Benchmarking multi-platform sequencing technologies for human genome assembly.

Genome assembly is a computational technique that involves piecing together deoxyribonucleic acid (DNA) fragments generated by sequencing technologies to create a comprehensive and precise representation of the entire genome. Generating a high-quality human reference genome is a crucial prerequisite for comprehending human biology, and it is also vital for downstream genomic variation analysis. Many efforts have been made over the past few decades to create a complete and gapless reference genome for humans by using a diverse range of advanced sequencing technologies. Several available tools are aimed at enhancing the quality of haploid and diploid human genome assemblies, which include contig assembly, polishing of contig errors, scaffolding and variant phasing. Selecting the appropriate tools and technologies remains a daunting task despite several studies have investigated the pros and cons of different assembly strategies. The goal of this paper was to benchmark various strategies for human genome assembly by combining sequencing technologies and tools on two publicly available samples (NA12878 and NA24385) from Genome in a Bottle. We then compared their performances in terms of continuity, accuracy, completeness, variant calling and phasing. We observed that PacBio HiFi long-reads are the optimal choice for generating an assembly with low base errors. On the other hand, we were able to produce the most continuous contigs with Oxford Nanopore long-reads, but they may require further polishing to improve on quality. We recommend using short-reads rather than long-reads themselves to improve the base accuracy of contigs from Oxford Nanopore long-reads. Hi-C is the best choice for chromosome-level scaffolding because it can capture the longest-range DNA connectedness compared to 10× linked-reads and Bionano optical maps. However, a combination of multiple technologies can be used to further improve the quality and completeness of genome assembly. For diploid assembly, hifiasm is the best tool for human diploid genome assembly using PacBio HiFi and Hi-C data. Looking to the future, we expect that further advancements in human diploid assemblers will leverage the power of PacBio HiFi reads and other technologies with long-range DNA connectedness to enable the generation of high-quality, chromosome-level and haplotype-resolved human genome assemblies.

A Semi-Automatic Environmental Monitoring Device for Mercury and Cobalt Ion Detection.

A syringe-based, semi-automatic environmental monitoring device is developed for on-site detection of harmful heavy metal ions in water. This portable device consists of a spring-embedded syringe and a polydimethylsiloxane (PDMS) membrane-based flow regulator for semi-automatic fix-and-release fluidic valve actuation, and a paper-based analytical device (PAD) with two kinds of gold nanoclusters (AuNCs) for sensitive Hg2+ and Co2+ ion detection, respectively. The thickness of the elastic PDMS membrane can be adjusted to stabilize and modulate the flow rates generated by the pushing force provided by the spring attached to the plunger. Also, different spring constants can drastically alter the response time. People of all ages can extract the fix-volume sample solutions and then release them to automatically complete the detection process, ensuring high reliability and repeatability. The PAD comprises two layers of modified paper, and each layer is immobilized with bovine serum albumin-capped gold nanoclusters (R-AuNCs) and glutathione-capped gold clusters (G-AuNCs), respectively. The ligands functionalized on the surface of the AuNCs not only can fine-tune the optical properties of the nanoclusters but also enable specific and simultaneous detection of Hg2+ and Co2+ ions via metallophilic Au+ -Hg2+ interaction and the Co2+ -thiol complexation effect, respectively. The feasibility of the device for detecting heavy metal ions at low concentrations in various environmental water samples is demonstrated. The Hg2+ and Co2+ ions can be seen simultaneously within 20 min with detection limits as low as 1.76 nm and 0.27 µm, respectively, lower than those of the regulatory restrictions on water by the US Environmental Protection Agency and the European Union. we expect this sensitive, selective, portable, and easy-to-use device to be valid for on-site multiple heavy metal ion pollution screenings in resource-constrained settings.

Combination therapy based on dual-target biomimetic nano-delivery system for overcoming cisplatin resistance in hepatocellular carcinoma.

