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https://www.readbyqxmd.com/read/28647701/aberrant-methylation-of-t-cadherin-can-be-a-diagnostic-biomarker-for-colorectal-cancer
#1
Bo-Shi Duan, Long-Fei Xie, Yue Wang
BACKGROUND/AIM: T-cadherin is a tumor suppressor gene, its predictive value in colorectal cancer (CRC) still remains controversial. In this study, we aimed to evaluate the association between T-cadherin promoter methylation and CRC by performing a meta-analysis. MATERIALS AND METHODS: The relevant literature was searched using the PubMed, Cochrane Library, Web of Science and Google Scholar databases for articles published until December 2016. The effect sizes were estimated by measuring an odds ratio (OR) with a 95% confidence interval (CI)...
July 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28647584/transforaminal-lumbar-interbody-fusion-tlif-versus-posterior-lumbar-interbody-fusion-plif-in-lumbar-spondylolisthesis-a-systematic-review-and-meta-analysis
#2
REVIEW
Suzanne L de Kunder, Sander Mj van Kuijk, Kim Rijkers, Inge Jmh Caelers, Wouter Lw van Hemert, Rob A de Bie, Henk van Santbrink
BACKGROUND CONTEXT: Transforaminal lumbar interbody fusion (TLIF) and posterior lumbar interbody fusion (PLIF) are both frequently used as surgical treatment for lumbar spondylolisthesis. Due to the unilateral transforaminal route to the intervertebral space used in TLIF, opposed to the bilateral route used in PLIF, TLIF could be associated with fewer complications, shorter duration of surgery, and less blood loss, while effectiveness of both techniques on back and/or leg pain is equal...
June 21, 2017: Spine Journal: Official Journal of the North American Spine Society
https://www.readbyqxmd.com/read/28646085/generation-of-a-collection-of-mutant-tomato-lines-using-pooled-crispr-libraries
#3
Thomas B Jacobs, Ning Zhang, Dhruv Patel, Gregory B Martin
The high efficiency of CRIPSR-mediated mutagenesis in plants enables the development of high-throughput mutagenesis strategies. By transforming pooled CRISPR libraries into tomato, collections of mutant lines were generated with minimal transformation attempts and in a relatively short period of time. Identification of the targeted gene(s) was easily determined by sequencing the incorporated gRNA(s) in the primary transgenic events. From a single transformation with a CRISPR library targeting the immunity-associated leucine-rich repeat subfamily XII genes, heritable mutations were recovered in 15 of the 54 genes targeted...
June 23, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28645181/the-clinical-benefits-of-perioperative-antioxidant-vitamin-therapy-in-patients-undergoing-cardiac-surgery-a-meta-analysis
#4
Jun Geng, Ju Qian, Weijun Si, Hao Cheng, Fuhai Ji, Zhenya Shen
The clinical benefits of perioperative antioxidant vitamin therapy in cardiac patients remain controversial. Here, we conducted a meta-analysis to determine the strength of the evidence supporting the perioperative use of antioxidant vitamins in patients undergoing cardiac surgery. We searched 4 databases (PubMed, EMBASE, Science Citation Index and Cochrane Library) for randomized controlled trials that reported the effects of antioxidant vitamin therapy on patients undergoing cardiac surgery until 6 June 2016...
June 22, 2017: Interactive Cardiovascular and Thoracic Surgery
https://www.readbyqxmd.com/read/28644563/gas-phase-dissociation-study-of-erythrinian-alkaloids-by-electrospray-ionization-mass-spectrometry-and-computational-methods
#5
T Guaratini, L G P Feitosa, D B Silva, N P Lopes, J L C Lopes, R Vessecchi
Alkaloids from plants of the genus Erythrina display important biological activities, including anxiolytic action. Characterization of these alkaloids by mass spectrometry (MS) has contributed to the construction of a spectral library, has improved understanding of their structures, and has supported the proposal of fragmentation mechanisms in light of density functional calculations (DFT). In this study, we have used low- and high-resolution MS(n) analyses to investigate the fragmentation patterns of erythrinian alkaloids; we have employed the B3LYP/6-31+G(d,p) model to obtain their reactive sites...
