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https://www.readbyqxmd.com/read/28203245/small-rnas-derived-from-the-t-dna-of-agrobacterium-rhizogenes-in-hairy-roots-of-phaseolus-vulgaris
#1
Pablo Peláez, Alejandrina Hernández-López, Georgina Estrada-Navarrete, Federico Sanchez
Agrobacterium rhizogenes is a pathogenic bacteria that causes hairy root disease by transferring bacterial DNA into the plant genome. It is an essential tool for industry and research due to its capacity to produce genetically modified roots and whole organisms. Here, we identified and characterized small RNAs generated from the transfer DNA (T-DNA) of A. rhizogenes in hairy roots of common bean (Phaseolus vulgaris). Distinct abundant A. rhizogenes T-DNA-derived small RNAs (ArT-sRNAs) belonging to several oncogenes were detected in hairy roots using high-throughput sequencing...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28198902/microvalve-based-bioprinting-process-bio-inks-and-applications
#2
REVIEW
Wei Long Ng, Jia Min Lee, Wai Yee Yeong, May Win Naing
Bioprinting is an emerging research field that has attracted tremendous attention for various applications; it offers a highly automated, advanced manufacturing platform for the fabrication of complex bioengineered constructs. Different bio-inks comprising multiple types of printable biomaterials and cells are utilized during the bioprinting process to improve the homology to native tissues and/or organs in a highly reproducible manner. This paper, presenting a first-time comprehensive yet succinct review of microvalve-based bioprinting, provides an in-depth analysis and comparison of different drop-on-demand bioprinting systems and highlights the important considerations for microvalve-based bioprinting systems...
February 15, 2017: Biomaterials Science
https://www.readbyqxmd.com/read/28197907/regulation-of-cellular-processes-by-sumo-understudied-topics
#3
Jorrit M Enserink
SUMO plays a multiple role in maintenance of cellular homeostasis, both under normal conditions and under cell stress . Considerable effort has been devoted to unraveling the functions of SUMO in regulation of transcription and preservation of genome stability. However, it is clear from high-throughput SUMO proteome studies that SUMO likely regulates many more cellular processes. The function of SUMO in these processes has hardly been explored. This review will focus on the emerging function of SUMO in regulation of several of these processes...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28194764/commentary-what-is-the-case-for-candidate-gene-approaches-in-the-era-of-high-throughput-genomics-a-response-to-border-and-keller-2017
#4
Sarah R Moore
Border and Keller argue that candidate gene approaches are outdated and out-of-touch with the current understanding of the genetic architecture of complex behavioral traits and should be abandoned in favor of unbiased, genome-wide approaches. Border and Keller further suggest that a candidate gene should not be selected for in-depth investigation unless identified by a well-powered genome-wide association study (GWAS). An alternative perspective is offered that candidate approaches can be sensible for developmental and deep-phenotyping studies aimed at elucidating particular biological pathways responsible for the emergence of psychological phenotypes, and that candidates should not necessarily be expected to be confirmed by, or solely selected based on, GWAS...
March 2017: Journal of Child Psychology and Psychiatry, and Allied Disciplines
https://www.readbyqxmd.com/read/28191931/laser-synthesis-and-processing-of-colloids-fundamentals-and-applications
#5
Dongshi Zhang, Bilal Gökce, Stephan Barcikowski
Driven by functionality and purity demand for applications of inorganic nanoparticle colloids in optics, biology, and energy, their surface chemistry has become a topic of intensive research interest. Consequently, ligand-free colloids are ideal reference materials for evaluating the effects of surface adsorbates from the initial state for application-oriented nanointegration purposes. After two decades of development, laser synthesis and processing of colloids (LSPC) has emerged as a convenient and scalable technique for the synthesis of ligand-free nanomaterials in sealed environments...
