Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing

Prediction of Loss of Muscle Mass in Sarcopenia Using Ultrasonic Diaphragm Excursion

February 13, 2022 Lieven Leave a comment

Background: The diagnosis of sarcopenia is based on the mass and function of appendicular skeletal muscle. It is not clear whether diaphragm excursion is related to muscle mass loss. We try to fill the gap by measuring ultrasonic diaphragm excursion during quiet breathing (Dq) and forced deep breathing (Df) and test whether they could predict the muscle mass loss in sarcopenia.

Methods: The subjects are recruited from the elderly patients diagnosed with pulmonary nodules in community physical examination. According to the definition, the subjects were divided into group A (who did not meet the diagnostic criteria for muscle mass loss in sarcopenia) and group B (who met the criteria). Participants were assessed for ultrasonic diaphragm excursion, pulmonary function, and cardiopulmonary exercise testing. Logistic regression was used to assess the correlation between right diaphragm excursion and skeletal muscle mass, and receiver-operating characteristic curve (ROC) was applied to determine the best threshold.

Results: We recruited 64 elderly participants: 52 in group A (39 males) and 12 in group B (8 males). The Df in group A were higher than in group B (6.02 (5.44-6.60) vs. 4.31 (3.53-5.09) cm, P=0.008). The difference also exists in FVC, FEV1.0, PEF, Pimax, WRmax, and VO₂max, but neither in Dq. Logical regression showed that Df was negatively related to muscle mass (B = -0.525, OR = 0.591 (0.378-0.926), P=0.022), even after adjusted age. Based on ROC, a cutoff value of 5.27 cm (AUC = 0.7783, P=0.0028) was selected, and Df ≤ 5.27 cm indicates the increase in odds https://biodas.org/ of existing muscle mass loss.

Conclusion: Ultrasonic diaphragm excursion in forced deep breath is helpful for predicting muscle mass loss in sarcopenia.

Application and Validation of the Tricuspid Annular Plane Systolic Excursion/Systolic Pulmonary Artery Pressure Ratio in Patients with Ischemic and Non-Ischemic Cardiomyopathy

The main aim of this study was to assess the prognostic utility of TAPSE/PASP as an echocardiographic parameter of maladaptive RV remodeling in cardiomyopathy patients using cardiac magnetic resonance (CMR) imaging. Furthermore, we sought to compare TAPSE/PASP to TAPSE. The association of the echocardiographic parameters TAPSE/PASP and TAPSE with CMR parameters of RV and LV remodeling was evaluated in 111 patients with ischemic and non-ischemic cardiomyopathy and cut-off values for maladaptive RV remodeling were defined.

In a second step, the prognostic value of TAPSE/PASP and its cut-off value were analyzed regarding mortality in a validation cohort consisting of 221 patients with ischemic and non-ischemic cardiomyopathy. A low TAPSE/PASP (<0.38 mm/mmHg) and TAPSE (<16 mm) were associated with a lower RVEF and a long-axis RV global longitudinal strain (GLS) as well as higher RVESVI, RVEDVI and NT-proBNP.

A low TAPSE/PASP, but not TAPSE, was associated with a lower LVEF and long-axis LV GLS, and a higher LVESVI, LVEDVI and T1 relaxation time at the interventricular septum and the RV insertion points. Furthermore, in the validation cohort, low TAPSE/PASP was associated with a higher mortality and TAPSE/PASP was an independent predictor of mortality. TAPSE/PASP is a predictor of maladaptive RV and LV remodeling associated with poor outcomes in cardiomyopathy patients.

Preoperative Computed Tomography Angiography Reveals Leaflet-Specific Calcification and Excursion Patterns in Aortic Stenosis

Background: Computed tomography-based evaluation of aortic stenosis (AS) by calcium scoring does not consider interleaflet differences in leaflet characteristics. Here, we sought to examine the functional implications of these differences.

Methods: We retrospectively reviewed the computed tomography angiograms of 200 male patients with degenerative calcific AS undergoing transcatheter aortic valve replacement and 20 male patients with normal aortic valves. We compared the computed tomography angiography (CTA)-derived aortic valve leaflet calcification load (AVLC_CTA), appearance, and systolic leaflet excursion (LE_sys) of individual leaflets. We performed computer simulations of normal valves to investigate how interleaflet differences in LE_sys affect aortic valve area. We used linear regression to identify predictors of leaflet-specific calcification in patients with AS.

