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https://www.readbyqxmd.com/read/27936513/probing-the-structural-dynamics-of-the-crispr-cas9-rna-guided-dna-cleavage-system-by-coarse-grained-modeling
#1
Wenjun Zheng
In the adaptive immune systems of many bacteria and archaea, the Cas9 endonuclease forms a complex with specific guide/scaffold RNA to identify and cleave complementary target sequences in foreign DNA. This DNA targeting machinery has been exploited in numerous applications of genome editing and transcription control. However, the molecular mechanism of the Cas9 system is still obscure. Recently, high-resolution structures have been solved for Cas9 in different structural forms (e.g., unbound forms, RNA-bound binary complexes, and RNA-DNA-bound tertiary complexes, corresponding to an inactive state, a pre-target-bound state, and a cleavage-competent or product state), which offered key structural insights to the Cas9 mechanism...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27936442/label-free-colorimetric-detection-of-cancer-related-gene-based-on-two-step-amplification-of-molecular-machine
#2
Huo Xu, Dong Wu, Chen-Qiao Li, Zheng Lu, Xiao-Yun Liao, Jie Huang, Zai-Sheng Wu
Highly sensitive detection of K-ras gene is of great significance in biomedical research and clinical diagnosis. Here, we developed a colorimetric biosensing system for the detection of proto-oncogene K-ras based on enhanced amplification effect of DNA molecular machine, where dual isothermal circular strand-displacement amplification (D-SDA) occurs on two arms in one-to-one correspondence. Specifically, we designed a primer-locked hairpin probe (HP) and a primer-contained linear polymerization template (PPT)...
December 2, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27936411/a-network-analysis-of-dsm-5-posttraumatic-stress-disorder-symptoms-and-correlates-in-u-s-military-veterans
#3
Cherie Armour, Eiko I Fried, Marie K Deserno, Jack Tsai, Robert H Pietrzak
OBJECTIVE: Recent developments in psychometrics enable the application of network models to analyze psychological disorders, such as PTSD. Instead of understanding symptoms as indicators of an underlying common cause, this approach suggests symptoms co-occur in syndromes due to causal interactions. The current study has two goals: (1) examine the network structure among the 20 DSM-5 PTSD symptoms, and (2) incorporate clinically relevant variables to the network to investigate whether PTSD symptoms exhibit differential relationships with suicidal ideation, depression, anxiety, physical functioning/quality of life (QoL), mental functioning/QoL, age, and sex...
November 27, 2016: Journal of Anxiety Disorders
https://www.readbyqxmd.com/read/27936379/clinical-and-epidemiological-characteristics-associated-with-unfavorable-tuberculosis-treatment-outcomes-in-tb-hiv-co-infected-patients-in-brazil-a-hierarchical-polytomous-analysis
#4
Thiago Nascimento do Prado, Jayant V Rajan, Angélica Espinosa Miranda, Elias Dos Santos Dias, Lorrayne Beliqui Cosme, Lia Gonçalves Possuelo, Mauro N Sanchez, Jonathan E Golub, Lee W Riley, Ethel Leonor Maciel
BACKGROUND: TB patients co-infected with HIV have worse treatment outcomes than non-coinfected patients. How clinical characteristics of TB and socioeconomic characteristics influence these outcomes is poorly understood. Here, we use polytomous regression analysis to identify clinical and epidemiological characteristics associated with unfavorable treatment outcomes among TB-HIV co-infected patients in Brazil. METHODS: TB-HIV cases reported in the Brazilian information system (SINAN) between January 1, 2001 and December 31, 2011 were identified and categorized by TB treatment outcome (cure, default, death, and development of MDR TB)...
December 6, 2016: Brazilian Journal of Infectious Diseases
https://www.readbyqxmd.com/read/27936274/spatiotopic-buildup-of-saccade-target-representation-depends-on-target-size
#5
Eckart Zimmermann
How we maintain spatial stability across saccade eye movements is an open question in visual neuroscience. A phenomenon that has received much attention in the field is our seemingly poor ability to discriminate the direction of transsaccadic target displacements. We have recently shown that discrimination performance increases the longer the saccade target has been previewed before saccade execution (Zimmermann, Morrone, & Burr, 2013). We have argued that the spatial representation of briefly presented stimuli is weak but that a strong representation is needed for transsaccadic, i...