February 13, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28188894/emerging-rna-editing-biomarkers-will-foster-drug-development
#6
REVIEW
Siem van der Laan, Nicolas Salvetat, Dinah Weissmann, Franck Molina
Unanticipated adverse drug reactions (ADRs) on the central nervous system are a major cause of clinical attrition and market withdrawal. Current practices for their prospective assessment still lean on extensive analysis of rodent behaviour despite their highly controversial predictive value. Human-derived in vitro models that objectively quantify mechanism-related biomarkers can greatly contribute to better ADR prediction at early developmental stages. Adenosine-to-inosine RNA editing constitutes a physiological cellular process that translates environmental cues by regulating protein function at the synaptic level in health and disease...
February 7, 2017: Drug Discovery Today
https://www.readbyqxmd.com/read/28187425/computational-lipidomics-and-lipid-bioinformatics-filling-in-the-blanks
#7
Josch Pauling, Edda Klipp
Lipids are highly diverse metabolites of pronounced importance in health and disease. While metabolomics is a broad field under the omics umbrella that may also relate to lipids, lipidomics is an emerging field which specializes in the identification, quantification and functional interpretation of complex lipidomes. Today, it is possible to identify and distinguish lipids in a high-resolution, high-throughput manner and simultaneously with a lot of structural detail. However, doing so may produce thousands of mass spectra in a single experiment which has created a high demand for specialized computational support to analyze these spectral libraries...
December 22, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28176006/development-of-a-high-throughput-colorimetric-zika-virus-infection-assay
#8
Janis A Müller, Mirja Harms, Axel Schubert, Benjamin Mayer, Stephanie Jansen, Jean-Philippe Herbeuval, Detlef Michel, Thomas Mertens, Olli Vapalahti, Jonas Schmidt-Chanasit, Jan Münch
Zika virus (ZIKV) is an emerging pathogen that causes congenital infections which may result in birth defects, such as microcephaly. Currently, no approved treatment or vaccination is available. ZIKV can be readily detected in cell culture where virally infected cells are normally stained by specific antibodies. As ZIKV regularly causes a cytopathic effect, we were wondering whether this viral property can be used to quantitatively determine viral infectivity. We here describe the use of an 3-[4,5-dimethyl-2-thiazolyl]-2,5-diphenyl-2H-tetrazolium bromide-(MTT)-based cell viability assay that allows to determine ZIKV-induced cell death...
February 7, 2017: Medical Microbiology and Immunology
https://www.readbyqxmd.com/read/28174021/biogenesis-and-function-of-ago-associated-rnas
#9
REVIEW
Iben Daugaard, Thomas Birkballe Hansen
Numerous sophisticated high-throughput sequencing technologies have been developed over the past decade, and these have enabled the discovery of a diverse catalog of small non-coding (nc)RNA molecules that function as regulatory entities by associating with Argonaute (Ago) proteins. MicroRNAs (miRNAs) are currently the best-described class of post-transcriptional regulators that follow a specific biogenesis pathway characterized by Drosha/DGCR8 and Dicer processing. However, more exotic miRNA-like species that bypass particular steps of the canonical miRNA biogenesis pathway continue to emerge, with one of the most recent additions being the agotrons, which escape both Drosha/DGCR8- and Dicer-processing...
February 4, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28158969/diversity-analysis-of-cotton-gossypium-hirsutum-l-germplasm-using-the-cottonsnp63k-array
#10
Lori L Hinze, Amanda M Hulse-Kemp, Iain W Wilson, Qian-Hao Zhu, Danny J Llewellyn, Jen M Taylor, Andrew Spriggs, David D Fang, Mauricio Ulloa, John J Burke, Marc Giband, Jean-Marc Lacape, Allen Van Deynze, Joshua A Udall, Jodi A Scheffler, Steve Hague, Jonathan F Wendel, Alan E Pepper, James Frelichowski, Cindy T Lawley, Don C Jones, Richard G Percy, David M Stelly
BACKGROUND: Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured...
