ANXA5: A Key Regulator of Immune Cell Infiltration in Hepatocellular Carcinoma.

BACKGROUND Hepatocellular carcinoma (HCC) poses a significant threat to human life and is the most prevalent form of liver cancer. The intricate interplay between apoptosis, a common form of programmed cell death, and its role in immune regulation stands as a crucial mechanism influencing tumor metastasis. MATERIAL AND METHODS Utilizing HCC samples from the TCGA database and 61 anoikis-related genes (ARGs) sourced from GeneCards, we analyzed the relationship between ARGs and immune cell infiltration in HCC. Subsequently, we identified long non-coding RNAs (lncRNAs) associated with ARGs, using the least absolute shrinkage and selection operator (LASSO) regression analysis to construct a robust prognostic model. The predictive capabilities of the model were then validated through examination in a single-cell dataset. RESULTS Our constructed prognostic model, derived from lncRNAs linked to ARGs, comprised 11 significant lncRNAs: NRAV, MCM3AP-AS1, OTUD6B-AS1, AC026356.1, AC009133.1, DDX11-AS1, AC108463.2, MIR4435-2HG, WARS2-AS1, LINC01094, and HCG18. The risk score assigned to HCC samples demonstrated associations with immune indicators and the infiltration of immune cells. Further, we identified Annexin A5 (ANXA5) as the pivotal gene among ARGs, with it exerting a prominent role in regulating the lncRNA gene signature. Our validation in a single-cell database elucidated the involvement of ANXA5 in immune cell infiltration, specifically in the regulation of mononuclear cells. CONCLUSIONS This study delves into the intricate correlation between ARGs and immune cell infiltration in HCC, culminating in the development of a novel prognostic model reliant on 11 ARGs-associated lncRNAs. Furthermore, our findings highlight ANXA5 as a promising target for immune regulation in HCC, offering new perspectives for immune therapy in the context of HCC.

In Situ Fabrication of Electrospun Magnetic Film Under Laparoscopic Guidance for Preventing Postoperative Recurrence of Hepatocellular Carcinoma.

Despite laparoscopic-guided minimally invasive hepatectomy emerging as the primary approach for resecting hepatocellular carcinoma (HCC), there's still a significant gap in suitable biomaterials that seamlessly integrate with these techniques to achieve effective hemostasis and suppress residual tumors at the surgical margin. Electrospun films are increasingly used for wound closure, yet the employment of prefabricated electrospun films for hemostasis during minimally invasive HCC resection is hindered by prolonged operation times, complexity in implementation, limited visibility during surgery, and inadequate postoperative prevention of HCC recurrence. In this study, we integrated montmorillonite-iron oxide sheets into the PVP polymer framework, enhancing the resulting electrospun polyvinylpyrrolidone (PVP) /montmorillonite-iron oxide (MI) film (abbreviated as PMI) with robustness, hemostatic capability, and magnetocaloric properties. In contrast to the in vitro prefabricated electrospun films, the electrospun PMI film is designed to be formed in situ on liver wounds under laparoscopic guidance during hepatectomy. This design affords superior wound adaptability, facilitating meticulous wound closure and expeditious hemostasis, thereby simplifying the operative process and ultimately alleviating the workload of healthcare professionals. Moreover, when exposed to an alternating magnetic field, the film can efficiently ablate residual tumors, significantly augmenting the treatment efficacy of HCC. This article is protected by copyright. All rights reserved.

Preparation of NIR-II Polymer Nanoprobe Through Twisted Intramolecular Charge Transfer and Förster Resonance Energy Transfer of NIR-I Dye.

