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https://www.readbyqxmd.com/read/28918434/improved-dna-purification-with-quality-assurance-for-evaluation-of-the-microbial-genetic-content-of-constructed-wetlands
#1
Wenda Huang, Jingjing Guo, Ran Tao, Ying Man, Yunv Dai, Yang Yang
Efficient isolation of target DNA is a crucial first step of DNA-based metagenomic analyses of environmental samples. Insufficient quantity and purity of DNA isolated using commercial kits result in missing genetic information, especially for large-diameter substrates in constructed wetlands (CWs). Here, we addressed this problem by devising a cost-effective calcium chloride lysozyme-sodium dodecyl sulfate (SDS) method (CCLS), with key improvements in the steps of humic acid removal and cell lysis. The buffer comprising Tris, EDTA, Na2O2P7 and PVPP (TENP), and skim milk, could reduce adsorption between microorganisms and substrates, and calcium chloride precipitated and removed over 94% of humic acid...
September 16, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28918039/crispr-cas9-mediated-knockin-application-in-cell-therapy-a-non-viral-procedure-for-bystander-treatment-of-glioma-in-mice
#2
Oscar Meca-Cortés, Marta Guerra-Rebollo, Cristina Garrido, Salvador Borrós, Nuria Rubio, Jeronimo Blanco
The use of non-viral procedures, together with CRISPR/Cas9 genome-editing technology, allows the insertion of single-copy therapeutic genes at pre-determined genomic sites, overcoming safety limitations resulting from random gene insertions of viral vectors with potential for genome damage. In this study, we demonstrate that combination of non-viral gene delivery and CRISPR/Cas9-mediated knockin via homology-directed repair can replace the use of viral vectors for the generation of genetically modified therapeutic cells...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28917662/successful-optic-nerve-regeneration-in-the-senescent-zebrafish-despite-age-related-decline-of-cell-intrinsic-and-extrinsic-response-processes
#3
Jessie Van Houcke, Ilse Bollaerts, Emiel Geeraerts, Benjamin Davis, An Beckers, Inge Van Hove, Kim Lemmens, Lies De Groef, Lieve Moons
Dysfunction of the central nervous system (CNS) in neurodegenerative diseases or after brain lesions seriously affects life quality of a growing number of elderly, since the adult CNS lacks the capacity to replace or repair damaged neurons. Despite intensive research efforts, full functional recovery after CNS disease and/or injury remains challenging, especially in an aging environment. As such, there is a rising need for an aging model in which the impact of aging on successful regeneration can be studied...
August 24, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/28916329/ecological-extension-of-the-theory-of-evolution-by-natural-selection-from-a-perspective-of-western-and-eastern-holistic-philosophy
#4
REVIEW
Toshiyuki Nakajima
Evolution by natural selection requires the following conditions: (1) a particular selective environment, (2) variation of traits in the population; (3) differential survival/reproduction among types of organisms; and (4) heritable traits. However, the traditional (standard) model does not unclearly explain how and why these conditions are generated or determined. What generates a selective environment? What generates new types? How does a certain type replace, or coexist, with others? In this paper, based on the holistic philosophy in Western and Eastern traditions, I focus on the ecosystem as a higher-level system and generator of conditions that induce the evolution of local populations; I also aim to identify the ecosystem processes that generate those conditions...
September 12, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28916285/profiling-of-bisphenol-s-towards-nuclear-receptors-activities-in-human-reporter-cell-lines
#5
Ondrej Zenata, Zdenek Dvorak, Radim Vrzal
Bisphenol S (BPS) is heat-stable structural analog of bisphenol A (BPA), a known endocrine disruptor. Due to the effort to replace BPA with BPS, it is essential to know if BPS is suitable non-toxic replacement without reported deleterious effects of BPA. Since most of the BPA effects are ascribed to its ability to activate nuclear receptors, we screened some prominent members of this family in order to confirm or refute some recent findings. We found that BPS insignificantly activated aryl hydrocarbon receptor (AhR) in reporter gene assay and no induction of AhR target gene CYP1A1 was observed in human hepatocytes (HH)...
