keyword
MENU ▼
Read by QxMD icon Read
search

Library construction

keyword
https://www.readbyqxmd.com/read/28813447/the-use-of-high-throughput-small-rna-sequencing-reveals-differentially-expressed-micrornas-in-response-to-aster-yellows-phytoplasma-infection-in-vitis-vinifera-cv-chardonnay
#1
Marius C Snyman, Marie-Chrystine Solofoharivelo, Rose Souza-Richards, Dirk Stephan, Shane Murray, Johan T Burger
Phytoplasmas are cell wall-less plant pathogenic bacteria responsible for major crop losses throughout the world. In grapevine they cause grapevine yellows, a detrimental disease associated with a variety of symptoms. The high economic impact of this disease has sparked considerable interest among researchers to understand molecular mechanisms related to pathogenesis. Increasing evidence exist that a class of small non-coding endogenous RNAs, known as microRNAs (miRNAs), play an important role in post-transcriptional gene regulation during plant development and responses to biotic and abiotic stresses...
2017: PloS One
https://www.readbyqxmd.com/read/28807055/transcriptomic-profiling-of-microbe-microbe-interactions-reveals-the-specific-response-of-the-biocontrol-strain-p-fluorescens-in5-to-the-phytopathogen-rhizoctonia-solani
#2
Rosanna C Hennessy, Mikkel A Glaring, Stefan Olsson, Peter Stougaard
BACKGROUND: Few studies to date report the transcriptional response of biocontrol bacteria toward phytopathogens. In order to gain insights into the potential mechanism underlying the antagonism of the antimicrobial producing strain P. fluorescens In5 against the phytopathogens Rhizoctonia solani and Pythium aphanidermatum, global RNA sequencing was performed. METHODS: Differential gene expression profiling of P. fluorescens In5 in response to either R. solani or P...
August 10, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28806924/essential-genome-of-campylobacter-jejuni
#3
Rabindra K Mandal, Tieshan Jiang, Young Min Kwon
BACKGROUND: Campylobacter species are a leading cause of bacterial foodborne illness worldwide. Despite the global efforts to curb them, Campylobacter infections have increased continuously in both developed and developing countries. The development of effective strategies to control the infection by this pathogen is warranted. The essential genes of bacteria are the most prominent targets for this purpose. In this study, we used transposon sequencing (Tn-seq) of a genome-saturating library of Tn5 insertion mutants to define the essential genome of C...
August 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28805368/pyrophosphate-recognition-and-sensing-in-water-using-bis-zinc-ii-dipicolylamino-functionalized-peptides
#4
Katrina A Jolliffe
Phosphate oxoanions and phosphorylated biomolecules (such as nucleotides, lipids, and proteins) play key roles in a wide range of biological processes. The ability to selectively detect these ions in the presence of each other has numerous applications in biochemistry and biomedicine. However, receptors and sensors that can discriminate between polyphosphate species with high selectivity and in biologically relevant conditions are rare. In this Account, we show how peptides (both cyclic and linear) can be used to position two zinc(II)dipicolylamine [Zn(II)DPA] binding sites in an appropriate arrangement to provide selective binding of pyrophosphate (PPi) in the presence of other polyphosphate species, including ATP, and in complex media such as cell growth buffer...
August 14, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28804478/the-entomopathogenic-fungi-isaria-fumosorosea-plays-a-vital-role-in-suppressing-the-immune-system-of-plutella-xylostella-rna-seq-and-dge-analysis-of-immunity-related-genes
#5
Jin Xu, Xiaoxia Xu, Muhammad Shakeel, Shuzhong Li, Shuang Wang, Xianqiang Zhou, Jialin Yu, Xiaojing Xu, Xiaoqiang Yu, Fengliang Jin
Most, if not all, entomopathogenic fungi have been used as alternative control agents to decrease the insect resistance and harmful effects of the insecticides on the environment. Among them, Isaria fumosorosea has also shown great potential to control different insect pests. In the present study, we explored the immune response of P. xylostella to the infection of I. fumosorosea at different time points by using RNA-Sequencing and differential gene expression technology at the genomic level. To gain insight into the host-pathogen interaction at the genomic level, five libraries of P...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28803463/bacterial-microcolonies-in-gel-beads-for-high-throughput-screening-of-libraries-in-synthetic-biology
#6
José M Duarte, Içvara Barbier, Yolanda Schaerli
Synthetic biologists increasingly rely on directed evolution to optimize engineered biological systems. Applying an appropriate screening or selection method for identifying the potentially rare library members with the desired properties is a crucial step for success in these experiments. Special challenges include substantial cell-to-cell variability and the requirement to check multiple states (e.g. being ON or OFF depending on the input). Here, we present a high-throughput screening method that addresses these challenges...
