Analysis of risk factors and development of predictive model for malnutrition in patients with traumatic brain injury

Malnutrition is a highly prevalent complication in patients with traumatic brain injury (TBI), and it is closely related to the prognosis of patients. Accurate identification of patients at high risk of malnutrition is essential. Therefore, we analyzed the risk factors of malnutrition in patients with TBI and developed a model to predict the risk of malnutrition. A retrospective collection of 345 patients with TBI, and they were divided into malnutrition and comparison groups according to the occurrence of malnutrition. Univariate correlation and multifactor logistic regression analyses were performed to determine patients' malnutrition risk factors. We used univariate and logistic regression (forward stepwise method) analyses to identify significant predictors associated with malnutrition in patients with TBI and developed a predictive model for malnutrition prediction. The model's discrimination, calibration, and clinical utility were evaluated using the receiver operating characteristic (ROC) curve, calibration plots, and decision curve analysis (DCA). A total of 216 patients (62.6%) developed malnutrition. Multifactorial logistic regression analysis showed that pulmonary infection, urinary tract infection, dysphagia, application of NGT, GCS score ≤ 8, and low ADL score were independent risk factors for malnutrition in patients with TBI (P < 0.05). The area under the curve of the model was 0.947. Calibration plots showed good discrimination of model calibration. DCA showed that the column line plot models were all clinically meaningful when nutritional interventions were performed over a considerable range of threshold probabilities (0-0.98). Malnutrition is widespread in patients with TBI, and the nomogram is a good predictor of whether patients develop malnutrition.

Factors and predictive model for malnutrition in poststroke disabled patients: A multicenter cross-sectional study

BACKGROUND

Although malnutrition has been shown to influence the clinical outcome of poststroke disabled patients, the associated factors and the prediction model have yet to be uncovered.

OBJECTIVES

This study aims to assess the current prevalence and factors associated with malnutrition in poststroke disabled patients and establish a prediction model.

METHODS

A multicenter cross-sectional survey among Chinese poststroke disabled patients (≥18 y old) was conducted in 2021. Information on patients' basic data, medical history, Barthel Index, dysphagia, and nutritional status was collected. A multivariable logistic regression model was used to identify the factors that influence malnutrition. Nomogram was developed and internal validation was conducted using 5-fold cross-validation. External validation was performed using the data from a preliminary survey. Receiver operating characteristic (ROC) analysis, calibration curves, and decision curve analysis (DCA) were used to analyze the predictive value of the nomogram.

RESULTS

Four hundred fifty-seven cases were enrolled, with the prevalence of malnutrition as 71.77%. Age (aOR = 1.039, 95% CI: 1.006-1.078), pulmonary infection (aOR = 4.301, 95% CI: 2.268-14.464), dysphagia (aOR = 24.605, 95% CI: 4.966-191.058), total intake volume (aOR = 0.997, 95% CI: 0.995-0.999), Barthel Index (aOR = 0.965, 95% CI: 0.951-0.980), and nasogastric tube (aOR = 16.529, 95% CI: 7.418-52.518) as nutrition support mode (compared to oral intake) were identified as the associated factors of malnutrition in stroke-disabled patients (P < 0.05). ROC analysis showed that the area under the curve (AUC) for nomogram was 0.854 (95% CI: 0.816-0.892). Fivefold cross-validation showed the mean AUC as 0.829 (95% CI: 0.784-0.873). There were no significant differences between predicted and actual probabilities. The DCA revealed that the model exhibited a net benefit when the risk threshold was between 0 and 0.4.

CONCLUSIONS

Age, pulmonary infection, dysphagia, nutrition support mode, total intake volume, and Barthel Index were factors associated with malnutrition in stroke-related disabled patients. The nomogram based on the result exhibited good accuracy, consistency and values.

Conformation-dependent lesion bypass of bulky arylamine-dG adducts generated from 2-nitrofluorene in epigenetic sequence contexts

Sequence context influences structural characteristics and repair of DNA adducts, but there is limited information on how epigenetic modulation affects conformational heterogeneity and bypass of DNA lesions. Lesions derived from the environmental pollutant 2-nitrofluorene have been extensively studied as chemical carcinogenesis models; they adopt a sequence-dependent mix of two significant conformers: major groove binding (B) and base-displaced stacked (S). We report a conformation-dependent bypass of the N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene (dG-FAF) lesion in epigenetic sequence contexts (d[5'-CTTCTC#G*NCCTCATTC-3'], where C# is C or 5-methylcytosine (5mC), G* is G or G-FAF, and N is A, T, C or G). FAF-modified sequences with a 3' flanking pyrimidine were better bypassed when the 5' base was 5mC, whereas sequences with a 3' purine exhibited the opposite effect. The conformational basis behind these variations differed; for -CG*C- and -CG*T-, bypass appeared to be inversely correlated with population of the duplex-destabilizing S conformer. On the other hand, the connection between conformation and a decrease in bypass for flanking purines in the 5mC sequences relative to C was more complex. It could be related to the emergence of a disruptive non-S/B conformation. The present work provides novel conformational insight into how 5mC influences the bypass efficiency of bulky DNA damage.