Near-infrared-II (NIR-II) fluorescence imaging is pivotal in biomedical research. Organic probes exhibit high potential in clinical translation, due to advantages such as precise structure design, low toxicity, and post-modifications convenience. In related preparation, enhancement of NIR-II tail emission from NIR-I dyes is an efficient method. In particular, the promotion of twisted intramolecular charge transfer (TICT) of relevant NIR-I dyes is a convenient protocol. However, present TICT-type probes still show disadvantages in relatively low emission, large particle sizes, or limited choice of NIR-I dyes, etc. Herein, the synthesis of stable small-sized polymer NIR-II fluoroprobes (e.g., 7.2 nm), integrating TICT and Förster resonance energy transfer process to synergistically enhance the NIR-II emission is reported. Strong enhanced emissions can be obtained from various NIR-I dyes and lanthanide elements (e.g., twelvefold at 1250 nm from Nd-DTPA/IR-808 sample). The fluorophore provides high-resolution angiography, with high-contrast imaging on middle cerebral artery occlusion model mice for distinguishing occlusion. The fluorophore can be rapidly excreted from the kidney (urine ≈65% within 4 h) in normal mice and exhibits long-term renal retention on acute kidney injury mice, showing potential applications in the prognosis of kidney diseases. This development provides an effective strategy to design and synthesize effective NIR-II fluoroprobes.

Minimally Invasive Delivery of Percutaneous Ablation Agent via Magnetic Colloidal Hydrogel Injection for Treatment of Hepatocellular Carcinoma.

Percutaneous thermotherapy, a minimally invasive operational procedure, is employed in the ablation of deep tumor lesions by means of target-delivering heat. Conventional thermal ablation methods, such as radiofrequency or microwave ablation, to a certain extent, are subjected to extended ablation time as well as biosafety risks of unwanted overheating. Given its effectiveness and safety, percutaneous thermotherapy gains a fresh perspective, thanks to magnetic hyperthermia. In this respect, an injectable- and magnetic-hydrogel-construct-based thermal ablation agent is likely to be a candidate for the aforementioned clinical translation. Adopting a simple and environment-friendly strategy, a magnetic colloidal hydrogel injection is introduced by a binary system comprising super-paramagnetic Fe3O4 nanoparticles and gelatin nanoparticles. The colloidal hydrogel constructs, unlike conventional bulk hydrogel, can be easily extruded through a percutaneous needle and then self-heal in a reversible manner owing to the unique electrostatic cross-linking. The introduction of magnetic building blocks is exhibited with a rapid magnetothermal response to an alternating magnetic field. Such hydrogel injection is capable of generating heat without limitation of deep penetration. The materials achieve outstanding therapeutic results in mouse and rabbit models. These findings constitute a new class of locoregional interventional thermal therapies with minimal collateral damages.

Methylation changes of liver DNA during the formation of gallstones.

Aim: To explore the overall methylation changes in liver tissues during the formation of gallstones, as well as the key pathways and genes involved in the process. Methods: Reduced-representation bisulfite sequencing and RNA sequencing were conducted on the liver tissues of mice with gallstones and control normal mice. Results: A total of 8705 differentially methylated regions in CpG and 1410 differentially expressed genes were identified. The joint analysis indicated that aberrant DNA methylation may be associated with dysregulated gene expression in key pathways such as cholesterol metabolism and bile secretion. Conclusion: We propose for the first time that methylation changes in some key pathway genes in liver tissue may be involved in the formation of gallstones.

Injectable Hydrogels Including Magnetic Nanosheets for Multidisciplinary Treatment of Hepatocellular Carcinoma via Magnetic Hyperthermia.

Relapse and unresectability have become the main obstacle for further improving hepatocellular carcinoma (HCC) treatment effect. Currently, single therapy for HCC in clinical practice is limited by postoperative recurrence, intraoperative blood loss and poor patient outcomes. Multidisciplinary therapy has been recognized as the key to improving the long-term survival rate for HCC. However, the clinical application of HCC synthetic therapy is restricted by single functional biomaterials. In this study, a magnetic nanocomposite hydrogel (CG-IM) with iron oxide nanoparticle-loaded mica nanosheets (Iron oxide nanoparticles@Mica, IM) is reported. This biocompatible magnetic hydrogel integrated high injectability, magnetocaloric property, mechanical robustness, wet adhesion, and hemostasis, leading to efficient HCC multidisciplinary therapies including postoperative tumor margin treatment and percutaneous locoregional ablation. After minimally invasive hepatectomy of HCC, the CG-IM hydrogel can facilely seal the bleeding hepatic margin, followed by magnetic hyperthermia ablation to effectively prevent recurrence. In addition, CG-IM hydrogel can inhibit unresectable HCC by magnetic hyperthermia through the percutaneous intervention under ultrasound guidance.

