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1.
BMC Genomics ; 21(1): 711, 2020 Oct 14.
Artigo em Inglês | MEDLINE | ID: mdl-33054712

RESUMO

BACKGROUND: Genes are regulated by various types of regulators and most of them are still unknown or unobserved. Current gene regulatory networks (GRNs) reverse engineering methods often neglect the unknown regulators and infer regulatory relationships in a local and sub-optimal manner. RESULTS: This paper proposes a global GRNs inference framework based on dictionary learning, named dlGRN. The method intends to learn atomic regulators (ARs) from gene expression data using a modified dictionary learning (DL) algorithm, which reflects the whole gene regulatory system, and predicts the regulation between a known regulator and a target gene in a global regression way. The modified DL algorithm fits the scale-free property of biological network, rendering dlGRN intrinsically discern direct and indirect regulations. CONCLUSIONS: Extensive experimental results on simulation and real-world data demonstrate the effectiveness and efficiency of dlGRN in reverse engineering GRNs. A novel predicted transcription regulation between a TF TFAP2C and an oncogene EGFR was experimentally verified in lung cancer cells. Furthermore, the real application reveals the prevalence of DNA methylation regulation in gene regulatory system. dlGRN can be a standalone tool for GRN inference for its globalization and robustness.

2.
Placenta ; 103: 16-23, 2020 Oct 08.
Artigo em Inglês | MEDLINE | ID: mdl-33068962

RESUMO

OBJECTIVE: To analyze the effects of the Human Chorionic Gonadotropin beta (ß-hCG) and the VEGF-MEK/ERK signaling pathway on villi angiogenesis in early missed abortion. METHODS: A total of 12 cases of women with missed abortion and 12 cases of women who had induced abortion voluntarily without any disease were included in the present study. The age, pregnancy time and gestation period in the control group corresponded to the missed abortion group. Wes Simple Western system and qRT-PCR were used to detect the expression of VEGF-MEK/ERK signaling pathway related proteins and genes in villous. Radioimmunoassay and Enzyme-linked immunosorbent assay were used to detect ß-hCG and VEGF levels in serum. The microvascular density (MVD) in villous tissue was analyzed by immunohistochemical staining. RESULTS: The levels of ß-hCG and VEGF in serum, the expression of VEGF-MEK/ERK signaling pathway and MVD in villous tissue of the missed abortion group were lower than those of the control group. In addition, compared with the control group, the layers of trophoblasts of the villous tissue in the missed abortion group became thinner significantly, the number of cells reduced, the cell structures were disorganized, and parts of the trophoblast cells were absent. Correlational analysis showed that the protein expression of ERK1/2 was positively correlated with MVD in missed abortion group. CONCLUSIONS: Our results reveal that decreased production of ß-hCG in early pregnant women could down-regulate the expression of VEGF-MEK/ERK signal pathway, then reduce angiogenesis and eventually leading to the abnormal angiogenesis of villous, which may be an important mechanism of missed abortion.

3.
Artigo em Inglês | MEDLINE | ID: mdl-32865395

RESUMO

Nanobubbles have been widely studied for their use in water treatments. Conventional methods for producing nanobubbles require significantly high levels of electric power. A system that involves inducing an alternative magnetic field (AMF) in flowing water has been developed which has relatively low power requirements compared to other methods. Experimental results are presented that indicate nanobubbles are generated by this AMF system. These results include zeta potential measurements in deionized water, light scattering observations and nanoparticle tracking analysis (NTA) measurements of object size and relative scattering intensity for water containing 5´10-4 M CaCO3. The NTA results also suggest the formation of nanobubble-nanoparticle clusters. Finally, an earlier work is reviewed which demonstrated that this AMF treatment led to the removal of tubercles on the inner walls of pipe samples. This prior result is discussed in light of the present evidence of nanobubble formation and a hypothesis is proposed based on the dissolution of CaCO3 as a result of nanobubble-nanoparticle clustering.