MiR-1275 Targeting SPARC Promotes Gambogic Acid-Induced Inhibition of Gastric Cancer

Gambogic acid (GA) has been observed to effectively impede the progression of numerous types of cancers. In this study, we investigated the effects of miR-1275 and Secreted Protein Acidic and Cysteine Rich (SPARC) on GA in gastric cancer (GC). miR-1275 and SPARC expression were determined in GC cell lines and tissues using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The correlation between miR-1275 and SPARC expression was ascertained using Pearson's correlation coefficient. Cell proliferation was assessed using the cell counting kit-8 (CCK-8) assay. The Transwell assay was conducted to examine cell migration. A dual-luciferase reporter assay was used to verify the regulatory relationship between miR-1275 and SPARC. The levels of SPARC, Bcl-2, and Bax proteins were estimated using western blotting. To verify the effects of GA on the growth of GC cells in vivo, a tumorigenesis experiment was performed in nude mice. GA suppressed GC cell viability and migration, facilitated apoptosis, and inhibited tumor growth in vivo and in vitro. Low levels of miR-1275 been observed in GC cell lines and tissues. GA-treated GC cells manifested high miR-1275 levels. In functional experiments, miR-1275 enhanced the influence of GA on cell apoptosis, migration, and proliferation. Furthermore, GA treatment suppressed SPARC upregulation in GC cell lines and tissues. Pearson's correlation coefficient revealed that miR-1275 expression negatively correlated with SPARC expression. Mechanistically, miR-1275 promoted growth inhibition in GA-treated GC cells by targeting SPARC. Our study indicates that miR-1275 enhances the suppressive effect of GA on GC progression by inhibiting SPARC expression. Through this study, we contribute to the knowledge of a new mechanism by which GA suppresses GC progression.

Investigating cannabinoids as P2X purinoreceptor 4 ligands by using surface plasmon resonance and computational docking

P2X purinoceptor 4 (P2X4) is an ATP-gated ion channel receptor with diverse neurophysiological functions, and P2X4 modulators hold promise as potential therapeutics for neuropathic pain, neuroinflammation, and neurodegenerative diseases. While several cannabinoids have been reported as modulators of purinoreceptors, their specific purinoreceptor-binding characteristics remain elusive. In this study, we established a comprehensive workflow that included a binding screening platform and a novel surface plasmon resonance (SPR) competitive assay, complemented by computational docking, to identify potential P2X4 binders among a panel of twenty-eight cannabinoids. Through SPR, we determined the binding affinities of cannabinoids (KD values ranging from 3.4 × 10-4 M to 1 × 10-6 M), along with two known P2X4 antagonists, BX430 (KD = 4.5 × 10-6 M) and 5-BDBD (KD = 7.8 × 10-6 M). The competitive SPR assay validated that BX430 and 5-BDBD acted as non-competitive binders with P2X4. In the following competitive assays, two cannabinoids including cannabidiol (CBD) and cannabivarin (CBV) were identified as competitive P2X4-binders with 5-BDBD, while the remaining cannabinoids exhibited non-competitive binding with either BX430 or 5-BDBD. Our molecular docking experiments further supported these findings, demonstrating that both CBD and CBV shared identical binding sites with residues in the 5-BDBD binding pocket on P2X4. In conclusion, this study provides valuable insights into the P2X4-binding affinity of cannabinoids through SPR and sheds light on the interactions between cannabinoids (CBD and CBV) and P2X4.

Erratum: Correction Notice: Establishment of Human PD-1/PD-L1 Blockade Assay Based on Surface Plasmon Resonance (SPR) Biosensor

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Establishment of Human PD-1/PD-L1 Blockade Assay Based on Surface Plasmon Resonance (SPR) Biosensor

Blockade of the programmed cell death protein 1 (PD-1)/PD-ligand 1 (PD-L1) axis is a promising strategy for cancer immunotherapy. Although antibody-based PD-1/PD-L1 inhibitors have shown remarkable results in clinical cancer studies, their inherent limitations underscore the significance of developing novel PD-1/PD-L1 inhibitors. Small molecule inhibitors have several advantages over antibody-based inhibitors, including favorable tumor penetration and oral bioavailability, fewer side effects, easier administration, preferred biological half-life, and lower cost. However, small molecule inhibitors that directly target the PD-1/PD-L1 interaction are still in the early development stage, partially due to the lack of reliable biophysical assays. Herein, we present a novel PD-1/PD-L1 blockade assay using a surface plasmon resonance (SPR)-based technique. This blockade assay immobilizes human PD-1 on a sensor chip, which interacts with PD-L1 inhibitors or negative PD-L1 binders with human PD-L1 protein at a range of molecular ratios. The binding kinetics of PD-L1 to PD-1 and the blockade rates of small molecules were determined. Compared to other techniques such as PD-1/PD-L1 pair enzyme-linked immunosorbent assay (ELISA) and AlphaLISA immunoassays, our SPR-based method offers real-time and label-free detection with advantages including shorter experimental runs and smaller sample quantity requirements. Key features A SPR protocol screens compounds for their capacity to block the PD-1/PD-L1 interaction. Validation of PD-1/PD-L1 interaction, followed by assessing blockade effects with known inhibitors BMS-1166 and BMS-202, and a negative control NO-Losartan A. Analysis of percentage blockade of PD-1/PD-L1 of the samples to obtain the IC50. Broad applications in the discovery of small molecule-based PD-1/PD-L1 inhibitors for cancer immunotherapy. Graphical overview.