Injectable magnetic montmorillonite colloidal gel for the postoperative treatment of hepatocellular carcinoma.

Bioactive materials have been extensively developed for the adjuvant therapy of cancer. However, few materials can meet the requirements for the postoperative resection of hepatocellular carcinoma (HCC) due to massive bleeding and high recurrence. In particular, combination therapy for HCC has been highly recommended in clinical practice, including surgical resection, interventional therapy, ablation therapy and chemotherapy. Herein, an injectable magnetic colloidal gel (MCG) was developed by controllable electrostatic attraction between clinically available magnetic montmorillonites and amphoteric gelatin nanoparticles. The optimized MCG exhibited an effective magnetic heating effect, remarkable rheological properties, and high gel network stability, realizing the synergistic treatment of postoperative HCC by stimuli-responsive drug delivery, hemostasis and magnetic hyperthermia. Furthermore, a minimal invasive MCG-induced interventional magnetic hyperthermia therapy (MHT) under ultrasound guidance was realized on hepatic tumor rabbits, providing an alternative therapeutics to treat the postoperative recurrence. Overall, MCG is a clinically available injectable formulation for adjuvant therapy after HCC surgical resection.

Risk prediction models for difficult cholecystectomy.

Introduction: In some cases, laparoscopic cholecystectomy (LC) may be very difficult and easily converted to laparotomy, causing many complications to patients and prolonging the prognosis time. Thus, to evaluate the difficulty of LC before operation is extremely important. Aim: To explore the risk factors of difficult cholecystectomy (DC) and to establish a risk prediction model of DC. Material and methods: The data of 201patients who underwent cholecystectomy from 1 January 2018 to 10 November 2019 were analysed retrospectively. The highest quartile (P75) of cholecystectomy operation time was used as a cutting point of DC (≥ P75) and NLC (< P75). Logistic regression was used to analyse the influencing factors of DC, and its risk model was constructed for prediction. Results: Multivariate logistic regression analysis showed that body mass index (BMI) > 25 kg/m2, white blood cell (WBC) > 10 × 109/l, calculus incarcerated in neck of gallbladder, frequency of acute cholecystitis in the last 2 months > 4 times, thickness of gallbladder wall > 0.5 cm, and maximum diameter of gallstone > 2 cm were independent risk factors for DC. The prediction efficiency of the logistic regression equation was 0.879 (χ 2 = 1.457, p > 0.05). Conclusions: Based on analysis of risk factors, a logistic risk prediction model for difficult cholecystectomy was established. This model can be used to predict the difficulty of cholecystectomy.

In situ Thermal-Responsive Magnetic Hydrogel for Multidisciplinary Therapy of Hepatocellular Carcinoma.

Current surgical single modality treatments for hepatocellular carcinoma (HCC) were restricted by recurrence, blood loss, significant trauma, and poor prognostic. Although multidisciplinary strategies for HCC treatment have been highly recommended by the clinical guidelines, there was limited choice of materials and treatments. Herein, we reported an in situ formed magnetic hydrogel with promising bioapplicable thermal-responsiveness, strong adhesion in wet conditions, high magnetic hyperthermia, and biocompatibility, leading to efficient HCC multidisciplinary treatment including postoperative treatment and transarterial embolization therapy. In vivo results indicated that this hydrogel could reduce the postoperative recurrence rate. The hemostatic ability of the thermal-responsive hydrogel was further demonstrated in both the liver scratch model and liver tumor resection. Computed tomography imaging suggested that the hydrogel could completely embolize the arterial vessels of rabbit liver tumor by vascular intervention operation, which could serve as multidisciplinary responsive materials to external magnetic field and body temperature for HCC treatment.