4.
J Sci Food Agric ; 2020 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-32869299

RESUMO

BACKGROUND: Phospholipids, the main lipid component in marine shellfish, mainly comprise glycerophosphocholine (GPC) and glycerophosphoethanolamine (GPE). GPC and GPE in marine shellfish, especially scallop, carry n-3 long-chain polyunsaturated fatty acids, such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), although different types of glycerophospholipids (GP) have different health benefits on human health. Moreover, different GP subclasses such as GPC and GPE have different oxidative susceptibilities in complex food systems. The present study compared the oxidative susceptibilities of GPC and GPE in dried scallop during storage by high-performance liquid chromatography-tandem mass spectrometry and kinetic models, and also investigated the effects of natural phenolic antioxidant on their susceptibilities. RESULTS: The results showed that GPC and GPE molecular species (carrying EPA or DHA) contents in samples continuously reduced during storage at two different temperatures. The first-order kinetic model better reflected the changes of GPC and GPE molecular species (carrying EPA or DHA) in samples than the zero-order kinetic model during storage. According to the oxidation rate (k) obtained from first-order kinetic models, GPE possessed a greater oxidation rate than GPC during storage. Moreover, the results showed that antioxidants of bamboo leaves (AOB, polar polyphenolic antioxidants) significantly decreased the oxidation rates of GPC and GPE molecular species (carrying EPA or DHA) in samples during storage, and GPC could be more effectively protected by AOB compared to GPE. CONCLUSION: The present study provides a practical method for accurately evaluating the oxidative susceptibility of different phospholipid classes in complex food systems. © 2020 Society of Chemical Industry.

5.
Medicine (Baltimore) ; 99(33): e21628, 2020 Aug 14.
Artigo em Inglês | MEDLINE | ID: mdl-32872023

RESUMO

RATIONABLE: Large cell neuroendocrine carcinoma of the lung is rare, especially in the area of the foramen magnum. No previous studies have reported metastatic large cell neuroendocrine lung cancer to the foramen magnum. This paper will be the first time to report this special case. PATIENT CONCERNS: A case of a 37-year-old woman presented with headache that had developed 20 days previously. Imaging examination revealed a circular abnormal signal at the posterior margin of the foramen magnum. DIAGNOSES: The patient we report was diagnosed with a metastatic intracranial tumor. INTERVENTIONS: The patient underwent occipital craniotomy. Pathological results showed metastatic neuroendocrine carcinoma of the brain. Whole body PET-CT examination showed that fusiform soft tissue shadows could be seen near the hilum of the lower lobe of the left lung. OUTCOMES: The final bronchoscopy pathological results showed the large cell neuroendocrine carcinoma of the lung. The patient underwent further chemotherapy and radiotherapy in the oncology department. LESSONS: Diagnosis and treatment of large cell neuroendocrine carcinoma of the lung are difficult. The prognosis is poorer, and effective treatment is urgently needed.


Assuntos
Neoplasias Encefálicas/secundário , Carcinoma Neuroendócrino/patologia , Forame Magno/patologia , Neoplasias Pulmonares/patologia , Adulto , Neoplasias Encefálicas/diagnóstico por imagem , Neoplasias Encefálicas/cirurgia , Carcinoma Neuroendócrino/diagnóstico por imagem , Carcinoma Neuroendócrino/terapia , Feminino , Humanos , Neoplasias Pulmonares/diagnóstico por imagem , Neoplasias Pulmonares/terapia , Tomografia Computadorizada com Tomografia por Emissão de Pósitrons , Tomografia Computadorizada por Raios X
6.
Oncogene ; 39(43): 6704-6718, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32958832