August 14, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28801904/constructing-strong-cell-type-specific-promoters-through-informed-design
#7
Adam J Brown, David C James
Promoter functionality is highly context dependent, as exemplified by gene-specific expression profiles across different tissues and cell types. Cell type-specific promoter regulation is a function of each cell's unique complement of transcriptional machinery components. Accordingly, to achieve high levels of transcriptional activity within a particular cell type, synthetic promoters must be specifically designed to harness those cells discrete repertoire of available transcription factors . Here, we describe a method for constructing very strong cell type-specific synthetic promoters for use in any given mammalian host cell...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28801902/bioinformatically-informed-design-of-synthetic-mammalian-promoters
#8
Michael L Roberts, Polyxeni Katsoupi, Vivian Tseveleki, Era Taoufik
Synthetic promoters have been developed in a number of different organisms and are capable of mediating specific and enhanced levels of gene expression. Typically, cis-regulatory regions from a few genes are randomly combined to generate a synthetic promoter library, and the sequences with the highest activity are selected for in target cell lines. Here we describe a novel approach that can be employed in the construction of synthetic promoters . Specifically, we use gene expression profiles obtained from microarray datasets to select the cis-regulatory elements that comprise the synthetic promoter library...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28801417/optic-nerve-sheath-diameter-sonography-for-the-diagnosis-of-increased-intracranial-pressure-a-systematic-review-and-meta-analysis-protocol
#9
Alex Koziarz, Niv Sne, Fraser Kegel, Waleed Alhazzani, Siddharth Nath, Jetan H Badhiwala, Timothy Rice, Paul Engels, Faidi Samir, Andrew Healey, Kamyar Kahnamoui, Laura Banfield, Sunjay Sharma, Kesava Reddy, Gregory W J Hawryluk, Andrew W Kirkpatrick, Saleh A Almenawer
INTRODUCTION: Increased intracranial pressure (ICP) is a significant neurological issue that may lead to permanent neurological sequelae. When evaluating patients with traumatic brain injury, it is crucial to identify those with high ICP in order to expedite ICP lowering measures and maintain adequate cerebral perfusion. Several measures are used to recognise patients with increased ICP including CT scan, MRI, ICP monitor, and lumbar puncture (LP). However, these tests can be invasive, associated with radiation exposure, contraindicated, or not readily available...
August 11, 2017: BMJ Open
https://www.readbyqxmd.com/read/28800965/the-crispr-cas9-facilitated-multiplex-pathway-optimization-cfpo-technique-and-its-application-to-improve-the-escherichia-coli-xylose-utilization-pathway
#10
Xinna Zhu, Dongdong Zhao, Huanna Qiu, Feiyu Fan, Shuli Man, Changhao Bi, Xueli Zhang
One of the most important research subjects of metabolic engineering is the pursuit of balanced metabolic pathways, which requires the modulation of expression of many genes. However, simultaneously modulating multiple genes on the chromosome remains challenging in prokaryotic organisms, including the industrial workhorse - Escherichia coli. In this work, the CRISPR/Cas9-facilitated multiplex pathway optimization (CFPO) technique was developed to simultaneously modulate the expression of multiple genes on the chromosome...
