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Background: Cell-free DNA (cfDNA) analysis offers an attractive noninvasive means of detecting and monitoring diseases. cfDNA cleavage patterns within a short range (e.g., 11 nucleotides) have been reported to correlate with cytosine-phosphate-guanine (CpG) methylation, allowing fragmentomics-based methylation analysis (FRAGMA). Here, we adopted FRAGMA to the extended region harboring multiple nucleosomes, termed FRAGMAXR., Methods: We profiled cfDNA nucleosomal patterns over the genomic regions from -800 to 800 bp surrounding differentially methylated CpG sites, harboring approximately 8 nucleosomes, referred to as CpG-associated cfDNA nucleosomal patterns. Such nucleosomal patterns were analyzed by FRAGMAXR in cancer patients and pregnant women., Results: We identified distinct cfDNA nucleosomal patterns around differentially methylated CpG sites. Compared with subjects without cancer, patients with hepatocellular carcinoma (HCC) showed reduced amplitude of nucleosomal patterns, with a gradual decrease over tumor stages. Nucleosomal patterns associated with differentially methylated CpG sites could be used to train a machine learning model, resulting in the detection of HCC patients with an area under the receiver operating characteristic curve of 0.93. We further demonstrated the feasibility of multicancer detection using a dataset comprising lung, breast, and ovarian cancers. The tissue-of-origin analysis of plasma cfDNA from pregnant women and cancer patients revealed that the placental DNA and tumoral DNA contributions deduced by FRAGMAXR correlated well with values measured using genetic variants (Pearson r: 0.85 and 0.94, respectively)., Conclusions: CpG-associated cfDNA nucleosomal patterns of cfDNA molecules are influenced by DNA methylation and might be useful for biomarker developments for cancer liquid biopsy and noninvasive prenatal testing., (© Association for Diagnostics & Laboratory Medicine 2024.)

The analysis of tissues of origin of cell-free DNA (cfDNA) is of research and diagnostic interest. Many studies focused on bisulfite treatment or immunoprecipitation protocols to assess the tissues of origin of cfDNA. DNA loss often occurs during such processes. Fragmentomics of cfDNA molecules has uncovered a wealth of information related to tissues of origin of cfDNA. There is still much room for the development of tools for assessing contributions from various tissues into plasma using fragmentomic features. Hence, we developed an approach to analyze the relative contributions of DNA from different tissues into plasma, by identifying characteristic fragmentation patterns associated with selected histone modifications. We named this technique as FRAGmentomics-based Histone modification Analysis (FRAGHA). Deduced placenta-specific histone H3 lysine 27 acetylation (H3K27ac)-associated signal correlated well with the fetal DNA fraction in maternal plasma (Pearson's r = 0.96). The deduced liver-specific H3K27ac-associated signal correlated with the donor-derived DNA fraction in liver transplantation recipients (Pearson's r = 0.92) and was significantly increased in patients with hepatocellular carcinoma (HCC) ( P < 0.01, Wilcoxon rank-sum test). Significant elevations of erythroblasts-specific and colon-specific H3K27ac-associated signals were observed in patients with β-thalassemia major and colorectal cancer, respectively. Furthermore, using the fragmentation patterns from tissue-specific H3K27ac regions, a machine learning algorithm was developed to enhance HCC detection, with an area under the curve (AUC) of up to 0.97. Finally, genomic regions with H3K27ac or histone H3 lysine 4 trimethylation (H3K4me3) were found to exhibit different fragmentomic patterns of cfDNA. This study has shed light on the relationship between cfDNA fragmentomics and histone modifications, thus expanding the armamentarium of liquid biopsy., Competing Interests: Competing interests statement:J.B., P.J., L.J., M.Y., K.C.A.C., and Y.M.D.L. filed patent applications based on the data in this study. Reviewer S.B. is an inventor on patents related to cfDNA mutation and methylation analysis technologies that have been licensed to Roche and Adela, respectively, and is a co-founder and has ownership in Adela.

Aim: To characterize the distribution of meibomian gland (MG) area loss (MGL) and its relationship with demographic characteristics, mites, and symptoms., Methods: This retrospective observational study included patients who visited the Dry Eye Clinic of Shenzhen Eye Hospital between June 2020 and August 2021. General patient characteristics, ocular symptoms, Demodex test results of the eyelid edges, and the results of a comprehensive ocular surface analysis were collected. MGL was analyzed using Image J software., Results: This study enrolled 1204 outpatients aged 20-80 (40.70±13.44)y, including 357 males (29.65%) and 847 females (70.35%). The patients were classified into mild ( n =155; 12.87%), moderate ( n =795; 66.03%), severe ( n =206; 17.11%), and extremely severe ( n =48; 3.99%) MGL groups. MGL was significantly larger in female than in male ( P =0.006). The degree of MGL also significantly differed in age ( P <0.001) and the more numbers of mites with severity ( P <0.001). Multivariate disordered multinomial logistic regression analysis identified that female sex, older age, secretory symptoms, and a large number of mites were risk factors for MGL ( P <0.05)., Conclusion: Patients with MGL are more likely to be older, female, more numbers of mites, and increased secretion., Competing Interests: Conflicts of Interest: Ding SC, None; Su JJ, None; Zhan Q, None; Wang JM, None; Zheng F, None; Fang XX, None; Cheng D, None; Guo P, None., (International Journal of Ophthalmology Press.)