STING agonist enhances the efficacy of programmed death-ligand 1 monoclonal antibody in breast cancer immunotherapy by activating the interferon-ß signalling pathway.

This study aimed to explore the role of a stimulator of interferon (IFN) gene (STING) agonist in breast cancer (BCa) immunotherapy. Clinical samples were collected from 37 patients with BCa. A tumor-bearing mouse model was established by injecting 4T1 cells into the mammary fat pad of mice. STING agonist and atezolizumab were injected in the mice twice a week for 2 weeks. Peripheral blood, tumor mass, lung, liver, brain cortex and kidney samples of the tumor-bearing mice were collected. Anti-IFN alpha receptor subunit 1 (IFNAR1) was used to treat 4T1 cells. Tumor tissues of patients with BCa exhibited lower STING and high programmed cell death protein 1 and programmed death-ligand 1 protein expressions. The STING agonist inhibited 4T1 cell growth in mice (P < 0.001) and increased the IFN-ß level and phosphorylation of STING, TBK1, IRF3 and STAT1 in tumor mass of tumor-bearing mice (P < 0.001). It synergized with atezolizumab to inhibit 4T1 cell growth in mice and increased tumor necrosis factor-α, IFN-ß, interleukin-10 and IFN-γ levels in the peripheral blood and tumor mass (P < 0.01). It synergized with atezolizumab to increase CD8+ cytotoxic T cells and decrease FOXP3+ Treg cells in the tumor-bearing mouse model. The STING agonist was nontoxic to the lung, liver, brain cortex and kidney. Anti-IFNAR1 reversed the STING agonist promotion on TBK1, IRF3 and STAT1 phosphorylation in 4T1 cells (P < 0.01). STING agonists enhance the efficacy of atezolizumab in BCa immunotherapy by activating the IFN-ß signaling pathway.

Simultaneous single-cell phenotype analysis of hepatocellular carcinoma CTCs using a SERS-aptamer based microfluidic chip.

Hepatocellular carcinoma (HCC) is a harmful malady that truly debilitates human health, and hence it is of significance to isolate and on-line profile the phenotype of HCC cells for further diagnosis and therapy. We developed a novel strategy for efficient capture and in situ heterogeneous phenotype analysis of circulating tumor cells (CTCs) at the single-cell level based on surface-enhanced Raman scattering (SERS) fingerprint characteristics. Herein, a new microfluidic chip with lantern-like bypass structure was designed to capture CTCs by their large size from whole blood. Furthermore, two types of SERS-aptamer nanotags were fabricated, realizing spectral recognition of single CTCs in accordance with the surface membrane protein expression. Up to 84% of CTCs with a purity of 95% were captured from whole blood samples using the present SERS-aptamer based microfluidic chip at 20 µL min-1. The results showed that the proposed strategy can successfully identify HCC cell subtypes by SERS measurements, which was related to the clinical surface biomarkers. This may open a new avenue for serving as a powerful tool of cancer diagnosis and prognosis evaluation.

Injectable ferrimagnetic silk fibroin hydrogel for magnetic hyperthermia ablation of deep tumor.