Strategies to overcome toxicity and drug resistance caused by chemotherapeutic drugs for targeted therapy against hepatocellular carcinoma (HCC) are urgently needed. Previous studies revealed that high oxidored-nitro domain-containing protein 1(NOR1) expression in HCC was associated with cisplatin (DDP) resistance. Herein, a novel dual-targeting nanocarrier system AR-NADR was generated for the treatment of DDP resistance in HCC. The core of the nanocarrier system is the metal-organic frameworks (MOF) modified with nuclear location sequence (NLS), which loading with DDP and NOR1 shRNA (R). The shell is an A54 peptide inserted into the erythrocyte membrane (AR). Our results show that AR-NADR efficiently internalized by tumor cells due to its specific binding to the A54 receptors that are abundantly expressed on the surface of HCC cells and NLS peptide-mediated nuclear entry. Additionally, DDP is more likely to be released due to the degradation of Ag-MOF in the acidic tumor microenvironment. Moreover, by acting as a vector for gene delivery, AR-NADR effectively inhibits tumor drug resistance by suppressing the expression of NOR1, which induces intracellular DDP accumulation and makes cells sensitive to DDP. Finally, the anti-HCC efficacy and mechanisms of AR-NADR were systematically elucidated by a HepG2/DDP cell model as well as a tumor model. Therefore, AR-NADR constitutes a key strategy to achieve excellent gene silencing and antitumor efficacy, which provides effective gene therapy and precise treatment strategies for cisplatin resistance in HCC.

Bioengineered stem cell membrane functionalized nanoparticles combine anti-inflammatory and antimicrobial properties for sepsis treatment.

BACKGROUND: Sepsis is a syndrome of physiological, pathological and biochemical abnormalities caused by infection. Although the mortality rate is lower than before, many survivors have persistent infection, which means sepsis calls for new treatment. After infection, inflammatory mediators were largely released into the blood, leading to multiple organ dysfunction. Therefore, anti-infection and anti-inflammation are critical issues in sepsis management. RESULTS: Here, we successfully constructed a novel nanometer drug loading system for sepsis management, FZ/MER-AgMOF@Bm. The nanoparticles were modified with LPS-treated bone marrow mesenchymal stem cell (BMSC) membrane, and silver metal organic framework (AgMOF) was used as the nanocore for loading FPS-ZM1 and meropenem which was delivery to the infectious microenvironments (IMEs) to exert dual anti-inflammatory and antibacterial effects. FZ/MER-AgMOF@Bm effectively alleviated excessive inflammatory response and eliminated bacteria. FZ/MER-AgMOF@Bm also played an anti-inflammatory role by promoting the polarization of macrophages to M2. When sepsis induced by cecal ligation and puncture (CLP) challenged mice was treated, FZ/MER-AgMOF@Bm could not only reduce the levels of pro-inflammatory factors and lung injury, but also help to improve hypothermia caused by septic shock and prolong survival time. CONCLUSIONS: Together, the nanoparticles played a role in combined anti-inflammatory and antimicrobial properties, alleviating cytokine storm and protecting vital organ functions, could be a potential new strategy for sepsis management.

Correlation between the salivary microbiology and H2 S concentration of the oral cavity.

BACKGROUND: Hydrogen sulfide (H2 S) is the most important compound causing oral malodor, and its concentration is thought to be closely correlated with oral microorganism activity. Therefore, clarifying the correlation between oral microbes and metabolites is important. METHODS: This study tested with 16S rRNA gene amplicon and shotgun metagenomic sequencing of oral microorganisms and oral malodor tests. RESULTS: There were different of the microbial taxa between the low and high H2 S groups. And in the high H2 S group, most of the enriched taxa were genera which abundance was correlated with H2 S concentration. Fusobacterium periodonticum and Prevotella nanceiensis were significantly different in coverage breadth and depth and in LPS biosynthesis contributions between the two groups. The contribution of F. periodonticum to sulfur metabolism was significantly different between the two groups, and the relative F. periodonticum abundance was higher in the high H2 S group. CONCLUSIONS: The H2 S content is significantly associated with the oral cavity microorganism composition and abundance. Most microorganisms enriched in people with high H2 S levels are associated with oral diseases such as caries and periodontal diseases.