Background: Osteosarcomas (OS) is a kind of malignant bone tumor which occurs primarily in children and adolescents, and the clinical therapeutics remain disappointing. As a new programmed cell death, ferroptosis is characterized by iron dependent and intracellular oxidative accumulation, which provides a potential alternative intervene for the OS treatment. Baicalin, a major bioactive flavone derived from traditional Chinese medicine Scutellaria baicalensis, has been proved to have anti-tumor properties in OS. Whether ferroptosis participated in the baicalin mediated anti-OS activity is an interesting project., Purpose: To explore the pro-ferroptosis effect and mechanisms of baicalin in OS., Methods/study Design: Pro-ferroptosis effect of baicalin on cell death, cell proliferation, iron accumulation, lipid peroxidation production was determined in MG63 and 143B cells. The levels of glutathione (GSH), oxidized (GSSG) glutathione and malondialdehyde (MDA) were determined by enzyme linked immunosorbent assay (ELISA). The expression levels of nuclear factor erythroid 2-related factor 2 (Nrf2), Glutathione peroxidase 4 (GPX4) and xCT were detected by western blot in baicalin-mediated ferroptosis regulation. In vivo, a xenograft mice model was adopted to explore the anticancer effect of baicalin., Results: In the present study, it was found that baicalin significantly suppress tumor cell growth in vitro and in vivo. By promoting the Fe accumulation, ROS formation, MDA production and suppressing the ratio of GSH/GSSG, baicalin was found to trigger ferroptosis in OS and ferroptosis inhibitor ferrostatin-1 (Fer-1) successfully reversed these suppressive effects, indicating that ferroptosis participated in the baicalin mediated anti-OS activity. Mechanistically, baicalin physically interacted with Nrf2, a critical regulator of ferroptosis, and influenced its stability via inducing ubiquitin degradation, which suppressed the Nrf2 downstream targets GPX4 and xCT expression, and led to stimulating ferroptosis., Conclusions: Our findings for the first time indicated that baicalin exerted anti-OS activity through a novel Nrf2/xCT/GPX4-dependent ferroptosis regulatory axis, which hopefully provides a promising candidate for OS treatment., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier GmbH.)

Cell-free DNA (cfDNA) fragmentation is nonrandom, at least partially mediated by various DNA nucleases, forming characteristic cfDNA end motifs. However, there is a paucity of tools for deciphering the relative contributions of cfDNA cleavage patterns related to underlying fragmentation factors. In this study, through non-negative matrix factorization algorithm, we used 256 5' 4-mer end motifs to identify distinct types of cfDNA cleavage patterns, referred to as "founder" end-motif profiles (F-profiles). F-profiles were associated with different DNA nucleases based on whether such patterns were disrupted in nuclease-knockout mouse models. Contributions of individual F-profiles in a cfDNA sample could be determined by deconvolutional analysis. We analyzed 93 murine cfDNA samples of different nuclease-deficient mice and identified six types of F-profiles. F-profiles I, II, and III were linked to deoxyribonuclease 1 like 3 (DNASE1L3), deoxyribonuclease 1 (DNASE1), and DNA fragmentation factor subunit beta (DFFB), respectively. We revealed that 42.9% of plasma cfDNA molecules were attributed to DNASE1L3-mediated fragmentation, whereas 43.4% of urinary cfDNA molecules involved DNASE1-mediated fragmentation. We further demonstrated that the relative contributions of F-profiles were useful to inform pathological states, such as autoimmune disorders and cancer. Among the six F-profiles, the use of F-profile I could inform the human patients with systemic lupus erythematosus. F-profile VI could be used to detect individuals with hepatocellular carcinoma, with an area under the receiver operating characteristic curve of 0.97. F-profile VI was more prominent in patients with nasopharyngeal carcinoma undergoing chemoradiotherapy. We proposed that this profile might be related to oxidative stress.

Objective: To examine the application value of 3D Slicer software assisted domestic frameless stereotactic robot in biopsy of intracranial lesions. Methods: A retrospective analysis was performed on 80 patients who admitted consecutively and underwent intracerebral lesions biopsy with the domestic frameless stereotactic robot at Department of Neurosurgery, Aerospace Central Hospital from January 2019 to December 2021. There were 36 males and 44 females, with a mean age of (38.5±18.0) years (range: 6 to 71 years). Before surgery only enhanced T1-weighted three-dimensional magnetization prepared gradient echo sequences and diffusion tensor imaging scans were performed. Self-reconstruction of intracranial lesions, cerebral cortex and blood vessels was carried out using 3D Slicer software system after the DICOM format imaging data of 80 patients were collected. These imaging data were merged to the workstation of the domestic frameless stereotactic robot for preoperative surgical planning and the surgical puncture path was designed to avoid blood vessels in the brain functional area, cerebral cortex and sulcus. Results: All frameless stereotactic biopsy were successfully performed. Postoperative pathological diagnosis included 50 cases of diffuse astrocytic and oligodendroglioma, 15 cases of lymphoma, 5 cases of metastatic tumors, 5 cases of inflammatory demyelinating disease, 2 cases of inflammatory granuloma, 1 case of hemangioma, 1 case of acute lymphoblastic leukemia intracranial invasion and 1 case of seminoma. The positive diagnosis rate was 100% (80/80). Postoperative imaging confirmed that the puncture path and target were accurately implemented according to the preoperative planning, and the target error was (1.32±0.44) mm (range: 0.55 to 1.99 mm). One case of puncture-related bleeding occurred at the target after surgery and improved after treatment. Conclusion: The three-dimensional multimodal images reconstructed by the 3D Slicer software before operation could help the surgeons make the preoperative planning and reduce the risk of stereotactic brain biopsy.

