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Randomization gene circuit

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https://www.readbyqxmd.com/read/27664398/efficacy-and-role-of-inulin-in-mitigation-of-enteric-sulfur-containing-odor-in-pigs
#1
Yuan-Fan Deng, Yuan-Yuan Liu, Yi-Tao Zhang, Yan Wang, Juan-Boo Liang, Vincenzo Tufarelli, Vito Laudadio, Xin-Di Liao
BACKGROUND: The efficacy and role of inulin in the mitigation of enteric sulfur-containing odor gases hydrogen sulfide (H2 S) and methyl mercaptan (CH3 SH) in pigs were examined in this study. Twelve Duroc × Landrace × Yorkshire male finisher pigs (60.7 ± 1.9 kg), housed individually in open-circuit respiration chambers, were randomly assigned to two dietary groups, namely basal diet (control) and basal diet supplemented with 1% (w/w) inulin. At the end of the 45 day experiment, pigs were slaughtered and volatile fatty acid (VFA) concentration, sulfate radical (SO4(2)(-) ) concentration, population of sulfate-reducing bacteria (SRB) and expression of methionine gamma-lyase (MGL) gene were determined in contents from the caecum, colon (two segments) and rectum...
September 24, 2016: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/27630669/a-comparison-of-deterministic-and-stochastic-modeling-approaches-for-biochemical-reaction-systems-on-fixed-points-means-and-modes
#2
Sayuri K Hahl, Andreas Kremling
In the mathematical modeling of biochemical reactions, a convenient standard approach is to use ordinary differential equations (ODEs) that follow the law of mass action. However, this deterministic ansatz is based on simplifications; in particular, it neglects noise, which is inherent to biological processes. In contrast, the stochasticity of reactions is captured in detail by the discrete chemical master equation (CME). Therefore, the CME is frequently applied to mesoscopic systems, where copy numbers of involved components are small and random fluctuations are thus significant...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27529501/short-synthetic-terminators-for-assembly-of-transcription-units-in-vitro-and-stable-chromosomal-integration-in-yeast-s-cerevisiae
#3
Murray Iain MacPherson, Yasushi Saka
Assembly of synthetic genetic circuits is central to synthetic biology. Yeast S. cerevisiae in particular has proven to be an ideal chassis for synthetic genome assemblies by exploiting its efficient homologous recombination. However, this property of efficient homologous recombination poses a problem for multigene assemblies in yeast since repeated usage of standard parts, such as transcriptional terminators, can lead to rearrangements of the repeats in assembled DNA constructs in vivo. To address this issue in developing a library of orthogonal genetic components for yeast, we designed a set of short synthetic terminators based on a consensus sequence with random linkers to avoid repetitive sequences...
August 16, 2016: ACS Synthetic Biology
https://www.readbyqxmd.com/read/27508977/abnormal-blink-reflex-recovery-cycle-in-manifesting-and-nonmanifesting-carriers-of-the-dyt1-gene-mutation
#4
Po-Yu Fong, Mark J Edwards, Chin-Song Lu, Rou-Shayn Chen, John C Rothwell, Kailash P Bhatia, Ying-Zu Huang
The aim of this study is to evaluate the brainstem function in DYT1 carriers manifesting clinical dystonia (MDYT1) and those without clinical symptoms (NMDYT1). Motor cortical inhibition and plasticity were found to be abnormal in MDYT1, whereas these were less abnormal in NMDYT1. However, the spinal reciprocal inhibition was abnormal in MDYT1, but normal in NMDYT1. Moreover, protein accumulation and perinuclear inclusion bodies were found in the brainstem, but not in other brain areas, in DYT1 patients. Therefore, we designed this study to investigate the brainstem physiology using the blink reflex (BR) recovery cycle test in MDYT1 and NMDYT1...
September 28, 2016: Neuroreport
https://www.readbyqxmd.com/read/27380260/promoter-screening-from-bacillus-subtilis-in-various-conditions-hunting-for-synthetic-biology-and-industrial-applications
#5
Yafeng Song, Jonas M Nikoloff, Gang Fu, Jingqi Chen, Qinggang Li, Nengzhong Xie, Ping Zheng, Jibin Sun, Dawei Zhang
The use of Bacillus subtilis in synthetic biology and metabolic engineering is highly desirable to take advantage of the unique metabolic pathways present in this organism. To do this, an evaluation of B. subtilis' intrinsic biological parts is required to determine the best strategies to accurately regulate metabolic circuits and expression of target proteins. The strengths of promoter candidates were evaluated by measuring relative fluorescence units of a green fluorescent protein reporter, integrated into B...