Activation and thermal stabilization of a recombinant γ-glutamyltranspeptidase from Bacillus licheniformis ATCC 27811 by monovalent cations.

The regulation of enzyme activity through complexation with certain metal ions plays an important role in many biological processes. In addition to divalent metals, monovalent cations (MVCs) frequently function as promoters for efficient biocatalysis. Here, we examined the effect of MVCs on the enzymatic catalysis of a recombinant γ-glutamyltranspeptidase (BlrGGT) from Bacillus licheniformis ATCC 27,811 and the application of a metal-activated enzyme to L-theanine synthesis. The transpeptidase activity of BlrGGT was enhanced by Cs+ and Na+ over a broad range of concentrations with a maximum of 200 mM. The activation was essentially independent of the ionic radius, but K+ contributed the least to enhancing the catalytic efficiency. The secondary structure of BlrGGT remained mostly unchanged in the presence of different concentrations of MVCs, but there was a significant change in its tertiary structure under the same conditions. Compared with the control, the half-life (t1/2) of the Cs+-enriched enzyme at 60 and 65 °C was shown to increase from 16.3 and 4.0 min to 74.5 and 14.3 min, respectively. The simultaneous addition of Cs+ and Mg2+ ions exerted a synergistic effect on the activation of BlrGGT. This was adequately reflected by an improvement in the conversion of substrates to L-theanine by 3.3-15.1% upon the addition of 200 mM MgCl2 into a reaction mixture comprising the freshly desalted enzyme (25 µg/mL), 250 mM L-glutamine, 600 mM ethylamine, 200 mM each of the MVCs, and 50 mM borate buffer (pH 10.5). Taken together, our results provide interesting insights into the complexation of MVCs with BlrGGT and can therefore be potentially useful to the biocatalytic production of naturally occurring γ-glutamyl compounds. KEY POINTS: • The transpeptidase activity of B. licheniformis Î³-glutamyltranspeptidase can be activated by monovalent cations. • The thermal stability of the enzyme was profoundly increased in the presence of 200 mM Cs+. • The simultaneous addition of Cs+and Mg2+ions to the reaction mixture improves L-theanine production.

Self-redox reaction driven in situ formation of Cu2O/Ti3C2Tx nanosheets boost the photocatalytic eradication of multi-drug resistant bacteria from infected wound.

BACKGROUND: MXenes with interesting optical and electrical properties have been attractive in biomedical applications such as antibacterial and anticancer agents, but their low photogeneration efficiency of reactive oxygen species (ROS) and poor stability are major concerns against microbial resistance. METHODS: Water-dispersible single layer Ti3C2Tx-based MXene through etching tightly stacked MAX phase precursor using a minimally intensive layer delamination method. After addition of Cu(II) ions, the adsorbed Cu(II) ions underwent self-redox reactions with the surface oxygenated moieties of MXene, leading to in situ formation of Cu2O species to yield Cu2O/Ti3C2Tx nanosheets (heterostructures). RESULTS: Under NIR irradiation, the Cu2O enhanced generation of electron-hole pairs, which boosted the photocatalytic production of superoxide and subsequent transformation into hydrogen peroxide. Broad-spectrum antimicrobial performance of Cu2O/Ti3C2Tx nanosheets with sharp edges is attributed to the direct contact-induced membrane disruption, localized photothermal therapy, and in situ generated cytotoxic free radicals. The minimum inhibitory concentration of Cu2O/Ti3C2Tx nanosheets reduced at least tenfold upon NIR laser irradiation compared to pristine Cu2O/Ti3C2Tx nanosheets. The Cu2O/Ti3C2Tx nanosheets were topically administrated on the methicillin-resistant Staphylococcus aureus (MRSA) infected wounds on diabetic mice. CONCLUSION: Upon NIR illumination, Cu2O/Ti3C2Tx nanosheets eradicated MRSA and their associated biofilm to promote wound healing. The Cu2O/Ti3C2Tx nanosheets with superior catalytic and photothermal properties have a great scope as an effective antimicrobial modality for the treatment of infected wounds.