Background: Jagged ends of plasma DNA are a recently recognized class of fragmentomic markers for cell-free DNA, reflecting the activity of nucleases. A number of recent studies have also highlighted the importance of jagged ends in the context of pregnancy and oncology. However, knowledge regarding the generation of jagged ends is incomplete., Methods: Jaggedness of plasma DNA was analyzed based on Jag-seq, which utilized the differential methylation signals introduced by the DNA end-repair process. We investigated the jagged ends in plasma DNA using mouse models by deleting the deoxyribonuclease 1 (Dnase1), DNA fragmentation factor subunit beta (Dffb), or deoxyribonuclease 1 like 3 (Dnase1l3) gene., Results: Aberrations in the profile of plasma DNA jagged ends correlated with the type of nuclease that had been genetically deleted, depending on nucleosomal structures. The deletion of Dnase1l3 led to a significant reduction of jaggedness for those plasma DNA molecules involving more than 1 nucleosome (e.g., size ranges 240-290 bp, 330-380 bp, and 420-470 bp). However, less significant effects of Dnase1 and Dffb deletions were observed regarding different sizes of DNA fragments. Interestingly, the aberration in plasma DNA jagged ends related to multinucleosomes was observed in human subjects with familial systemic lupus erythematosus with Dnase1l3 deficiency and human subjects with sporadic systemic lupus erythematosus., Conclusions: Detailed understanding of the relationship between nuclease and plasma DNA jaggedness has opened up avenues for biomarker development., (© American Association for Clinical Chemistry 2022.)

Cell-free DNA (cfDNA) in bodily fluids has rapidly transformed the development of noninvasive prenatal testing, cancer liquid biopsy, and transplantation monitoring. Plasma cfDNA consists of a mixture of molecules originating from various bodily tissues. The study of the fragmentation patterns of cfDNA, also referred to as 'fragmentomics', is now an actively pursued area of biomarker research. Clues that cfDNA fragmentation patterns might carry information concerning the tissue of origin of cfDNA molecules have come from works demonstrating that circulating fetal, tumor-derived, and transplanted liver-derived cfDNA molecules have a shorter size distribution than the background mainly of hematopoietic origin. More recently, an improved understanding of cfDNA fragmentation has provided many emerging fragmentomic markers, including fragment sizes, preferred ends, end motifs, single-stranded jagged ends, and nucleosomal footprints. The intrinsic biological link between activities of various DNA nucleases and characteristic fragmentations has been demonstrated. In this review, we focus on the biological properties of cell-free DNA unveiled recently and their potential clinical applications.

Single-stranded ends of double-stranded DNA (jagged ends) are more abundant in urinary DNA than in plasma DNA. However, the lengths of jagged ends in urinary DNA remained undetermined, as a previous method used for urinary DNA jagged end sequencing analysis (Jag-seq) relied on unmethylation at CpG sites, limiting the resolution. Here, we performed high-resolution Jag-seq analysis using methylation at non-CpG cytosine sites, allowing determination of exact length of jagged ends. The urinary DNA bore longer jagged ends (~26-nt) than plasma DNA (~17-nt). The jagged end length distribution displayed 10-nt periodicities in urinary DNA, which were much less observable in plasma DNA. Amplitude of the 10-nt periodicities increased in patients with renal cell carcinoma. Heparin treatment of urine diminished the 10-nt periodicities. The urinary DNA jagged ends often extended into nucleosomal cores, suggesting potential interactions with histones. This study has thus advanced our knowledge of jagged ends in urine DNA., (© 2022. The Author(s).)

Background: Double-stranded DNA in plasma is known to carry single-stranded ends, called jagged ends. Plasma DNA jagged ends are biomarkers for pathophysiologic states such as pregnancy and cancer. It remains unknown whether urinary cell-free DNA (cfDNA) molecules have jagged ends., Methods: Jagged ends of cfDNA were detected by incorporating unmethylated cytosines during a DNA end-repair process, followed by bisulfite sequencing. Incorporation of unmethylated cytosines during the repair of the jagged ends lowered the apparent methylation levels measured by bisulfite sequencing and were used to calculate a jagged end index. This approach is called jagged end analysis by sequencing., Results: The jagged end index of urinary cfDNA was higher than that of plasma DNA. The jagged end index profile of plasma DNA displayed several strongly oscillating major peaks at intervals of approximately 165 bp (i.e., nucleosome size) and weakly oscillating minor peaks with periodicities of approximately 10 bp. In contrast, the urinary DNA jagged end index profile showed weakly oscillating major peaks but strongly oscillating minor peaks. The jagged end index was generally higher in nucleosomal linker DNA regions. Patients with bladder cancer (n = 46) had lower jagged end indexed of urinary DNA than participants without bladder cancer (n = 39). The area under the curve for differentiating between patients with and without bladder cancer was 0.83., Conclusions: Jagged ends represent a property of urinary cfDNA. The generation of jagged ends might be related to nucleosomal structures, with enrichment in linker DNA regions. Jagged ends of urinary DNA could potentially serve as a new biomarker for bladder cancer detection., (© American Association for Clinical Chemistry 2021.)

