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Novel dna extraction

Yanhong Shi, Hong Zhang, Zhe Tian, Min Yang, Yu Zhang
Studies on antibiotic production wastewater have shown that even a single antibiotic can select for multidrug resistant bacteria in aquatic environments. It is speculated that plasmids are an important mechanism of multidrug resistance (MDR) under high concentrations of antibiotics. Herein, two metagenomic libraries were constructed with plasmid DNA extracted from cultivable microbial communities in a biological wastewater treatment reactor supplemented with 0 (CONTROL) or 25 mg/L of oxytetracycline (OTC-25)...
January 13, 2018: Applied Microbiology and Biotechnology
RiBang Wu, CuiLing Wu, Dan Liu, XingHao Yang, JiaFeng Huang, Jiang Zhang, Binqiang Liao, HaiLun He
Extracted salmon skin collagen was hydrolysed with the free or immobilized extracellular protease of Vibrio sp. SQS2-3. The hydrolysate exhibited anti-freezing activity (>3 kDa) and antioxidant activity (<3000 Da) after ultrafiltration. The antioxidant peptide was further purified by size-exclusion chromatography and found to scavenge DPPH (73.29 ± 1.03%), OH (72.73 ± 3.34%,), and intracellular ROS in HUVECs; protect DNA against oxidation-induced damage; and have an ORAC of 2.78 ± 0...
May 15, 2018: Food Chemistry
Kai-Yao Huang, Tzu-Hao Chang, Jhih-Hua Jhong, Yu-Hsiang Chi, Wen-Chi Li, Chien-Lung Chan, K Robert Lai, Tzong-Yi Lee
BACKGROUND: Anti-microbial peptides (AMPs), naturally encoded by genes and generally containing 12-100 amino acids, are crucial components of the innate immune system and can protect the host from various pathogenic bacteria and viruses. In recent years, the widespread use of antibiotics has resulted in the rapid growth of antibiotic-resistant microorganisms that often induce critical infection and pathogenesis. Recently, the advent of high-throughput technologies has led molecular biology into a data surge in both the amount and scope of data...
December 21, 2017: BMC Systems Biology
J Fu, F Lai, Y Chen, X Wan, G Wei, Y Li, H Xiao, X Cao
BACKGROUND: Carney complex (CNC) is an extremely rare, multiple endocrine neoplasia syndrome that occurs in an autosomal dominant manner. Mutations in PRKAR1A have been reported to be a common genetic cause of CNC. METHODS: In this study, we reported a Chinese pedigree of CNC that manifests mainly as spotty skin pigmentation and primary pigmented nodular adrenocortical disease. Whole blood samples of this pedigree were collected for DNA/RNA analysis. Polymerase chain reaction (PCR) and reverse-transcription polymerase chain reaction analyses were performed to amplify the 11 exons and adjacent introns of PRKAR1A...
January 9, 2018: Journal of Endocrinological Investigation
Iman Jafari, Vahid Heravi Shargh, Maryam Shahryari, Azam Abbasi, Mahmoud Reza Jaafari, Ali Khamesipour, Ali Badiee
Although there have been numerous attempts to develop a successful vaccine against leishmaniasis, based on the clinical trial in this field, no vaccine against Leishmania in routine way can be found for globally effective vaccination in human. Amongst, first generation vaccines consisting of parasite fractions or whole killed Leishmania showed more successful results in clinical trials. It seems that the main reason for the low efficacy of these vaccines is lack of a suitable adjuvant. In this study, a crude extract of detergent-solubilized L...
December 28, 2017: Immunobiology
Takuya Okada, Gaku Okabe, Yon-Soo Tak, Satoru Mimura, Haruhiko Takisawa, Yumiko Kubota
Intact G0 nuclei isolated from quiescent cells are not capable of DNA replication in interphase Xenopus egg extracts, which allow efficient replication of permeabilized G0 nuclei. Previous studies have shown multiple control mechanisms for maintaining the quiescent state, but DNA replication inhibition of intact G0 nuclei in the extracts remains poorly understood. Here, we showed that pre-RC is assembled on chromatin, but its activation is inhibited after incubating G0 nuclei isolated from quiescent NIH3T3 cells in the extracts...
January 4, 2018: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Alyce Taylor-Brown, Danielle Madden, Adam Polkinghorne
The expanding field of bacterial genomics has revolutionized our understanding of microbial diversity, biology and phylogeny. For most species, DNA extracted from culture material is used as the template for genome sequencing; however, the majority of microbes are actually uncultivable, and others, such as obligate intracellular bacteria, require laborious tissue culture to yield sufficient genomic material for sequencing. Chlamydiae are one such group of obligate intracellular microbes whose characterization has been hampered by this requirement...