Lozenges with probiotic strains enhance oral immune response and health.

OBJECTIVE: Probiotics participate in regulating oral microbiota and reducing the prevalence of oral diseases; however, clinical research on probiotics is insufficient. Therefore, in this study, we performed in vitro screening of potential oral protective probiotic strains and then evaluated the clinical efficacy of the selected strains on maintaining oral health. MATERIALS AND METHODS: Fifty healthy individuals were recruited and randomly assigned into the placebo group and probiotics group, which included three strains of probiotics, Lactobacillus salivarius subs. salicinius AP-32, Lactobacillus paracasei ET-66, and Lactobacillus plantarum LPL28. Each group was blindly administered placebo or probiotics for four weeks. RESULTS: Next-generation sequencing results showed that the oral microbiota of Lactobacillus salivarius in the oral cavity were significantly increased in subjects supplemented with mixed probiotic lozenges. The anti-bacterial activities of viable probiotics were observed within two weeks. Both IgA levels and Lactobacillus and Bifidobacterium abundances in the oral cavity were significantly increased in the experimental groups, along with a reduced formation of plaque. Most participants reported that their oral health conditions and intestinal symptoms had improved. CONCLUSIONS: Overall, our clinical study suggests that oral probiotic lozenges may enhance oral immunity, modulate oral microbiota, and improve oral health.

Adequacy of care during interfacility transfer in Taiwan: A pilot study.

BACKGROUND/PURPOSE: Interfacility transfer (IFT) in Asian communities is seldom discussed. We aimed to describe the characteristics of IFT in Taiwan and to explore the adequacy of care during transfer. METHODS: A retrospective, cross-sectional, descriptive study was conducted using standardized, paper-based interfacility ambulance transfer records between 1 January 2018 and 31 January 2018 from Tainan City, Taiwan. The mode of patient care needed was classified as advanced life support (ALS) or basic life support (BLS) cares based on clinical conditions. ALS providers were defined as physicians and EMT-Paramedics, while BLS providers were defined as nurse practitioners, nurses, EMT-1s and EMT-2s. RESULTS: Of the 377 (227 [60.2%] were >65 years old; 219 [58.1%] were male) IFTs enrolled in the final analysis, 210 (55.7%) patients met the ALS transfer criteria, with poor consciousness (n = 158), tachypnea (n = 17), tachycardia (n = 5), bradycardia (n = 7), hypertension (n = 12), hypotension (n = 13), hypoxia (n = 4), endotracheal intubation (n = 18), a tracheostomy (n = 25), a precipitous labor (n = 1), and after resuscitation for out-of-hospital cardiac arrest (n = 10) or in-hospital cardiac arrest (n = 3). None of the patients who required ALS care had adequate ambulance staffing. Of the 167 BLS IFTs, 9 (5.4%) patients deteriorated and required ALS care during transportation, which included worsened consciousness (n = 2), tachycardia (n = 1), hypertension (n = 2), hypotension (n = 1), and hypoxia (n = 3). The rates of deterioration during BLS-transferals from the emergency departments, general wards, nursing facilities, and unknown areas were 4.8%, 4.7%, 7.7%, and 7.1%, respectively (p = 0.93). CONCLUSION: The patient care during IFT in Taiwan is inadequate currently and should warrant attention.

Self-assisted wound healing using piezoelectric and triboelectric nanogenerators.