September 12, 2017: Toxicology Letters
https://www.readbyqxmd.com/read/28915787/mmquant-how-to-count-multi-mapping-reads
#6
Matthias Zytnicki
BACKGROUND: RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previously used (drop duplicated genes, distribute uniformly the reads, or estimate expression), but all of them provide biased results. RESULTS: We provide here a tool, called mmquant, for computing gene expression, included duplicated genes. If a read maps at different positions, the tool detects that the corresponding genes are duplicated; it merges the genes and creates a merged gene...
September 15, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28915335/ecm-related-myopathies-and-muscular-dystrophies-pros-and-cons-of-protein-therapies
#7
Pam M Van Ry, Tatiana M Fontelonga, Pamela Barraza-Flores, Apurva Sarathy, Andreia M Nunes, Dean J Burkin
Extracellular matrix (ECM) myopathies and muscular dystrophies are a group of genetic diseases caused by mutations in genes encoding proteins that provide critical links between muscle cells and the extracellular matrix. These include structural proteins of the ECM, muscle cell receptors, enzymes, and intracellular proteins. Loss of adhesion within the myomatrix results in progressive muscle weakness. For many ECM muscular dystrophies, symptoms can occur any time after birth and often result in reduced life expectancy...
September 12, 2017: Comprehensive Physiology
https://www.readbyqxmd.com/read/28913944/the-more-you-test-the-more-you-find-the-smallest-p-values-become-increasingly-enriched-with-real-findings-as-more-tests-are-conducted
#8
Olga A Vsevolozhskaya, Chia-Ling Kuo, Gabriel Ruiz, Luda Diatchenko, Dmitri V Zaykin
The increasing accessibility of data to researchers makes it possible to conduct massive amounts of statistical testing. Rather than follow specific scientific hypotheses with statistical analysis, researchers can now test many possible relationships and let statistics generate hypotheses for them. The field of genetic epidemiology is an illustrative case, where testing of candidate genetic variants for association with an outcome has been replaced by agnostic screening of the entire genome. Poor replication rates of candidate gene studies have improved dramatically with the increase in genomic coverage, due to factors such as adoption of better statistical practices and availability of larger sample sizes...
September 14, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28913802/design-and-assembly-of-crispr-cas9-reagents-for-gene-knockout-targeted-insertion-and-replacement-in-wheat
#9
Tomáš Čermák, Shaun J Curtin
Advances in cereal transformation along with the completion of the wheat genome sequence assembly have increased the demand for tools that perform targeted and specific modifications in this crop plant. This protocol demonstrates the construction of reagents using a comprehensive genome engineering kit to create single and multiple gene "knockouts," site-specific chromosome deletions and gene replacement or "knockins" including the use of geminivirus replicons (GVRs). The reagents allow for both easy construction of simple genome engineering vectors, and "mix and match" swapping of components such as the Cas9, guide RNA and donor template cassettes for gene targeting...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28913343/exacerbating-and-reversing-lysosomal-storage-diseases-from-yeast-to-humans
#10
REVIEW
Tamayanthi Rajakumar, Andrew B Munkacsi, Stephen L Sturley
Lysosomal storage diseases (LSDs) arise from monogenic deficiencies in lysosomal proteins and pathways and are characterized by a tissue-wide accumulation of a vast variety of macromolecules, normally specific to each genetic lesion. Strategies for treatment of LSDs commonly depend on reduction of the offending metabolite(s) by substrate depletion or enzyme replacement. However, at least 44 of the ~50 LSDs are currently recalcitrant to intervention. Murine models have provided significant insights into our understanding of many LSD mechanisms; however, these systems do not readily permit phenotypic screening of compound libraries, or the establishment of genetic or gene-environment interaction networks...