Results: In patients with AS, the noncoronary cusp (NCC) carried the greatest AVLC_CTA (365.9 [237.3-595.4] Agatston unit), compared to the left coronary cusp (LCC, 278.5 [169.2-478.8] Agatston unit) and the right coronary cusp (RCC, 240.6 [137.3-439.0] Agatston unit; both P<0.001). However, LCC conferred the least LE_sys (42.8º [38.8º-49.0º]) compared to NCC (44.8º [41.1º-49.78º], P=0.001) and RCC (47.7º [42.0º-52.3º], P<0.001) and was more often characterized as predominantly thickened (23.5%) compared to NCC (12.5%) and RCC (16.5%). Computer simulations of normal valves revealed greater reductions in aortic valve area following closures of NCC (-32.2 [-38.4 to -25.8]%) and RCC (-35.7 [-40.2 to -32.9]%) than LCC (-24.5 [-28.5 to -18.3]%; both P<0.001). By linear regression, the AVLC_CTA of NCC and RCC, but not LCC, predicted LE_sys (both P<0.001) in patients with AS. Both ostial occlusion and ostial height of the right coronary artery predicted AVLC_{CTA, RCC} (P=0.005 and P=0.001).

Conclusions: In male patients, the AVLC_CTA of NCC and RCC contribute more to AS than that of LCC. LCC’s propensity for noncalcific leaflet thickening and worse LE_sys, however, should not be underestimated when using calcium scores to assess AS severity.

Keywords: aortic valve stenosis; calcium; computed tomography angiography; computer simulation; transcatheter aortic valve replacement.

Polysomnographic Plethysmography Excursions are Reduced in Obese Elderly Men

Sleep apnea is a widespread disorder and is defined by the complete or partial cessation of breathing. Obstructive sleep apnea (OSA) is caused by an obstruction in the upper airway while central sleep apnea (CSA) is characterized by a diminished or absent respiratory effort. It is crucial to differentiate between these respiratory subtypes as they require radically different treatments.

Currently, diagnostic polysomnography (PSG) is used to determine respiratory thoracic and abdominal movement patterns using plethysmography belt signals, to distinguish between OSA and CSA. There is significant manual technician interrater variability between these classifications, especially in the evaluation of CSA. We hypothesize that an increased body mass index (BMI) will cause decreased belt signal excursions that increase false scorings of CSA.

The hypothesis was investigated by calculating the envelope as a continuous signal of belt signals in 2833 subjects from the MrOS Sleep Study and extracting a mean value of each of the envelopes for each subject. Using linear regression, we found that an increased BMI was associated with lower excursions during REM sleep (-0.013 [mV] thoracic and -0.018 [mV] abdominal, per BMI) and non-REM (-0.014 [mV] thoracic and -0.012 [mV] abdominal, per BMI). We conclude that increased BMI leads to lower excursions in the belt signals during event-free sleep, and that OSA and CSA events are harder to distinguish in subjects with high BMI. This has a major implication for the correct identification of CSA/OSA and its treatment.

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An open source protein gel documentation system for proteome analyses

February 13, 2022 Lieven Leave a comment

Data organization and data mining represents one of the main challenges for modern high throughput technologies in pharmaceutical chemistry and medical chemistry. The presented open source documentation and analysis system provides an integrated solution (tutorial, setup protocol, sources, executables) aimed at substituting the traditionally used lab-book.

The data management solution provided incorporates detailed information about the processing of the gels and the experimental conditions used and includes basic data analysis facilities which can be easily extended.

Cost-effective gel documentation using a web-cam.

In search for a cost effective gel documentation system applicable for different fields of molecular biology, we analyzed the capabilities of a cheap CCD-camera originally designed to capture images for transmission through the internet (web-cam) with regard to gel documentation. The camera was connected to a personal computer https://biodas.org/ by universal serial bus (USB) and used for the documentation of DNA separated on agarose gels and stained by ethidium-bromide using the software provided with the camera.

The web-cam provided digital images of sufficient quality for routine documentation and combined the low set-up costs of a Polaroid system with the low running costs of video capture systems, hence is ideal as a start-up system and as augmentation to existing equipment.

Persistence of the same Candida albicans strain despite fluconazole therapy. Documentation by pulsed-field gel electrophoresis.

Candida albicans and other Candida species have emerged as major nosocomial pathogens associated with a high mortality. Therapeutic options for fungal infections are limited. Amphotericin B has been the mainstay of treatment for serious systemic candidal infections, but it is relatively toxic and associated with a variety of side effects. Fluconazole has been proposed as alternative therapy for the treatment of systemic candidiasis including candidemia. We report the case of a patient with fungemia in whom fluconazole failed to eradicate C. albicans and C. tropicalis.

These pathogens were recovered from sputum and urine cultures, respectively, on day 12 of intravenous fluconazole therapy. Molecular epidemiologic techniques employing pulsed-field gel electrophoresis confirmed the persistence of the same C. albicans strain. Susceptibility studies showed a marked change in MICs of fluconazole between 24 and 48 hr, with an increase from less than or equal to 1.25 to greater than 80 micrograms/ml. Controlled trials will be needed to delineate the role of fluconazole in the treatment of disseminated candidiasis and its efficacy in comparison with amphotericin B. Amphotericin B should remain the drug of choice for such infections until data from controlled trials are available.