The complex process of wound healing depends on the coordinated interaction between various immunological and biological systems, which can be aided by technology. This present review provides a broad overview of the medical applications of piezoelectric and triboelectric nanogenerators, focusing on their role in the development of wound healing technology. Based on the finding that the damaged epithelial layer of the wound generates an endogenous bioelectric field to regulate the wound healing process, development of technological device for providing an exogenous electric field has therefore been paid attention. Authors of this review focus on the design and application of piezoelectric and triboelectric materials to manufacture self-powered nanogenerators, and conclude with an outlook on the current challenges and future potential in meeting medical needs and commercialization.

Lineage-guided Notch-dependent gliogenesis by Drosophila multi-potent progenitors.

Macroglial cells in the central nervous system exhibit regional specialization and carry out region-specific functions. Diverse glial cells arise from specific progenitors in specific spatiotemporal patterns. This raises an interesting possibility that glial precursors with distinct developmental fates exist that govern region-specific gliogenesis. Here, we have mapped the glial progeny produced by the Drosophila type II neuroblasts, which, like vertebrate radial glia cells, yield both neurons and glia via intermediate neural progenitors (INPs). Distinct type II neuroblasts produce different characteristic sets of glia. A single INP can make both astrocyte-like and ensheathing glia, which co-occupy a relatively restrictive subdomain. Blocking apoptosis uncovers further lineage distinctions in the specification, proliferation and survival of glial precursors. Both the switch from neurogenesis to gliogenesis and the subsequent glial expansion depend on Notch signaling. Taken together, lineage origins preconfigure the development of individual glial precursors with involvement of serial Notch actions in promoting gliogenesis.

Viable and Heat-Killed Probiotic Strains Improve Oral Immunity by Elevating the IgA Concentration in the Oral Mucosa.

Oral-nasal mucosal immunity plays a crucial role in protecting the body against bacterial and viral invasion. Safe probiotic products have been used to enhance human immunity and oral health. In this study, we verified the beneficial effects of mixed viable probiotic tablets, consisting of Lactobacillus salivarius subsp. salicinius AP-32, Bifidobacterium animalis subsp. lactis CP-9, and Lactobacillus paracasei ET-66, and heat-killed probiotic tablets, consisting of L. salivarius subsp. salicinius AP-32 and L. paracasei ET-66, on oral immunity among 45 healthy participants. Participants were randomly divided into viable probiotic, heat-killed probiotic, and placebo groups. The administration of treatment lasted for 4 weeks. Saliva samples were collected at Weeks 0, 2, 4, and 6, and Lactobacillus, Bifidobacterium and Streptococcus mutans populations and IgA concentration were measured. IgA concentrations, levels of TGF-beta and IL-10 in PBMCs cells were quantified by ELISA method. Results showed that salivary IgA levels were significantly increased on administration of both the viable (119.30 ± 12.63%, ***P < 0.001) and heat-killed (116.78 ± 12.28%, ***P < 0.001) probiotics for 4 weeks. Among three probiotic strains, AP-32 would effectively increase the levels of TGF-beta and IL-10 in PBMCs. The oral pathogen Streptococcus mutans was significantly reduced on viable probiotic tablet administration (49.60 ± 31.01%, ***P < 0.001). The in vitro antibacterial test confirmed that viable probiotics effectively limited the survival rate of oral pathogens. Thus, this clinical pilot study demonstrated that oral probiotic tablets both in viable form or heat-killed form could exert beneficial effects on oral immunity via IL-10, TGB-beta mediated IgA secretion. The effective dosage of viable probiotic content in the oral tablet was 109 CFUs/g and the heat-killed oral tablet was 1 × 1010 cells/g.

The ratio of H/C is a useful parameter to predict adsorption of the herbicide metolachlor to biochars.