January 3, 2018: Microbial Genomics
Nawal Hijjawi, Rongchang Yang, Ma'mon Hatmal, Yasmeen Yassin, Taghrid Mharib, Rami Mukbel, Sameer Alhaj Mahmoud, Abdel-Ellah Al-Shudifat, Una Ryan
Little is known about the prevalence of Giardia duodenalis in human patients in Jordan and all previous studies have used direct microscopy, which lacks sensitivity. The present study developed a novel quantitative PCR (qPCR) assay at the β-giardin (bg) locus and evaluated its use as a frontline test for the diagnosis of giardiasis in comparison with a commercially available ELISA using nested PCR and sequencing of the glutamate dehydrogenase (gdh) locus (gdh nPCR) as the gold standard. A total of 96 human faecal samples were collected from 96 patients suffering from diarrhea from 5 regions of Jordan and were screened using the ELISA and qPCR...
January 5, 2018: Experimental Parasitology
Xiaoyu Han, Wei Li, Na He, Panpan Feng, Yihua Pang, Chunyan Ji, Daoxin Ma
PURPOSES: The conventional risk stratification of acute myeloid leukemia (AML), based on cytogenetics, cannot meet the demand for accurate prognostic evaluations. In recent years, gene mutations are found to be potential markers for more accurate risk stratification, but reports on mutation screening of Chinese AML are limited. We aim to display the mutation patterns of Chinese AML patients, reveal the genotype-phenotype correlation and make a comparison with Caucasians patients. METHODS: Genome DNA from 78 patients' bone marrow were extracted for targeted gene mutation panel by next-generation sequencing (NGS) technology...
January 5, 2018: Clinica Chimica Acta; International Journal of Clinical Chemistry
Ilaria Piazza, Karl Kochanowski, Valentina Cappelletti, Tobias Fuhrer, Elad Noor, Uwe Sauer, Paola Picotti
Metabolite-protein interactions control a variety of cellular processes, thereby playing a major role in maintaining cellular homeostasis. Metabolites comprise the largest fraction of molecules in cells, but our knowledge of the metabolite-protein interactome lags behind our understanding of protein-protein or protein-DNA interactomes. Here, we present a chemoproteomic workflow for the systematic identification of metabolite-protein interactions directly in their native environment. The approach identified a network of known and novel interactions and binding sites in Escherichia coli, and we demonstrated the functional relevance of a number of newly identified interactions...
January 3, 2018: Cell
Lichao Zhang, Liang Kong
Gene recombination is a key process to produce hereditary differences. Recombination spot identification plays an important role in revealing genome evolution and promoting DNA function study. However, traditional experiments are not good at identifying recombination spot with huge amounts of DNA sequences springed up by sequencing. At present, some machine learning methods have been proposed to speed up this identification process. However, the correlations between nucleotides pairs at different positions along DNA sequence is often ignored, which reflects the important sequence order information...
January 2, 2018: Journal of Theoretical Biology
Shuhei Hashiro, Koyu Fujiuchi, Daisuke Sugimori, Hisashi Yasueda
We have identified an enzyme, galactolipase (ckGL), which hydrolyzes the acyl ester bond of galactolipids such as digalactosyldiacylglycerol (DGDG), in the microalga Chlorella kessleri. Following purification of the enzyme to electrophoretic homogeneity from cell-free extract, the maximum activity toward DGDG was observed at pH 6.5 and 37 °C. ckGL was Ca2+-dependent enzyme and displayed an apparent molecular mass of approx. 53 kDa on SDS-PAGE. The substrate specificity was in the order: DGDG (100%) > monogalactosyldiacylglycerol ≈ phosphatidylglycerol (~ 40%) > sulfoquinovosyldiacylglycerol (~ 20%); the enzyme exhibited almost no activity toward glycerides and other phospholipids...
January 3, 2018: Applied Microbiology and Biotechnology
David C Earl, P Brent Ferrell, Nalin Leelatian, Jordan T Froese, Benjamin J Reisman, Jonathan M Irish, Brian O Bachmann
Discovering bioactive metabolites within a metabolome is challenging because there is generally little foreknowledge of metabolite molecular and cell-targeting activities. Here, single-cell response profiles and primary human tissue comprise a response platform used to discover novel microbial metabolites with cell-type-selective effector properties in untargeted metabolomic inventories. Metabolites display diverse effector mechanisms, including targeting protein synthesis, cell cycle status, DNA damage repair, necrosis, apoptosis, or phosphoprotein signaling...