Due to the well-recognized biocompatibility, silk fibroin hydrogels have been developed for biomedical applications including bone regeneration, drug delivery and cancer therapy. For the treatment of cancer, silk-based photothermal agents exhibit the high photothermal conversion efficiency, but the limited light penetration depth of photothermal therapy restricts the treatment of some tumors in deep positions, such as liver tumor and glioma. To provide an alternative strategy, here we developed an injectable magnetic hydrogel based on silk fibroin and iron oxide nanocubes (IONCs). The as-prepared ferrimagnetic silk fibroin hydrogel could be easily injected through a syringe into tumor, especially rabbit hepatocellular carcinoma in deeper positions using ultrasound-guided interventional treatment. Compared with photothermal agents, the embedded IONCs endowed the ferrimagnetic silk fibroin hydrogel with remote hyperthermia performance under an alternating magnetic field, resulting in the effective magnetic hyperthermia of deep tumors including subcutaneously implanted tumor model in Balb/c mouse after the coverage of a fresh pork tissue and orthotopic transplantation liver tumor in rabbit. Furthermore, due to the confinement of IONCs in silk fibroin hydrogel, the undesired thermal damage toward normal tissue could be avoided compared with directly administrating monodispersed magnetic nanoparticles.

Enzyme-Responsive Ag Nanoparticle Assemblies in Targeting Antibacterial against Methicillin-Resistant Staphylococcus Aureus.

The abuse of antibiotics resulted in the emergence of antibiotics-resistant bacteria, which has raised a great social concern together with the impetus to develop effective antibacterial materials. Herein, the synthesis of biocompatible enzyme-responsive Ag nanoparticle assemblies (ANAs) and their application in the high-efficiency targeted antimicrobial treatment of methicillin-resistant Staphylococcus aureus (MRSA) have been demonstrated. The ANAs could collapse and undergo stable/collapsed transition on approaching MRSA because of the serine protease-like B enzyme proteins (SplB)-triggered decomposition of the branched copolymers which have been employed as the macrotemplate in the synthesis of responsive ANAs. This transition contributed greatly to the high targeting affinity and efficiency of ANAs to MRSA. The minimum inhibitory concentration and minimum bactericidal concentration against MRSA were 2.0 and 32.0 µg mL-1, respectively. Skin wound healing experiments confirmed that the responsive ANAs could serve as an effective wound dressing to accelerate the healing of MRSA infection.

Activatable Cell-Penetrating Peptide Conjugated Polymeric Nanoparticles with Gd-Chelation and Aggregation-Induced Emission for Bimodal MR and Fluorescence Imaging of Tumors.

Activatable cell-penetrating peptide (ACPP) conjugated polymeric nanoparticles containing gadolinium (Gd)-chelates and aggregation-induced emission fluorogens (AIEgens) have been synthesized and applied as a magnetic resonance imaging (MRI) and fluorescence imaging (FI) bimodal imaging probe with active tumor targeting. The polymeric nanoparticles have been generated by dissolving presynthesized linear block copolymers into water directly. With AIEgens, N-BP5-Gd-ACPPs showed tumor cell penetration, which can be characterized by in vitro FI. Preliminary in vivo experiments of Gd-chelated nanoparticles have demonstrated promising characteristics as a tumor-targeting MRI contrast agent with good biocompatibility. This study impacts the synthesis of functional copolymers and polymeric nanoparticles for their applications in bioimaging.

Randomized trial of umbilical incisional hernia in high-risk patients: extraction of gallbladder through subxiphoid port vs. umbilical port after laparoscopic cholecystectomy.

INTRODUCTION: Trocar site incisional hernia (TSIH) is one of the most common complications of laparoscopic surgery. Using the umbilical port as a common hole for removing the gallbladder in laparoscopic cholecystectomy is more likely to lead to TSIH than other ports. Thus, extracting the gallbladder through other ports may reduce the incidence of TSIH. AIM: To ascertain whether extraction of the gallbladder through the subxiphoid port is more beneficial for reducing umbilical incisional hernia than the umbilical port. MATERIAL AND METHODS: From April 2014 to March 2017, a randomized clinical trial was conducted among patients with high risk of incisional hernia and accepted for three-port laparoscopic cholecystectomy (TLC) in our department. 182 patients with indications of cholecystectomy were allocated randomly to group A (subxiphoid port) and group B (umbilical port). Data collection was carried out on operative time, postoperative pain, hospital stay, wound infection and TSIH in the early postoperative course, and at 1, 10, and 24 months after surgery. RESULTS: The incidence of TSIH in group A was lower than that in group B (4.9% vs. 14.6%; odds ratio = 8.02; 95% CI: 2.15-47.6; p < 0.001). The mean operative time of group A was significantly shorter than that of group B (35 ±15.16 min vs. 42 ±14.58 min, p < 0.01). There was no significant difference in wound infection rate between group A and group B (p = 0.068). The data of hospital stay (p = 0.428) and postoperative pain (p = 0.349) of all analyzed patients were similar in the two groups. CONCLUSIONS: Extraction of the gallbladder through the subxiphoid port can reduce umbilical incisional hernia in high-risk patients effectively.