RESUMO

Autophagy can protect stressed cancer cell by degradation of damaged proteins and organelles. However, the regulatory mechanisms behind this cellular process remain incompletely understood. Here, we demonstrate that RSK2 (p90 ribosomal S6 kinase 2) plays a critical role in ER stress-induced autophagy in breast cancer cells. We demonstrated that the promotive effect of RSK2 on autophagy resulted from directly binding of AMPKα2 in nucleus and phosphorylating it at Thr172 residue. IRE1α, an ER membrane-associated protein mediating unfolded protein response (UPR), is required for transducing the signal for activation of ERK1/2-RSK2 under ER stress. Suppression of autophagy by knockdown of RSK2 enhanced the sensitivity of breast cancer cells to ER stress both in vitro and in vivo. Furthermore, we demonstrated that inhibition of RSK2-mediated autophagy rendered breast cancer cells more sensitive to paclitaxel, a chemotherapeutic agent that induces ER stress-mediated cell death. This study identifies RSK2 as a novel controller of autophagy in tumor cells and suggests that targeting RSK2 can be exploited as an approach to reinforce the efficacy of ER stress-inducing agents against cancer.

7.
Ultrasound Med Biol ; 46(12): 3179-3187, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32907771

RESUMO

This meta-analysis was aimed at investigating the value of using contrast-enhanced ultrasound (CEUS) in the differential diagnosis of benign and malignant soft tissue masses (STMs). Relevant studies published before March 24, 2020 were identified through a comprehensive search of PubMed, Ovid, Cochrane and Web of Science. According to the inclusion criteria, five studies were selected comprising 746 patients. In the differential diagnosis of benign and malignant STMs, the pooled sensitivity and specificity of CEUS were 76% (95% confidence interval [CI]: 71%-81%; heterogeneity [I2] = 74.5%) and 67% (95% CI: 62%-71%; I2 = 36.5%), respectively. The diagnostic odds ratio was 7.37 (95% CI: 3.78%-14.35; I2 = 66.6%). The overall area under the curve was 0.77 (standard error: 0.0392). Subgroup analysis revealed that different index tests of CEUS resulted in different diagnostic performance. Importantly, CEUS is an effective method for the differential diagnosis between benign and malignant STMs.

8.
J Hazard Mater ; 400: 123138, 2020 Dec 05.
Artigo em Inglês | MEDLINE | ID: mdl-32947735

RESUMO

Mercury (Hg) and its compounds are one of the most dangerous environmental pollutants and Hg pollution exists in soils in different degrees over the world. Phytoremediation of Hg-contaminated soils has attracted increasing attention for the advantages of low investment, in-situ remediation, potential economic benefits and so on. Searching for the hyperaccumulator of Hg and its application in practice become a research hotspot. In this context, we review the current literatures that introduce various experimental plant species for accumulating Hg and aided techniques improving the phytoremediation of Hg-contaminated soils. Experimental plant species for accumulating Hg and accumulation or translocation factor of Hg are listed in detail. The translocation factor (TF) is greater than 1.0 for some plant species, however, the bioaccumulation factor (BAF) is greater than 1.0 for Axonopus compressus only. Plant species, soil properties, weather condition, and the bioavailability and heterogeneity of Hg in soils are the main factors affecting the phytoremediation of Hg-contaminated soils. Chemical accelerator kinds and promoting effect of chemical accelerators for accumulating and transferring Hg by various plant species are also discussed. Potassium iodide, compost, ammonium sulphate, ammonium thiosulfate, sodium sulfite, sodium thiosulfate, hydrochloric acid and sulfur fertilizer may be selected to promote the absorption of Hg by plants. The review introduces transgenic gene kinds and promoting effect of transgenic plants for accumulating and transferring Hg in detail. Some transgenic plants can accumulate more Hg than non-transgenic plants. The composition of rhizosphere microorganisms of remediation plants and the effect of rhizosphere microorganisms on the phytoremediation of Hg-contaminated soils are also introduced. Some rhizosphere microorganisms can increase the mobility of Hg in soils and are beneficial for the phytoremediation.