Probing the Interactions of Perfluorocarboxylic Acids of Various Chain Lengths with Human Serum Albumin: Calorimetric and Spectroscopic Investigations

Despite an exponential increase in PFAS research over the past two decades, the mechanisms behind how PFAS cause adverse health effects are still poorly understood. Protein interactions are considered a significant driver of bioaccumulation and subsequent toxicity from re-exposure; however, most of the available literature is limited to legacy PFAS. We utilized microcalorimetric and spectroscopic methods to systematically investigate the binding between human serum albumin (HSA) and perfluorocarboxylic acids (PFCAs) of varying chain lengths and their nonfluorinated fatty acid (FA) counterparts. The results reveal the optimal chain length for significant PFCA-HSA binding and some fundamental interactions, i.e., the polar carboxylic head of PFCA is countered by ionizable amino acids such as arginine, and the fluorocarbon tails stabilized by hydrophobic residues like leucine and valine. Additionally, fluorine's unique polarizability contributes to PFCA's stronger binding affinities relative to the corresponding fatty acids. Based on these observations, we posit that PFCAs likely bind to HSA in a "cavity-filling" manner, provided they have an appropriate size and shape to accommodate the electrostatic interactions. The results reported herein widen the pool of structural information to explain PFAS bioaccumulation patterns and toxicity and support the development of more accurate computational modeling of protein-PFAS interactions. TOC graphic created with Biorender.com.

Electrochemically Enabled Intramolecular Amino- and Oxysulfonylation of Alkenes with Sodium Sulfinates to Access Sulfonylated Saturated Heterocycles

A practical and efficient electrochemical intramolecular amino- or oxysulfonylation of internal alkenes equipped with pendant nitrogen or oxygen-centered nucleophiles with sodium sulfinate was developed. Under undivided electrolytic cell conditions, a variety of sulfonylated N-heterocycles and O-heterocycles, such as tetrahydrofurans, tetrahydropyrans, oxepanes, tetrahydropyrroles, piperidines, δ-valerolactones, etc., were efficiently prepared from easily accessible unsaturated alcohols, carboxylic acids, and N-tosyl amines without the need for additional metal or exogenous oxidant. The robust electrochemical transformation features excellent redox economy, high diastereoselectivity, and broad substrate specificity, which provide a general and practical access to sulfone-containing heterocycles and would facilitate the related synthetic and biological studies based on this electrosynthesis.

Identification of SARS-CoV-2 Main Protease Inhibitors from a Library of Minor Cannabinoids by Biochemical Inhibition Assay and Surface Plasmon Resonance Characterized Binding Affinity

The replication of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is mediated by its main protease (M^pro), which is a plausible therapeutic target for coronavirus disease 2019 (COVID-19). Although numerous in silico studies reported the potential inhibitory effects of natural products including cannabis and cannabinoids on SARS-CoV-2 M^pro, their anti-M^pro activities are not well validated by biological experimental data. Herein, a library of minor cannabinoids belonging to several chemotypes including tetrahydrocannabinols, cannabidiols, cannabigerols, cannabichromenes, cannabinodiols, cannabicyclols, cannabinols, and cannabitriols was evaluated for their anti-M^pro activity using a biochemical assay. Additionally, the binding affinities and molecular interactions between the active cannabinoids and the M^pro protein were studied by a biophysical technique (surface plasmon resonance; SPR) and molecular docking, respectively. Cannabinoids tetrahydrocannabutol and cannabigerolic acid were the most active M^pro inhibitors (IC₅₀ = 3.62 and 14.40 μM, respectively) and cannabigerolic acid had a binding affinity KD=2.16×10-4 M). A preliminary structure and activity relationship study revealed that the anti-Mpro effects of cannabinoids were influenced by the decarboxylation of cannabinoids and the length of cannabinoids' alkyl side chain. Findings from the biochemical, biophysical, and computational assays support the growing evidence of cannabinoids' inhibitory effects on SARS-CoV-2 M^pro.

The Value of Negative-Pressure Wound Therapy and Flap Surgery in Hidradenitis Suppurativa – A Single Center Analysis of Different Treatment Options

Background

Hidradenitis suppurativa is manifested by painful abscesses and scarring of sweat glands. Axillary, inguinal and genital regions are mostly affected. Multiple options exist in the treatment of hidradenitis suppurativa. The aim of this retrospective, mono-center cohort study was to analyze the outcome of different treatment methods after radical excision of hidradenitis suppurativa.

Methods

We retrospectively evaluated the treatment strategy and recurrence rate of hidradenitis suppurativa. We included all eligible patients of legal age between February 2003 and October 2021, with the diagnosis of Hidradenitis suppurativa and the necessity for surgical treatment. All patients with surgical treatment and direct wound closure by suture were excluded. Bacterial load and flora were analyzed for primary and secondary reconstruction in combination with negative-pressure wound therapy. Patient data were analyzed for recurrence rate and remission time according to different reconstructive techniques.