The effects of 7-nitroindazole on serum neuron-specific enolase and astroglia-derived protein (S100ß) levels after traumatic brain injury.

We investigated the possible role of 7-nitroindazole (7-NI) in regulating serum neuron-specific enolase (NSE) and S100ß levels in a rat model of traumatic brain injury (TBI). We also explored the possible mechanism by which 7-NI may affect the level of NSE and S100ß. A total of 160 healthy adult male Sprague-Dawley rats were randomly divided into 2 groups: i) The saline-treated group and ii) the 7-NI-treated group. Using the random number table, the groups were further divided into four subgroups: i) The sham-injured group; ii) the TBI 6 h group; iii) the TBI 12 h group; and iv) the TBI 24 h group (n=20). Controlled cortical impact in rats was established. Serum NSE and S100ß levels, nitric oxide (NO) level, water content, Evans blue (EB) content, malondialdehyde (MDA) level and total superoxide dismutase (T-SOD) level in the brain tissue were measured. NO synthase (NOS) activity was measured at 6, 12 and 24 h after TBI. Pathological changes in brain tissue were studied by hematoxylin and eosin (H&E) staining at each time-point. NSE and S100ß levels, NO content, water content, EB content and MDA level in the brain tissue increased significantly after TBI. NOS activity was also increased significantly after TBI while T-SOD content in brain tissue was significantly reduced after TBI. H&E staining showed that brain damage was aggravated gradually after TBI. We concluded that the early application of 7-NI significantly reduced serum NSE and S100ß levels after TBI. The neuroprotective effects of 7-NI may be associated with reduced NOS activity, reduced NO content, alleviated brain edema, lower blood-brain barrier permeability and oxidative stress. Serum NSE and S100ß levels can reflect the therapeutic effect of 7-NI, which suggest a good diagnostic value.

Single-nucleotide polymorphism array coupled with multiple displacement amplification: accuracy and spatial resolution for analysis of chromosome copy numbers in few cells.

When coupled with multiple displacement amplification (MDA), microarray-based comparative genomic intensity allows detection of chromosome copy number aberrations even in single or few cells, but the actual performance of the system and their influencing factors have not been well defined. Here, using single-nucleotide polymorphism (SNP) array, we analyzed copy number profiles from DNA amplified by MDA in 1-10 cells and estimated the accuracy and spatial resolution of the analysis. Based on the concordance of SNP copy numbers for DNA with and without MDA, the accuracy of the system can be significantly enhanced by using MDA-amplified DNA as reference and also by increasing the cell numbers. Analyses under different smoothing treatments revealed a practical resolution of 2 Mb for 10 cells and 10 Mb for a single cell. When both cells with known chromosomal duplication and deletion were analyzed, this platform detected a copy number "loss" more accurately than a "gain" (P < 0.01), particularly in single-cell MDA products. Together, we demonstrated that SNP array coupled with MDA is reliable and efficient for detection of copy number aberrations in a small number of cells, and its accuracy and resolution can both be significantly enhanced with increasing the number of cells as MDA template.

Solvent and lipid accessibility prediction as a basis for model quality assessment in soluble and membrane proteins.