β-tubulin, a component of microtubules, is involved in a wide variety of roles in cell shape, motility, intracellular trafficking and regulating intracellular metabolism. It has been an important fungicide target to control plant pathogen, for example, Fusarium. However, the regulation of fungicide sensitivity by β-tubulin-interacting proteins is still unclear. Here, ASK1 was identified as a β-tubulin interacting protein. The ASK1 regulated the sensitivity of Fusarium to carbendazim (a benzimidazole carbamate fungicide), and multiple cellular processes, such as chromatin separation, conidiation and sexual production. Further, we found the point mutations at 50th and 198th of β 2 -tubulin which caused carbendazim resistance decreased the binding between β 2 -tubulin and ASK1, resulting in the deactivation of ASK1. ASK1, on the other hand, competed with carbendazim to bind to β 2 -tubulin. The point mutation F167Y in β 2 -tubulin broke the intermolecular H-bonds and salt bridges between β 2 -tubulin and ASK1, which reduced the competitive effect of ASK1 to carbendazim and resulted in the similar carbendazim sensitivities in F167Y-ΔASK1 and F167Y. These findings have powerful implications for efforts to understand the interaction among β 2 -tubulin, its interacting proteins and fungicide, as well as to discover and develop new fungicide against Fusarium.

Fusarium fungi are the cause of an array of devastating diseases affecting yield losses and accumulating mycotoxins. Fungicides can be exploited against Fusarium and deoxynivalenol (DON) production. However, Fusarium resistance to common chemicals has become a therapeutic challenge worldwide, which indicates that new control agents carrying different mechanisms of action are desperately needed. Here, we found that a nonantibiotic drug, ethylenediaminetetraacetic acid disodium salt (EDTANa 2 ), exhibited various antifungal activities against Fusarium species and DON biosynthesis. The infection of wheat seeding caused by F. graminearum was suppressed over 90% at 4 mM EDTANa 2 . A similar control effect was observed in field tests. Mycotoxin production assays showed DON production was significantly inhibited, 47% lower than the control, by 0.4 mM EDTANa 2 . In vitro experiments revealed a timely inhibition of H 2 O 2 production as quickly as 4 h after amending cultures with EDTANa 2 and the expression of several TRI genes significantly decreased. Chitin synthases of Fusarium were Mn 2+ -containing enzymes that were strongly inhibited by Mn 2+ deficiency. EDTANa 2 inhibited chitin synthesis and destroyed the cell wall and cytomembrane integrity of Fusarium , mainly via the chelation of Mn 2+ by EDTANa 2 , and thus led to Mn deficiency in Fusarium cells. Taken together, these findings uncover the potential of EDTANa 2 as a fungicide candidate to manage Fusarium head blight (FHB) and DON in agricultural production.

Cell-free DNA in plasma has been used for noninvasive prenatal testing and cancer liquid biopsy. The physical properties of cell-free DNA fragments in plasma, such as fragment sizes and ends, have attracted much recent interest, leading to the emerging field of cell-free DNA fragmentomics. However, one aspect of plasma DNA fragmentomics as to whether double-stranded plasma molecules might carry single-stranded ends, termed a jagged end in this study, remains underexplored. We have developed two approaches for investigating the presence of jagged ends in a plasma DNA pool. These approaches utilized DNA end repair to introduce differential methylation signals between the original sequence and the jagged ends, depending on whether unmethylated or methylated cytosines were used in the DNA end-repair procedure. The majority of plasma DNA molecules (87.8%) were found to bear jagged ends. The jaggedness varied according to plasma DNA fragment sizes and appeared to be in association with nucleosomal patterns. In the plasma of pregnant women, the jaggedness of fetal DNA molecules was higher than that of the maternal counterparts. The jaggedness of plasma DNA correlated with the fetal DNA fraction. Similarly, in the plasma of cancer patients, tumor-derived DNA molecules in patients with hepatocellular carcinoma showed an elevated jaggedness compared with nontumoral DNA. In mouse models, knocking out of the Dnase1 gene reduced jaggedness, whereas knocking out of the Dnase1l3 gene enhanced jaggedness. Hence, plasma DNA jagged ends represent an intrinsic property of plasma DNA and provide a link between nuclease activities and the fragmentation of plasma DNA., (© 2020 Jiang et al.; Published by Cold Spring Harbor Laboratory Press.)

General control nonderepressible 2 (GCN2) is a master regulator kinase of amino acid homeostasis and important for cancer survival in the tumor microenvironment under amino acid depletion. We initiated studies aiming at the discovery of novel GCN2 inhibitors as first-in-class antitumor agents and conducted modification of the substructure of sulfonamide derivatives with expected type I half binding on GCN2. Our synthetic strategy mainly corresponding to the αC-helix allosteric pocket of GCN2 led to significant enhancement in potency and a good pharmacokinetic profile in mice. In addition, compound 6d , which showed slow dissociation in binding on GCN2, demonstrated antiproliferative activity in combination with the asparagine-depleting agent asparaginase in an acute lymphoblastic leukemia (ALL) cell line, and it also displayed suppression of GCN2 pathway activation with asparaginase treatment in the ALL cell line and mouse xenograft model., Competing Interests: The authors declare no competing financial interest., (Copyright © 2019 American Chemical Society.)

