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https://www.readbyqxmd.com/read/29223136/allele-exchange-at-the-epsps-locus-confers-glyphosate-tolerance-in-cassava
#1
Aaron W Hummel, Raj Deepika Chauhan, Tomas Cermak, Andrew M Mutka, Anupama Vijayaraghavan, Adam Boyher, Colby G Starker, Rebecca Bart, Daniel F Voytas, Nigel J Taylor
Effective weed control can protect yields of cassava (Manihot esculenta) storage roots (Doll and Piedrahita Cañola, 1978). Farmers could benefit from using herbicide with a tolerant cultivar. We applied traditional transgenesis and gene editing to generate robust glyphosate tolerance in cassava. By comparing promoters regulating expression of transformed 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) genes with various paired amino acid substitutions, we found that strong constitutive expression is required to achieve glyphosate tolerance during in vitro selection and in whole cassava plants...
December 9, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29222989/disrupted-circuits-in-mouse-models-of-autism-spectrum-disorder-and-intellectual-disability
#2
REVIEW
Carla Em Golden, Joseph D Buxbaum, Silvia De Rubeis
Autism spectrum disorder (ASD) and intellectual disability (ID) are caused by a wide range of genetic mutations, a significant fraction of which reside in genes important for synaptic function. Studies have found that sensory, prefrontal, hippocampal, cerebellar, and striatal regions, as well as the circuits that connect them, are perturbed in mouse models of ASD and ID. Dissecting the disruptions in morphology and activity in these neural circuits might help us to understand the shared risk between the two disorders as well as their clinical heterogeneity...
December 5, 2017: Current Opinion in Neurobiology
https://www.readbyqxmd.com/read/29222839/decellularized-human-liver-extracellular-matrix-hdlm-mediated-hepatic-differentiation-of-human-induced-pluripotent-stem-cells-hipsc
#3
Maria Jaramillo, Heidi Yeh, Martin L Yarmush, Basak E Uygun
Liver tissue engineering has emerged as a promising approach in organ transplantation, but has been hampered by the lack of a reliable and readily available cell source. Induced pluripotent cells (hiPSC) have been highlighted a desirable source, due to their differentiation potential, ability to self-renew and the possibility of making patient specific cells. We developed a decellularization protocol that efficiently removes cellular material, while retaining extracellular matrix components. Subsequently, hiPSC were differentiated on the decellularized human liver matrix (hDLM) scaffolds using an established hepatic differentiation protocol...
December 8, 2017: Journal of Tissue Engineering and Regenerative Medicine
https://www.readbyqxmd.com/read/29222823/dominant-role-of-microglial-and-macrophage-innate-immune-responses-in-human-ischemic-infarcts
#4
Tobias Zrzavy, Joana Machado-Santos, Sheren Christine, Christoph Baumgartner, Howard L Weiner, Oleg Butovsky, Hans Lassmann
Inflammatory mechanisms, involving granulocytes, T-cells, B-cells, macrophages and activated microglia, have been suggested to play a pathogenic role in experimental models of stroke and may be targets for therapeutic intervention. However, knowledge on the inflammatory response in human stroke lesions is limited. Here, we performed a quantitative study on the inflammatory reaction in human ischemic infarct lesions. We found increased numbers of T-lymphocytes, mainly CD8+ cells, but not of B-lymphocytes. Their number was very low in comparison to that seen in inflammatory diseases of the central nervous system and they did not show signs of activation...
December 8, 2017: Brain Pathology
https://www.readbyqxmd.com/read/29222813/reln-signaling-modulates-glioblastoma-growth-and-substrate-dependent-migration
#5
Markus Schulze, Christ Violonchi, Stefan Swoboda, Tobias Welz, Eugen Kerkhoff, Sabine Hoja, Susanne Brüggemann, Johann Simbürger, Jörg Reinders, Markus J Riemenschneider
Glioblastoma (GBM) represents the most common and most malignant type of primary brain tumor and significantly contributes to cancer morbidity and mortality. Invasion into the healthy brain parenchyma is a major feature of glioblastoma aggressiveness. Reelin (RELN) is a large secreted extracellular matrix glycoprotein that regulates neuronal migration and positioning in the developing brain and sustains functionality in the adult brain. We here show that both RELN and its main downstream effector DAB1 are silenced in glioblastoma as compared to non-neoplastic tissue and mRNA expression is inversely correlated with malignancy grade...
December 8, 2017: Brain Pathology
https://www.readbyqxmd.com/read/29222807/long-non-coding-rna-expression-in-bladder-cancer
#6
REVIEW
Mohammad Taheri, Mir Davood Omrani, Soudeh Ghafouri-Fard
The advent of novel high-throughput sequencing methods has facilitated identification of non-coding RNAs with fundamental roles in cellular biological and pathological conditions. A group of these consisting of at least 200 nucleotides are called long non-coding RNAs (lncRNAs). Their participation in the pathogenesis of cancer has been highlighted in recent years. Bladder cancer, one of the most prevalent cancers worldwide, exhibits altered expression levels of several lncRNAs. Several in vitro and in vivo studies have assessed the effects of silencing RNAs on cancer cell phenotypes and in vivo tumor growth...