June 23, 2017: Journal of Mass Spectrometry: JMS
https://www.readbyqxmd.com/read/28643317/-effect-of-metformin-on-colorectal-carcinoma-in-type-2-diabetes-mellitus-patients-a-markov-model-analysis
#6
Tianhong Su, Bing Liao, Yu Dong, Zhenwei Peng, Qian Zhou, Bin Li, Sui Peng, Ning Zhang
OBJECTIVE: To evaluate the colorectal cancer (CRC) prevention effect of metformin in comparison with that of other T2DM medications from a Markov model perspective. METHODS: Literature concerning CRC morbidity of T2DM patients with metformin or other diabetes medications treatment was reviewed in PubMed and Cochrane Library database from September 2010 to December 2016. INCLUSION CRITERIA: (1)enrolled population was adult patients with T2DM but without CRC; (2) any of the parameters applied in our model was reported; (3) randomized clinical trials (RCTs), quasi-randomized trials, prospective or retrospective cohort studies...
June 25, 2017: Zhonghua Wei Chang Wai Ke za Zhi, Chinese Journal of Gastrointestinal Surgery
https://www.readbyqxmd.com/read/28641411/development-of-an-lc-hrms-metabolomics-method-with-high-specificity-for-metabolite-identification-using-all-ion-fragmentation-aif-acquisition
#7
Shama Naz, Hector Gallart-Ayala, Stacey Reinke, Caroline Mathon, Richard Blankley, Romanas Chaleckis, Craig Edward Wheelock
High-resolution mass spectrometry (HRMS)-based metabolomics approaches have made significant advances. However, metabolite identification is still a major challenge and significant bottleneck in translating metabolomics data into biological context. In the current study, a liquid chromatography (LC)-HRMS metabolomics method was developed using an all ion fragmentation (AIF) acquisition approach. In order to increase the specificity in metabolite annotation, four criteria were considered: i) accurate mass (AM), ii) retention time (RT), iii) MS/MS spectrum, and iv) product/precursor ion intensity ratios...
June 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28638397/generation-annotation-and-analysis-of-a-large-scale-expressed-sequence-tag-library-from-arabidopsis-pumila-to-explore-salt-responsive-genes
#8
Xianzhong Huang, Lifei Yang, Yuhuan Jin, Jun Lin, Fang Liu
Arabidopsis pumila is an ephemeral plant, and a close relative of the model plant Arabidopsis thaliana, but it possesses higher photosynthetic efficiency, higher propagation rate, and higher salinity tolerance compared to those A. thaliana, thus providing a candidate plant system for gene mining for environmental adaption and salt tolerance. However, A. pumila is an under-explored resource for understanding the genetic mechanisms underlying abiotic stress adaptation. To improve our understanding of the molecular and genetic mechanisms of salt stress adaptation, more than 19,900 clones randomly selected from a cDNA library constructed previously from leaf tissue exposed to high-salinity shock were sequenced...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28634080/nong-a-constituent-of-the-nonactin-biosynthetic-gene-cluster-regulates-nocardamine-synthesis-in-streptomyces-albus-j1074
#9
Wanki Park, Jung-Kyun Woo, Jongheon Shin, Ki-Bong Oh
Many factors regulate the expression of specialised secondary metabolite biosynthetic gene clusters, which have been recognised as important for the discovery of novel microbial natural products. A cosmid library based on genomic DNA of the marine-derived Streptomyces puniceus Act1085 was constructed and screened to identify a short gene cluster similar to the nonactin biosynthetic cluster. The ORFs of the gene cluster isolated had high amino acid sequence identity, from 82% to 96%, with corresponding ORFs of the nonactin biosynthetic gene cluster from S...
June 17, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28630098/comparative-micrornaome-analysis-of-the-testis-and-ovary-of-the-chinese-giant-salamander
#10
Rui Chen, Jian Du, Lin Ma, Li-Qing Wang, Sheng-Song Xie, Chang-Ming Yang, Xian-Yong Lan, Chuan-Ying Pan, Wu-Zi Dong
MicroRNAs (miRNAs) are 18-24 nucleotides non-coding RNAs that regulate gene expression by post-transcriptional suppression of mRNA. The Chinese giant salamander (CGS, Andrias davidianus), which is an endangered species, has become one of important models of animal evolution; however, no miRNA studies on this species have been conducted. In this study, two small RNA libraries of CGS ovary and testis were constructed using deep sequencing technology. A bioinformatics pipeline was developed to distinguish miRNA sequences from other classes of small RNAs represented in the sequencing data...