February 3, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28158186/a-high-throughput-phenotypic-screen-identifies-clofazimine-as-a-potential-treatment-for-cryptosporidiosis
#11
Melissa S Love, Federico C Beasley, Rajiv S Jumani, Timothy M Wright, Arnab K Chatterjee, Christopher D Huston, Peter G Schultz, Case W McNamara
Cryptosporidiosis has emerged as a leading cause of non-viral diarrhea in children under five years of age in the developing world, yet the current standard of care to treat Cryptosporidium infections, nitazoxanide, demonstrates limited and immune-dependent efficacy. Given the lack of treatments with universal efficacy, drug discovery efforts against cryptosporidiosis are necessary to find therapeutics more efficacious than the standard of care. To date, cryptosporidiosis drug discovery efforts have been limited to a few targeted mechanisms in the parasite and whole cell phenotypic screens against small, focused collections of compounds...
February 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28155690/high-dimensional-omics-data-analysis-using-a-variable-screening-protocol-with-prior-knowledge-integration-ski
#12
Cong Liu, Jianping Jiang, Jianlei Gu, Zhangsheng Yu, Tao Wang, Hui Lu
BACKGROUND: High-throughput technology could generate thousands to millions biomarker measurements in one experiment. However, results from high throughput analysis are often barely reproducible due to small sample size. Different statistical methods have been proposed to tackle this "small n and large p" scenario, for example different datasets could be pooled or integrated together to provide an effective way to improve reproducibility. However, the raw data is either unavailable or hard to integrate due to different experimental conditions, thus there is an emerging need to develop a method for "knowledge integration" in high-throughput data analysis...
December 23, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28145469/high-throughput-screen-detects-calcium-signaling-dysfunction-in-typical-sporadic-autism-spectrum-disorder
#13
Galina Schmunk, Rachel L Nguyen, David L Ferguson, Kenny Kumar, Ian Parker, J Jay Gargus
Autism spectrum disorder (ASD) is a heterogeneous group of neurodevelopmental disorders without any defined uniting pathophysiology. Ca(2+) signaling is emerging as a potential node in the genetic architecture of the disorder. We previously reported decreased inositol trisphosphate (IP3)-mediated Ca(2+) release from the endoplasmic reticulum in several rare monogenic syndromes highly comorbid with autism - fragile X and tuberous sclerosis types 1 and 2 syndromes. We now extend those findings to a cohort of subjects with sporadic ASD without any known mutations...
February 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28142321/understanding-human-autoimmunity-and-autoinflammation-through-transcriptomics
#14
Romain Banchereau, Alma-Martina Cepika, Jacques Banchereau, Virginia Pascual
Transcriptomics, the high-throughput characterization of RNAs, has been instrumental in defining pathogenic signatures in human autoimmunity and autoinflammation. It enabled the identification of new therapeutic targets in IFN-, IL-1- and IL-17-mediated diseases. Applied to immunomonitoring, transcriptomics is starting to unravel diagnostic and prognostic signatures that stratify patients, track molecular changes associated with disease activity, define personalized treatment strategies, and generally inform clinical practice...
January 30, 2017: Annual Review of Immunology
https://www.readbyqxmd.com/read/28139751/no-effect-of-bt-cry1ie-toxin-on-bacterial-diversity-in-the-midgut-of-the-chinese-honey-bees-apis-cerana-cerana-hymenoptera-apidae
#15
Hui-Ru Jia, Ping-Li Dai, Li-Li Geng, Cameron J Jack, Yun-He Li, Yan-Yan Wu, Qing-Yun Diao, James D Ellis
Cry1Ie protein derived from Bacillus thuringiensis (Bt) has been proposed as a promising candidate for the development of a new Bt-maize variety to control maize pests in China. We studied the response of the midgut bacterial community of Apis cerana cerana to Cry1Ie toxin under laboratory conditions. Newly emerged bees were fed one of the following treatments for 15 and 30 days: three concentrations of Cry1Ie toxin (20 ng/mL, 200 ng/mL, and 20 μg/mL) in sugar syrup, pure sugar syrup as a negative control and 48 ng/mL imidacloprid as a positive control...