Inhibition of post-surgery tumour recurrence via a sprayable chemo-immunotherapy gel releasing PD-L1 antibody and platelet-derived small EVs

Background: Melanoma is the most serious type of skin cancer, and surgery is an effective method to treat melanoma. Unfortunately, local residual micro-infiltrated tumour cells and systemic circulating tumour cells (CTCs) are significant causes of treatment failure, leading to tumour recurrence and metastasis.

Methods: Small EVs were isolated from platelets by differential centrifugation, and doxorubicin-loaded small EVs (PexD) was prepared by mixing small EVs with doxorubicin (DOX). PexD and an anti-PD-L1 monoclonal antibody (aPD-L1) were co-encapsulated in fibrin gel. The synergistic antitumour efficacy of the gel containing PexD and aPD-L1 was assessed both in vitro and in vivo.

Results: Herein, we developed an in situ-formed bioresponsive gel combined with chemoimmunotherapeutic agents as a drug reservoir that could effectively inhibit both local tumour recurrence and tumour metastasis. In comparison with a DOX solution, PexD could better bind to tumour cells, induce more tumour immunogenic cell death (ICD) and promote a stronger antitumour immune response. PexD could enter the blood circulation through damaged blood vessels to track and eliminate CTCs. The concurrent release of aPD-L1 at the tumour site could impair the PD-1/PD-L1 pathway and restore the tumour-killing effect of cytotoxic T cells. This chemoimmunotherapeutic strategy triggered relatively strong T cell immune responses, significantly improving the tumour immune microenvironment.

Conclusion: Our findings indicated that the immunotherapeutic fibrin gel could “awaken” the host innate immune system to inhibit both local tumour recurrence post-surgery and metastatic potential, thus, it could serve as a promising approach to prevent tumour recurrence.

Clinical Comparison of I-gel and Laryngeal Mask Airway-Supreme Airway Devices During General Anaesthesia in the Paediatric Population

Objectives: Both the Supreme Laryngeal Mask Airway (SLMA) and the I-gel (I-gel) are supraglottic airway devices (SADs) commonly used for airway management in paediatric patients. This study aims to compare the efficacy in terms of insertion and ventilation profiles of size 2 SLMA and the I-gel in anaesthetised paediatric patients.

Methods: 100 children were prospectively allocated to two groups depending upon the device inserted as SLMA (n = 50) and I-gel (n = 50). The primary outcomes were studied in terms of ease of insertion, haemodynamic changes, ventilation parameters, leak pressure and incidences of complications during general anaesthesia.

Results: There were no failed attempts in the insertion of the airways in either group. The SLMA was more easily inserted in the majority of cases compared to the I-gel group. The number of attempts for insertion and the time taken for insertion were comparable in the I-gel and the SLMA group (13.8462.38 vs. 14.0261.7) (P .57, .66). Securing an effective airway took <30 seconds in both the groups with an overall median duration of 15 seconds. There was no difficulty in passing the gastric tube in either group (P<.30). There was a statistical difference between the oropharyngeal seal pressure (OSP), which was 25.1861.59 and 22.1061.36 cmH2O for SLMA and I-gel, respectively (P<.001). Haemodynamic parameters after the insertion of the device were comparable, and there were no clinically important complications in the post-operative period.

Conclusions: Both the devices appeared to be simple and suitable for airway management during elective surgery in paediatric patients. However, the SLMA was easily inserted with less insertion time in the majority of patients. Also, it provides higher OSP during anaesthesia and is better tolerated during emergence, with minimal risk of injury to the oropharynx.

Transfer and Fixation of Denatured RNA in Agarose Gels to Membranes by Capillary Transfer

In most cases, fractionation of RNA by agarose gel electrophoresis is but a prelude to hybridization of the fractionated population to specific labeled probes that detect particular target mRNAs. RNA is first transferred from an agarose gel to a 2D support, usually a nylon membrane.

This protocol presents the steps involved in the transfer of RNA from an agarose gel to a membranous support, facilitated by the upward flow of buffer, followed by various methods for fixation of the RNA to the membrane in preparation for hybridization. An alternative method for transfer by downward capillary flow is also given.