2016: PloS One
https://www.readbyqxmd.com/read/27197833/effect-of-genome-position-on-heterologous-gene-expression-in-bacillus-subtilis-an-unbiased-analysis
#6
Christopher Sauer, Simon Syvertsson, Laura C Bohorquez, Rita Cruz, Colin R Harwood, Tjeerd van Rij, Leendert W Hamoen
A fixed gene copy number is important for the in silico construction of engineered synthetic networks. However, the copy number of integrated genes depends on their genomic location. This gene dosage effect is rarely addressed in synthetic biology. Two studies in Escherichia coli presented conflicting data on the impact of gene dosage. Here, we investigate how genome location and gene orientation influences expression in Bacillus subtilis. An important difference with the E. coli studies is that we used an unbiased genome integration approach mediated by random transposon insertion...
September 16, 2016: ACS Synthetic Biology
https://www.readbyqxmd.com/read/27167409/quorum-quenching-strategy-targeting-gram-positive-pathogenic-bacteria
#7
Ravindra Pal Singh, Said E Desouky, Jiro Nakayama
Quorum sensing (QS) is a cell density-dependent regulatory system that orchestrates the group behavior of unicellular organisms by synchronizing the expression of certain gene(s) within the clonal community of same species. Bacterial pathogens often employ QS system to establish efficiently an infection. A large part of low GC Gram-positive bacteria belonging to phylum Firmicutes use thiolactone/lactone peptides as communication signals so-called autoinducing peptides (AIPs) to coordinate QS circuit. In particular, QS of staphylococci, enterococci, and clostridia have been intensively studied in terms of alternative target of anti-pathogenic chemotherapy independent of bactericidal antibiotics...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27125681/advances-in-surgery-for-movement-disorders
#8
Nathan C Rowland, Francesco Sammartino, Andres M Lozano
Movement disorder surgery has evolved throughout history as our knowledge of motor circuits and ways in which to manipulate them have expanded. Today, the positive impact on patient quality of life for a growing number of movement disorders such as Parkinson's disease is now well accepted and confirmed through several decades of randomized, controlled trials. Nevertheless, residual motor symptoms after movement disorder surgery such as deep brain stimulation and lack of a definitive cure for these conditions demand that advances continue to push the boundaries of the field and maximize its therapeutic potential...
April 29, 2016: Movement Disorders: Official Journal of the Movement Disorder Society
https://www.readbyqxmd.com/read/27092132/phenotypic-variability-in-synthetic-biology-applications-dealing-with-noise-in-microbial-gene-expression
#9
REVIEW
Lucia Bandiera, Simone Furini, Emanuele Giordano
The stochasticity due to the infrequent collisions among low copy-number molecules within the crowded cellular compartment is a feature of living systems. Single cell variability in gene expression within an isogenic population (i.e., biological noise) is usually described as the sum of two independent components: intrinsic and extrinsic stochasticity. Intrinsic stochasticity arises from the random occurrence of events inherent to the gene expression process (e.g., the burst-like synthesis of mRNA and protein molecules)...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27076218/mammalian-synthetic-biology-time-for-big-macs
#10
Andrea Martella, Steven M Pollard, Junbiao Dai, Yizhi Cai
The enabling technologies of synthetic biology are opening up new opportunities for engineering and enhancement of mammalian cells. This will stimulate diverse applications in many life science sectors such as regenerative medicine, development of biosensing cell lines, therapeutic protein production, and generation of new synthetic genetic regulatory circuits. Harnessing the full potential of these new engineering-based approaches requires the design and assembly of large DNA constructs-potentially up to chromosome scale-and the effective delivery of these large DNA payloads to the host cell...