August 25, 2017: Microbial Cell
https://www.readbyqxmd.com/read/28912524/precise-insertion-and-guided-editing-of-higher-plant-genomes-using-cpf1-crispr-nucleases
#11
Matthew B Begemann, Benjamin N Gray, Emma January, Gina C Gordon, Yonghua He, Haijun Liu, Xingrong Wu, Thomas P Brutnell, Todd C Mockler, Mohammed Oufattole
Precise genome editing of plants has the potential to reshape global agriculture through the targeted engineering of endogenous pathways or the introduction of new traits. To develop a CRISPR nuclease-based platform that would enable higher efficiencies of precise gene insertion or replacement, we screened the Cpf1 nucleases from Francisella novicida and Lachnospiraceae bacterium ND2006 for their capability to induce targeted gene insertion via homology directed repair. Both nucleases, in the presence of a guide RNA and repairing DNA template flanked by homology DNA fragments to the target site, were demonstrated to generate precise gene insertions as well as indel mutations at the target site in the rice genome...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28912070/recombinant-influenza-h7-hemagglutinin-containing-cfllc-minidomain-in-the-transmembrane-domain-showed-enhanced-cross-protection-in-mice
#12
Yang Wang, Yun Zhang, Jialing Wu, Ying Lin, Zhihui Wu, Ying Wei, Xiaona Wei, Jianru Qin, Chunyi Xue, George Dacai Liu, Yongchang Cao
Since February 2013, H7N9 influenza virus, causing human infections with high mortality in China, has been a potential pandemic threat. The H7N9 viruses are found to diverge into distinct genotypes as other influenza viruses; thus a vaccine that can provide sufficient cross-protection against different genotypes of H7N9 viruses is urgently needed. Our previous studies demonstrated that the HA-based structural design approach by introducing a CFLLC minidomain into transmembrane domain (TM) of H1, H5 or H9 hemagglutinin (HA) proteins by replacing with H3 subtype HA TM could enhance their cross-protection...
September 11, 2017: Virus Research
https://www.readbyqxmd.com/read/28911202/pathogenicity-of-a-novel-missense-variant-associated-with-choroideremia-and-its-impact-on-gene-replacement-therapy
#13
Simona Torriano, Nejla Erkilic, Valérie Faugère, Krishna Damodar, Christian P Hamel, Anne-Francoise Roux, Vasiliki Kalatzis
Choroideremia (CHM) is an inherited retinal dystrophy characterised by progressive degeneration of photoreceptors, retinal pigment epithelium (RPE) and underlying choroid. It is caused by loss-of-function mutations in CHM, which has an X-linked inheritance, and is thus an ideal candidate for gene replacement strategies. CHM encodes REP1, which plays a key role in the prenylation of Rab GTPases. We recently showed that an induced pluripotent stem cell (iPSc)-derived RPE model for CHM is fully functional and reproduces the underlying prenylation defect...
September 15, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28911098/the-smap2-rna-binding-motif-in-the-3-utr-affects-mrna-stability-in-the-crenarchaeum-sulfolobus-solfataricus
#14
Birgit Märtens, Kundan Sharma, Henning Urlaub, Udo Bläsi
Sm and Sm-like proteins represent an evolutionarily conserved family with key roles in RNA metabolism in Pro- and Eukaryotes. In this study, a collection of 53 mRNAs that co-purified with Sulfolobus solfataricus (Sso) SmAP2 were surveyed for a specific RNA binding motif (RBM). SmAP2 was shown to bind with high affinity to the deduced consensus RNA binding motif (SmAP2-cRBM) in vitro. Residues in SmAP2 interacting with the SmAP2-cRBM were mapped by UV-induced crosslinking in combination with mass-spectrometry, and verified by mutational analyses...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28911069/clinical-utility-of-circulating-dna-analysis-for-rapid-detection-of-actionable-mutations-to-select-metastatic-colorectal-patients-for-anti-egfr-treatment
#15
A R Thierry, S El Messaoudi, C Mollevi, J L Raoul, R Guimbaud, D Pezet, P Artru, E Assenat, C Borg, M Mathonnet, C De La Fouchardière, O Bouché, C Gavoille, C Fiess, B Auzemery, R Meddeb, E Lopez-Crapez, C Sanchez, B Pastor, M Ychou
Background: While tumor-tissue remains the 'gold standard' for genetic analysis in cancer patients, it is challenged with the advent of circulating cell-free tumor DNA (ctDNA) analysis from blood samples. Here, we broaden our previous study on the clinical validation of plasma DNA in metastatic colorectal cancer patients, by evaluating its clinical utility under standard management care. Patients and methods: Concordance and data turnaround-time of ctDNA when compared with tumor-tissue analysis were studied in a real-time blinded prospective multicenter clinical study (n = 140 metastatic colorectal patients)...