Results

In 44 affected anatomical sites (n = 23 patients) we treated 15 patients with negative-pressure wound therapy. Bacterial load and flora were lower in the last wound swab of patients with multi-surgical procedures (22 localizations) compared to the first wound swab independent of the use of negative-pressure wound therapy.

Wound closure, independent of a direct and multi-stage procedure was achieved by local fasciocutaneous flaps (n = 12), secondary intention healing (n = 7), secondary intention healing with buried chip skin grafts (n = 10), or split-thickness skin grafts (n = 15). Radical excision combined with split-thickness skin grafts showed the lowest recurrence rate in the follow-up (16%; n = 4).

Conclusion

Radical excision of hidradenitis suppurativa as gold standard for surgical treatment combined with negative-pressure wound therapy as multi-stage procedures ultimately reduced bacterial load and flora in our study. The use of split-thickness skin grafts showed the lowest recurrence rate.

Complementary Copper-Catalyzed and Electrochemical Aminosulfonylation of O-Homoallyl Benzimidates and N-Alkenyl Amidines with Sodium Sulfinates

A complementary copper-catalyzed and electrochemical aminosulfonylation of O-homoallyl benzimidates and N-alkenyl amidines with sodium sulfinates was developed. The terminal alkene substrate produced sulfone-containing 1,3-oxazines and tetrahydropyrimidines in the presence of Cu(OAc)₂, Ag₂CO₃, and DPP, and under similar reaction conditions, sulfonylated tetrahydro-1,3-oxazepines were prepared from 1-aryl-substituted O-homoallyl benzimidates in moderate to good yields. For certain electron-rich 1,1-diaryl-substituted alkene substrates, the corresponding tetrahydro-1,3-oxazepines could also be obtained in similar or even higher yields via a green electrochemical technique.

Inhibitory Effects and Surface Plasmon Resonance-Based Binding Affinities of Dietary Hydrolyzable Tannins and Their Gut Microbial Metabolites on SARS-CoV-2 Main Protease

Severe acute respiratory syndrome coronavirus (SARS-CoV-2) main protease (Mpro) inhibitors are considered as potential treatments for coronavirus disease 2019, and dietary polyphenols show promise in SARS-CoV-2 Mpro inhibition based on in silico studies. In the present study, we utilize a combination of biochemical-, surface plasmon resonance-, and docking-based assays to evaluate the inhibition and binding affinities of a series of tannins and their gut microbial metabolites on SARS-CoV-2 Mpro. The tested compounds (2-50 μM) were hydrolyzable tannins, including ellagitannins (punicalagin and ellagic acid) and gallotannins (tannic acid, pentagalloyl glucose, ginnalin A, and gallic acid), and their gut microbial metabolites, urolithins and pyrogallol, respectively. They inhibited SARS-CoV-2 Mpro (by 6.6-100.0% at 50 μM) and bound directly to the Mpro protein (with dissociation constants from 1.1 × 10-6 to 5.3 × 10-5 M). This study sheds light on the inhibitory effects of tannins and their metabolites on SARS-CoV-2 Mpro.

Three CircRNAs Function as Potential Biomarkers for Colorectal Cancer

BACKGROUND

Colorectal cancer (CRC) is one of the most frequently diagnosed cancers worldwide. Based on clinical data, CRC could be cured by surgery with favorable outcomes if diagnosed at an early stage. The present study aimed to determine whether circ-FMN2, circ-LMNB1, and circ-ZNF609 may serve as potential biomarkers for CRC.

METHODS

Expression levels of circ-FMN2, circ-LMNB1, and circ-ZNF609 were detected in serum samples from 88 CRC patients and 68 healthy volunteers by real-time quantitative PCR (RT-qPCR). The correlation between circRNA expressions and clinicopathological parameters was analyzed subsequently. The ROC curve analysis and survival curves were calculated and compared in order to explore the diagnostic and prognostic values of circ-RNAs in CRC.

RESULTS

The results verified that circ-FMN2, circ-LMNB1, and circ-ZNF609 were significantly elevated in serum samples of CRC patients compared with healthy controls (p < 0.01). Increased circ-FMN2, circ-LMNB1, and circ-ZNF609 expressions were markedly positively correlated with histological grade (p < 0.0001, p = 0.0014, p = 0.0303), lymph nodes metastasis (p < 0.0001, p < 0.0001, p = 0.0093), and TNM stage (p = 0.0055, p = 0.0110, p < 0.000). Meanwhile, the ROC curve analysis verified the diagnostic accuracy of circ-FMN2, circ-LMNB1, and circ-ZNF609 with AUC of 0.9153 (95% CI = 0.8707 ~ 0.9599), 0.9627 (95% CI = 0.9351 ~ 0.9903), and 0.8711 (95% CI = 0.8151 ~ 0.9270), respectively. Furthermore, the CRC patients with high circ-FMN2, circ-LMNB1, and circ-ZNF609 had significantly worse outcomes than those with low expression (p = 0.0267, p = 0.0145, p = 0.0194).

