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Y Feng, S Y Mei, N Liu, R X Guo
No abstract text is available yet for this article.
March 14, 2018: Zhonghua Xue Ye Xue za Zhi, Zhonghua Xueyexue Zazhi
Brant Gracia, Hashim M Al-Hashimi, Namita Bisaria, Rhiju Das, Daniel Herschlag, Rick Russell
Large-scale, cooperative rearrangements underlie the functions of RNA in RNA-protein machines and gene regulation. To understand how such rearrangements are orchestrated, we used high-throughput chemical footprinting to dissect a seemingly concerted rearrangement in P5abc RNA, a paradigm of RNA folding studies. With mutations that systematically disrupt or restore putative structural elements, we found that this transition reflects local folding of structural modules, with modest and incremental cooperativity that results in concerted behavior...
March 20, 2018: Cell Reports
Kathrin Theil, Margareta Herzog, Nikolaus Rajewsky
In mRNA sequences, 3' UTRs are thought to contain most elements that specifically regulate localization, turnover, and translation. Although high-throughput experiments indicate that many RNA-binding proteins (RBPs) also bind 5' UTRs, much less is known about specific post-transcriptional control exerted by 5' UTRs. GLD-1 is a conserved RBP and a translational repressor with essential roles in Caenorhabditis elegans germ cell development. Previously, we showed that GLD-1 binds highly conserved sites in both 3' and 5' UTRs...
March 20, 2018: Cell Reports
Walderik W Zomerman, Sabine L A Plasschaert, Siobhan Conroy, Frank J Scherpen, Tiny G J Meeuwsen-de Boer, Harm J Lourens, Sergi Guerrero Llobet, Marlinde J Smit, Lorian Slagter-Menkema, Annika Seitz, Corrie E M Gidding, Esther Hulleman, Pieter Wesseling, Lisethe Meijer, Leon C van Kempen, Anke van den Berg, Daniël O Warmerdam, Frank A E Kruyt, Floris Foijer, Marcel A T M van Vugt, Wilfred F A den Dunnen, Eelco W Hoving, Victor Guryev, Eveline S J M de Bont, Sophia W M Bruggeman
The brain cancer medulloblastoma consists of different transcriptional subgroups. To characterize medulloblastoma at the phosphoprotein-signaling level, we performed high-throughput peptide phosphorylation profiling on a large cohort of SHH (Sonic Hedgehog), group 3, and group 4 medulloblastomas. We identified two major protein-signaling profiles. One profile was associated with rapid death post-recurrence and resembled MYC-like signaling for which MYC lesions are sufficient but not necessary. The second profile showed enrichment for DNA damage, as well as apoptotic and neuronal signaling...
March 20, 2018: Cell Reports
Xiaowei Wu, Changxin Li, Jinming Mao, Ling Li, Yan Liu, Yao Hou
The aim of this study was to find related pathogenic genes in cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy in (CADASIL)-like patients. The direct sequencing and high-throughput multiplex polymerase chain reaction (PCR) was performed to screen for related genes. The clinical and imaging data of a CADASIL-like patient (the pro-band) and his family members were collected. At first, the known hereditary cerebral vascular genes of the pro-band were screened with direct sequencing to find candidate gene mutations...
March 15, 2018: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
Svetlana Ferreira Lima, Marcela Lucas de Souza Bicalho, Rodrigo Carvalho Bicalho
Amplicon sequencing technique has been increasingly applied to the clinical setting as a sensitive diagnostic tool. Therefore, it is of great importance to develop a DNA extraction method that accurate isolates DNA from complex host-associated microbiota. Given the multifactorial etiology of clinical mastitis and the diversified lifestyle of bacterial species harboring in milk, here four distinct milk sample fractions: raw whole milk, milk fat, casein-pellet, and casein-pellet + fat from healthy cows and cows with clinical mastitis, were subjected to bead-beating DNA extraction, followed by high-throughput sequencing...
2018: PloS One
Beatrice Xuan Ho, Nicole Min Qian Pek, Boon-Seng Soh
The rising interest in human induced pluripotent stem cell (hiPSC)-derived organoid culture has stemmed from the manipulation of various combinations of directed multi-lineage differentiation and morphogenetic processes that mimic organogenesis. Organoids are three-dimensional (3D) structures that are comprised of multiple cell types, self-organized to recapitulate embryonic and tissue development in vitro. This model has been shown to be superior to conventional two-dimensional (2D) cell culture methods in mirroring functionality, architecture, and geometric features of tissues seen in vivo...