August 9, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28798837/automated-modification-and-fusion-of-voxel-models-to-construct-body-phantoms-with-heterogeneous-breast-tissue-application-to-mri-simulations
#11
Joseph V Rispoli, Steven M Wright, Craig R Malloy, Mary P McDougall
BACKGROUND: Human voxel models incorporating detailed anatomical features are vital tools for the computational evaluation of electromagnetic (EM) fields within the body. Besides whole-body human voxel models, phantoms representing smaller heterogeneous anatomical features are often employed; for example, localized breast voxel models incorporating fatty and fibroglandular tissues have been developed for a variety of EM applications including mammography simulation and dosimetry, magnetic resonance imaging (MRI), and ultra-wideband microwave imaging...
2017: Journal of Biomedical Graphics and Computing
https://www.readbyqxmd.com/read/28795278/frozen-tissue-preparation-for-high-resolution-multiplex-histological-analyses-of-human-brain-specimens
#12
Fangjie Shao, Wenhong Jiang, Qingqing Gao, Baizhou Li, Chongran Sun, Qiyuan Wang, Qin Chen, Bing Sun, Hong Shen, Keqing Zhu, Jianmin Zhang, Chong Liu
The availability of a comprehensive tissue library is essential for elucidating the function and pathology of human brains. Considering the irreplaceable status of the formalin-fixation-paraffin-embedding (FFPE) preparation in routine pathology and the advantage of ultra-low temperature to preserve nucleic acids and proteins for multi-omics studies, these methods have become major modalities for the construction of brain tissue libraries. Nevertheless, the use of FFPE and snap-frozen samples is limited in high-resolution histological analyses because the preparation destroys tissue integrity and/or many important cellular markers...
August 9, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28791871/toward-an-architecture-of-attachment-disorganization-john-bowlby-s-published-and-unpublished-reflections
#13
Judith Solomon, Robbie Duschinsky, Lianne Bakkum, Carlo Schuengel
This article examines the construct of disorganized attachment originally proposed by Main and Solomon, developing some new conjectures based on inspiration from a largely unknown source: John Bowlby's unpublished texts, housed at the Wellcome Trust Library Archive in London (with permission from the Bowlby family). We explore Bowlby's discussions of disorganized attachment, which he understood from the perspective of ethological theories of conflict behavior. Bowlby's reflections regarding differences among the behaviors used to code disorganized attachment will be used to explore distinctions that may underlie the structure of the current coding system...
August 1, 2017: Clinical Child Psychology and Psychiatry
https://www.readbyqxmd.com/read/28791211/development-and-characterization-of-polymorphic-est-based-ssr-markers-in-barley-hordeum-vulgare
#14
Won-Sam Jo, Hye-Yeong Kim, Kyung-Min Kim
In barley, breeding using good genetic characteristics can improve the quality or quantity of crop characters from one generation to the next generation. The development of effective molecular markers in barley is crucial for understanding and analyzing the diversity of useful alleles. In this study, we conducted genetic relationship analysis using expressed sequence tag-simple sequence repeat (EST-SSR) markers for barley identification and assessment of barley cultivar similarity. Seeds from 82 cultivars, including 31 each of naked and hulled barley from the Korea Seed and Variety Service and 20 of malting barley from the RDA-Genebank Information Center, were analyzed in this study...
August 2017: 3 Biotech
https://www.readbyqxmd.com/read/28791203/development-and-characterization-of-microsatellite-primers-for-zanthoxylum-schinifolium-rutaceae
#15
Young Mi Kim, Aruna Jo, Ji Hee Jeong, Yong Rak Kwon, Ho Bang Kim
PREMISE OF THE STUDY: Polymorphic microsatellite markers of Zanthoxylum schinifolium (Rutaceae), a promising medicinal plant with effective antibacterial, anticancer, and anti-inflammatory compounds, were developed and evaluated for further genetic studies based on genetic variation among individuals or populations. METHODS AND RESULTS: Following the selective hybridization method, microsatellite-enrichment libraries were constructed. Using these libraries, we obtained 15 polymorphic and three monomorphic microsatellite markers for Z...