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An activatable chemiluminescence probe based on phenoxy-dioxetane scaffold for biothiol imaging in living systems

February 13, 2022 Lieven Leave a comment

Quantification of biothiols in living systems is essential to understand their biological applications. Here, we developed two activatable chemiluminescence probes (SHCL and NCCL) and investigated their utility in the bioimaging of intracellular biothiols by directly tethering 2,4-dinitrobenzenesulfonyl to the hydroxyl group of phenoxy-dioxetane. The design of these two probes differed in substituents of phenol-dioxetane, i.e., SHCL contained the ortho chlorine, whereas NCCL had the para hydroxymethyl. Upon glutathione (GSH) cleavage, both probes emitted significantly “turn-on” chemiluminescent signals. However, the chemiluminescence intensity based on NCCL declined with increasing GSH level above 5 mM, while SHCL exhibited much higher chemiluminescent intensity and a wider concentration range (0.5 μM-50 mM), which was much more suitable for sensing endogenous biothiols.

We further demonstrated that chlorine substitution in SHCL played an important role in bioimaging owing to the halogen effect, providing a lower pK_a value and significant enhancement of the chemiluminescent emission. SHCL imaged the biothiols effectively in tumor cells and tumor-bearing mice. Additionally, this novel chemiluminescence probe can be easily used to evaluate the in vitro activity of acetylcholinesterase. Overall, we anticipate that SHCL may provide a facile and intuitive tool for https://biodas.org/ studying the role of biothiols in diseases.

Nitrogen doped graphene quantum dots based long-persistent chemiluminescence system for ascorbic acid imaging.

High photo-intensity and sluggish flight attenuation are important to highly sensitive chemluminescence imaging. Herein, we present a copper ion catalyzed long-persistent chemiluminescent imaging system of nitrogen-doped graphene quantum dots (NGQDs) for ascorbic acid detection in fruit. NGQDs as luminescent probe are fabricated, emitting out chemluminescence with the direct oxidation by H2O2.
In addition, Cu2+ ion enlarges over two order magnitudes of NGQDs CL intensity (214 times) due to its catalyzed Fenton-like reaction for H2O2 decomposition, and displaying unique specificity against other metal ions. As a result, the twinkling luminescence of NGQDs is boosted and changes to hold persistent with small decay in the presence of copper ion exhibiting potential for CL imaging.
As an imaging model, a visual sensor based on Cu2+/NGQDs/H2O2 is developed for AA quantitative monitoring with a limit of detection (LOD) of 0.5μM (S/N=3) and applied in real AA detection in fruit. The CL imaging method demonstrated with high stability and proper sensitivity would provide a convenient and visual tool for AA determination, displaying promising candidates for imaging sensing.

Imaging systems for westerns: chemiluminescence vs. infrared detection.

Western blot detection methods have traditionally used X-ray films to capture chemiluminescence. The increasing costs for film, reagents, and maintenance have driven researchers away from darkrooms to more sensitive and technologically advanced digital imaging systems. Cooled charge coupled devices (CCD) cameras capture both chemiluminescence and fluorescence images, with limitations for each detection method. Chemiluminescence detection is highly sensitive and relies on an enzymatic reaction that produces light, which can be detected by a CCD camera that records photons and displays an image based on the amount of light generated. However, the enzymatic reaction is dynamic and changes over time making it necessary to optimize reaction times and imaging.

Fluorescent detection with a CCD camera offers a solution to this problem since the signal generated by the proteins on the membrane is measured in a static state. Despite this advantage, many researchers continue to use chemiluminescent detection methods due to the generally poor performance of fluorophores in the visible spectrum. Infrared imaging systems offer a solution to the dynamic reactions of chemiluminescence and the poor performance of fluorophores detected in the visible spectrum by imaging fluorphores in the infrared spectrum.

Infrared imaging is equally sensitive to chemiluminescence and more sensitive to visible fluorescence due in part to reduced autofluorescence in the longer infrared wavelength. Furthermore, infrared detection is static, which allows a wider linear detection range than chemiluminescence without a loss of signal.

A distinct advantage of infrared imaging is the ability to simultaneously detect proteins on the same blot, which minimizes the need for stripping and reprobing leading to an increase in detection efficiency. Here, we describe the methodology for chemiluminescent (UVP BioChemi) and infrared (LI-COR Odyssey) imaging, and briefly discuss their advantages and disadvantages.

Line scanning system for direct digital chemiluminescence imaging of DNA sequencing blots.

A cryogenically cooled charge-coupled device (CCD) camera equipped with an area CCD array is used in a line scanning system for low-light-level imaging of chemiluminescent DNA sequencing blots. Operating the CCD camera in time-delayed integration (TDI) mode results in continuous data acquisition independent of the length of the CCD array. Scanning is possible with a resolution of 1.4 line pairs/mm at the 50% level of the modulation transfer function. High-sensitivity, low-light-level scanning of chemiluminescent direct-transfer electrophoresis (DTE) DNA sequencing blots is shown.

