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https://www.readbyqxmd.com/read/28336855/behavior-and-potential-impacts-of-metal-based-engineered-nanoparticles-in-aquatic-environments
#1
REVIEW
Cheng Peng, Wen Zhang, Haiping Gao, Yang Li, Xin Tong, Kungang Li, Xiaoshan Zhu, Yixiang Wang, Yongsheng Chen
The specific properties of metal-based nanoparticles (NPs) have not only led to rapidly increasing applications in various industrial and commercial products, but also caused environmental concerns due to the inevitable release of NPs and their unpredictable biological/ecological impacts. This review discusses the environmental behavior of metal-based NPs with an in-depth analysis of the mechanisms and kinetics. The focus is on knowledge gaps in the interaction of NPs with aquatic organisms, which can influence the fate, transport and toxicity of NPs in the aquatic environment...
January 22, 2017: Nanomaterials
https://www.readbyqxmd.com/read/28333914/genome-scale-crispr-cas9-knockout-and-transcriptional-activation-screening
#2
Julia Joung, Silvana Konermann, Jonathan S Gootenberg, Omar O Abudayyeh, Randall J Platt, Mark D Brigham, Neville E Sanjana, Feng Zhang
Forward genetic screens are powerful tools for the unbiased discovery and functional characterization of specific genetic elements associated with a phenotype of interest. Recently, the RNA-guided endonuclease Cas9 from the microbial CRISPR (clustered regularly interspaced short palindromic repeats) immune system has been adapted for genome-scale screening by combining Cas9 with pooled guide RNA libraries. Here we describe a protocol for genome-scale knockout and transcriptional activation screening using the CRISPR-Cas9 system...
April 2017: Nature Protocols
https://www.readbyqxmd.com/read/28333622/constrained-inversion-and-spectral-unmixing-in-multispectral-optoacoustic-tomography
#3
Lu Ding, Xose Luis Dean Ben, Neal C Burton, Robert W Sobol, Vasilis Ntziachristos, Daniel Razansky
Accurate extraction of physical and biochemical parameters from optoacoustic images is often impeded due to the use of unrigorous inversion schemes, incomplete tomographic detection coverage or other experimental factors that cannot be readily accounted for during the image acquisition and reconstruction process. For instance, inaccurate assumptions in the physical forward model may lead to negative optical absorption values in the reconstructed images. Any artifacts present in the single wavelength optoacoustic images can be significantly aggravated when performing a two-step reconstruction consisting in acoustic inversion and spectral unmixing aimed at rendering the distributions of spectrally-distinct absorbers...
March 22, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28325765/caenorhabditis-elegans-rig-i-homolog-mediates-antiviral-rna-interference-downstream-of-dicer-dependent-biogenesis-of-viral-small-interfering-rnas
#4
Stephanie R Coffman, Jinfeng Lu, Xunyang Guo, Jing Zhong, Hongshan Jiang, Gina Broitman-Maduro, Wan-Xiang Li, Rui Lu, Morris Maduro, Shou-Wei Ding
Dicer enzymes process virus-specific double-stranded RNA (dsRNA) into small interfering RNAs (siRNAs) to initiate specific antiviral defense by related RNA interference (RNAi) pathways in plants, insects, nematodes, and mammals. Antiviral RNAi in Caenorhabditis elegans requires Dicer-related helicase 1 (DRH-1), not found in plants and insects but highly homologous to mammalian retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs), intracellular viral RNA sensors that trigger innate immunity against RNA virus infection...
March 21, 2017: MBio
https://www.readbyqxmd.com/read/28325749/the-nca-1-and-nca-2-ion-channels-function-downstream-of-gq-and-rho-to-regulate-locomotion-in-caenorhabditis-elegans
#5
Irini Topalidou, Pin-An Chen, Kirsten Cooper, Shigeki Watanabe, Erik M Jorgensen, Michael Ailion
The heterotrimeric G protein Gq positively regulates neuronal activity and synaptic transmission. Previously, the Rho guanine nucleotide exchange factor Trio was identified as a direct effector of Gq that acts in parallel to the canonical Gq effector phospholipase C. Here we examine how Trio and Rho act to stimulate neuronal activity downstream of Gq in the nematode Caenorhabditis elegans Through two forward genetic screens, we identify the cation channels NCA-1 and NCA-2, orthologs of mammalian NALCN, as downstream targets of the Gq/Rho pathway...