Objectives: To establish a convenient and rapid method for extracting DNA from bone., Methods: Fifteen long bone samples were washed and sterilized. The skeletal fragments were obtained by electric drill, and lysed by PrepFiler Express BTA™ lysis buffer. DNA was then manually extracted by silicon microbeads for further analysis., Results: STR genotyping was successfully obtained in 14 out of the 15 samples, and the detection rate was 93.33%., Conclusions: The method for DNA extraction from bone established in present study is convenient, quick, effective, and with a strong applicability, which is worth spreading and applying., Competing Interests: The authors of this article and the planning committee members and staff have no relevant financial relationships with commercial interests to disclose., (Copyright© by the Editorial Department of Journal of Forensic Medicine)

Objective: To assess the clinical significance of cerebrospinal fluid (CSF) free fatty acid (FFA) levels in Chinese patients with acute ischemic stroke., Methods: From December 2011 to October 2014, all patients with first-ever acute ischemic stroke were recruited to participate in the study. CSF levels of FFAs were assayed at 4 time points, and severity of stroke was evaluated with the National Institutes of Health Stroke Scale (NIHSS) score on admission., Results: Median CSF FFA levels were significantly (P < 0.0001) higher in patients with stroke compared with control subjects. CSF FFA levels reflected the disease severity of acute ischemic stroke. There were significant positive associations between CSF FFA levels and NIHSS scores (r = 0.424, P < 0.0001) and infarct volume (r = 0.289, P < 0.0001). CSF FFA levels in patients with cardioembolic (CE) stroke were significantly higher compared with patients with non-CE stroke (0.34 mmol/L [interquartile range, 0.26-0.42] vs. 0.14 mmol/L [interquartile range, 0.08-0.23]; P < 0.0001). Based on the receiver operating characteristic curve, the optimal cutoff value of CSF FFA levels as an indicator for the diagnosis of CE stroke was projected to be 0.22 mmol/L, which yielded a sensitivity of 83.3% and a specificity of 75.3%, and the area under the curve was 0.873 (95% confidence interval, 0.810-0.935)., Conclusions: CSF FFA levels at the time of admission were associated with stroke severity and lesion volumes. In addition, CE stroke can be distinguished from other stroke etiologies by measuring CSF FFA levels very early., (Copyright © 2015 Elsevier Inc. All rights reserved.)

Objective: To establish an accurate, rapid and efficient method for authentication of Panax species by using PCR amplification of specific alleles., Methods: The samples of Panax species were collected for extracting the total DNA. matK sequence from the Panax species was amplified by PCR and sequenced directionally, and then aligned by using Clustal W. Specific primers were designed and amplified by two-steps PCR amplification method., Results: By optimizing the denatured and annealing temperature and time, cycle numbers, the rapid PCR methods for authentication of Panax species were established respectively. When SYBR Green I was added in the PCR product, strong green fluorescence was visualized under 365 nm UV lamp whereas adulterants were not., Conclusion: The rapid PCR method can identify the Panax species rapidly. This study provides the technical support for authentication of Chinese medicinal materials.

Retinoic acid-inducible gene I (RIG-I) is a pattern recognition receptor expressed in metazoan cells that is responsible for eliciting the production of type I interferons and pro-inflammatory cytokines upon detection of intracellular, non-self RNA. Structural studies of RIG-I have identified a novel Pincer domain composed of two alpha helices that physically tethers the C-terminal domain to the SF2 helicase core. We find that the Pincer plays an important role in mediating the enzymatic and signaling activities of RIG-I. We identify a series of mutations that additively decouple the Pincer motif from the ATPase core and show that this decoupling results in impaired signaling. Through enzymological and biophysical analysis, we further show that the Pincer domain controls coupled enzymatic activity of the protein through allosteric control of the ATPase core. Further, we show that select regions of the HEL1 domain have evolved to potentiate interactions with the Pincer domain, resulting in an adapted ATPase cleft that is now responsive to adjacent domains that selectively bind viral RNA., (© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Hepatitis C virus (HCV) NS3-4A is required for viral replication and assembly. We establish that virus assembly is sensitive to mutations in the linker region between the helicase and protease domains of NS3-4A. However, we find that the protease cleavage, RNA binding, and unwinding rates of NS3 are minimally affected in vitro. Thus, we conclude that the NS3 linker is critical for mediating protein-protein interactions and dynamic control rather than for modulating the enzymatic functions of NS3-4A., (Copyright © 2014, American Society for Microbiology. All Rights Reserved.)

Objective: To evaluate the effectiveness of whole-genome array comparative genomic hybridization (aCGH) in prenatal diagnosis in Hong Kong., Methods: Array CGH was performed on 220 samples recruited prospectively as the first-tier test study. In addition 150 prenatal samples with abnormal fetal ultrasound findings found to have normal karyotypes were analyzed as a 'further-test' study using NimbleGen CGX-135K oligonucleotide arrays., Results: Array CGH findings were concordant with conventional cytogenetic results with the exception of one case of triploidy. It was found in the first-tier test study that aCGH detected 20% (44/220) clinically significant copy number variants (CNV), of which 21 were common aneuploidies and 23 had other chromosomal imbalances. There were 3.2% (7/220) samples with CNVs detected by aCGH but not by conventional cytogenetics. In the 'further-test' study, the additional diagnostic yield of detecting chromosome imbalance was 6% (9/150). The overall detection for CNVs of unclear clinical significance was 2.7% (10/370) with 0.9% found to be de novo. Eleven loci of common CNVs were found in the local population., Conclusion: Whole-genome aCGH offered a higher resolution diagnostic capacity than conventional karyotyping for prenatal diagnosis either as a first-tier test or as a 'further-test' for pregnancies with fetal ultrasound anomalies. We propose replacing conventional cytogenetics with aCGH for all pregnancies undergoing invasive diagnostic procedures after excluding common aneuploidies and triploidies by quantitative fluorescent PCR. Conventional cytogenetics can be reserved for visualization of clinically significant CNVs.