March 21, 2018: International Journal of Molecular Sciences
Marta Maciejewska, Magdalena Całusińska, Luc Cornet, Delphine Adam, Igor S Pessi, Sandrine Malchair, Philippe Delfosse, Denis Baurain, Hazel A Barton, Monique Carnol, Sébastien Rigali
Moonmilk are cave carbonate deposits that host a rich microbiome, including antibiotic-producing Actinobacteria, making these speleothems appealing for bioprospecting. Here, we investigated the taxonomic profile of the actinobacterial community of three moonmilk deposits of the cave "Grotte des Collemboles" via high-throughput sequencing of 16S rRNA amplicons. Actinobacteria was the most common phylum after Proteobacteria, ranging from 9% to 23% of the total bacterial population. Next to actinobacterial operational taxonomic units (OTUs) attributed to uncultured organisms at the genus level (~44%), we identified 47 actinobacterial genera with Rhodoccocus (4 OTUs, 17%) and Pseudonocardia (9 OTUs, ~16%) as the most abundant in terms of the absolute number of sequences...
March 21, 2018: Antibiotics
Xia Liu, Yongdong Xu, Zhi Li, Shengwei Jiang, Shuo Yao, Rina Wu, Yingfeng An
A silica sands-based method has been developed to isolate high quality genomic DNAs from cells of animals, plants and microorganisms, such as Hemisalanx prognathus, Spinacia oleracea, Pichia pastoris, Bacillus licheniformis and Escherichia coli. To the best of our knowledge, no DNA isolation method has so wide application until now. In addition, this method and a commercially available kit were compared in analysis of microbial communities using high-throughput 16 s rDNA sequencing. As a result, the silica sands-based method was found to be even more efficient in isolating genomic DNA from gram-positive bacteria than the kit, indicating that it would become a very valuable choice to faithfully reflect the composition of microbial communities...
March 21, 2018: Preparative Biochemistry & Biotechnology
Forough Ghasemi, M Reza Hormozi-Nezhad, Morteza Mahmoudi
Monitoring the ratio of 40- and 42-residue amyloid β peptides (i.e., Aβ40 and Aβ42) in human plasma is considered one of the hallmarks of detection of the early stage of Alzheimer's disease (AD). Therefore, development of a specific, yet non-antibody-based method for simultaneous detection of Aβ40 and Aβ42 may have considerable clinical applications. Here, we developed a 'nanoparticle-based colorimetric sensor array' utilizing label-free gold and silver nanoparticles for visual detection of Aβ42 and Aβ40...
March 21, 2018: Nanoscale
Inuk Jung, Hyejin Kang, Jang Uk Kim, Hyeonsook Chang, Sun Kim, Woosuk Jung
BACKGROUND: Ginseng is a popular traditional herbal medicine in north-eastern Asia. It has been used for human health for over thousands of years. With the rise in global temperature, the production of Korean ginseng (Panax ginseng C.A.Meyer) in Korea have migrated from mid to northern parts of the Korean peninsula to escape from the various higher temperature related stresses. Under the high ambient temperature, vegetative growth was accelerated, which resulted in early flowering. This precocious phase change led to yield loss...
March 19, 2018: BMC Systems Biology
Minseok Kwon, Sangseob Leem, Joon Yoon, Taesung Park
BACKGROUND: With the rapid advancement of array-based genotyping techniques, genome-wide association studies (GWAS) have successfully identified common genetic variants associated with common complex diseases. However, it has been shown that only a small proportion of the genetic etiology of complex diseases could be explained by the genetic factors identified from GWAS. This missing heritability could possibly be explained by gene-gene interaction (epistasis) and rare variants. There has been an exponential growth of gene-gene interaction analysis for common variants in terms of methodological developments and practical applications...
March 19, 2018: BMC Systems Biology
Doulaye Dembélé
High-throughput biological technologies are routinely used to generate gene expression profiling or cytogenetics data. To achieve high performance, methods available in the literature become more specialized and often require high computational resources. Here, we propose a new versatile method based on the data-ordering rank values. We use linear algebra, the Perron-Frobenius theorem and also extend a method presented earlier for searching differentially expressed genes for the detection of recurrent copy number aberration...