December 8, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29222801/culture-of-human-primary-bone-cells-and-phenotype-assessment
#7
Paola Brun
Bone engineering scaffolds and biomimetic substitutes are currently the leading techniques to repair and regenerate bone defects. Ideally, bone grafts should imitate the structure and properties of bone extracellular matrix, house osteoprogenitor cells, and provide all the necessary environmental cues to orchestrate the functions of osteoblast and osteoclast cells. Consequently, there is an increasing demand for preclinical models based on in vitro bone-derived cell cultures for screening of novel biomaterials...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222764/optimization-of-multi-omic-genome-scale-models-methodologies-hands-on-tutorial-and-perspectives
#8
Supreeta Vijayakumar, Max Conway, Pietro Lió, Claudio Angione
Genome-scale metabolic models are valuable tools for assessing the metabolic potential of living organisms. Being downstream of gene expression, metabolism is increasingly being used as an indicator of the phenotypic outcome for drugs and therapies. We here present a review of the principal methods used for constraint-based modelling in systems biology, and explore how the integration of multi-omic data can be used to improve phenotypic predictions of genome-scale metabolic models. We believe that the large-scale comparison of the metabolic response of an organism to different environmental conditions will be an important challenge for genome-scale models...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222759/techniques-for-large-scale-bacterial-genome-manipulation-and-characterization-of-the-mutants-with-respect-to-in-silico-metabolic-reconstructions
#9
George C diCenzo, Turlough M Finan
The rate at which all genes within a bacterial genome can be identified far exceeds the ability to characterize these genes. To assist in associating genes with cellular functions, a large-scale bacterial genome deletion approach can be employed to rapidly screen tens to thousands of genes for desired phenotypes. Here, we provide a detailed protocol for the generation of deletions of large segments of bacterial genomes that relies on the activity of a site-specific recombinase. In this procedure, two recombinase recognition target sequences are introduced into known positions of a bacterial genome through single cross-over plasmid integration...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222755/integrated-host-pathogen-metabolic-reconstructions
#10
Anu Raghunathan, Neema Jamshidi
The science and art of Genome scale metabolic network reconstructions have been explicitly documented in the literature for organisms across all the three kingdoms of life. Constraints-based models derived from such reconstructions have been used to assess metabolic phenotypes of their complex connections to genotype accurately. The problem of infectious disease is complex due to the multifactorial response of the host to the pathogen. Systems biology approaches and modeling allow one to study, understand, and predict emergent properties of such complex responses...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222754/template-assisted-metabolic-reconstruction-and-assembly-of-hybrid-bacterial-models
#11
Tiziano Vignolini, Alessio Mengoni, Marco Fondi
Intraspecific genomic exchanges happen frequently between bacteria living in the same natural environment and can also be performed artificially in the laboratory for basic research or genetic/metabolic engineering purposes. In silico metabolic reconstruction and simulation of the metabolism of the hybrid strains that result from these processes can be used to predict the phenotypic outcome of such genomic rearrangements; this can be especially helpful as a designing tool in the purview of synthetic biology...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222753/integration-of-comparative-genomics-with-genome-scale-metabolic-modeling-to-investigate-strain-specific-phenotypical-differences
#12
Jonathan Monk, Emanuele Bosi
Genome-scale metabolic reconstructions are powerful resources that allow translation biological knowledge and genomic information to phenotypical predictions using a number of constraint-based methods. This approach has been applied in recent years to gain deep insights into the cellular phenotype role of the genes at a systems-level, driving the design of targeted experiments and paving the way for knowledge-based synthetic biology.The identification of genetic determinants underlying the variability at the phenotypical level is crucial to understand the evolutionary trajectories of a bacterial species...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222740/a-case-of-maturity-onset-diabetes-of-the-young-mody3-in-a-family-with-a-novel-hnf1a-gene-mutation-in-five-generations
#13
A K Ovsyannikova, O D Rymar, D E Ivanoshchuk, Svetlana V Mikhailova, E V Shakhtshneider, P S Orlov, E S Malakhina, M I Voevoda
Diabetes mellitus with autosomal dominant inheritance, i.e., maturity-onset diabetes of the young (MODY), is a genetic form of diabetes mellitus. The MODY phenotype is associated with gene mutations leading to pancreatic β-cell dysfunction. Here, we present the clinical case of a 50-year-old proband with familial diabetes mellitus in five generations (proband, her mother, grandmother, great-grandfather, and son). This disease is most likely associated with the novel Ser6Arg mutation in the HNF1A gene, which was identified in four family members...
December 8, 2017: Diabetes Therapy: Research, Treatment and Education of Diabetes and related Disorders
https://www.readbyqxmd.com/read/29222693/neuroblastoma-pathogenesis-deregulation-of-embryonic-neural-crest-development
#14
REVIEW
Julie A Tomolonis, Saurabh Agarwal, Jason M Shohet
Neuroblastoma (NB) is an aggressive pediatric cancer that originates from neural crest tissues of the sympathetic nervous system. NB is highly heterogeneous both from a clinical and a molecular perspective. Clinically, this cancer represents a wide range of phenotypes ranging from spontaneous regression of 4S disease to unremitting treatment-refractory progression and death of high-risk metastatic disease. At a cellular level, the heterogeneous behavior of NB likely arises from an arrest and deregulation of normal neural crest development...