9.
Methods ; 2020 Aug 10.
Artigo em Inglês | MEDLINE | ID: mdl-32791338

RESUMO

Ubiquitination is one of the most important post-translational modifications which involves in many biological processes. Because mass spectrometry-based ubiquitination site identification methods are costly and time consuming, computational approaches provide alternative ways to the determination of ubiquitination sites. Although machine learning based methods can effectively predict ubiquitination sites, most of them rely on feature engineering, which may lead to bias or incomplete feature. Recently, deep learning has achieved great success in prediction of post-translational modification sites. However, deep learning method has not been explored in the prediction of species-specific ubiquitination sites. In this paper, we propose a novel transfer deep learning method, named DeepTL-Ubi, for predicting ubiquitination sites of multiple species. DeepTL-Ubi enhances the performance of species-specific ubiquitination site prediction by transferring common knowledge from the large amount of human data to other species, which effectively solves the problem of insufficient training data for other species. Besides, we train and test our model by collecting ubiquitination sites for multiple species from several sources. Experiment results show that our transfer learning technique can effectively improve the predictive performance of species with small sample size, and DeepTL-Ubi is superior to existing tools in many species. The source code and training data of DeepTL-Ubi are publicly deposited at https://github.com/USTC-HIlab/DeepTL-Ubi.

10.
Chemosphere ; 263: 127914, 2020 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-32822940

RESUMO

The MSWI fly ash (FA) is classified as hazardous waste and electrolytic manganese residue (EMR) as the harmful industrial waste. FA, water-washed FA (WFA), EMR and coal fly ash (CFA) were co-recycled to form lightweight MFCE ceramisites. The effects of FA, WFA and mixed MSWI fly ash on ceramisites were discussed. The approach to mixing FA and WFA increased the recycling amount of MSWI fly ash. The optimal mixture of 34.5% EMR, 24.1% CFA, 20.7% FA and 20.7% WFA sintered at 1160 °C for 12 min with a procedural heating rate (10 °C/min) and belonged to Class 800 artificial lightweight aggregate (GB/T 17431.1-2010); the quantity of MSWI fly ash in ceramisite was as high as 41.4%. Volatilization rates of Cd, Pb, Cu, Zn, Mn and Cr for ceramisite were higher 75.0, 24.2, 62.7, 133, 343 and 764% than FA respectively, attributed to the co-existence of chlorides and sulfates. The remained Zn, Cu, Pb, Mn and Cr were exchanged with Mg2+/Ca2+/Al3+ of diopside and wollastonite to form residual fractions. Our findings provided a feasibility method of co-recycling MSWI fly ash and electrolytic manganese residue to produce green lightweight aggregates.

11.
Heredity (Edinb) ; 2020 Aug 17.
Artigo em Inglês | MEDLINE | ID: mdl-32807851

RESUMO

Epigenetic mechanisms such as DNA methylation have the potential to affect organism acclimatization and adaptation to environmental changes by influencing their phenotypic plasticity; however, little is known about the role of methylation in the adaptive phenotypic divergence of marine invertebrates. Therefore, in this study, a typical intertidal species, the Pacific oyster (Crassostrea gigas), was selected to investigate the epigenetic mechanism of phenotypic plasticity in marine invertebrates. Intertidal and subtidal oysters subjected to one-generation common garden experiments and exhibited phenotypic divergence were used. The methylation landscape of both groups of oysters was investigated under temperate and high temperature. The two tidal oysters exhibited divergent methylation patterns, regardless of the temperature, which was mainly original environment-induced. Intertidal samples exhibited significant hypomethylation and more plasticity of methylation in response to heat shock, while subtidal samples showed hypermethylation and less plasticity. Combined with RNA-seq data, a positive relationship between methylation and expression in gene bodies was detected on a genome-wide scale. In addition, approximately 11% and 7% of differentially expressed genes showed significant methylation variation under high temperatures in intertidal and subtidal samples, respectively. Genes related to apoptosis and organism development may be regulated by methylation in response to high temperature in intertidal oysters, whereas oxidation-reduction and ion homeostasis-related genes were involved in subtidal oysters. The results also suggest that DNA methylation mediates phenotypic divergence in oysters adapting to different environments. This study provides new insight into the epigenetic mechanisms underlying phenotypic plasticity in adaptation to rapid climate change in marine organisms.