October 21, 2016: ACS Synthetic Biology
https://www.readbyqxmd.com/read/27040780/an-expression-refinement-process-ensures-singular-odorant-receptor-gene-choice
#11
Ishmail Abdus-Saboor, Mohammed J Al Nufal, Maha V Agha, Marion Ruinart de Brimont, Alexander Fleischmann, Benjamin M Shykind
Odorant receptor (OR) gene choice in mammals is a paradigmatic example of monogenic and monoallelic transcriptional selection, in which each olfactory sensory neuron (OSN) chooses to express one OR allele from over 1,000 encoded in the genome [1-3]. This process, critical for generation of the circuit from nose to brain [4-6], is thought to occur in two steps: a slow initial phase that randomly activates a single OR allele, followed by a rapid feedback that halts subsequent expression [7-14]. Inherent in this model is a finite failure rate wherein multiple OR alleles may be activated prior to feedback suppression [15, 16]...
April 25, 2016: Current Biology: CB
https://www.readbyqxmd.com/read/26983548/glutamatergic-medication-in-the-treatment-of-obsessive-compulsive-disorder-ocd-and-autism-spectrum-disorder-asd-study-protocol-for-a-randomised-controlled-trial
#12
Alexander Häge, Tobias Banaschewski, Jan K Buitelaar, Rick M Dijkhuizen, Barbara Franke, David J Lythgoe, Konstantin Mechler, Steven C R Williams, Ralf W Dittmann
BACKGROUND: Compulsivity is a cross-disorder trait underlying phenotypically distinct psychiatric disorders that emerge in childhood or adolescence. Despite the effectiveness of serotonergic compounds in the treatment of obsessive-compulsive disorder, treatment-resistant symptoms remaining in 40 to 60 % of patients present a pressing clinical problem. There are currently no medications that effectively treat the core impairments of autism spectrum disorder. There is an urgent need for the development of conceptually novel pharmacological strategies...
2016: Trials
https://www.readbyqxmd.com/read/26779340/effect-of-supplementation-of-allicin-on-methanogenesis-and-ruminal-microbial-flora-in-dorper-crossbred-ewes
#13
Tao Ma, Dandan Chen, Yan Tu, Naifeng Zhang, Bingwen Si, Kaidong Deng, Qiyu Diao
BACKGROUND: Garlic extracts have been reported to be effective in reducing methanogenesis. Related mechanisms are not well illustrated, however, and most studies have been conducted in vitro. This study investigates the effects of supplementary allicin (AL) in sheep diet on in vivo digestibility, rumen fermentation, and shifts of microbial flora. METHODS: Two experiments were conducted using Dorper × thin-tailed Han crossbred ewes. In experiment 1, eighteen ewes (60...
2016: Journal of Animal Science and Biotechnology
https://www.readbyqxmd.com/read/26709012/jejunum-ileum-circuit-procedure-improves-glucose-metabolism-in-diabetic-rats-independent-of-weight-loss
#14
Yanmin Wang, Xiang Zhang, Teng Liu, Mingwei Zhong, Houmin Wan, Shaozhuang Liu, Guangyong Zhang, Ghassan S Kassab, Sanyuan Hu
OBJECTIVE: To introduce a lower-risk novel surgical procedure to achieve diabetes reversal along with associated hormonal changes. METHODS: Diabetic rats were randomly assigned to jejunum-ileum circuit (JIC), sham-JIC, ileal interposition (IT), and sham-IT groups. The JIC group included two subgroups: short (JIC-S) and long (JIC-L), based on the length between anastomosis and Treitz ligament (LAT ). The body weight, food intake, blood glucose, glucose and insulin tolerance, and gut hormones were measured...
February 2016: Obesity
https://www.readbyqxmd.com/read/26689263/engineering-an-allosteric-transcription-factor-to-respond-to-new-ligands
#15
Noah D Taylor, Alexander S Garruss, Rocco Moretti, Sum Chan, Mark A Arbing, Duilio Cascio, Jameson K Rogers, Farren J Isaacs, Sriram Kosuri, David Baker, Stanley Fields, George M Church, Srivatsan Raman
Genetic regulatory proteins inducible by small molecules are useful synthetic biology tools as sensors and switches. Bacterial allosteric transcription factors (aTFs) are a major class of regulatory proteins, but few aTFs have been redesigned to respond to new effectors beyond natural aTF-inducer pairs. Altering inducer specificity in these proteins is difficult because substitutions that affect inducer binding may also disrupt allostery. We engineered an aTF, the Escherichia coli lac repressor, LacI, to respond to one of four new inducer molecules: fucose, gentiobiose, lactitol and sucralose...