January 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28137568/drug-target-identification-using-an-itraq-based-quantitative-chemical-proteomics-approach-based-on-a-target-profiling-study-of-andrographolide
#16
J Wang, Y K Wong, J Zhang, Y-M Lee, Z-C Hua, H-M Shen, Q Lin
Identifying the cellular binding targets of drugs and other bioactive small molecules is a crucial step for understanding their molecular mechanisms of action as well as potential off-target effects. The field of chemical proteomics is an emerging discipline in chemical biology using synthetic chemistry and high-throughput detection techniques to study small molecule-protein interactions. In this chapter, we describe a quantitative chemical proteomics protocol combining bioorthogonal click chemistry and quantitation by isobaric tags for relative and absolute quantification (iTRAQ) to identify the specific binding targets of drugs and bioactive small molecules such as natural products...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28137240/ascidians-an-emerging-marine-model-for-drug-discovery-and-screening
#17
Rémi Dumollard, Ievgeniia Gazo, Isa D L Gomes, Lydia Besnardeau, Alex McDougall
Ascidians (tunicates; sea squirts) are marine animals which provide a source of diverse, bioactive natural products, and a model for toxicity screenings. Compounds isolated from ascidians comprise an approved anti-tumor drug and many others are potent drug leads. Furthermore, the use of invertebrate embryos for toxicological screening tests or analysis offers the possibility to image a large number of samples for high throughput screens. Ascidians are members of a sister clade to the vertebrates and make a vertebrate-like tadpole larva composed of less than 3000 cells in 18 hours...
January 29, 2017: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/28137236/the-use-of-the-zebrafish-model-to-aid-in-drug-discovery-and-target-validation
#18
Prusothman Yoganantharjah, Yann Gibert
The zebrafish is fast becoming a leading and prominent model organism used by researchers for developmental biology, and research in modeling human diseases in zebrafish is being undertaken at a fast pace. Many therapeutic areas, including oncology and cardiovascular diseases to name a few all have zebrafish models based on known disease mechanisms that are translatable to modes of action in humans. Many novel assays have been and are continuing to be developed to study human disease in zebrafish. Prominent methods to identify novel drug targets within the organism include, chemical mutagenesis, insertional mutagenesis and high throughput small molecule screens...
January 30, 2017: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/28134443/challenges-and-opportunities-for-whole-genome-sequencing-based-surveillance-of-antibiotic-resistance
#19
Anita C Schürch, Willem van Schaik
Infections caused by drug-resistant bacteria are increasingly reported across the planet, and drug-resistant bacteria are recognized to be a major threat to public health and modern medicine. In this review, we discuss how whole-genome sequencing (WGS)-based approaches can contribute to the surveillance of the emergence and spread of antibiotic resistance. We outline the characteristics of sequencing technologies that are currently most used for WGS (Illumina short-read technologies and the long-read sequencing platforms developed by Pacific Biosciences and Oxford Nanopore)...
January 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28133416/understanding-and-controlling-cu-catalyzed-graphene-nucleation-the-role-of-impurities-roughness-and-oxygen-scavenging
#20
Philipp Braeuninger-Weimer, Barry Brennan, Andrew J Pollard, Stephan Hofmann
The mechanism by which Cu catalyst pretreatments control graphene nucleation density in scalable chemical vapor deposition (CVD) is systematically explored. The intrinsic and extrinsic carbon contamination in the Cu foil is identified by time-of-flight secondary ion mass spectrometry as a major factor influencing graphene nucleation and growth. By selectively oxidizing the backside of the Cu foil prior to graphene growth, a drastic reduction of the graphene nucleation density by 6 orders of magnitude can be obtained...
December 27, 2016: Chemistry of Materials: a Publication of the American Chemical Society
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