Biochar adsorbent was produced by pyrolyzing traditional Chinese medicinal herb residue at 300, 500 and 750 °C (referred to as biochar-300, biochar-500 and biochar-750). Basic physical and chemical analyses, Fourier transform infrared spectroscopy (FT-IR), and thermodynamic analyses were performed to elucidate adsorption and properties of biochar. Biochar adsorption capacity of herbicide metolochlor, as measured by batch-type adsorption experiments by Freundlich constant Kf (mg1-n Ln kg-1), followed the order: biochar-750 > biochar-300 > biochar-500. Thermodynamic analysis suggested that adsorption of metolachlor on biochar was a spontaneous process. The adsorption isotherm for the biochar produced at the highest pyrolysis temperature was characteristic for adsorption process driven by a high surface area of biochar (85.30 m2 g-1), while the adsorption process for the biochar produced at the lowest temperature was controlled by its higher content of organic matter (39.06%) and abundant functional groups. The FT-IR spectra also showed that the biochar prepared at the lowest temperature had the highest number of surface groups. In general, pore-filling induced by the large surface area of the biochar was the dominant adsorption mechanism. When the H/C value was >0.5, the adsorption mechanism of biochar was dominated by surface chemical bond, while pore-filling played a major role when the H/C value was <0.5.

A Preliminary Study of Microbiota Diversity in Saliva and Bronchoalveolar Lavage Fluid from Patients with Primary Bronchogenic Carcinoma.

BACKGROUND The present study aimed to evaluate the difference in microbiota diversity in the oral cavity and fluid bronchoalveolar lavage (BALF) of patients with lung cancer. MATERIAL AND METHODS Buccal (saliva) and lower respiratory tract BALF samples were collected from 51 patients with primary bronchogenic carcinoma and 15 healthy controls, and bacterial genomic DNA was extracted. High-throughput 16S rDNA amplicon sequencing was performed, and microbial diversity, composition, and functions of microbiota were analyzed by bioinformatics methods. RESULTS Patients with lung cancer have lower microbial diversity than healthy controls in both saliva and BALF samples. Significant segregation was observed between the different pathological types of lung cancer groups and the control group regardless of the sampling site. Treponema and Filifactor were identified as potential bacterial biomarkers in BALF samples, while Filifactor was ideal to distinguish healthy controls from lung cancer patients. Moreover, the predictive variation analysis of the KEGG (Kyoto Encyclopedia of Genes and Genomes) metabolic pathway showed that the metabolic differences in microbiota varied by sampling site. CONCLUSIONS Lung cancer patients carry a different and less diverse microorganism community than healthy controls. Certain bacterial taxa might be associated with lung cancer, but the exact species depends on the sampling site and the pathological type. This study provides basic data on the microbiota diversity in BALF and saliva samples from lung cancer patients. Further investigation with a larger sample size should help validate the enriched species in different pathological types of lung cancers.

Regulation of H+-pyrophosphatase by 14-3-3 Proteins from Arabidopsis thaliana.

Plant vacuolar H+-transporting inorganic pyrophosphatase (V-PPase; EC 3.6.1.1) is a crucial enzyme that exists on the tonoplast to maintain pH homeostasis across the vacuolar membrane. This enzyme generates proton gradient between cytosol and vacuolar lumen by hydrolysis of a metabolic byproduct, pyrophosphate (PP i ). The regulation of V-PPase at protein level has drawn attentions of many workers for decades, but its mechanism is still unclear. In this work, we show that AVP1, the V-PPase from Arabidopsis thaliana, is a target protein for regulatory 14-3-3 proteins at the vacuolar membrane, and all twelve 14-3-3 isoforms were analyzed for their association with AVP1. In the presence of 14-3-3ν, -µ, -ο, and -ι, both enzymatic activities and its associated proton pumping of AVP1 were increased. Among these 14-3-3 proteins, 14-3-3 µ shows the highest stimulation on coupling efficiency. Furthermore, 14-3-3ν, -µ, -ο, and -ι exerted protection of AVP1 against the inhibition of suicidal substrate PP i at high concentration. Moreover, the thermal profile revealed the presence of 14-3-3ο improves the structural stability of AVP1 against high temperature deterioration. Additionally, the 14-3-3 proteins mitigate the inhibition of Na+ to AVP1. Besides, the binding sites/motifs of AVP1 were identified for each 14-3-3 protein. Taken together, a working model was proposed to elucidate the association of 14-3-3 proteins with AVP1 for stimulation of its enzymatic activity.