December 1, 2016: Journal of Vision
https://www.readbyqxmd.com/read/27936239/a-broad-spectrum-chemokine-binding-protein-of-bovine-papular-stomatitis-virus-inhibits-neutrophil-and-monocyte-infiltration-in-inflammatory-and-wound-models-of-mouse-skin
#6
Saeed Sharif, Yoshio Nakatani, Lyn Wise, Michael Corbett, Nicola C Real, Gabriella S Stuart, Zabeen Lateef, Kurt Krause, Andrew A Mercer, Stephen B Fleming
Bovine papular stomatitis virus (BPSV) is a Parapoxvirus that induces acute pustular skin lesions in cattle and is transmissible to humans. Previous studies have shown that BPSV encodes a distinctive chemokine-binding protein (CBP). Chemokines are critically involved in the trafficking of immune cells to sites of inflammation and infected tissue, suggesting that the CBP plays a role in immune evasion by preventing immune cells reaching sites of infection. We hypothesised that the BPSV-CBP binds a wide range of inflammatory chemokines particularly those involved in BPSV skin infection, and inhibits the recruitment of immune cells from the blood into inflamed skin...
2016: PloS One
https://www.readbyqxmd.com/read/27936220/effects-of-ion-irradiation-on-seedlings-growth-monitored-by-ultraweak-delayed-luminescence
#7
Rosaria Grasso, Tomoko Abe, Giuseppe A P Cirrone, Giacomo Cuttone, Marisa Gulino, Francesco Musumeci, Francesco Romano, Hiromichi Ryuto, Agata Scordino
The optical technique based on the measurement of delayed luminescence emitted from the biological samples has demonstrated its ability to provide valid and predictive information on the functional status of various biological systems. We want to extend this technique to study the effect of ionizing radiation on biological systems. In particular we are interested in the action of ion beams, used for therapeutic purposes or to increase the biological diversity. In general, the assessment of the damage that radiation produces both in the target objects and in the surrounding tissues, requires considerable time because is based on biochemical analysis or on the examination of the evolution of the irradiated systems...
2016: PloS One
https://www.readbyqxmd.com/read/27936218/a-key-role-for-inhibins-in-dendritic-cell-maturation-and-function
#8
Roxana Olguín-Alor, Marisol de la Fuente-Granada, Laura C Bonifaz, Laura Antonio-Herrera, Eduardo A García-Zepeda, Gloria Soldevila
Inhibins are members of the TGFβ superfamily, which regulate many cellular processes including differentiation, proliferation, survival and apoptosis. Although initially described as hormones regulating the hypothalamus-pituitary-gonadal axis, based on their ability to antagonize Activins, our group has recently reported that they play a role in thymocyte differentiation and survival, as well as in thymic stromal cell maturation and nTreg generation. Here, we used Inhibin knock out mice (Inhα-/-) to investigate the role of Inhibins in peripheral dendritic cell maturation and function...
2016: PloS One
https://www.readbyqxmd.com/read/27936216/genetic-association-analysis-of-common-variants-in-foxo3-related-to-longevity-in-a-chinese-population
#9
Rong Lin, Yunxia Zhang, Dongjing Yan, Xiaoping Liao, Xianshou Wang, Yunxin Fu, Wangwei Cai
Recent studies suggested that forkhead box class O3 (FOXO3) functions as a key regulator for the insulin/insulin-like growth factor-1signaling pathway that influence aging and longevity. This study aimed to comprehensively elucidate the association of common genetic variants in FOXO3 with human longevity in a Chinese population. Eighteen single-nucleotide polymorphisms (SNPs) in FOXO3 were successfully genotyped in 616 unrelated long-lived individuals and 846 younger controls. No nominally significant effects were found...
2016: PloS One
https://www.readbyqxmd.com/read/27936192/insecticidal-activity-of-melaleuca-alternifolia-essential-oil-and-rna-seq-analysis-of-sitophilus-zeamais-transcriptome-in-response-to-oil-fumigation
#10
Min Liao, Jin-Jing Xiao, Li-Jun Zhou, Yang Liu, Xiang-Wei Wu, Ri-Mao Hua, Gui-Rong Wang, Hai-Qun Cao
BACKGROUND: The cereal weevil, Sitophilus zeamais is one of the most destructive pests of stored cereals worldwide. Frequent use of fumigants for managing stored-product insects has led to the development of resistance in insects. Essential oils from aromatic plants including the tea oil plant, Melaleuca alternifolia may provide environmentally friendly alternatives to currently used pest control agents. However, little is known about molecular events involved in stored-product insects in response to plant essential oil fumigation...