December 8, 2017: Cell and Tissue Research
https://www.readbyqxmd.com/read/29222551/neutrophil-and-t-cell-homeostasis-in-the-closed-eye
#15
Cameron K Postnikoff, Kelly K Nichols
Purpose: This study sought to examine the changes and phenotype of the tear neutrophil and T-cell populations between early eyelid closure and after a full night of sleep. Methods: Fourteen healthy participants were recruited and trained to wash the ocular surface with PBS for at-home self-collection of ocular surface and tear leukocytes following up to 1 hour of sleep and a full night of sleep (average 7 hours), on separate days. Cells were isolated, counted, and incubated with fluorescently labeled antibodies to identify neutrophils, monocytes, and T cells...
December 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29222496/genome-wide-and-gene-based-association-mapping-for-rice-eating-and-cooking-characteristics-and-protein-content
#16
Xiaoqian Wang, Yunlong Pang, Jian Zhang, Zhichao Wu, Kai Chen, Jauhar Ali, Guoyou Ye, Jianlong Xu, Zhikang Li
Rice eating and cooking quality and protein content (PC) are important properties affecting consumers' preferences, nutrition and health. Linkage QTL mapping and association studies are usually applied to genetically dissect related traits, which could be further facilitated by high density SNP markers and gene annotation based on reference genome to rapid identify candidate genes associated with interested traits. Here, we carried out an association study for apparent amylose content (AC), gel consistency (GC), gelatinization temperature (GT) and PC evaluated in two environments using a diverse panel of 258 accessions from 3 K Rice Genome Project...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29222433/the-evolution-of-phenotypic-plasticity-under-global-change
#17
Emma M Gibbin, Gloria Massamba N'Siala, Leela J Chakravarti, Michael D Jarrold, Piero Calosi
Marine ecosystems are currently in a state of flux, with ocean warming and acidification occurring at unprecedented rates. Phenotypic plasticity underpins acclimatory responses by shifting the mean phenotype in a population, which may buffer the negative effects of global change. However, little is known about how phenotypic plasticity evolves across multiple generations. We tested this by reciprocally-transplanting the polychaete Ophryotrocha labronica between control and global change scenarios (ocean warming and acidification in isolation and combined) over five generations...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29222418/heb-is-required-for-the-specification-of-fetal-il-17-producing-%C3%AE-%C3%AE-t-cells
#18
Tracy S H In, Ashton Trotman-Grant, Shawn Fahl, Edward L Y Chen, Payam Zarin, Amanda J Moore, David L Wiest, Juan Carlos Zúñiga-Pflücker, Michele K Anderson
IL-17-producing γδ T (γδT17) cells are critical components of the innate immune system. However, the gene networks that control their development are unclear. Here we show that HEB (HeLa E-box binding protein, encoded by Tcf12) is required for the generation of a newly defined subset of fetal-derived CD73- γδT17 cells. HEB is required in immature CD24+CD73- γδ T cells for the expression of Sox4, Sox13, and Rorc, and these genes are repressed by acute expression of the HEB antagonist Id3. HEB-deficiency also affects mature CD73+ γδ T cells, which are defective in RORγt expression and IL-17 production...
December 8, 2017: Nature Communications
https://www.readbyqxmd.com/read/29222416/functional-analysis-of-human-intrafusal-fiber-innervation-by-human-%C3%AE-motoneurons
#19
A Colón, X Guo, N Akanda, Y Cai, J J Hickman
Investigation of neuromuscular deficits and diseases such as SMA, as well as for next generation prosthetics, utilizing in vitro phenotypic models would benefit from the development of a functional neuromuscular reflex arc. The neuromuscular reflex arc is the system that integrates the proprioceptive information for muscle length and activity (sensory afferent), to modify motoneuron output to achieve graded muscle contraction (actuation efferent). The sensory portion of the arc is composed of proprioceptive sensory neurons and the muscle spindle, which is embedded in the muscle tissue and composed of intrafusal fibers...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29222412/ancestral-perinatal-obesogen-exposure-results-in-a-transgenerational-thrifty-phenotype-in-mice
#20
Raquel Chamorro-Garcia, Carlos Diaz-Castillo, Bassem M Shoucri, Heidi Käch, Ron Leavitt, Toshi Shioda, Bruce Blumberg
Ancestral environmental exposures to non-mutagenic agents can exert effects in unexposed descendants. This transgenerational inheritance has significant implications for understanding disease etiology. Here we show that exposure of F0 mice to the obesogen tributyltin (TBT) throughout pregnancy and lactation predisposes unexposed F4 male descendants to obesity when dietary fat is increased. Analyses of body fat, plasma hormone levels, and visceral white adipose tissue DNA methylome and transcriptome collectively indicate that the F4 obesity is consistent with a leptin resistant, thrifty phenotype...
December 8, 2017: Nature Communications
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