Retinoic acid-inducible gene-I (RIG-I) is an intracellular RNA sensor that activates the innate immune machinery in response to infection by RNA viruses. Here, we report the crystal structure of distinct conformations of a RIG-I:dsRNA complex, which shows that HEL2i-mediated scanning allows RIG-I to sense the length of RNA targets. To understand the implications of HEL2i scanning for catalytic activity and signalling by RIG-I, we examined its ATPase activity when stimulated by duplex RNAs of varying lengths and 5' composition. We identified a minimal RNA duplex that binds one RIG-I molecule, stimulates robust ATPase activity, and elicits a RIG-I-mediated interferon response in cells. Our results reveal that the minimal functional unit of the RIG-I:RNA complex is a monomer that binds at the terminus of a duplex RNA substrate. This behaviour is markedly different from the RIG-I paralog melanoma differentiation-associated gene 5 (MDA5), which forms cooperative filaments.

Objective: To investigate the effect and indication of one stage posterior debridement and bone grafting fusion and internal fixation for thoracic tuberculosis., Methods: From January 2005 to May 2011,12 patients with thoracic tuberculosis were treated with one stage posterior debridement and pedicle screw fixation combined with regular anti-tuberculosis treatment before and after operation. There were 7 males and 5 females,with an average age of 45 years and average course of 15 months. Information of operative time, blood loss, bony fusion, local kyphosis and neurologic functional were evaluated., Results: All infective focus were thoroughly removed and bone graft obtained fusion. The mean of operative time and blood loss were 170 min (120-210 min) and 510 ml (200-1 000 ml),respectively. Cobb angle from (28.7 +/- 9.2) degrees preoperatively decreased to (8.2 +/- 3.5) degrees postoperatively(P<0.05). No kyphosis correction loss,tubercular recurrence or failure of internal fixation was found. According to Frankel grade to evaluate neurological function, all patients arrived to grade E., Conclusion: One stage posterior debridement and bone grafting fusion and internal fixation is an effective method in treating thoracic tuberculosis. It has advantages such as thorough debridement, short operative time, less blood loss, more kyphosis correction and higher bony fusion rate.

The type I interferon (IFN) signaling pathway restricts infection of many divergent families of RNA and DNA viruses by inducing hundreds of IFN-stimulated genes (ISGs), some of which have direct antiviral activity. We screened 813 short hairpin RNA (shRNA) constructs targeting 245 human ISGs using a flow cytometry approach to identify genes that modulated infection of West Nile virus (WNV) in IFN-β-treated human cells. Thirty ISGs with inhibitory effects against WNV were identified, including several novel genes that had antiviral activity against related and unrelated positive-strand RNA viruses. We also defined one ISG, activating signal cointegrator complex 3 (ASCC3), which functioned as a negative regulator of the host defense response. Silencing of ASCC3 resulted in upregulation of multiple antiviral ISGs, which correlated with inhibition of infection of several positive-strand RNA viruses. Reciprocally, ectopic expression of human ASCC3 or mouse Ascc3 resulted in downregulation of ISGs and increased viral infection. Mechanism-of-action and RNA sequencing studies revealed that ASCC3 functions to modulate ISG expression in an IRF-3- and IRF-7-dependent manner. Compared to prior ectopic ISG expression studies, our shRNA screen identified novel ISGs that restrict infection of WNV and other viruses and defined a new counterregulatory ISG, ASCC3, which tempers cell-intrinsic immunity.

Objective: To explore a new method in order to extract DNA from bones and teeth automatically., Methods: Samples of 33 bones and 15 teeth were acquired by freeze-mill method and manual method, respectively. DNA materials were extracted and quantified from the triturated samples by AutoMate Express forensic DNA extraction system., Results: DNA extraction from bones and teeth were completed in 3 hours using the AutoMate Express forensic DNA extraction system. There was no statistical difference between the two methods in the DNA concentration of bones. Both bones and teeth got the good STR typing by freeze-mill method, and the DNA concentration of teeth was higher than those by manual method., Conclusion: AutoMate Express forensic DNA extraction system is a new method to extract DNA from bones and teeth, which can be applied in forensic practice.

RIG-I is a cytoplasmic surveillance protein that contributes to the earliest stages of the vertebrate innate immune response. The protein specifically recognizes 5'-triphosphorylated RNA structures that are released into the cell by viruses, such as influenza and hepatitis C. To understand the energetic basis for viral RNA recognition by RIG-I, we studied the binding of RIG-I domain variants to a family of dsRNA ligands. Thermodynamic analysis revealed that the isolated RIG-I domains each make important contributions to affinity and that they interact using different strategies. Covalent linkage between the domains enhances RNA ligand specificity while reducing overall binding affinity, thereby providing a mechanism for discriminating virus from host RNA.