February 2016: Nature Methods
https://www.readbyqxmd.com/read/26481028/-randomness-and-cell-fate
#16
REVIEW
Philippe Nghe
Thermal fluctuations at the molecular scale cause random fluctuations of gene expression, which, in association with differentiation circuits, can lead to phenotypic diversification in cell populations. In this synthesis article, we detail the mechanisms that generate this diversification and illustrate their consequences in various organisms. In bacteria, random phenotypic diversification allows to anticipate environmental changes that are otherwise unpredictable, in particular during metabolic transitions and stress responses, for example inducing a transient form of antibiotic resistance...
October 2015: Médecine Sciences: M/S
https://www.readbyqxmd.com/read/26410354/chronic-administration-of-the-n-methyl-d-aspartate-receptor-antagonist-ketamine-improves-rett-syndrome-phenotype
#17
Annarita Patrizi, Nathalie Picard, Alex Joseph Simon, Georgia Gunner, Eleonora Centofante, Nick Arthur Andrews, Michela Fagiolini
BACKGROUND: Rett syndrome (RTT) is a neurological disorder caused by mutation of the X-linked MECP2 gene, which results in the progressive disruption of excitatory and inhibitory neuronal circuits. To date, there is no effective treatment available for the disorder. Studies conducted in RTT patients and murine models have shown altered expression of N-methyl-D-aspartate receptors (NMDARs). Genetic deletion of the NMDAR subunit, GluN2A, in mice lacking Mecp2 is sufficient to prevent RTT phenotypes, including regression of vision...
May 1, 2016: Biological Psychiatry
https://www.readbyqxmd.com/read/26357038/an-integrated-approach-to-anti-cancer-drug-sensitivity-prediction
#18
Noah Berlow, Saad Haider, Qian Wan, Mathew Geltzeiler, Lara E Davis, Charles Keller, Ranadip Pal
A framework for design of personalized cancer therapy requires the ability to predict the sensitivity of a tumor to anticancer drugs. The predictive modeling of tumor sensitivity to anti-cancer drugs has primarily focused on generating functions that map gene expressions and genetic mutation profiles to drug sensitivity. In this paper, we present a new approach for drug sensitivity prediction and combination therapy design based on integrated functional and genomic characterizations. The modeling approach when applied to data from the Cancer Cell Line Encyclopedia shows a significant gain in prediction accuracy as compared to elastic net and random forest techniques based on genomic characterizations...
November 2014: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/26336146/conditional-moment-closure-schemes-for-studying-stochastic-dynamics-of-genetic-circuits
#19
Mohammad Soltani, Cesar Augusto Vargas-Garcia, Abhyudai Singh
Inside individual cells, stochastic expression drives random fluctuations in gene product copy numbers, which corrupts functioning of both natural and synthetic genetic circuits. Dynamic models of genetic circuits are formulated stochastically using the chemical master equation framework. Since obtaining probability distributions can be computationally expensive in these models, noise is typically investigated through lower-order statistical moments (mean, variance, correlation, skewness, etc.) of mRNA/proteins levels...
August 2015: IEEE Transactions on Biomedical Circuits and Systems
https://www.readbyqxmd.com/read/26332088/stochastic-switching-of-cell-fate-in-microbes
#20
REVIEW
Thomas M Norman, Nathan D Lord, Johan Paulsson, Richard Losick
Microbes transiently differentiate into distinct, specialized cell types to generate functional diversity and cope with changing environmental conditions. Though alternate programs often entail radically different physiological and morphological states, recent single-cell studies have revealed that these crucial decisions are often left to chance. In these cases, the underlying genetic circuits leverage the intrinsic stochasticity of intracellular chemistry to drive transition between states. Understanding how these circuits transform transient gene expression fluctuations into lasting phenotypic programs will require a combination of quantitative modeling and extensive, time-resolved observation of switching events in single cells...
2015: Annual Review of Microbiology
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