12.
Ying Yong Sheng Tai Xue Bao ; 31(7): 2195-2201, 2020 Jul.
Artigo em Chinês | MEDLINE | ID: mdl-32715681

RESUMO

We extracted Eucalyptus essential oil by steam distillation and analyzed its chemical components by GC-MS. The inhibitory effects of α-terpineol, a component in Eucalyptus essential oil, were tested in Petri dishes on the germination and growth of Amaranthus retroflexus. The allelopathic effects of α-terpineol on A. retroflexus were examined with a pot experiment by measuring germination rate and biomass. The yield of essential oil was 0.04%. Ninety-two chemical components were detected from the essential oil. In Petri dish experiment, the germination inhibitory effect under 5 µL and 7.5 µL of α-terpineol per dish reached 100%. In pot experiment, germination, aboveground fresh and dry weights of A. retroflexus were significantly affected by α-terpineol. At the concentration of 1.6 µL·cm-3, the inhibition effect was strongest, with the allelopathic response index being -0.51 for germination, -0.62 for aboveground fresh weight, and -0.44 for aboveground dry weight, and the inhibition ratio being 51%, 62% and 44%, respectively.


Assuntos
Eucalyptus , Óleos Voláteis , Monoterpenos Cicloexânicos , Óleo de Eucalipto , Monoterpenos
13.
Microb Genom ; 6(10)2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32667876

RESUMO

Mannoside phosphorylases are involved in the intracellular metabolization of mannooligosaccharides, and are also useful enzymes for the in vitro synthesis of oligosaccharides. They are found in glycoside hydrolase family GH130. Here we report on an analysis of 6308 GH130 sequences, including 4714 from the human, bovine, porcine and murine microbiomes. Using sequence similarity networks, we divided the diversity of sequences into 15 mostly isofunctional meta-nodes; of these, 9 contained no experimentally characterized member. By examining the multiple sequence alignments in each meta-node, we predicted the determinants of the phosphorolytic mechanism and linkage specificity. We thus hypothesized that eight uncharacterized meta-nodes would be phosphorylases. These sequences are characterized by the absence of signal peptides and of the catalytic base. Those sequences with the conserved E/K, E/R and Y/R pairs of residues involved in substrate binding would target ß-1,2-, ß-1,3- and ß-1,4-linked mannosyl residues, respectively. These predictions were tested by characterizing members of three of the uncharacterized meta-nodes from gut bacteria. We discovered the first known ß-1,4-mannosyl-glucuronic acid phosphorylase, which targets a motif of the Shigella lipopolysaccharide O-antigen. This work uncovers a reliable strategy for the discovery of novel mannoside-phosphorylases, reveals possible interactions between gut bacteria, and identifies a biotechnological tool for the synthesis of antigenic oligosaccharides.

14.
Transl Oncol ; 13(10): 100818, 2020 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-32592902

RESUMO

OBJECTIVE: This study aims to evaluate the efficacy and safety of stereotactic body radiation therapy (SBRT) using Cyber Knife (CK) in the treatment of patients with recurrent pancreatic cancer after surgery, and analyze its survival-related factors. METHODS: The primary endpoint was freedom from local progression (FFLP) and local control (LC) rate after CK. The secondary endpoints were overall survival (OS), progression-free survival (PFS), symptom relief and toxicities. Receiver operating characteristic (ROC) curves were used to determine the optimal cut-off values of inflammatory composite indicators NLR, PLR, SII and PNI. The prognostic factors that affected these patients were analyzed by univariate and multivariate analysis, respectively. RESULTS: A total of 27 patients were enrolled. Median local recurrence disease free interval(DFI)was 11.3 (1.3-30.6) months, LC was 81.5% and 37.0% at 6 and 12 months, respectively. Median PFS was 7.1 (1.3-27.1) months. Median OS was 11.3 (1.3-30.6) months. Symptom alleviation was observed in 16 of 17 patients (94.1%) within 2 weeks after CK. Subsequent chemotherapy, CA199≥50% decrease after CK were independent prognostic factors for OS (all P <0.05). CONCLUSION: SBRT is a safe and effective treatment approach for recurrent pancreatic adenocarcinoma. Encouraging local control rate, low toxicity, and effective symptom relief suggests the vital role of CK in the treatment of these patients. This clinical application needs to be further studied in the combination of CK and multimodal therapy.