The detection of DNA fragments on the blot involves DNA-DNA hybridization with oligonucleotide-alkaline phosphatase conjugate and 1,2-dioxetane-based chemiluminescence. The width of the scan allows the recording of up to four sequencing reactions (16 lanes) on one scan. The scan speed of 52 cm/h used for the sequencing blots corresponds to a data acquisition rate of 384 pixels/s. The chemiluminescence detection limit on the scanned images is 3.9 x 10(-18) mol of plasmid DNA. A conditional median filter is described to remove spikes caused by cosmic ray events from the CCD images.

New advanced oxidation progress with chemiluminescence behavior based on NaClO triggered by WS ₂ nanosheets

As one integral part of coping strategies for addressing water pollution, advanced oxidation progresses (AOPs) get enormous attentions in recent years. However, the complex synthesis and high cost of H₂O₂ and K₂S₂O₈ hampered their developments. Herein, a novel AOP with the chemiluminescence (CL) property based on economic NaClO and WS₂ nanosheets was proposed to achieve efficient decomposition of organic pollutants.

In this AOP, WS₂ nanosheets exhibited a dual-function feature of the catalyst and energy acceptor. It demonstrated that the reaction order of WS₂ nanosheets was equal to 0.8271 and enormous singlet oxygen (¹O₂),·ClO and hydroxyl radical (·OH) were generated in rhodamine B (RhB) degradation process. Interestingly, a strong CL emission was observed and reflected the relative concentration of ¹O₂ and·OH for adjusting the oxidizing capability in WS₂ nanosheets-NaClO system.

Through a series of degradation tests, RhB, methylene blue (MB), p-nitrophenol and phenol were decomposed and the degradation efficiency of over 90% was achieved. Therefore, this study not only builds a chemiluminescent AOPs to eliminate organic pollutants, but also broadens the applications of WS₂ nanomaterials and CL in environmental field.

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Highly Tough, Stretchable, and Solvent-Resistant Cellulose Nanocrystal Photonic Films for Mechanochromism and Actuator Properties

February 13, 2022 Lieven Leave a comment

Cellulose nanocrystals (CNCs)-derived photonic materials have confirmed great potential in producing renewable optical and engineering areas. However, it remains challenging to simultaneously possess toughness, strength, and multiple responses for developing high-performance sensors, intelligent coatings, flexible textiles, and multifunctional devices. Herein, the authors report a facile and robust strategy that poly(ethylene glycol) dimethacrylate (PEGDMA) can be converged into the chiral nematic structure of CNCs by ultraviolet-triggered free radical polymerization in an N,N-dimethylformamide solvent system.

The resulting CNC-poly(PEGDMA) composite exhibits impressive strength (42 MPa), stretchability (104%), toughness (31 MJ m^-3 ), and solvent resistance. Notably, it preserves vivid optical iridescence, displaying stretchable variation from red, yellow, to green responding to the applied mechanical stimuli. More interestingly, upon exposure to spraying moisture, it executes sensitive actuation (4.6° s^-1 ) and multiple complex 3D deformation behaviors, accompanied by synergistic iridescent appearances.

Due to its structural anisotropy of CNC with typical left-handedness, the actuation shows the capability to generate a high probability (63%) of right-handed helical shapes, mimicking a coiled tendril. The authors envision that this versatile system with sustainability, robustness, mechanochromism, and specific actuating ability will open a https://biodas.org/ sustainable avenue in mechanical sensors, stretchable optics, intelligent actuators, and soft robots.

Understanding the Drying Behavior of Regenerated Cellulose Gel Beads: The Effects of Concentration and Nonsolvents

The drying behavior of regenerated cellulose gel beads swollen with different nonsolvents (e.g., water, ethanol, water/ethanol mixtures) is studied in situ on the macroscopic scale with an optical microscope as well as on nanoscale using small-angle/wide-angle X-ray scattering (SAXS/WAXS) techniques. Depending on the cellulose concentration, the structural evolution of beads during drying follows one of three distinct regimes.

First, when the cellulose concentration is lower than 0.5 wt %, the drying process comprises three steps and, regardless of the water/ethanol mixture composition, a sharp structural transition corresponding to the formation of a cellulose II crystalline structure is observed. Second, when the cellulose concentration is higher than 5.0 wt %, a two-step drying process is observed and no structural transition occurs for any of the beads studied. Third, when the cellulose concentration is between 0.5 and 5.0 wt %, the drying process is dependent on the nonsolvent composition.

A three-step drying process takes place for beads swollen with water/ethanol mixtures with a water content higher than 20%, while a two-step drying process is observed when the water content is lower than 20%. To describe the drying behavior governed by the cellulose concentration and nonsolvent composition, a simplified phase diagram is proposed.

