burden and thus serve as important targets for immunotherapy. Identification of novel TSAs can provide new strategies for immunotherapies. In this study, we demonstrated that the upstream open reading frame (uORF) of RNF10 encodes an antigenic peptide (RNF10 uPeptide), capable of eliciting a T cell-mediated anti-tumor immune response. We initially demonstrated the immunogenicity of the RNF10 uPeptide in a CT26 tumor mouse model, by showing that its epitope was specifically recognized by CD8+ T cells. Vaccination of mice with the long form of the RNF10 uPeptide conferred strong anti-tumor activity. Next, we proved that the human RNF10 uORF could be translated. In addition, we predicted the binding of an RNF10 uPeptide epitope to HLA-A∗02:01 (HLA-A2). This HLA-A2-restricted epitope of the RNF10 uPeptide induced a potent specific human T cell response. Finally, we showed that an HLA-A2-restricted cytotoxic T cell (CTL) clone, derived from a pancreatic cancer patient, recognized the RNF10 uPeptide epitope (RLFGQQQRA) and lysed HLA-A2+ pancreatic carcinoma cells expressing the RNF10 uPeptide. These results indicate that the RNF10 uPeptide could be a promising target for pancreatic carcinoma immunotherapy.

Case report: Hereditary spastic paraplegia with a novel homozygous mutation in ZFYVE26.

Hereditary spastic paraplegia (HSP) is a group of neurodegenerative diseases with genetic and clinical heterogeneity characterized by spasticity and weakness of the lower limbs. It includes four genetic inheritance forms: autosomal dominant inheritance (AD), autosomal recessive inheritance (AR), X-linked inheritance, and mitochondrial inheritance. To date, more than 82 gene loci have been found to cause HSP, and SPG15 (ZFYVE26) is one of the most common autosomal recessive hereditary spastic paraplegias (ARHSPs) with a thin corpus callosum (TCC), presents with early cognitive impairment and slowly progressive leg weakness. Here, we reported a homozygous pathogenic variant in ZFYVE26. A 19-year-old Chinese girl was admitted to our hospital presenting with a 2-year progressive bilateral leg spasticity and weakness; early cognitive impairment; corpus callosum dysplasia; chronic neurogenic injury of the medulla oblongata supplied muscles; and bilateral upper and lower limbs on electromyogram (EMG). Based on these clinical and electrophysiological features, HSP was suspected. Exome sequencing of the family was performed by high-throughput sequencing, and an analysis of the patient showed a ZFYVE26 NM_015346: c.7111dupA p.(M2371Nfs*51) homozygous mutation. This case reported a new ZFYVE26 pathogenic variant, which was different from the SPG15 gene mutation reported earlier.

[Research Progress of Klotho in Lung Neoplasms].

Klotho gene was originally discovered as an anti-aging gene, Klotho protein encoded by Klotho gene is expressed in multiple human tissues, and its most prominent function is the regulation of phosphate homeostasis. Klotho protein possesses various activities, including inhibition of multiple signaling pathways, reducing oxidative stress and suppressing inflammation, and these activities are associated with cancer. Klotho protein is discovered as a universal tumor suppressor, and its expression is associated with tumorigenesis and prognosis of patients. Lung cancer is the most common malignancy tumor, and it is the leading cause of cancer deaths worldwide because of its high incidence and mortality. This article summarizes the research progress of the role of Klotho on pathogenesis, therapeutic effect and prognosis in lung cancer, in order to provide new biomarker and target for diagnosis, treatment and prognosis of lung cancer.
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