15.
Biomed Pharmacother ; 127: 110229, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32559853

RESUMO

There are limited options for targeted therapies for colorectal cancer (CRC). Anti-EGFR therapy is limited to CRC without KRAS mutations. Even worse, most of CRC are refractory to currently immune checkpoint blockade. DKK2, which is upregulated in CRC, was recently found to suppress host immune responses, and its blockage effectively impeded tumor progression in benign genetic CRC models in our previous study. Here, our recent study demonstrated that in human CRC tumor samples expressing high levels of DKK2, DKK2 blockade caused stronger activation of tumor infiltrating CD8+ T cells in ex vivo culture. Intriguingly, we observed a correlation of high DKK2 expression with increased lymph node metastasis prevalence in these CRC patients as well. Furthermore, in a mouse genetic CRC model with mutations in APC and KRAS, which more closely mimics advanced human CRC, we confirmed the tumor inhibitory effect of DKK2 blockade, which significantly retarded tumor progression and extended survival, with increased immune effector cell activation and reduced angiogenesis. Based on this, we performed a combined administration of DKK2 blockade with sub-optimal anti-VEGFR treatment and observed a synergetic effect on suppressing tumor angiogenesis and progression, as well as extending survival, better than those of every single therapy. Thus, this study provides further evidence for the potential therapeutic application of DKK2 blockade in the clinical treatment of human CRC.

16.
Sleep ; 2020 Jun 17.
Artigo em Inglês | MEDLINE | ID: mdl-32556242

RESUMO

STUDY OBJECTIVE: The frequency of cortical arousals is an indicator of sleep quality. Additionally, cortical arousals are used to identify hypopneic events. However, it is inconvenient to record electroencephalogram (EEG) data during home sleep testing. Fortunately, most cortical arousal events are associated with autonomic nervous system activity that could be observed on an electrocardiography (ECG) signal. ECG data have lower noise and are easier to record at home than EEG. In this study, we developed a deep learning-based cortical arousal detection (DeepCAD) algorithm that uses a single-lead ECG to detect arousal during sleep. METHODS: This study included 1547 polysomnography records that met study inclusion criteria and were selected from the Multi-Ethnic Study of Atherosclerosis (MESA) database. We developed an end-to-end deep learning model consisting of convolutional neural networks and recurrent neural networks which: (1) accepted varying length physiological data; (2) directly extracted features from the raw ECG signal; (3) captured long-range dependencies in the physiological data; and (4) produced arousal probability in one second resolution. RESULTS: We evaluated the model on a test set (n=311). The model achieved a gross area under precision-recall curve score of 0.62 and a gross area under receiver operating characteristic curve score of 0.93. CONCLUSION: This study demonstrated the end-to-end deep learning approach with a single-lead ECG has the potential to be used to accurately detect arousals in home sleep tests.

17.
Water Sci Technol ; 81(6): 1114-1129, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32597399

RESUMO

In this study, an efficient route to synthesizing polyethyleneimine-modified ultrasonic-assisted acid hydrochar (PEI-USAH) is developed and reported. Ultrasonic irradiation technique was used as surface modification method to shorten the crosslinking reaction for hydrochar and polyethyleneimine (PEI). The PEI-USAH showed an excellent adsorption capacity for Cr(VI) from aqueous solution. The physicochemical properties of this PEI-modified adsorbent were comparatively characterized by Fourier transform infrared spectroscopy, scanning electron microscopy, X-ray photoelectron spectroscopy, Brunauer-Emmett-Teller analysis and CNHS analysis. The effects of contact time, initial pH, and biosorbent dose on adsorption capacities were investigated. The batch adsorption experiments showed that PEI-USAH possessed the maximum adsorption capacities of 94.38 mg/g and 330.84 mg/g for initial Cr(VI) concentration of 100 mg/L and 500 mg/L, respectively. Furthermore, this adsorption process could be fitted to Langmuir adsorption and described by the pseudo second order kinetic model. Based on the above findings, PEI-USAH could be used as a potential adsorbent for removal of Cr(VI) from wastewater.