Cellular Flocculation Using Concentrated Polymer Brush-Modified Cellulose Nanofibers with Different Fiber Lengths

In this study, concentrated polymer brush-modified cellulose nanofibers (CNFs) with different fiber lengths were used for the flocculation of cells for systematically studying the mechanism of this unique cellular flocculation based on colloidal flocculation theory. Concentrated poly(p-styrenesulfonic acid sodium salt) brush-grafted CNF (CNF-PSSNa) with different fiber lengths were cultured with three different cell types to examine their influence on floc (cell clusters formed by cellular flocculation) characteristics. The floc size and survival rate could be controlled by modifying the CNF-PSSNa fiber lengths.

The three cell types showed the same flocculation tendency after culture, indicating the applicability of the method in different cell lines. After 2 weeks of culture, CNF-PSSNa increased the specific expression of hepatocytes compared to the two-dimensional cell culture. Thus, owing to its wide applicability, high cell viability, and ability to control cell size and improve cell function, this technology could be used as a new three-dimensional cell culture method.

Gold nanoparticles spontaneously grown on cellulose nanofibrils as a reusable nanozyme for colorimetric detection of cholesterol in human serum

Recently, gold nanoparticles (AuNPs) are extensively used as peroxidase mimics. However, low catalytic activity, high synthesis cost, substrate-induced aggregation in reaction medium and difficulty in recovery and reuse still remain as major challenges. Here, a novel, simple, spontaneous, and reagent-less in-situ method for the production of AuNPs using dialdehyde cellulose nanofibrils (DACNF) is proposed. AuNPs synthesis time and size were greatly influenced by aldehyde content and the optimal aldehyde content for ultra-small AuNPs (≈10 nm) was 2.1 mM/g. AuNPs@DACNFs exhibited broad-spectrum peroxidase activity and steady-state kinetics revealed their better kinetic parameters (low K_m and high V_max) over horseradish peroxidase (HRP). AuNPs@DACNFs was further converted into paper strip, which served as a biosensor for H₂O₂ and cholesterol detection.

The proposed method exhibited wide linear response in the range of 10-90 μM and 0.05-0.45 mM, and detection limit of 0.39 μM and 1.9 μM for H₂O₂ and cholesterol, respectively. Great shelf life and reusability were evident by FE-SEM and ICP-OES analysis. The smartphone application “Color Grab” was used to enable the portable onsite detection. The results of cholesterol detection in human serum samples were in agreement with clinically observed values, suggesting the great potential of the probe in disease diagnosis.

COBL9 and COBL7 synergistically regulate root hair tip growth via controlling apical cellulose deposition

Root hairs are cylindrical extensions of root epidermal cells that are important for the acquisition of water and minerals, interactions between plant and microbes. The deposition of cell wall materials in the tip enables root hairs to maintain elongation constantly. To date, our knowledge of the regulators that connect the architecture of cell wall and the root hair development remains very limited.

Here, we demonstrated that COBL9 and COBL7, two genes of COBRA-Like family in Arabidopsis as well as their counterparts in rice, OsBC1L1 and OsBC1L8, regulate root hair growth. Single mutant cobl9, double mutants cobl7 cobl9 and double mutants osbc1l1 osbc1l8 all displayed prematurely terminated root hair elongation, though at varying levels. COBL7-YFP and COBL9-YFP accumulate prominently in the growing tips of newly emerged root hairs.

Furthermore, cobl9, cobl7 cobl9 and osbc1l1 osbc1l8 mutants were defective in the enrichment of cellulose in the tips of the growing root hairs. We also discovered that overexpression of COBL9 could promote root hair elongation and salinity tolerance. Taken together, these results provide compelling evidence that the polarized COBL7 and COBL9 in the tip of the emerging root hairs have conserved roles in regulating root hair development and stress adaptation in dicots and monocots.

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Efficacy and safety of endovascular brachytherapy combined with transarterial chemoembolization for the treatment of hepatocellular carcinoma patients with type III or IV portal vein tumor thrombosis

February 13, 2022 Lieven Leave a comment

Background: The purpose of this study was to evaluate the efficacy and safety of endovascular brachytherapy (EVBT) combined with transarterial chemoembolization (TACE) for the treatment of hepatocellular carcinoma (HCC) complicated with type III OR IV portal vein tumor thrombosis (PVTT) and to further analyze the prognostic predictors for the patients with HCC and PVTT.

Methods: We retrospectively analyzed the medical records of 54 patients who were diagnosed with HCC complicated with type III or IV PVTT and received EVBT combined with modified TACE treatment from January 2017 to June 2019. Adverse events, treatment response, overall survival (OS), progression-free survival (PFS), and stent patency were analysed to evaluate the efficacy and safety of this treatment. The independent prognostic predictors of OS were also statistically analyzed by the cox regression model.