CONCLUSIONS

The present study elucidated that circ-FMN2, circ-LMNB1, and circ-ZNF609 may function as potential diagnostic and prognostic indicators for CRC detection.

CNN-based qualitative detection of bone mineral density via diagnostic CT slices for osteoporosis screening

The features extracted from diagnostic computed tomography (CT) slices were used to qualitatively detect bone mineral density (BMD) through neural network models, and the evaluation results indicated that it may be a promising approach to perform osteoporosis screening in clinical practice.

INTRODUCTION

The purpose of this study is to design a novelty diagnostic method for osteoporosis screening by using the convolutional neural network (CNN), which can be incorporated into the procedure of routine CT diagnostic in medical examination thereby improving the osteoporosis diagnosis and reducing the patient burden.

METHODS

The proposed CNN-based method mainly comprises two functional modules to perform qualitative detection of BMD by analyzing the diagnostic 2D CT slice. The first functional module aims to locate and segment the ROI of diagnostic 2D CT slice, called Mark-Segmentation-Network (MS-Net). The second functional module is used to determine the category of BMD by the features of ROI, called BMD-Classification-Network (BMDC-Net). The diagnostic 2D CT slice of pedicle level in lumbar vertebrae (L1) was selected from 3D CT image in our experiments firstly. Then, the trained MS-Net can get the mark image of input original 2D CT slice, thereby obtain the segmentation image. Finally, the trained BMDC-Net can obtain the probability value of normal bone mass, low bone mass, and osteoporosis by inputting the segmentation image. On the basis of network results, the radiologists can provide preliminary qualitative diagnosis results of BMD.

RESULTS

Training of the network was performed on diagnostic 2D CT slices of 150 patients. The network was tested on 63 patients. Each patient corresponds to a 2D CT slice. The proposed MS-Net has an excellent segmentation precision on the shape preservation of different lumbar vertebra. The dice index (DI), pixel accuracy (PA), and intersection over union (IOU) of segmentation results are greater than 0.8. The proposed BMDC-Net achieved an accuracy of 76.65% and an area under the receiver operating characteristic curve of 0.9167.

CONCLUSIONS

This study proposed a novel method for qualitative detection of BMD via diagnostic CT slices and it has great potential in clinical applications for osteoporosis screening. The method can potentially reduce the manual burden to radiologists and diagnostic cost to patients.

Effect of <i>Evodia rutaecarpa</i> (Juss) Benth extract on Alzheimer disease in mice

Purpose: To investigate the protective effect of Evodia rutaecarpa (Juss.) Benth. extract (ERBE) against Alzheimer's disease in 3xTg-AD mice. Methods: The cognitive function of 3xTg-AD mice was assessed using Morris water maze test. The levels of amyloid beta deposits and NeuN in the mouse hippocampus were evaluated by immunohistochemistry. Brain neurotrophic derived factor (BDNF) and tyrosine kinase B (TrkB) expressions were determined by western blot analysis. Results: ERBE treatment significantly ameliorated learning and memory deficits in AD mice, as shown by increased time spent in the target zone during probe tests. The escape latency in the animals treated with 400 mg/kg ERBE (20.5 ± 1.3 s) was significantly higher than untreated 3xTg-AD mice (12.4 ± 1.3 s, p < 0.01). In addition, ERBE significantly decreased Aβ deposits, increased NeuN-positive cells, and upregulated the expressions of BDNF (1.4 ± 0.2, p < 0.05) and TrkB (1.1 ± 0.2, p < 0.05) in 3xTg AD mice. Conclusion: The results suggest that ERBE administration may be a useful strategy for treating memory impairment induced by several neurodegenerative diseases. Keywords: Evodia rutaecarpa, Alzheimer, Memory impairment, NeuN-positive cells

Dynamical Scaling of Charge and Spin Responses at a Kondo Destruction Quantum Critical Point

Quantum critical points often arise in metals perched at the border of an antiferromagnetic order. The recent observation of singular and dynamically scaling charge conductivity in an antiferromagnetic quantum critical heavy fermion metal implicates beyond-Landau quantum criticality. Here we study the charge and spin dynamics of a Kondo destruction quantum critical point (QCP), as realized in an SU(2)-symmetric Bose-Fermi Kondo model. We find that the critical exponents and scaling functions of the spin and single-particle responses of the QCP in the SU(2) case are essentially the same as those of the large-N limit, showing that 1/N corrections are subleading. Building on this insight, we demonstrate that the charge responses at the Kondo destruction QCP are singular and obey ω/T scaling. This property persists at the Kondo destruction QCP of the SU(2)-symmetric Kondo lattice model.

Sequential localization of a complex electron fluid

Complex and correlated quantum systems with promise for new functionality often involve entwined electronic degrees of freedom. In such materials, highly unusual properties emerge and could be the result of electron localization. Here, a cubic heavy fermion metal governed by spins and orbitals is chosen as a model system for this physics. Its properties are found to originate from surprisingly simple low-energy behavior, with 2 distinct localization transitions driven by a single degree of freedom at a time. This result is unexpected, but we are able to understand it by advancing the notion of sequential destruction of an SU(4) spin-orbital-coupled Kondo entanglement. Our results implicate electron localization as a unified framework for strongly correlated materials and suggest ways to exploit multiple degrees of freedom for quantum engineering.