March 21, 2017: Genetics
https://www.readbyqxmd.com/read/28323890/establishment-of-transient-gene-expression-systems-in-protoplasts-from-liriodendron-hybrid-mesophyll-cells
#6
Ailing Huo, Zhenyu Chen, Pengkai Wang, Liming Yang, Guangping Wang, Dandan Wang, Suchan Liao, Tielong Cheng, Jinhui Chen, Jisen Shi
Liriodendron is a genus of the magnolia family comprised of two flowering tree species that produce hardwoods of great ecological and economic value. However, only a limited amount of genetic research has been performed on the Liriodendron genus partly because transient or stable transgenic trees have been difficult to produce. In general, transient expression systems are indispensable for rapid, high-throughput screening and systematic characterization of gene functions at a low cost; therefore, development of such a system for Liriodendron would provide a necessary step forward for research on Magnoliaceae and other woody trees...
2017: PloS One
https://www.readbyqxmd.com/read/28323300/a-walk-on-the-wild-side-oryza-species-as-source-for-rice-abiotic-stress-tolerance
#7
Paloma Koprovski Menguer, Raul Antonio Sperotto, Felipe Klein Ricachenevsky
Oryza sativa, the common cultivated rice, is one of the most important crops for human consumption, but production is increasingly threatened by abiotic stresses. Although many efforts have resulted in breeding rice cultivars that are relatively tolerant to their local environments, climate changes and population increase are expected to soon call for new, fast generation of stress tolerant rice germplasm, and current within-species rice diversity might not be enough to overcome such needs. The Oryza genus contains other 23 wild species, with only Oryza glaberrima being also domesticated...
March 20, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28320289/cancer-bad-luck-or-punishment
#8
REVIEW
A V Lichtenstein
Contrasting opinions on the role of extrinsic and intrinsic factors in cancer etiology (Tomasetti, C., and Vogelstein, B. (2015) Science, 347, 78-81; Wu, S., et al. (2016) Nature, 529, 43-47) variously define priorities in the war on cancer. The correlation between the lifetime risk of several types of cancer and the total number of divisions of normal self-renewing cells revealed by the authors has given them grounds to put forward the "bad luck" hypothesis. It assumes that ~70% of cancer variability is attributed to random errors arising during DNA replication in normal, noncancerous stem cells, i...
January 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/28318085/inflammatory-double-hit-model-of-temporomandibular-joint-disorder-with-elevated-ccl2-cxcl9-cxcl10-rantes-and-behavioural-hypersensitivity-in-tnfr1-r2-mice
#9
S L McIlwrath, R Nesemeier, F Ma, H S Oz, L Zhang, K N Westlund
BACKGROUND: Patients with temporomandibular joint disorders (TMD), reactive arthritis and rheumatoid arthritis often have combined etiology of hereditary and microenvironmental factors contributing to joint pain. Multiple clinical and animal studies indicate 'double-hit' inflammatory insults can cause chronic inflammation. The first inflammatory insult primes the immune system and subsequent insults elicit amplified responses. The present 'double hit' study produced a chronic orofacial pain model in mice with genetic deletion of both TNFα receptors (TNFR1/R2-/-), investigating the main nociceptive signalling pathways in comparisons to wild type mice...
March 20, 2017: European Journal of Pain: EJP
https://www.readbyqxmd.com/read/28317264/a-collection-of-enhancer-trap-insertional-mutants-for-functional-genomics-in-tomato
#10
Fernando Pérez-Martín, Fernando J Yuste-Lisbona, Benito Pineda, María Pilar Angarita-Díaz, Begoña García-Sogo, Teresa Antón, Sibilla Sánchez, Estela Giménez, Alejandro Atarés, Antonia Fernández-Lozano, Ana Ortíz-Atienza, Manuel García-Alcázar, Laura Castañeda, Rocío Fonseca, Carmen Capel, Geraldine Goergen, Jorge Sánchez, Jorge L Quispe, Juan Capel, Trinidad Angosto, Vicente Moreno, Rafael Lozano
With the completion of genome sequencing projects, the next challenge is to close the gap between gene annotation and gene functional assignment. Genomic tools to identify gene functions are based on the analysis of phenotypic variations between a wild-type and its mutant; hence, mutant collections are a valuable resource. In this sense, T-DNA collections allow for an easy and straightforward identification of the tagged gene, serving as the basis of both forward and reverse genetic strategies. This study reports on the phenotypic and molecular characterization of an enhancer trap T-DNA collection in tomato (Solanum lycopersicum L...