Results: No adverse events occurred in the enrolled patients receiving EVBT combined with TACE treatment. The objective response and disease control rates were 42.6% and 96.3% respectively within 4 weeks after the treatment. The median OS and PFS were 209 days and 138 days, respectively. Cumulative stent patency rate was 70.4% at the last follow-up. AFP ≥ 400 ng/ml, ECOG PS > 1, Child Pugh grade B, and non-hemihepatic HCC were independent risk predictors to https://biodas.org/ evaluate the OS of HCC patient with type III or IV PVTT.

Conclusions: EVBT combined with TACE was a relatively effective and safe strategy to treat HCC patients with type III or IV PVTT.

Dual immune checkpoint blockade in hepatocellular carcinoma: where do we stand?

Hepatocellular carcinoma (HCC) represents the fourth most common cause of cancer-related death. Surgery, local ablative therapies and liver transplantation are the only potentially curative strategies, but the majority of patients present with advanced disease at diagnosis or develop recurrence after surgery.

In recent years, immunotherapy for HCC has received growing interest, and one of the most promising strategies is the association of two immune checkpoint inhibitors (ICIs), which has already demonstrated its potential in other solid tumors such as melanoma and renal cell carcinoma. Herein, we discuss the role and the biologic rationale of dual immune checkpoint blockade in HCC patients, focusing on the two ICI combinations: nivolumab plus ipilimumab and durvalumab plus tremelimumab.

Exposome and Skin. Part 2. The Influential Role of the Exposome, Beyond UVR, in Actinic Keratosis, Bowen’s Disease and Squamous Cell Carcinoma: A Proposal

Actinic keratosis (AK) is the main risk factor for the development of cutaneous invasive squamous cell carcinoma (SCC). It represents the first sign of severe chronic ultraviolet radiation exposure, which has a clear significant effect. Nevertheless, the skin is exposed to many other exposome factors which should be thoroughly considered. Our aim was to assess the impact of exposome factors other than ultraviolet radiation (UVR) on the etiopathology of AK and Bowen’s disease (BD) and progression of AK to SCC and to design tailored prevention strategies.

We performed an exhaustive literature search in September 2021 through PubMed on the impact of exposome factors other than UVR on AK, BD and SCC. We conducted several parallel searches combining terms of the following topics: AK, BD, SCC and microbiome, hormones, nutrition, alcohol, tobacco, viral infections, chemical contaminants and air pollution. Notably, skin microbiome studies have shown how Staphylococcus aureus infections are associated with AK and AK-to-SCC progression by the production of chronic inflammation. Nutritional studies have demonstrated how a caloric restriction in fat intake, oral nicotinamide and moderate consumption of wine significantly reduce the number of premalignant keratoses and SCC.

Regarding lifestyle factors, both alcohol and smoking are associated with the development of SCC in a dose-dependent manner. Relevant environmental factors are viral infections and chemical contaminants. Human papillomavirus infections induce deregulation of cellular proliferation and are associated with AK, BD and SCC. In addition to outdoor jobs, occupations such as industrial processing and farming also increase the risk of developing keratoses and SCC. The exposome of AK will undoubtedly help the understanding of its etiopathology and possible progression to SCC and will serve as a basis to design tailored prevention strategies.

A Genome-Wide Investigation of Effects of Aberrant DNA Methylation on the Usage of Alternative Promoters in Hepatocellular Carcinoma

Background: The alternative usage of promoters provides a way to regulate gene expression, has a significant influence on the transcriptome, and contributes to the cellular transformation of cancer. However, the function of alternative promoters (APs) in hepatocellular carcinoma (HCC) has not been systematically studied yet. In addition, the potential mechanism of regulation to the usage of APs remains unclear. DNA methylation, one of the most aberrant epigenetic modifications in cancers, is known to regulate transcriptional activity. Whether DNA methylation regulates the usage of APs needs to be explored. Here, we aim to investigate the effects of DNA methylation on usage of APs in HCC.

Methods: Promoter activities were calculated based on RNA-seq data. Functional enrichment analysis was implemented to conduct GO terms. Correlation tests were used to detect the correlation between promoter activity and methylation status. The LASSO regression model was used to generate a diagnostic model. Kaplan-Meier analysis was used to compare the overall survival between high and low methylation groups. RNA-seq and whole-genome bisulfite sequencing (WGBS) in HCC samples were performed to validate the correlation of promoter activity and methylation.