DNA base sequence effects on bulky lesion-induced conformational heterogeneity during DNA replication

4-Aminobiphenyl (ABP) and its structure analog 2-aminofluorene (AF) are well-known carcinogens. In the present work, an unusual sequence effect in the 5′-CTTCTG₁G₂TCCTCATTC-3′ DNA duplex is reported for ABP- and AF-modified G. Specifically, the ABP modification at G₁ resulted in a mixture of 67% major groove B-type (B) and 33% stacked (S) conformers, while at the ABP modification at G₂ exclusively resulted in the B-conformer. The AF modification at G₁ and G₂ lead to 25%:75% and 83%:17% B:S population ratios, respectively. These differences in preferred conformation are due to an interplay between stabilizing (hydrogen bonding and stacking that is enhanced by lesion planarity) and destabilizing (solvent exposure) forces at the lesion site. Furthermore, while the B-conformer is a thermodynamic stabilizer and the S-conformer is a destabilizer in duplex settings, the situation is reversed at the single strands/double strands (ss/ds) junction. Specifically, the twisted biphenyl is a better stacker at the ss/ds junction than the coplanar AF. Therefore, the ABP modification leads to a stronger strand binding affinity of the ss/ds junction than the AF modification. Overall, the current work provides conformational insights into the role of sequence and lesion effects in modulating DNA replication.

Probing the Effect of Bulky Lesion-Induced Replication Fork Conformational Heterogeneity Using 4-Aminobiphenyl-Modified DNA

Bulky organic carcinogens are activated in vivo and subsequently react with nucleobases of cellular DNA to produce adducts. Some of these DNA adducts exist in multiple conformations that are slowly interconverted to one another. Different conformations have been implicated in different mutagenic and repair outcomes. However, studies on the conformation-specific inhibition of replication, which is more relevant to cell survival, are scarce, presumably due to the structural dynamics of DNA lesions at the replication fork. It is difficult to capture the exact nature of replication inhibition by existing end-point assays, which usually detect either the ensemble of consequences of all the conformers or the culmination of all cellular behaviors, such as mutagenicity or survival rate. We previously reported very unusual sequence-dependent conformational heterogeneities involving FABP-modified DNA under different sequence contexts (TG₁*G₂T [67%B:33%S] and TG₁G₂*T [100%B], G*, N-(2′-deoxyguanosin-8-yl)-4′-fluoro-4-aminobiphenyl) (Cai et al. Nucleic Acids Research, 46, 6356–6370 (2018)). In the present study, we attempted to correlate the in vitro inhibition of polymerase activity to different conformations from a single FABP-modified DNA lesion. We utilized a combination of surface plasmon resonance (SPR) and HPLC-based steady-state kinetics to reveal the differences in terms of binding affinity and inhibition with polymerase between these two conformers (67%B:33%S and 100%B).

Characterization of Byproducts from Chemical Syntheses of Oligonucleotides Containing 1-Methyladenine and 3-Methylcytosine

Oligonucleotides serve as important tools for biological, chemical, and medical research. The preparation of oligonucleotides through automated solid-phase synthesis is well-established. However, identification of byproducts generated from DNA synthesis, especially from oligonucleotides containing site-specific modifications, is sometimes challenging. Typical high-performance liquid chromatography (HPLC), mass spectrometry (MS), and gel electrophoresis methods alone are not sufficient for characterizing unexpected byproducts, especially for those having identical or very similar molecular weight (MW) to the products. We used a rigorous quality control procedure to characterize byproducts generated during oligonucleotide syntheses: (1) purify oligonucleotides by different HPLC systems; (2) determine exact MW by high-resolution MS; (3) locate modification position by MS/MS or exonuclease digestion with matrix-assisted laser desorption ionization-time of flight analysis; and (4) conduct, where applicable, enzymatic assays. We applied these steps to characterize byproducts in the syntheses of oligonucleotides containing biologically important methyl DNA adducts 1-methyladenine (m1A) and 3-methylcytosine (m3C). In m1A synthesis, we differentiated a regioisomeric byproduct 6-methyladenine, which possesses a MW identical to uncharged m1A. As for m3C, we identified a deamination byproduct 3-methyluracil, which is only 1 Da greater than uncharged m3C in the ∼4900 Da context. The detection of these byproducts would be very challenging if the abovementioned procedure was not adopted.