Historically, research on RNA helicase and translocation enzymes has seemed like a footnote to the extraordinary progress in studies on DNA-remodeling enzymes. However, during the past decade, the rising wave of activity in RNA science has engendered intense interest in the behaviors of specialized motor enzymes that remodel RNA molecules. Functional, mechanistic, and structural investigations of these RNA enzymes have begun to reveal the molecular basis for their key roles in RNA metabolism and signaling. In this chapter, we highlight the structural and mechanistic similarities among monomeric RNA translocase enzymes, while emphasizing the many divergent characteristics that have caused this enzyme family to become one of the most important in metabolism and gene expression., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Intracellular RIG-I-like receptors (RLRs, including RIG-I, MDA-5, and LGP2) recognize viral RNAs as pathogen-associated molecular patterns (PAMPs) and initiate an antiviral immune response. To understand the molecular basis of this process, we determined the crystal structure of RIG-I in complex with double-stranded RNA (dsRNA). The dsRNA is sheathed within a network of protein domains that include a conserved "helicase" domain (regions HEL1 and HEL2), a specialized insertion domain (HEL2i), and a C-terminal regulatory domain (CTD). A V-shaped pincer connects HEL2 and the CTD by gripping an α-helical shaft that extends from HEL1. In this way, the pincer coordinates functions of all the domains and couples RNA binding with ATP hydrolysis. RIG-I falls within the Dicer-RIG-I clade of the superfamily 2 helicases, and this structure reveals complex interplay between motor domains, accessory mechanical domains, and RNA that has implications for understanding the nanomechanical function of this protein family and other ATPases more broadly., (Copyright © 2011 Elsevier Inc. All rights reserved.)

The nonstructural protein 3 (NS3) helicase/protease is an important component of the hepatitis C virus (HCV) replication complex. We hypothesized that a specific β-strand tethers the C terminus of the helicase domain to the protease domain, thereby maintaining HCV NS3 in a compact conformation that differs from the extended conformations observed for other Flaviviridae NS3 enzymes. To test this hypothesis, we removed the β-strand and explored the structural and functional attributes of the truncated NS3 protein (NS3ΔC7). Limited proteolysis, hydrodynamic, and kinetic measurements indicate that NS3ΔC7 adopts an extended conformation that contrasts with the compact form of the wild-type (WT) protein. The extended conformation of NS3ΔC7 allows the protein to quickly form functional complexes with RNA unwinding substrates. We also show that the unwinding activity of NS3ΔC7 is independent of the substrate 3'-overhang length, implying that a monomeric form of the protein promotes efficient unwinding. Our findings indicate that an open, extended conformation of NS3 is required for helicase activity and represents the biologically relevant conformation of the protein during viral replication.

Objective: To investigate the value of carcinoembryonic antigen (CEA) or cytokeratin 19 fragment (CYFRA21-1) as an assessment indicator of therapeutic efficacy in advanced non-small cell lung cancer (NSCLC) patients., Methods: 228 cases of advanced NSCLC with chemotherapy were enrolled into this retrospective study. The serum CEA or CYFRA21-1 levels of all patients were above the cut-off limit before treatment. The relationship between changes of tumor markers (TMs) and imaging therapeutic efficacy or progression-free survival (PFS) was analyzed, and the value of TMs in therapeutic efficacy assessment was evaluated., Results: According to RECIST criteria, partial response (PR) occurred in 40 cases, stable disease (SD) in 151 and PD (progressive disease) in 37. The cut-off values of the changes of TMs between pre- and post-treatment were determined according to the above mentioned criteria. The CEA down (D), stable (S), above (A) groups were 90, 49 and 66 cases, respectively. CYFRA21-1 down (D), stable (S), above (A) groups were 84, 26 and 37 cases, respectively. PR groups were 68.4% and 88.9% in CEA and cyfra21-1 down groups, respectively, 7.9% and 5.6% in the above groups, respectively. PD groups were 59.4% and 76.2% in CEA and CYFRA21-1 above groups, respectively. No PD cases were in the down groups. The changes of TMs in SD group were between them. Statistically significant correlations were observed between changes of TMs and imaging therapeutic efficacy (r(CEA) = 0.45, P = 0.00; r(CYFRA21-1) = 0.44, P = 0.00). PFS among different TMs groups were significantly different (all P < 0.05), which can be used to further distinguish the prognosis among SD subgroups., Conclusion: Changes of TMs can be used to predict the imaging therapeutic effect and PFS of the patients, and if the SD group is divided into subgroups according to different therapeutic efficacy and prognosis, it may help the patients to receive individualized treatment.

By the methods of fixed point, line intercept, and random investigation, the vertical distribution and community diversity of butterflies in Yaoluoping National Nature Reserve were investigated from 2005 to 2008. A total of 3681 specimen were collected, belonging to 111 species, 69 genera, and 10 families, among which, Nymphalidae had the higher species number, individual's number, and diversity index than the other families. The butterflies in the study area were a mixture of Oriental and Palaearetic species, with the Oriental species diminished gradually and the Palaearetic components increased gradually with increasing altitude. Among the three vertical zones ( <800 m, 800-1200 m, and >1200 m in elevation), that of 800-1200 m had the most abundant species of butterflies; and among the six habitat types (deciduous broad-leaved forest, evergreen conifer forest, conifer-broad leaf mixed forest, bush and secondary forest, farmland, and residential area), bush and secondary forest had the higher species number, individual's number, and diversity index of butterflies, while farmland had the lowest diversity index. The similarity coefficient of butterfly species between the habitats was mainly dependent on vegetation type, i.e., the more the difference of vegetation type, the lesser the species similarity coefficient between the habitats, which was the highest (0.61) between conifer-broad leaf mixed forest and bush and secondary forest, and the lowest (0. 20) between evergreen conifer forest and bush and secondary forest.