Assuntos
Sargassum , Poluentes Químicos da Água , Adsorção , Cromo , Concentração de Íons de Hidrogênio , Cinética , Polietilenoimina , Espectroscopia de Infravermelho com Transformada de Fourier , Ultrassom
18.
Acta Crystallogr C Struct Chem ; 76(Pt 5): 389-397, 2020 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-32367818

RESUMO

The crystal structures of the antimicrobial drug tinidazole [TNZ; systematic name: 1-(2-ethylsulfonylethyl)-2-methyl-5-nitroimidazole, C8H13N3O4S] and the 1:1 cocrystal of TNZ with the naturally occurring compound vanillic acid (VA; systematic name: 4-hydroxy-3-methoxybenzoic acid, C8H8O4), namely, the TNZ-VA cocrystal, were determined by single-crystal X-ray analysis at 100 K. The supramolecular structure of the TNZ-VA cocrystal is composed of a carboxylic acid dimer and an O-H...N(heterocycle) synthon in the form of layers made up of O-H...N and O-H...O hydrogen bonds. The layers are joined via C-H...O hydrogen bonds, π-π stacking and C-H...π interactions. The energy framework analysis, together with interaction energy calculations using the DLPNO-CCSD(T) method, indicates that the TNZ-VA cocrystal inherits strong interactions from the TNZ and VA crystals, which accounts for the enhanced thermal stability and reduced dissolution rate. To the best of our knowledge, this is the first example of a cocrystal containing TNZ.

19.
Brief Bioinform ; 2020 May 11.
Artigo em Inglês | MEDLINE | ID: mdl-32393981

RESUMO

With the advances of next-generation sequencing technology, the field of disease research has been revolutionized. However, pinpointing the disease-causing variants from millions of revealed variants is still a tough task. Here, we have reviewed the existing linkage analysis tools and presented PedMiner, a web-based application designed to narrow down candidate variants from family based whole-exome sequencing (WES) data through linkage analysis. PedMiner integrates linkage analysis, variant annotation and prioritization in one automated pipeline. It provides graphical visualization of the linked regions along with comprehensive annotation of variants and genes within these linked regions. This efficient and comprehensive application will be helpful for the scientific community working on Mendelian inherited disorders using family based WES data.

20.
Small ; 16(20): e2000949, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32323494

RESUMO

Minimal residual disease (MRD) offers a highly independent prognostic factor for leukemia patients. However, challenges confronting conventional MRD assays are high invasiveness, as well as limited detection sensitivity and clinical applicability. Inspired by the self-adaptive skeleton and multiple suckers or tendrils of climbing plants, a biomimetic Multivalent Aptamer Nanoclimber (MANC)-functionalized microfluidic chip (MANC-Chip) is reported for minimally invasive, highly sensitive and clinically applicable MRD detection in the peripheral blood of T-cell acute lymphoblastic leukemia patients. The MANCs are synthesized by a simple co-polymerization reaction. Due to their flexible structure and cooperative multivalent effect, MANCs dramatically enhance the binding affinity of aptamers targeting leukemia cells. A deterministic lateral displacement-patterned microfluidic chip is designed to further increase the collision probability between MANCs and leukemia cells. Benefiting from the synergistic effect of multivalent binding and enhanced collision, a high capture efficiency of 92.2% for leukemia cells is achieved. Moreover, the captured leukemia cells can be released with high efficiency of 88.9% and high viability of 93.8% via nuclease treatment prior to downstream analysis. Overall, the excellent features of MANC-Chip make it very useful for precise detection of MRD and better understanding of leukemia.

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