Anti-glycation and anti-oxidative effects of a phenolic-enriched maple syrup extract and its protective effects on normal human colon cells

Oxidative stress and free radical generation accelerate the formation of advanced glycation endproducts (AGEs) which are linked to several chronic diseases. Published data suggest that phenolic-rich plant foods, show promise as natural anti-AGEs agents due to their anti-oxidation capacities. A phenolic-enriched maple syrup extract (MSX) has previously been reported to show anti-inflammatory and neuroprotective effects but its anti-AGE effects remain unknown. Therefore, herein, we investigated the anti-glycation and anti-oxidation effects of MSX using biochemical and biophysical methods. MSX (500 μg mL^-1) reduced the formation of AGEs by 40% in the bovine serum albumin (BSA)-fructose assay and by 30% in the BSA-methylglyoxal (MGO) assay. MSX also inhibited the formation of crosslinks typically seen in the late stage of glycation. Circular dichroism and differential scanning calorimeter analyses demonstrated that MSX maintained the structure of BSA during glycation. In the anti-oxidant assays, MSX (61.7 μg mL^-1) scavenged 50% of free radicals (DPPH assay) and reduced free radical generation by 20% during the glycation process (electron paramagnetic resonance time scan). In addition, the intracellular levels of hydrogen peroxide induced reactive oxygen species were reduced by 27-58% with MSX (50-200 μg mL^-1) in normal/non-tumorigenic human colon CCD-18Co cells. Moreover, in AGEs and MGO challenged CCD-18Co cells, higher cellular viabilities and rapid extracellular signal-regulated kinase (ERK) phosphorylation were observed in MSX treated cells, indicating its protective effects against AGEs-induced cytotoxicity. Overall, this study supports the biological effects of MSX, and warrants further investigation of its potential as a dietary agent against diseases mediated by oxidative stress and inflammation.

Mesenchymal stem cells and myoblast differentiation under HGF and IGF-1 stimulation for 3D skeletal muscle tissue engineering

Background

Volumetric muscle loss caused by trauma or after tumour surgery exceeds the natural regeneration capacity of skeletal muscle. Hence, the future goal of tissue engineering (TE) is the replacement and repair of lost muscle tissue by newly generating skeletal muscle combining different cell sources, such as myoblasts and mesenchymal stem cells (MSCs), within a three-dimensional matrix. Latest research showed that seeding skeletal muscle cells on aligned constructs enhance the formation of myotubes as well as cell alignment and may provide a further step towards the clinical application of engineered skeletal muscle.

In this study the myogenic differentiation potential of MSCs upon co-cultivation with myoblasts and under stimulation with hepatocyte growth factor (HGF) and insulin-like growth factor-1 (IGF-1) was evaluated. We further analysed the behaviour of MSC-myoblast co-cultures in different 3D matrices.

Results

Primary rat myoblasts and rat MSCs were mono- and co-cultivated for 2, 7 or 14 days. The effect of different concentrations of HGF and IGF-1 alone, as well as in combination, on myogenic differentiation was analysed using microscopy, multicolour flow cytometry and real-time PCR. Furthermore, the influence of different three-dimensional culture models, such as fibrin, fibrin-collagen-I gels and parallel aligned electrospun poly-ε-caprolacton collagen-I nanofibers, on myogenic differentiation was analysed. MSCs could be successfully differentiated into the myogenic lineage both in mono- and in co-cultures independent of HGF and IGF-1 stimulation by expressing desmin, myocyte enhancer factor 2, myosin heavy chain 2 and alpha-sarcomeric actinin. An increased expression of different myogenic key markers could be observed under HGF and IGF-1 stimulation. Even though, stimulation with HGF/IGF-1 does not seem essential for sufficient myogenic differentiation. Three-dimensional cultivation in fibrin-collagen-I gels induced higher levels of myogenic differentiation compared with two-dimensional experiments. Cultivation on poly-ε-caprolacton-collagen-I nanofibers induced parallel alignment of cells and positive expression of desmin.

Conclusions

In this study, we were able to myogenically differentiate MSC upon mono- and co-cultivation with myoblasts. The addition of HGF/IGF-1 might not be essential for achieving successful myogenic differentiation. Furthermore, with the development of a biocompatible nanofiber scaffold we established the basis for further experiments aiming at the generation of functional muscle tissue.

Electronic supplementary material

The online version of this article (doi:10.1186/s12860-017-0131-2) contains supplementary material, which is available to authorized users.

DNA-binding studies of the natural β-carboline eudistomin U

Eudistomin U is a member of the β-carboline class of heterocyclic amine-containing molecules that are capable of binding to DNA. The structure of eudistomin U is unique since it contains an indole ring at the 1-position of the pyridine ring. While simple β-carbolines are reported to intercalate DNA, an examination of the mode of binding of eudistomin U has been lacking. We report preliminary spectroscopic (UV-Vis, thermal denaturation, CD) and calorimetric (DSC) data on the binding of eudistomin U to DNA, which suggest that eudistomin U binds weakly according to a mechanism that is more complicated than other members of its class.

A Pilot Metabolic Profiling Study of Patients With Neonatal Jaundice and Response to Phototherapy

Phototherapy has been widely used in treating neonatal jaundice, but detailed metabonomic profiles of neonatal jaundice patients and response to phototherapy have not been characterized. Our aim was to depict the serum metabolic characteristics of neonatal jaundice patients relative to controls and changes in response to phototherapy. A (1) H nuclear magnetic resonance (NMR)-based metabonomic approach was employed to study the metabolic profiling of serum from healthy infants (n = 25) and from infants with neonatal jaundice (n = 30) pre- and postphototherapy. The acquired data were processed by multivariate principal component analysis (PCA) and orthogonal partial least-squares-discriminant analysis (OPLS-DA). The PLS-DA and OPLS-DA model identified nine metabolites capable of distinguishing patients from controls. In addition, 28 metabolites such as β-glucose, α-glucose, valine, and pyruvate changed in response to phototherapy. This study offers useful information on metabolic disorders in neonatal jaundice patients and the effects of phototherapy on lipids, amino acid, and energy metabolism.