Objectives: To construct the expression vector pGenesil-3-shRNA that can express the short hairpin RNAs (shRNA) silencing Kir6.2 gene and to study its influence on the proliferation and invasion of HepG2 cells., Methods: Two shRNA silencing Kir6.2 genes were transcript synthesized intracellularly by expressed templates of plasmid vector pSilence-3, and the target sequence of Kir6.2 gene was inserted into the upstream of the reporter gene in order to construct the recombinant plasmid vector pGenesil-3. Plasmids containing 2 different sequences of human Kir6.2 mRNA coding region were constructed and transfected into HepG2 cells by using lipofectamine 2000 methods. The experiment was divided into 4 groups: SK (normal), SK-HK (negative control), SK-K1 (transfected with the interfering sequence 1) and SK-K2 (transfected with the interfering sequence 2) groups. A selected single clone was cultured after screening by G418. The expression of Kir6.2 protein was detected by Western blot. MTT assay and Transwell system were used to observe the proliferation and invasion of HepG2 cells., Results: The recombinant expression plasmid pGenesil-3 was successfully constructed and underexpression of Kir6.2 gene in HepG2 cells was detected by Western blot. Underexpression of Kir6.2 gene significantly decreased the proliferation and invasion of the HepG2 cells., Conclusion: shRNA can inhibit the expression of Kir6.2 gene in the HepG2 cells, and underexpression of Kir6.2 gene decreased the proliferation and invasion of the HepG2 cells.

The aim is to investigate biological features of porcine endogenous retrovirus (PERV) of pigs in China and to provide basic parameters for evaluation of biological safety of xenotransplantation from pig to human. In this study, basic biologic features of PERV of DNA of peripheral blood white cells of 12 species of domestic pigs in China were examined by polymerase chain reaction; Analysis of difference of PERV gene sequence was investigated by sliver-stained single stranded conformational polymorphism and restriction fragment length polymorphism; Difference of PERV mRNA from a variety of tissue of two species of mini-pig was analysized by reverse transcriptase-PCR and semi-quantitative analysis. These results showed that Sequences of PERV-A, -B genes are ubiquitous in DNA genome of peripheral blood white cells in the examined pigs; There was no single stranded conformational polymorphism in PERV-A, -B gene sequences. There is the phenomenon of restriction fragment length polymorphism of sequence of PERV env gene in DNA genome of peripheral blood white cells in some pigs of the examined pigs. The PERV-A, -B and -C are expressive in a variety of tissues from two species of mini-pig, higher in kidneys, lymph nodes and livers, lower in pancreas and brains. It is deserved that the phenomenon of restriction fragment length polymorphism of PERV and the absence and mismatch of base of sequence of PERV-A may induce potential hazard of infection of PERV during xenotransplantation.

To understand the infectivity by porcine endogenous retrovirus with porcine skin fibroblast cell in vitro and in vivo, porcine skin fibroblast cell established by our laboratory were co-cultured with neo/HEK293 cell for the infection of PERV in vitro, and were subcutaneously transplantated to SCID (severe combined immuno-deficiency) mice for the infection of PERV in vivo, laying the foundation for valuation of biologic safety of xenotransplantation. The event of neo/HEK293 cells infected by PERV occurred during co-culture of porcine skin fibroblast cells with neo/HEK293 cells, expanding the rang of the infection of porcine endogenous retrovirus. After pig cells transplantated subcutaneously in SCID mice, the microchimerism (78.57%) of pig cells occurred widely, and there was phenomena of integration of PERV provirus (85.71%) in several organs or tissues remote from the injected sites, indicating infection of PERV in SCID mice in vivo, yet, there is no evidence of active viral replication in analysis of PERV env RNA of these tissues or organs. The infectivity of porcine endogenous retrovirus with porcine skin fibroblast cells in vitro and in vivo were demonstrated in this study, and there is no evidence of active viral replication of PERV in vivo. It is an important event of biologic safety which attention must be paid to potential hazard of infectious interspecies transmission of PERV during xenotransplantation.

Objective: To assess the efficacy of Fuganlin (FGL) oral liquid, a pure Chinese medicinal recipe in treating the repeated infantile respiratory tract infection., Methods: FGL was used for repeated infantile respiratory tract infections. The children who took the antipyretic oral liquid as the control. Before and after treatment, immune function and other test were determined in both groups. Wistar rats taking FGL for three months was also observed., Results: The curative and marked effective rates of the treated group were 76.8%, and the curative and marked effective rates of the control group were 48.0%. There are significant differences between the two groups (P < 0.01)., Conclusions: FGL could not only modulate immune function but also could serve as a tonic as well as symptomatic relief for fever, cough, asthma, anti-viral, anti-bacterial infection and anti-inflammatory function.