Results: We identified 855 APs in total, which could be well used to distinguish cancer from normal samples. The correlation of promoter activity and DNA methylation in APs was observed, and the APs with negative correlation were defined as methylation-regulated APs (mrAPs). Six mrAPs were identified to generate a diagnostic model with good performance (AUC = 0.97). Notably, the majority of mrAPs had CpG sites that could be used to predict clinical outcomes by methylation status. Finally, we verified 85.6% of promoter activity variation and 92.3% of methylation changes in our paired RNA-seq and WGBS samples, respectively. The negative correlation between promoter activity and methylation status was further confirmed in our HCC samples.

Conclusion: The aberrant methylation status plays a critical role in the precision usage of APs in HCC, which sheds light on the mechanism of cancer development and provides a new insight into cancer screening and treatment.

A case of locally advanced adenosquamous carcinoma of the cecum with long-term survival

A 63-year-old woman was admitted to our hospital with a right lower abdominal mass and general fatigue. Preoperative examination suggested a large ovarian tumor or cecal carcinoma. However, her intraoperative diagnosis was colon cancer; we therefore performed an ileocecal resection with oophorectomy. The tumor was pathologically diagnosed as adenosquamous carcinoma T4bN1M-stage IIIa.

We administrated CapeOX adjuvant chemotherapy for 6 months. Adenosquamous carcinoma is extremely rare, at around 0.1% of all colorectal cancers, and usually has a poor prognosis. The patient is still alive without recurrence after 84 post-operative months, even with later developments of metachronous early colorectal cancer and breast cancer. We herein report a rare case of cecal ASC with good prognosis.

Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing

May 6, 2020 Lieven Leave a comment

The PacBio RS II supplies for single molecule, real-time DNA know-how to sequence genomes and detect DNA modifications. The start line for high-quality sequence manufacturing is excessive molecular weight genomic DNA. To automate the librarypreparation course of, there should be high-throughput strategies in place to evaluate the genomic DNA, to make sure the dimensions and quantities of the sheared DNA fragments and ultimate library.

RESULTS

The library building automation was completed utilizing the Agilent NGS workstation with Bravo equipment for heating, shaking, cooling, and magnetic bead manipulations for template purification. The high quality management strategies from gDNA enter to ultimate library utilizing the Agilent Bioanalyzer System and Agilent TapeStation System had been evaluated.

Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing

CONCLUSIONS

Automated protocols of PacBio 10 kb librarypreparation produced libraries with comparable technical efficiency to these generated manually. The TapeStation System proved to be a dependable technique that may very well be utilized in a 96-well plate format to QC the DNA equal to the usual Bioanalyzer System outcomes. The DNA Integrity Number that’s calculated within the TapeStation System software program upon evaluation of genomic DNA is sort of useful to guarantee that the beginning genomic DNA just isn’t degraded. In this respect, the gDNA assay on the TapeStation System is preferable to the DNA 12000 assay on the Bioanalyzer System, which can not run genomic DNA, nor can the Bioanalyzer work instantly from the 96-well plates.

Emulsion PCR (EmPCR) is a generally employed technique for template amplification in a number of NGS-based sequencing platforms. The fundamental precept of emPCR is dilution and compartmentalization of template molecules in water droplets in a water-in-oil emulsion. Ideally, the dilution is to a level the place every droplet accommodates a single template molecule and features as a micro-PCR reactor.

Here, we focus on the fundamental ideas, benefits, and challenges of purposes of emPCR in medical testing. We describe the strategies of preparation and enrichment of template-positive Ion PGM™ Template OT2 200 Ion Sphere™ Particles (ISPs) on the Ion Personal Genome Machine(®) (PGM™) System.

For routine medical testing, following library era, we make use of the automated Ion OneTouch™ System that features the Ion OneTouch™ 2 and the Ion OneTouch™ ES devices for template era and enrichment of template-positive ISPs, respectively.

A new analytical technique was developed that integrates a generic pattern preparation into a liquid chromatography-multistage ion lure/time-of-flight mass spectrometry (LC-IT(MS(n))/TOF), allowing for large-scale screening and qualitative confirmation of wide-scope unlawful adulterants in different meals matrices. Samples had been pretreated by a quick single-tube multifunction extraction for correct multistage mass measurement on the hybrid LC-IT/TOF system.

A qualitative validation carried out for over 500 analyte-matrix pairs confirmed the strategy can scale back most of the matrix results and obtain a decrease restrict of confirmation at 0.1 mg/kg for 73% of the goal compounds.

A unique combination of dual-polarity detection, retention time, isotopic profile, and correct MS(n) spectra enables extra comprehensive and exact confirmation, based mostly on the multiparameter matching by automatedlibrary searching against the user-created database. Finally, the applicability of this LC-IT(MS(n))/TOF-based screening process for discriminating coeluting isobars, identifying nongoal adulterants, and even tentatively elucidating unanticipated species in actual samples is demonstrated.