ZnRF3 induces apoptosis of gastric cancer cells by antagonizing Wnt and Hedgehog signaling

AIM

The aim of this paper was to investigate the function an importance of E3-ubiquitin ligase ZnRF3 in the progression of cancer cell growth.

METHODS

A total of 58 patients (44 males and 14 females) were enrolled in the study and their gastric tumors were removed surgically and were staged by the TNM approach. Among these patients, 43 patients died and 15 survived at the time of this study. The tumors and the paracancerous tissues were examined by immunohostochemistry for the expression of ZnRF3. We assessed the expression of ZnRF3 in gastric tumors and paracancerous tissues from our patients and related this to patient survival.

RESULTS

A large proportion of malignant cancers of the stomach are gastric adenocarcinoma type. In spite of many studies, the molecular basis for this cancer is still unclear. Deregulated cell proliferative signaling via Wnt/β-catenin and Hedgehog pathways is considered important in the pathogenesis of many cancers including the gastric cancer. Recent studies identified ZnRF3 protein, which is a E3-ubiquitin ligase and which is either deleted or mutated in cancers, to inhibit Wnt signaling. However, the significance of ZnRF3 in the control of gastric cancer and whether it also regulates Hedgehog signaling pathway, is not known. ZnRF3 expression was much higher in tumors from aged patients. Male patients showed higher mortality than the females. Mechanistic studies using normal gastric cells (GES1) and gastric cancer cells (MGC-803) infected with either AdZnRF3 or AdGFP viral vectors, revealed that ZnRF3 overexpression causes significantly more apoptosis and lowered proliferation of cancer cells. ZnRF3 overexpression led to greatly reduced levels of Lgr5, a component of Wnt signaling and also Gli1, a component of Hedgehog signaling. Thus, ZnRF3 negatively influences both the Wnt and Hedgehog proliferative pathways and probably this way it negatively regulates cancer progression. These results suggest the importance of normal ZnRF3 function in checking the progression of cancer cell growth and indicate that a lack of this protein can lead to poorer clinical outcomes for gastric cancer patients.

CONCLUSION

We observed a clear relationship between ZnRF3 expression in paracancerous tissue and tumor size.

Structure Activity Related, Mechanistic, and Modeling Studies of Gallotannins containing a Glucitol-Core and α-Glucosidase

Gallotannins containing a glucitol core, which are only produced by members of the maple (Acer) genus, are more potent α-glucosidase inhibitors than the clinical drug, acarbose. While this activity is influenced by the number of substituents on the glucitol core (e.g. more galloyl groups leads to increased activity), the mechanisms of inhibitory action are not known. Herein, we investigated ligand-enzyme interactions and binding mechanisms of a series of 'glucitol-core containing gallotannins (GCGs)' against the α-glucosidase enzyme. The GCGs included ginnalins A, B and C (containing two, one, and one galloyl/s, respectively), maplexin F (containing 3 galloyls) and maplexin J (containing 4 galloyls). All of the GCGs were noncompetitive inhibitors of α-glucosidase and their interactions with the enzyme were further explored using biophysical and spectroscopic measurements. Thermodynamic parameters (by isothermal titration calorimetry) revealed a 1:1 binding ratio between GCGs and α-glucosidase. The binding regions between the GCGs and α-glucosidase, probed by a fluorescent tag, 1,1'-bis(4-anilino-5-napththalenesulfonic acid, revealed that the GCGs decreased the hydrophobic surface of the enzyme. In addition, circular dichroism analyses showed that the GCGs bind to α-glucosidase and lead to loss of the secondary α-helix structure of the protein. Also, molecular modeling was used to predict the binding site between the GCGs and the α-glucosidase enzyme. This is the first study to evaluate the mechanisms of inhibitory activities of gallotannins containing a glucitol core on α-glucosidase.

Aerobic granulation in a modified oxidation ditch with an adjustable volume intraclarifier

A modified oxidation ditch (MOD) with an adjustable volume intraclarifier was proposed and used to achieve aerobic sludge granulation in continuous flow process. This MOD with working volume of 60L treated onsite wastewater from a town. Excellent aerobic granules with mean diameter of 600μm and sludge volume index (SVI) of 44mL/g were obtained in 120day. Bacterial community analysis revealed that most species from seed sludge were preserved in both MOD and granule SBR (G-SBR) except bacteria (Bacteroidetes) might be easily washed out during granulation. Some different bacterial communities were found in sludges from sequencing batch and continuous flow reactors. Presence of metal ions and inorganics in raw wastewater had positive effect on granule formation, but an adjustable volume intraclarifier for controlling selection pressure and deleting return sludge pump played a key role in aerobic sludge granulation.