2016: PloS One
https://www.readbyqxmd.com/read/27936190/two-isoforms-of-yersinia-pestis-plasminogen-activator-pla-intraspecies-distribution-intrinsic-disorder-propensity-and-contribution-to-virulence
#11
Svetlana V Dentovskaya, Mikhail E Platonov, Tat'yana E Svetoch, Pavel Kh Kopylov, Tat'yana I Kombarova, Sergey A Ivanov, Rima Z Shaikhutdinova, Lyubov' V Kolombet, Sadhana Chauhan, Vitaly G Ablamunits, Vladimir L Motin, Vladimir N Uversky, Andrey P Anisimov
It has been shown previously that several endemic Y. pestis isolates with limited virulence contained the I259 isoform of the outer membrane protease Pla, while the epidemic highly virulent strains possessed only the T259 Pla isoform. Our sequence analysis of the pla gene from 118 Y. pestis subsp. microtus strains revealed that the I259 isoform was present exclusively in the endemic strains providing a convictive evidence of more ancestral origin of this isoform. Analysis of the effects of the I259T polymorphism on the intrinsic disorder propensity of Pla revealed that the I259T mutation slightly increases the intrinsic disorder propensity of the C-terminal tail of Pla and makes this protein slightly more prone for disorder-based protein-protein interactions, suggesting that the T259 Pla could be functionally more active than the I259 Pla...
2016: PloS One
https://www.readbyqxmd.com/read/27936160/a-cbl-interacting-protein-kinase-tacipk2-confers-drought-tolerance-in-transgenic-tobacco-plants-through-regulating-the-stomatal-movement
#12
Yan Wang, Tao Sun, Tingting Li, Meng Wang, Guangxiao Yang, Guangyuan He
In plants, the CBL-CIPK signaling pathways play key roles in the response to abiotic stresses. However, functional studies of CIPKs in the important staple crop wheat are very rare. In this study, we identified a CIPK gene from wheat, designated TaCIPK2. Expression analysis results showed that TaCIPK2 could be up-regulated in wheat leaves by polyethylene glycol, abscisic acid and H2O2 treatments. Subcellular localization analyses revealed that TaCIPK2 was present in whole wheat epidermal cells. A yeast two-hybrid assay indicated that TaCIPK2 interacted with TaCBL1, 2, 3 and 4 in vitro...
2016: PloS One
https://www.readbyqxmd.com/read/27936113/preoperative-csf-melatonin-concentrations-and-the-occurrence-of-delirium-in-older-hip-fracture-patients-a-preliminary-study
#13
Rikie M Scholtens, Sophia E J A de Rooij, Annelies E Vellekoop, Bart C Vrouenraets, Barbara C van Munster
BACKGROUND: Delirium is characterized by disturbances in circadian rhythm. Melatonin regulates our circadian rhythm. Our aim was to compare preoperative cerebrospinal fluid (CSF) melatonin levels in patients with and without postoperative delirium. METHODS: Prospective cohort study with hip fracture patients ≥ 65 years who were acutely admitted to the hospital for surgical treatment and received spinal anaesthesia. CSF was collected after cannulation, before administering anaesthetics...
2016: PloS One
https://www.readbyqxmd.com/read/27936112/genome-wide-association-of-heroin-dependence-in-han-chinese
#14
Gursharan Kalsi, Jack Euesden, Jonathan R I Coleman, Francesca Ducci, Fazil Aliev, Stephen J Newhouse, Xiehe Liu, Xiaohong Ma, Yingcheng Wang, David A Collier, Philip Asherson, Tao Li, Gerome Breen
Drug addiction is a costly and recurring healthcare problem, necessitating a need to understand risk factors and mechanisms of addiction, and to identify new biomarkers. To date, genome-wide association studies (GWAS) for heroin addiction have been limited; moreover they have been restricted to examining samples of European and African-American origin due to difficulty of recruiting samples from other populations. This is the first study to test a Han Chinese population; we performed a GWAS on a homogeneous sample of 370 Han Chinese subjects diagnosed with heroin dependence using the DSM-IV criteria and 134 ethnically matched controls...
2016: PloS One
https://www.readbyqxmd.com/read/27936107/structural-analysis-of-thymidylate-synthase-from-kaposi-s-sarcoma-associated-herpesvirus-with-the-anticancer-drug-raltitrexed
#15
Yong Mi Choi, Hyun Ku Yeo, Young Woo Park, Jae Young Lee
Kaposi's sarcoma-associated herpesvirus (KSHV) is a highly infectious human herpesvirus that causes Kaposi's sarcoma. KSHV encodes functional thymidylate synthase, which is a target for anticancer drugs such as raltitrexed or 5-fluorouracil. Thymidylate synthase catalyzes the conversion of 2'-deoxyuridine-5'-monophosphate (dUMP) to thymidine-5'-monophosphate (dTMP) using 5,10-methylenetetrahydrofolate (mTHF) as a co-substrate. The crystal structures of thymidylate synthase from KSHV (apo), complexes with dUMP (binary), and complexes with both dUMP and raltitrexed (ternary) were determined at 1...