September 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28910371/surveillance-of-norovirus-among-children-with-diarrhea-in-four-major-hospitals-in-bhutan-replacement-of-gii-21-by-gii-3-as-a-dominant-genotype
#16
Sonam Wangchuk, Takashi Matsumoto, Hidekatsu Iha, Kamruddin Ahmed
BACKGROUND: Diarrhea is a major cause of morbidity and mortality among Bhutanese children. The etiology of diarrhea is not well known due to the challenges of conducting routine surveillance with Bhutan's modest research facilities. Establishing an etiology is crucial toward generating evidence that will contribute to policy discussions on a diarrheal disease control program. Our previous study, during 2010-2012, revealed that norovirus (NoV) is an important cause of diarrhea among Bhutanese children, and that GII...
2017: PloS One
https://www.readbyqxmd.com/read/28904736/beer-polyphenols-and-menopause-effects-and-mechanisms-a-review-of-current-knowledge
#17
REVIEW
Berner Andrée Sandoval-Ramírez, Rosa M Lamuela-Raventós, Ramon Estruch, Gemma Sasot, Monica Doménech, Anna Tresserra-Rimbau
Beer is one of the most frequently consumed fermented beverages in the world, and it has been part of the human diet for thousands of years. Scientific evidence obtained from the development of new techniques of food analysis over the last two decades suggests that polyphenol intake derived from moderate beer consumption may play a positive role in different health outcomes including osteoporosis and cardiovascular risk and the relief of vasomotor symptoms, which are commonly experienced during menopause and are an important reason why women seek medical care during this period; here, we review the current knowledge regarding moderate beer consumption and its possible effects on menopausal symptoms...
2017: Oxidative Medicine and Cellular Longevity
https://www.readbyqxmd.com/read/28904531/potential-therapeutic-mechanisms-and-tracking-of-transplanted-stem-cells-implications-for-stroke-treatment
#18
REVIEW
Yanhong Zhang, Honghong Yao
Stem cell therapy is a promising potential therapeutic strategy to treat cerebral ischemia in preclinical and clinical trials. Currently proposed treatments for stroke employing stem cells include the replacement of lost neurons and integration into the existing host circuitry, the release of growth factors to support and promote endogenous repair processes, and the secretion of extracellular vesicles containing proteins, noncoding RNA, or DNA to regulate gene expression in recipient cells and achieve immunomodulation...
2017: Stem Cells International
https://www.readbyqxmd.com/read/28904414/identification-of-arsenic-resistance-genes-from-marine-sediment-metagenome
#19
Nar Singh Chauhan, Sonam Nain, Rakesh Sharma
A metagenomic library of sea sediment metagenome containing 245,000 recombinant clones representing ~ 2.45 Gb of sea sediment microbial DNA was constructed. Two unique arsenic resistance clones, A7 and A12, were identified by selection on sodium arsenite containing medium. Clone A7 showed a six-fold higher resistance to arsenate [As(V)], a three-fold higher resistance to arsenite [As(III)] and significantly increased resistance to antimony [Sb(III)], while clone A12 showed increased resistance only to sodium arsenite and not to the other two metalloids...
September 2017: Indian Journal of Microbiology
https://www.readbyqxmd.com/read/28901190/transcriptome-analysis-of-induced-pluripotent-stem-cell-ipsc-derived-pancreatic-%C3%AE-like-cell-differentiation
#20
Yan Huang, Jian Wan, Yibing Guo, Shajun Zhu, Yao Wang, Lei Wang, Qingsong Guo, Yuhua Lu, Zhiwei Wang
Diabetes affects millions of people worldwide, and β-cell replacement is one of the promising new strategies for treatment. Induced pluripotent stem cells (iPSCs) can differentiate into any cell type, including pancreatic β cells, providing a potential treatment for diabetes. However, the molecular mechanisms underlying the differentiation of iPSC-derived β cells have not yet been fully elucidated. Here, we generated pancreatic β-like cells from mouse iPSCs using a 3-step protocol and performed deep RNA sequencing to get a transcriptional landscape of iPSC-derived pancreatic β-like cells during the selective differentiation period...
August 2017: Cell Transplantation
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