June 19, 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/28623587/generation-of-dtales-and-libraries-of-synthetic-tale-activated-promoters-for-engineering-of-gene-regulatory-networks-in-plants
#11
Tom Schreiber, Alain Tissier
Transcription factors with programmable DNA-binding specificity constitute valuable tools for the design of orthogonal gene regulatory networks for synthetic biology. Transcription activator-like effectors (TALEs), as natural transcription regulators, were used to design, build, and test libraries of synthetic TALE-activated promoters (STAPs) that show a broad range of expression levels in plants. In this chapter, we present protocols for the construction of artificial TALEs and corresponding STAPs.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28622855/b-cell-cross-epitope-of-propionibacterium-acnes-and-actinobacillus-pleuropneumonia-selected-by-phage-display-library-can-efficiently-protect-from-actinobacillus-pleuropneumonia-infection
#12
Jianfang Liu, Qiuyue Ma, Feng Yang, Rining Zhu, Jingmin Gu, Changjiang Sun, Xin Feng, Chongtao Du, Paul R Langford, Wenyu Han, Junling Yang, Liancheng Lei
Contagious porcine pleuropneumonia (CPP), caused by Actinobacillus pleuropneumoniae (APP), is a highly transmissible and fatal respiratory illness that causes tremendous economic losses for the pig breeding industry worldwide. Propionibacterium acnes (PA) has a strong cross-reaction with anti-APP1 and anti-APP5 serum and can efficiently prevent APP infection, which was fortuitously found in researching the differential gene between the different APP serotypes. There seems to be some natural cross-protection between PA and APP...
June 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28622611/de-novo-transcriptome-sequencing-and-comparative-analysis-to-discover-genes-involved-in-ovarian-maturity-in-strongylocentrotus-nudus
#13
Zhiying Jia, Qiai Wang, Kaikai Wu, Zhenlin Wei, Zunchun Zhou, Xiaolin Liu
Strongylocentrotus nudus is an edible sea urchin, mainly harvested in China. Correlation studies indicated that S. nudus with larger diameter have a prolonged marketing time and better palatability owing to their precocious gonads and extended maturation process. However, the molecular mechanism underlying this phenomenon is still unknown. Here, transcriptome sequencing was applied to study the ovaries of adult S. nudus with different shell diameters to explore the possible mechanism. In this study, four independent cDNA libraries were constructed, including two from the big size urchins and two from the small ones using a HiSeq™2500 platform...
May 30, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28621534/construction-of-an-immunized-rabbit-phage-display-library-for-selecting-high-activity-of-against-bacillus-thuringiensis-cry1f-toxin-single-chain-antibodies
#14
Chongxin Xu, Cunzheng Zhang, Jianfeng Zhong, Hui Hu, Shimin Luo, Xiaoqin Liu, Xiao Zhang, Yuan Liu, Xianjin Liu
In the present study, a Cry1F-immunized rabbit phage display library (6.96×108) was constructed for selecting high activity of anti-Cry1F toxin single-chain antibody (scFv) by bio-panning. Total 16 positive monoclonal phage scFvs were obtained after 4 rounds panning which identified by enzyme-linked immunoassay (ELISA), PCR and DNA sequencing. The most positive phage scFv (named RF4) was expressed in E.coli.HB2151 and the purified soluble protein approximate 30 kDa with sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE)...
June 16, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28620550/generation-of-recombinant-antibodies-against-the-beta-1-6-branched-beta-1-3-d-glucan-schizophyllan-from-immunized-mice-via-phage-display
#15
Jörn Josewski, Sabine Buchmeier, André Frenzel, Philip Tinnefeld, Stefan Dübel, Udo Rau
beta-(1,6)-Branched beta-(1,3)-D-glucans like schizophyllan from the basidiomycete Schizophyllum commune excite various immunostimulatory effects and have been clinically tested as adjuvants. Some of the glucans are also applicable in food or petrol industry due to their viscosity and temperature stability in aqueous solution. Antibodies against these glucans could be used as tool for analysis of glucan preparations or for further research of its bioactivity. Therefore, an immune phage display library was constructed from mice immunized with schizophyllan...