On-going efforts to improve protein structure prediction stimulate the development of scoring functions and methods for model quality assessment (MQA) that can be used to rank and select the best protein models for further refinement. In this work, sequence-based prediction of relative solvent accessibility (RSA) is employed as a basis for a simple MQA method for soluble proteins, and subsequently extended to the much less explored case of (alpha-helical) membrane proteins. In analogy to soluble proteins, the level of exposure to the lipid of amino acid residues in transmembrane (TM) domains is captured in terms of the relative lipid accessibility (RLA), which is predicted from sequence using low-complexity Support Vector Regression models. On an independent set of 23 TM proteins, the new SVR-based predictor yields correlation coefficient (CC) of 0.56 between the predicted and observed RLA profiles, as opposed to CC of 0.13 for a baseline predictor that utilizes TMLIP2H empirical lipophilicity scale (with standard deviations of about 0.15). A simple MQA approach is then defined by ranking models of membrane proteins in terms of consistency between predicted and observed RLA profiles, as a measure of similarity to the native structure. The new method does not require a set of decoy models to optimize parameters, circumventing current limitations in this regard. Several different sets of models, including those generated by fragment based folding simulations, and decoys obtained by swapping TM helices to mimic errors in template based assignment, are used to assess the new approach. Predicted RLA profiles can be used to successfully discriminate near native models from non-native decoys in most cases, significantly improving the separation of correct and incorrectly folded models compared to a simple baseline approach that utilizes TMLIP2H. As suggested by the robust performance of a simple MQA method for soluble proteins that utilizes more accurate RSA predictions, further significant improvements are likely to be achieved. The steady growth in the number of resolved membrane protein structures is expected to yield enhanced RLA predictions, facilitating further efforts to improve de novo and template based prediction of membrane protein structure.

[Evaluation of the fidelity of multiple displacement amplification from small number of cells].

OBJECTIVE: To evaluate the fidelity of multiple displacement amplification (MDA) from small number of cells (1-10 cells) by 10K 2.0 SNP mapping array. METHODS: A fibroblast cell line (Tri-18; GM02732, 47, XY, +18) was used as the template, and 6 groups were set up in the study. Groups A and B were positive and negative control, respectively; groups C-F were experimental groups involving the MDA products from 1, 2, 5 and 10 cells respectively. In combination of single nucleotide polymorphism (SNP) array, the product of each group was assessed based on the genome coverage, loss of heterozygosity (LOH) rate and allele dropout (ADO) rate. RESULTS: The nonspecific product of negative control presented an average call rate of 3.2%. The genome coverage of the MDA product increased from 86.4% to 96.4% with the increasing number of template from 1 to 10 cells, while the LOH rate and ADO rate decreased significantly (P<0.05). CONCLUSION: MDA is a highly efficient and reliable method for whole genome amplification. The fidelity of MDA will be improved significantly with the increasing number of template cells. 10K 2.0 SNP mapping array is a quick, accurate and comprehensive method to evaluate the fidelity of amplified DNA products, but the ADO SNPs should be distinguished from those of preferential amplification from the LOH loci to avoid errors.

Computational exploration of the network of sequence flow between protein structures.

We investigate small sequence adjustments (of one or a few amino acids) that induce large conformational transitions between distinct and stable folds of proteins. Such transitions are intriguing from evolutionary and protein-design perspectives. They make it possible to search for ancient protein structures or to design protein switches that flip between folds and functions. A network of sequence flow between protein folds is computed for representative structures of the Protein Data Bank. The computed network is dense, on an average each structure is connected to tens of other folds. Proteins that attract sequences from a higher than expected number of neighboring folds are more likely to be enzymes and alpha/beta fold. The large number of connections between folds may reflect the need of enzymes to adjust their structures for alternative substrates. The network of the Cro family is discussed, and we speculate that capacity is an important factor (but not the only one) that determines protein evolution. The experimentally observed flip from all alpha to alpha + beta fold is examined by the network tools. A kinetic model for the transition of sequences between the folds (with only protein stability in mind) is proposed. Proteins 2010. (c) 2009 Wiley-Liss, Inc.