March 19, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28316112/molecular-ecology-studies-of-species-radiations-current-research-gaps-opportunities-and-challenges
#11
Marylaure de la Harpe, Margot Paris, Dirk N Karger, Jonathan Rolland, Michael Kessler, Nicolas Salamin, Christian Lexer
Understanding the drivers and limits of species radiations is a crucial goal of evolutionary genetics and molecular ecology, yet research on this topic has been hampered by the notorious difficulty of connecting micro- and macro-evolutionary approaches to studying the drivers of diversification. To chart the current research gaps, opportunities, and challenges of molecular ecology approaches to studying radiations, we examine the literature in the journal Molecular Ecology and re-visit recent high-profile examples of evolutionary genomic research on radiations...
March 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28306505/identification-of-an-rna-polymerase-iii-regulator-linked-to-disease-associated-protein-aggregation
#12
Olga Sin, Tristan de Jong, Alejandro Mata-Cabana, Michelle Kudron, Mohamad Amr Zaini, Francesco A Aprile, Renée I Seinstra, Esther Stroo, Roméo Willinge Prins, Céline N Martineau, Hai Hui Wang, Wytse Hogewerf, Anne Steinhof, Erich E Wanker, Michele Vendruscolo, Cornelis F Calkhoven, Valerie Reinke, Victor Guryev, Ellen A A Nollen
Protein aggregation is associated with age-related neurodegenerative disorders, such as Alzheimer's and polyglutamine diseases. As a causal relationship between protein aggregation and neurodegeneration remains elusive, understanding the cellular mechanisms regulating protein aggregation will help develop future treatments. To identify such mechanisms, we conducted a forward genetic screen in a C. elegans model of polyglutamine aggregation and identified the protein MOAG-2/LIR-3 as a driver of protein aggregation...
March 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28303933/vector-integration-sites-identification-for-gene-trap-screening-in-mammalian-haploid-cells
#13
Jian Yu, Constance Ciaudo
Forward genetic screens using retroviral (or transposon) gene-trap vectors in a haploid genome revolutionized the investigation of molecular networks in mammals. However, the sequencing data generated by Phenotypic interrogation followed by Tag sequencing (PhiT-seq) were not well characterized. The analysis of human and mouse haploid screens allowed us to describe PhiT-seq data and to define quality control steps. Moreover, we identified several blind spots in both haploid genomes where gene-trap vectors can hardly integrate...
March 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28302654/palmitate-induced-vacuolar-type-h-atpase-inhibition-feeds-forward-into-insulin-resistance-and-contractile-dysfunction
#14
Yilin Liu, Laura K M Steinbusch, Miranda Nabben, Dimitris Kapsokalyvas, Marc van Zandvoort, Patrick Schönleitner, Gudrun Antoons, Peter J Simons, Will A Coumans, Amber Geomini, Dipanjan Chanda, Jan F C Glatz, Dietbert Neumann, Joost J F P Luiken
Dietary fat overconsumption leads to myocardial lipid accumulation through mechanisms that are incompletely resolved. Previously, we identified increased translocation of the fatty acid transporter CD36 from its endosomal storage compartment to the sarcolemma as primary mechanism of excessive myocellular lipid import. Here, we show that increased CD36 translocation is caused by alkalinization of endosomes due to inhibition of proton pumping activity of vacuolar-type H(+)-ATPase (v-ATPase). Endosomal alkalinization was observed in hearts from rats fed a lard-based high fat-diet and in rodent and human cardiomyocytes upon palmitate overexposure, and appeared as early lipid-induced event preceding the onset of insulin resistance...
March 16, 2017: Diabetes
https://www.readbyqxmd.com/read/28296914/evolutionary-and-natural-history-of-the-turtle-frog-myobatrachus-gouldii-a-bizarre-myobatrachid-frog-in-the-southwestern-australian-biodiversity-hotspot
#15
Samantha Vertucci, Mitzy Pepper, Danielle L Edwards, J Dale Roberts, Nicola Mitchell, J Scott Keogh
Southwest Australia (SWA) is a global biodiversity hotspot and a centre of diversity and endemism for the Australo-Papuan myobatrachid frogs. Myobatrachus gouldii (the turtle frog) has a highly derived morphology associated with its forward burrowing behaviour, largely subterranean habit, and unusual mode of reproduction. Its sister genera Metacrinia and Arenophryne have restricted distributions in Western Australia with significant phylogeographic structure, leading to the recent description of a new species in the latter...