Type of adjuvant chemotherapy and treatment frequency in survival outcome of patients with colorectal liver metastases who underwent liver metastasectomy: an 8-year cohort study in Taiwan.

PURPOSE: The role of adjuvant chemotherapy (ACT) in treating patients who have colorectal liver metastases (CLM) and undergo liver metastasectomy (LMS) is unclear in this patient population. We aimed to compare the mortality of patients receiving different ACT (i.e., oxaliplatin-based, irinotecan-based, and 5-fluorouracil-only (5FU)) and different treatment frequencies. METHODS: We included 2583 patients with CLM who underwent LMS (including synchronous LMS [SLMS] and metachronous LMS [MLMS]) in this retrospective cohort study. We used Cox proportional hazard model to obtain hazard ratios (HRs) for mortality. The reference group was 5FU-only ACT when comparing ACT type and the reference group was treatment for ≤ 3 times when comparing ACT frequency. RESULTS: In SLMS patients, oxaliplatin-based ACT (HR = 0.78) and receiving ACT for ≥ 4 times (4-6 times, HR = 0.61; 7-9 times, HR = 0.69; 10-12 times, HR = 0.66) were associated with lower risk of mortality. In MLMS patients, oxaliplatin-based ACT (HR = 0.52), irinotecan-based ACT (HR = 0.64), and receiving ACT for 10-12 times (HR = 0.65) were associated with lower risk of mortality. CONCLUSIONS: In SLMS and MLMS patients, patients who received oxaliplatin-based ACT were more likely to survive than patients who received 5FU-only ACT. In MLMS patients, patients who received irinotecan-based ACT were also more likely to survive than those who received 5FU-only ACT. We recommend a course of at least four to six times of ACT after LMS in this patient population.

Electrophoretic and Electroosmotic Motion of a Charged Spherical Particle within a Cylindrical Pore Filled with Debye-Bueche-Brinkman Polymeric Solution.

Electrophoretic and electroosmotic motion of a charged spherical particle within a cylindrical pore filled with a Debye-Bueche-Brinkman (DBB) polymeric solution is investigated theoretically, which is of high relevance in capillary electrophoresis as well as micro- and nanofluidic applications involving polymeric solutions in a micro- or nanopore. The DBB model describes the rheological response of a polymeric solution with a linear polymer dissolved in a homogeneous solvent. It is a well-known non-Newtonian model in liquid physics based on rigorous theoretical derivations. By Debye and Bueche, corresponding governing fundamental electrokinetic equations are solved numerically with a patched pseudo-spectral method based on Chebyshev polynomials. We found that the double-layer polarization effect reduces the particle mobility severely when the Debye parameter, κa, is around unity, especially in narrow pores. This is attributed to the extra confinement effect from the nearby wall, which tends to sweep the predominant counterions within the double layer to the wake of the moving particle, resulting in a motion-deterring induced electric field. The electrophoretic mobility in a polymer solution is smaller than that in an aqueous electrolyte solution in general as a result of the much stronger viscous drag effect in a polymer solution. Moreover, electroosmotic flow (EOF) as a result of a charged pore wall is found to exhibit a highly non-Newtonian behavior. Unlike the corresponding plug-like flow for a Newtonian solution, an axisymmetric flow with a large local maximum in the velocity profile in the region near the pore wall is observed. This radial-varying velocity profile offers a potential extra separation mechanism, which favors the elution of smaller particles in general. The results obtained here provide fundamental understandings and insights of the electrophoresis and electroosmosis phenomena in a cylindrical pore filled with polymeric solution.