2017: Biotechnology Research International
https://www.readbyqxmd.com/read/28613262/antimicrobial-activity-of-truncated-and-polyvalent-peptides-derived-from-the-fkcrrqwqwrmkkgla-sequence-against-escherichia-coli-atcc-25922-and-staphylococcus-aureus-atcc-25923
#16
Nataly de Jesús Huertas, Zuly Jenny Rivera Monroy, Ricardo Fierro Medina, Javier Eduardo García Castañeda
Peptides derived from LfcinB were designed and synthesized, and their antibacterial activity was tested against Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 25923. Specifically, a peptide library was constructed by systemically removing the flanking residues (N or C-terminal) of Lfcin 17-31 ((17)FKCRRWQWRMKKLGA(31)), maintaining in all peptides the (20)RRWQWR(25) sequence that corresponds to the minimal antimicrobial motif. For this research, also included were (i) a peptide containing an Ala instead of Cys ([Ala(19)]-LfcinB 17-31) and (ii) polyvalent peptides containing the RRWQWR sequence and a non-natural amino acid (aminocaproic acid)...
June 14, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28613176/derivative-kernels-numerics-and-applications
#17
Mahdi S Hosseini, Konstantinos N Plataniotis
A generalized framework for numerical differentiation (ND) is proposed for constructing a finite impulse response (FIR) filter in closed form. The framework regulates the frequency response of ND filters for arbitrary derivative-order and cutoff frequency selected parameters relying on interpolating power polynomials and maximally flat design techniques. Compared to the state-of-the-art solutions such as Gaussian kernels, the proposed ND filter is sharply localized in the Fourier domain with ripple-free artifacts...
June 8, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28611392/targeted-sequencing-of-both-dna-strands-barcoded-and-captured-individually-by-rna-probes-to-identify-genome-wide-ultra-rare-mutations
#18
Qing Wang, Xu Wang, Pheobe S Tang, Grace M O'leary, Ming Zhang
Next Generation Sequencing (NGS) has been widely implemented in biological research and has made a profound impact on patient care. One of the essential NGS applications is to identify disease-causing sequence variants, where high coverage and accuracy are needed. Here, we reported a novel NGS pipeline, termed a Sequencing System of Digitalized Barcode Encrypted Single-stranded Library from Extremely Low (quality and quantity) DNA Input with Probe-based DNA Enrichment by RNA probes targeting DNA duplex (DEEPER-Seq)...
June 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28609783/balancing-gene-expression-without-library-construction-via-a-reusable-srna-pool
#19
Amar Ghodasara, Christopher A Voigt
Balancing protein expression is critical when optimizing genetic systems. Typically, this requires library construction to vary the genetic parts controlling each gene, which can be expensive and time-consuming. Here, we develop sRNAs corresponding to 15nt 'target' sequences that can be inserted upstream of a gene. The targeted gene can be repressed from 1.6- to 87-fold by controlling sRNA expression using promoters of different strength. A pool is built where six sRNAs are placed under the control of 16 promoters that span a ∼103-fold range of strengths, yielding ∼107 combinations...
June 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28607440/an-arabidopsis-mutant-with-high-operating-efficiency-of-photosystem-ii-and-low-chlorophyll-fluorescence
#20
Niels van Tol, Martijn Rolloos, Dieuwertje Augustijn, A Alia, Huub J de Groot, Paul J J Hooykaas, Bert J van der Zaal
The overall light energy to biomass conversion efficiency of plant photosynthesis is generally regarded as low. Forward genetic screens in Arabidopsis have yielded very few mutants with substantially enhanced photochemistry. Here, we report the isolation of a novel Arabidopsis mutant with a high operating efficiency of Photosystem II (φPSII) and low chlorophyll fluorescence from a library of lines harboring T-DNA constructs encoding artificial transcription factors. This mutant was named Low Chlorophyll Fluorescence 1 (LCF1)...
June 12, 2017: Scientific Reports
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