2017: PloS One
https://www.readbyqxmd.com/read/28296572/srna154-a-newly-identified-regulator-of-nitrogen-fixation-in-methanosarcina%C3%A2-mazei-strain-g%C3%A3-1
#16
Daniela Prasse, Konrad U Förstner, Dominik Jäger, Rolf Backofen, Ruth A Schmitz
Trans-encoded sRNA154 is exclusively expressed under nitrogen (N)-deficiency in Methanosarcina mazei strain Gö1. The sRNA154 deletion strain showed a significant decrease in growth under N-limitation, pointing towards a regulatory role of sRNA154 in N-metabolism. Aiming to elucidate its regulatory function we characterized sRNA154 by means of biochemical and genetic approaches. 24 homologs of sRNA154 were identified in recently reported draft genomes of Methanosarcina strains, demonstrating high conservation in sequence and predicted secondary structure with two highly conserved single stranded loops...
March 15, 2017: RNA Biology
https://www.readbyqxmd.com/read/28293850/analysis-of-growth-and-molecular-responses-to-ethylene-in-etiolated-rice-seedlings
#17
Biao Ma, Jin-Song Zhang
Ethylene plays a key role in various submergence responses of rice plants, but the mechanism of ethylene action remains largely unclear in rice. Regarding the differences between rice and Arabidopsis in ethylene-regulated processes, rice plants may possess divergent mechanisms in ethylene signaling in addition to the conserved aspects. Forward genetic analysis is essential to fully understand the ethylene signaling mechanism in rice. Here, we describe a method for screening ethylene-response mutants and evaluating ethylene responsiveness in etiolated rice seedlings...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28293236/interferon-lambda-modulating-immunity-in-infectious-diseases
#18
REVIEW
Mohammedyaseen Syedbasha, Adrian Egli
Interferon lambdas (IFN-λs; IFNL1-4) modulate immunity in the context of infections and autoimmune diseases, through a network of induced genes. IFN-λs act by binding to the heterodimeric IFN-λ receptor (IFNLR), activating a STAT phosphorylation-dependent signaling cascade. Thereby hundreds of IFN-stimulated genes are induced, which modulate various immune functions via complex forward and feedback loops. When compared to the well-characterized IFN-α signaling cascade, three important differences have been discovered...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28292857/awake1-an-abc-type-transporter-reveals-an-essential-role-for-suberin-in-the-control-of-seed-dormancy
#19
Fabio Fedi, Carmel O'Neil, Guillaume Menard, Martin Trick, Francoise Corbineau, Christophe Bailly, Peter J Eastmond, Steven Penfield
The mother plant plays an important dynamic role in the control of dormancy of her progeny seed, in response to environmental signals. In order to further understand the mechanisms by which this dormancy control takes place we conducted a forward genetic screen to isolate mutants which fail to enter dormancy in response to variation in temperature during seed set. We show that for the first of these mutants, designated AWAKE1, the maternal allele is required for entry into strongly dormant states, and that awake1 mutants show seed phenotypes previously shown to be associated with loss of suberin the seed...
March 14, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28288099/nlrp12-attenuates-colon-inflammation-by-maintaining-colonic-microbial-diversity-and-promoting-protective-commensal-bacterial-growth
#20
Liang Chen, Justin E Wilson, Mark J Koenigsknecht, Wei-Chun Chou, Stephanie A Montgomery, Agnieszka D Truax, W June Brickey, Christopher D Packey, Nitsan Maharshak, Glenn K Matsushima, Scott E Plevy, Vincent B Young, R Balfour Sartor, Jenny P-Y Ting
Inflammatory bowel diseases involve the dynamic interaction of host genetics, the microbiome and inflammatory responses. Here we found lower expression of NLRP12 (which encodes a negative regulator of innate immunity) in human ulcerative colitis, by comparing monozygotic twins and other patient cohorts. In parallel, Nlrp12 deficiency in mice caused increased basal colonic inflammation, which led to a less-diverse microbiome and loss of protective gut commensal strains (of the family Lachnospiraceae) and a greater abundance of colitogenic strains (of the family Erysipelotrichaceae)...
March 13, 2017: Nature Immunology
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