July 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28790989/a-proposal-for-a-structural-model-of-the-feline-calicivirus-protease-bound-to-the-substrate-peptide-under-physiological-conditions
#16
Masaru Yokoyama, Tomoichiro Oka, Hirotaka Takagi, Hirotatsu Kojima, Takayoshi Okabe, Tetsuo Nagano, Yukinobu Tohya, Hironori Sato
Feline calicivirus (FCV) protease functions to cleave viral precursor proteins during productive infection. Previous studies have mapped a protease-coding region and six cleavage sites in viral precursor proteins. However, how the FCV protease interacts with its substrates remains unknown. To gain insights into the interactions, we constructed a molecular model of the FCV protease bound with the octapeptide containing a cleavage site of the capsid precursor protein by homology modeling and docking simulation...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28790814/bacteriological-incidence-in-pneumonia-patients-with-pulmonary-emphysema-a-bacterial-floral-analysis-using-the-16s-ribosomal-rna-gene-in-bronchoalveolar-lavage-fluid
#17
Keisuke Naito, Kei Yamasaki, Kazuhiro Yatera, Kentaro Akata, Shingo Noguchi, Toshinori Kawanami, Kazumasa Fukuda, Takashi Kido, Hiroshi Ishimoto, Hiroshi Mukae
Pulmonary emphysema is an important radiological finding in chronic obstructive pulmonary disease patients, but bacteriological differences in pneumonia patients according to the severity of emphysematous changes have not been reported. Therefore, we evaluated the bacteriological incidence in the bronchoalveolar lavage fluid (BALF) of pneumonia patients using cultivation and a culture-independent molecular method. Japanese patients with community-acquired pneumonia (83) and healthcare-associated pneumonia (94) between April 2010 and February 2014 were evaluated...
2017: International Journal of Chronic Obstructive Pulmonary Disease
https://www.readbyqxmd.com/read/28789787/relationship-between-perceived-fatigue-and-performance-fatigability-in-people-with-multiple-sclerosis-a-systematic-review-and-meta-analysis
#18
REVIEW
Bryan D Loy, Ruby L Taylor, Brett W Fling, Fay B Horak
BACKGROUND: Perceived fatigue (i.e., subjective perception of reduced capacity) is one of the most common and disabling symptoms for people with multiple sclerosis (MS). Perceived fatigue may also be related to performance fatigability (i.e., decline in physical performance over time), although study findings have been inconsistent. OBJECTIVE: To locate all studies reporting the relationship between perceived fatigue and fatigability in people with MS, determine the population correlation, and examine moderating variables of the correlation size...
September 2017: Journal of Psychosomatic Research
https://www.readbyqxmd.com/read/28789614/comparative-transcriptome-analysis-reveals-key-cadmium-transport-related-genes-in-roots-of-two-pak-choi-brassica-rapa-l-ssp-chinensis-cultivars
#19
Rugang Yu, Dan Li, Xueling Du, Shenglan Xia, Caifeng Liu, Gangrong Shi
BACKGROUND: Cadmium translocation from roots to shoots is a complex biological process that is controlled by gene regulatory networks. Pak choi exhibits wide cultivar variations in Cd accumulation. However, the molecular mechanism involved in cadmium translocation and accumulation is still unclear. To isolate differentially expressed genes (DEGs) involved in transporter-mediated regulatory mechanisms of Cd translocation in two contrasting pak choi cultivars, Baiyewuyueman (B, high Cd accumulator) and Kuishan'aijiaoheiye (K, low Cd accumulator), eight cDNA libraries from the roots of two cultivars were constructed and sequenced by RNA-sequencing...
August 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28771149/culture-independent-methods-reveal-high-diversity-of-oxa-48-like-genes-in-water-environments
#20
Marta Tacão, Isabel Silva, Isabel Henriques
The carbapenemase OXA-48 was identified for the first time in 2001 and is now one of the greatest concerns in terms of antibiotic resistance. While many studies report clinical OXA-48-like producers, few reports refer blaOXA-48-like genes in environmental bacteria. The main goal of this study was to evaluate the diversity of blaOXA-48-like genes in aquatic systems, using culture-independent approaches. For that, environmental DNA was obtained from riverine and estuarine water and used to construct clone libraries of blaOXA-48-like gene polymerase chain reaction amplicons...
August 2017: Journal of Water and Health
keyword
keyword
52573
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"