Hinokitiol Inhibits Melanogenesis via AKT/mTOR Signaling in B16F10 Mouse Melanoma Cells.

H inokitiol purified from the heartwood of cupressaceous plants has had various biological functions of cell differentiation and growth. Hinokitiol has been demonstrated as having an important role in anti-inflammation and anti-bacteria effect, suggesting that it is potentially useful in therapies for hyperpigmentation. Previously, hinokitiol inhibited the production of melanin by inhibiting tyrosinase activity. The autophagic signaling pathway can induce hypopigmentation. This study is warranted to investigate the mechanism of hinokitiol-induced hypopigmentation through autophagy in B16F10 melanoma cells. The melanin contents and expression of microthphalmia associated transcription factor (MITF) and tyrosinase were inhibited by treatment with hinokitiol. Moreover, the phosphorylation of the protein express levels of phospho-protein kinase B (P-AKT) and phospho-mammalian targets of rapamycin (P-mTOR) were reduced after hinokitiol treatment. In addition, the microtubule associated protein 1 light chain 3 (LC3) -II and beclin 1 (autophagic markers) were increased after the B16F10 cell was treated with hinokitiol. Meanwhile, hinokitiol decreased cellular melanin contents in a dose-dependent manner. These findings establish that hinokitiol inhibited melanogenesis through the AKT/mTOR signaling pathway.

Functional and fluorescence analyses of tryptophan residues in H+-pyrophosphatase of Clostridium tetani.

Homodimeric proton-translocating pyrophosphatase (H+-PPase; EC 3.6.1.1) maintains the cytoplasmic pH homeostasis of many bacteria and higher plants by coupling pyrophosphate (PPi) hydrolysis and proton translocation. H+-PPase accommodates several essential motifs involved in the catalytic mechanism, including the PPi binding motif and Acidic I and II motifs. In this study, 3 intrinsic tryptophan residues, Trp-75, Trp-365, and Trp-602, in H+-PPase from Clostridium tetani were used as internal probes to monitor the local conformational state of the periplasm domain, transmembrane region, and cytoplasmic domain, respectively. Upon binding of the substrate analog Mg-imidodiphosphate (Mg-IDP), local structural changes prevented the modification of tryptophan residues by N-bromosuccinimide (NBS), especially at Trp-602. Following Mg-Pi binding, Trp-75 and Trp-365, but not Trp-602, were slightly protected from structural modifications by NBS. These results reveal the conformation of H+-PPase is distinct in the presence of different ligands. Moreover, analyses of the Stern-Volmer relationship and steady-state fluorescence anisotropy also indicate that the local structure around Trp-602 is more exposed to solvent and varied under different environments. In addition, Trp-602 was identified to be a crucial residue in the H+-PPase that may potentially be involved in stabilizing the structure of the catalytic region by site-directed mutagenesis analysis.

Investigation of C-terminal domain of SARS nucleocapsid protein-Duplex DNA interaction using transistors and binding-site models.

AlGaN/GaN high electron mobility transistors (HEMTs) were used to sense the binding between double stranded DNA (dsDNA) and the severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid protein (N protein). The sensing signals were the drain current change of the HEMTs induced by the protein-dsDNA binding. Binding-site models using surface coverage ratios were utilized to analyze the signals from the HEMT-based sensors to extract the dissociation constants and predict the number of binding sites. Two dissociation constants, K D1 = 0.0955 nM, K D2 = 51.23 nM, were obtained by fitting the experimental results into the two-binding-site model. The result shows that this technique is more competitive than isotope-labeling electrophoretic mobility shift assay (EMSA). We demonstrated that AlGaN/GaN HEMTs were highly potential in constructing a semiconductor-based-sensor binding assay to extract the dissociation constants of nucleotide-protein interaction.