January 2, 2018: Nature Communications
HyungJae Lee, Mihye Choi, Jiyun Lim, Minkyung Jo, Ji-Youn Han, Tae Min Kim, Youngnam Cho
Purpose: Recent developments in genomic and molecular methods have revolutionized the range of utilities of tumor-associated circulating biomarkers in both basic and clinical research. Herein, we present a novel approach for ultrasensitive extraction of cfDNA and CTCs, at high yield and purity, via the formation of magnetic nanowire networks. Materials and Methods: We fabricated and characterized biotinylated cationic polyethylenimine and biotinylated antibody cocktail-conjugated magnetic polypyrrole NWs (PEI/mPpy NW and Ab cocktail/mPpy NW, respectively)...
2018: Theranostics
HyungJae Lee, Mihye Choi, Sang-Hyun Hwang, Youngnam Cho
Purpose: As human papillomavirus (HPV) is primarily responsible for the development of cervical cancer, significant efforts have been devoted to develop novel strategies for detecting and identifying HPV DNA in urine. The analysis of target DNA sequences in urine offers a potential alternative to conventional methods as a non-invasive clinical screening and diagnostic assessment tool for the detection of HPV. However, the lack of efficient approaches to isolate and directly detect HPV DNA in urine has restricted its potential clinical use...
2018: Theranostics
Jee Won Lee, Ju Yeon Jung, Si-Keun Lim
In this paper, we describe the development of a novel method to detect oral bacteria by combining direct polymerase chain reaction (direct PCR) with an immunochromatographic strip (ICS), enabling the identification of saliva in forensic samples. Direct PCR was first used to directly amplify specific oral bacterial sequences (from Streptococcus sanguinis and Streptococcus salivarius) from swab samples, circumventing the need for tedious sample preparation steps such as cell lysis and DNA extraction and purification...
December 21, 2017: Forensic Science International. Genetics
Jia-Mei Guo, Ming-Yu Ba, Ying Yang, Chun-Suo Yao, Miao Yu, Jian-Gong Shi, Ying Guo
Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are essential components of highly active antiretroviral therapy (HAART) for human immunodeficiency virus type 1 (HIV-1) infection. In this study, we identified (+)-(7'S,8S,8'S)-3',4,4',5,5'-pentamethoxy-2,7'-cyclolignan (SG-1), a cyclolignan semi-synthesized from Machilus robusta and M. wangchiana extracts, as a potent NNRTI. SG-1 displayed anti-HIV-1 activity with an IC50 of 0.77 μmol/L by inhibiting reverse transcriptase (RT) RNA-dependent DNA polymerase activity through a direct binding...
December 27, 2017: Journal of Asian Natural Products Research
Warish Ahmed, Aldo Lobos, Jacob Senkbeil, Jayme Peraud, Javier Gallard, Valerie J Harwood
CrAssphage are recently-discovered DNA bacteriophages that are prevalent and abundant in human feces and sewage. We assessed the performance characteristics of a crAssphage quantitative PCR (qPCR) assay for quantifying sewage impacts in stormwater and surface water in subtropical Tampa, Florida. The mean concentrations of crAssphage in untreated sewage ranged from 9.08 to 9.98 log10 gene copies/L. Specificity was 0.927 against 83 non-human fecal reference samples and the sensitivity was 1.0. Cross-reactivity was observed in DNA extracted from soiled poultry litter but the concentrations were substantially lower than untreated sewage...
December 24, 2017: Water Research
T Onodera, M Kawai, K Obara, T Enomoto, K Sasaki, T Osabe, K Ogasawara, C Toyoda, H Tsuneyama, M Uchikawa, S Inaba, M Satake
BACKGROUND AND OBJECTIVE: The rare Ko phenotype lacks all 36 antigens in the Kell blood system. The molecular basis of the Ko phenotype has been investigated, and more than 40 silent KEL alleles are reported by many investigators. The majority of silent alleles are the KEL*02 background. Here, we report molecular genetic analysis of the KEL gene in Japanese individuals with the Ko phenotype. MATERIALS AND METHODS: The Ko phenotype was screened from Japanese blood donors for several years using monoclonal anti-Ku or anti-K14 by an automated blood grouping system PK7300...
December 27, 2017: Vox Sanguinis
Lizhen Zhu, Yanqin Huang, Xuefeng Fang, Chenglin Liu, Wanglong Deng, Chenhan Zhong, Jinghong Xu, Dong Xu, Ying Yuan
Two types of molecular tests have been established to assess the deficiency of DNA mismatch repair (MMR) system: microsatellite instability (MSI) and immunohistochemical (IHC) analysis. We have developed a reliable method to analyze the MSI status by next-generation sequencing (NGS) based on read count distribution. A total of 91 patients with primary colorectal cancer were recruited. These patients included 54 cases with the loss of expression of any MMR protein in IHC suggesting deficient MMR (dMMR), and 37 cases of colorectal cancer with staining of all four MMR proteins in IHC, suggesting proficient MMR (pMMR) in postoperative sample...
December 19, 2017: Journal of Molecular Diagnostics: JMD
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