2016: PloS One
https://www.readbyqxmd.com/read/27936099/characterization-of-arginase-expression-in-glioma-associated-microglia-and-macrophages
#16
Ian Zhang, Darya Alizadeh, Junling Liang, Leying Zhang, Hang Gao, Yanyan Song, Hui Ren, Mao Ouyang, Xiwei Wu, Massimo D'Apuzzo, Behnam Badie
Microglia (MG) and macrophages (MPs) represent a significant component of the inflammatory response to gliomas. When activated, MG/MP release a variety of pro-inflammatory cytokines, however, they also secrete anti-inflammatory factors that limit their cytotoxic function. The balance between pro and anti-inflammatory functions dictates their antitumor activity. To evaluate potential variations in MG and MP function in gliomas, we isolated these cells (and other Gr1+ cells) from intracranial GL261 murine gliomas by FACS and evaluated their gene expression profiles by microarray analysis...
2016: PloS One
https://www.readbyqxmd.com/read/27936065/kinase-screening-in-pichia-pastoris-identified-promising-targets-involved-in-cell-growth-and-alcohol-oxidase-1-promoter-paox1-regulation
#17
Wei Shen, Chuixing Kong, Ying Xue, Yiqi Liu, Menghao Cai, Yuanxing Zhang, Tianyi Jiang, Xiangshan Zhou, Mian Zhou
As one of the most commonly used eukaryotic recombinant protein expression systems, P. pastoris relies heavily on the AOX1 promoter (PAOX1), which is strongly induced by methanol but strictly repressed by glycerol and glucose. However, the complicated signaling pathways involved in PAOX1 regulation when supplemented with different carbon sources are poorly understood. Here we constructed a kinase deletion library in P. pastoris and identified 27 mutants which showed peculiar phenotypes in cell growth or PAOX1 regulation...
2016: PloS One
https://www.readbyqxmd.com/read/27936056/spatial-temporal-analysis-of-environmental-data-of-north-beijing-district-using-hilbert-huang-transform
#18
Yu Xiang, Xuezhi Wang, Lihua He, Wenyong Wang, William Moran
Temperature, solar radiation and water are major important variables in ecosystem models which are measurable via wireless sensor networks (WSN). Effective data analysis is necessary to extract significant spatial and temporal information. In this work, information regarding the long term variation of seasonal field environment conditions is explored using Hilbert-Huang transform (HHT) based analysis on the wireless sensor network data collection. The data collection network, consisting of 36 wireless nodes, covers an area of 100 square kilometres in Yanqing, the northwest of Beijing CBD, in China and data collection involves environmental parameter observations taken over a period of three months in 2011...
2016: PloS One
https://www.readbyqxmd.com/read/27936043/reproducibility-for-heart-rate-variability-analysis-during-6-min-walk-test-in-patients-with-heart-failure-and-agreement-between-devices
#19
Lays Magalhães Braga, Gustavo Faibischew Prado, Iracema Ioco Kikuchi Umeda, Tatiana Satie Kawauchi, Adriana Marques Fróes Taboada, Raymundo Soares Azevedo, Horacio Gomes Pereira Filho, César José Grupi, Hayala Cristina Cavenague Souza, Dalmo Antônio Ribeiro Moreira, Naomi Kondo Nakagawa
Heart rate variability (HRV) analysis is a useful method to assess abnormal functioning in the autonomic nervous system and to predict cardiac events in patients with heart failure (HF). HRV measurements with heart rate monitors have been validated with an electrocardiograph in healthy subjects but not in patients with HF. We explored the reproducibility of HRV in two consecutive six-minute walk tests (6MW), 60-minute apart, using a heart rate monitor (PolarS810i) and a portable electrocardiograph (called Holter) in 50 HF patients (mean age 59 years, NYHA II, left ventricular ejection fraction ~35%)...
2016: PloS One
https://www.readbyqxmd.com/read/27936036/the-rs3957357c-t-snp-in-gsta1-is-associated-with-a-higher-risk-of-occurrence-of-hepatocellular-carcinoma-in-european-individuals
#20
Hanane Akhdar, Said El Shamieh, Orlando Musso, Romain Désert, Wissam Joumaa, Dominique Guyader, Caroline Aninat, Anne Corlu, Fabrice Morel
Glutathione S-transferases (GSTs) detoxify toxic molecules by conjugation with reduced glutathione and regulate cell signaling. Single nucleotide polymorphisms (SNPs) of GST genes have been suggested to affect GST functions and thus to increase the risk of human hepatocellular carcinoma (HCC). As GSTA1 is expressed in hepatocytes and the rs3957357C>T (TT) SNP is known to downregulate GSTA1 mRNA expression, the aims of this study were: (i) to explore the relationship between the TT SNP in GSTA1 and the occurrence of HCC; (ii) to measure GSTA1 mRNA expression in HCCs...
2016: PloS One
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