January 1, 2018: Statistical Methods in Medical Research
Paul P Jung, Zhi Zhang, Nicole Paczia, Christian Jaeger, Tomasz Ignac, Patrick May, Carole L Linster
Aging is a complex trait of broad scientific interest, especially because of its intrinsic link with common human diseases. Pioneering work on aging-related mechanisms has been made in Saccharomyces cerevisiae , mainly through the use of deletion collections isogenic to the S288c reference strain. In this study, using a recently published high-throughput approach, we quantified chronological life span (CLS) within a collection of 58 natural strains across seven different conditions. We observed a broad aging variability suggesting the implication of diverse genetic and environmental factors in chronological aging control...
2018: NPJ Aging and Mechanisms of Disease
Keshi Ma, Wenshuo Shi, Mengyue Xu, Jiaxi Liu, Feixiong Zhang
It remains unclear whether plant lncRNAs are responsive to Ca2+ -channel blocking. When using the Ca2+ -channel blocker, LaCl3 , to treat germinated wheat seeds for 24 h, we found that both root length and mitosis were inhibited in the LaCl3 -treated groups. The effect of the Ca2+ -channel blocker was verified in three ways: a [Ca2+ ]cyt decrease detected using Fluo-3/AM staining, a decrease in the Ca content measured using inductively coupled plasma mass spectrometry, and an inhibition of Ca2+ influx detected using Non-invasive Micro-test Technology...
2018: Frontiers in Plant Science
Qiannan Peng, Shuaiming Jiang, Jieling Chen, Chenchen Ma, Dongxue Huo, Yuyu Shao, Jiachao Zhang
Fermented vegetables are typically traditional foods made of fresh vegetables and their juices, which are fermented by beneficial microorganisms. Herein, we applied high-throughput sequencing and culture-dependent technology to describe the diversities of microbiota and identify core microbiota in fermented vegetables from different areas of Hainan Province, and abundant metabolic pathways in the fermented vegetables were simultaneously predicted. At the genus level, Lactobacillus bacteria were the most abundant...
2018: Frontiers in Microbiology
Melissa L Sykes, Vicky M Avery
Using high throughput, high-content imaging, a proprietary library was screened against intracellular Trypanosoma cruzi amastigotes to identify compounds with novel activity against the parasite. Five inhibitors were discovered, which did not clear all of the parasites from 3T3 host cells following 48 hours exposure, and were identified as putative T. cruzi cytochrome P450 (TcCYP51) inhibitors. TcCYP51 inhibitors are not favourable for the drug discovery pipeline for treatment of Chagas Disease infection due to clinical and pre-clinical failures...
March 20, 2018: Scientific Reports
Daniel Maticzka, Ibrahim Avsar Ilik, Tugce Aktas, Rolf Backofen, Asifa Akhtar
RNA-binding proteins (RBPs) play important and essential roles in eukaryotic gene expression regulating splicing, localization, translation, and stability of mRNAs. We describe ultraviolet crosslinking and affinity purification (uvCLAP), an easy-to-use, robust, reproducible, and high-throughput method to determine in vivo targets of RBPs. uvCLAP is fast and does not rely on radioactive labeling of RNA. We investigate binding of 15 RBPs from fly, mouse, and human cells to test the method's performance and applicability...
March 20, 2018: Nature Communications
Xiang Li, Erchang Shang, Qiang Dong, Yingfeng Li, Jing Zhang, Shaohua Xu, Zuodong Zhao, Wei Shao, Cong Lv, Yong Zheng, Hailin Wang, Xiaoguang Lei, Bing Zhu, Zhuqiang Zhang
Regulation of gene expression by epigenetic modifications such as DNA methylation is crucial for developmental and disease processes, including cell differentiation and cancer development. Genes repressed by DNA methylation can be derepressed by various compounds that target DNA methyltransferases, histone deacetylases, and other regulatory factors. However, some additional, unknown mechanisms that promote DNA methylation-mediated gene silencing may exist. Chemical agents that can counteract the effects of epigenetic repression that is not regulated by DNA methyltransferases or histone deacetylases therefore may be of research interest...
March 20, 2018: Journal of Biological Chemistry
Jun Luo, Junping Yu, Hang Yang, Hongping Wei
OBJECTIVE: The methods combining culture and quantitative PCR(qPCR) offer new solutions for rapid antibiotic susceptibility testing(AST). However, the multiple steps of DNA extraction and cold storage of PCR reagents needed make them unsuitable for rapid high throughput AST. In this study, a parallel culture-qPCR method was developed to overcome above problems. METHOD: In this method, bacteria culture and DNA extraction automatically and simultaneously completed through using a common PCR instrument as a controllable heating device...
March 17, 2018: International Journal of Infectious Diseases: IJID
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