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Randomization gene circuit

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https://www.readbyqxmd.com/read/28841296/maltose-utilization-as-a-novel-selection-strategy-for-continuous-evolution-of-microbes-with-enhanced-metabolite-production
#1
Shu-De Liu, Yi-Nan Wu, Tian-Min Wang, Chong Zhang, Xin-Hui Xing
We have developed a novel selection circuit based on carbon source utilization that establishes and sustains growth-production coupling over several generations in a medium with maltose as the sole carbon source. In contrast to traditional antibiotic resistance-based circuits, we first proved that coupling of cell fitness to metabolite production by our circuit was more robust with a much lower escape risk even after many rounds of selection. We then applied the selection circuit to the optimization of L-tryptophan (l-Trp) production...
September 6, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28735588/mode-of-action-of-saccharomyces-cerevisiae-in-enteric-methane-mitigation-in-pigs
#2
Y L Gong, J B Liang, M F Jahromi, Y B Wu, A G Wright, X D Liao
The objectives of this study were to determine the effect and mode of action of Saccharomyces cerevisiae (YST2) on enteric methane (CH4) mitigation in pigs. A total of 12 Duroc×Landrace×Yorkshire male finisher pigs (60±1 kg), housed individually in open-circuit respiration chambers, were randomly assigned to two dietary groups: a basal diet (control); and a basal diet supplemented with 3 g/YST2 (1.8×1010 live cells/g) per kg diet. At the end of 32-day experiment, pigs were sacrificed and redox potential (Eh), pH, volatile fatty acid concentration, densities of methanogens and acetogens, and expression of methyl coenzyme-M reductase subunit A gene were determined in digesta contents from the cecum, colon and rectum...
July 24, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28645748/developmental-and-genetic-mechanisms-of-neural-circuit-evolution
#3
REVIEW
Maria Antonietta Tosches
No matter how a nervous system is genetically built, natural selection acts on the functional outcome of its activity. To understand how nervous systems evolve, it is essential to analyze how their functional units - the neural circuits - change and adapt over time. Different developmental and genetic mechanisms participate to the structural evolution of neural circuits. These mechanisms involve regulatory changes at the level of different gene sets. Functional constraints on neural circuit evolution suggest that these mechanisms are not employed randomly, and that the evolution of neuroanatomy might be biased...
June 20, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28426785/genome-wide-association-studies-identified-multiple-genetic-loci-for-body-size-at-four-growth-stages-in-chinese-holstein-cattle
#4
Xu Zhang, Qin Chu, Gang Guo, Ganghui Dong, Xizhi Li, Qin Zhang, Shengli Zhang, Zhiwu Zhang, Yachun Wang
The growth and maturity of cattle body size affect not only feed efficiency, but also productivity and longevity. Dissecting the genetic architecture of body size is critical for cattle breeding to improve both efficiency and productivity. The volume and weight of body size are indicated by several measurements. Among them, Heart Girth (HG) and Hip Height (HH) are the most important traits. They are widely used as predictors of body weight (BW). Few association studies have been conducted for HG and HH in cattle focusing on single growth stage...
2017: PloS One
https://www.readbyqxmd.com/read/28362798/interrogating-the-topological-robustness-of-gene-regulatory-circuits-by-randomization
#5
Bin Huang, Mingyang Lu, Dongya Jia, Eshel Ben-Jacob, Herbert Levine, Jose N Onuchic
One of the most important roles of cells is performing their cellular tasks properly for survival. Cells usually achieve robust functionality, for example, cell-fate decision-making and signal transduction, through multiple layers of regulation involving many genes. Despite the combinatorial complexity of gene regulation, its quantitative behavior has been typically studied on the basis of experimentally verified core gene regulatory circuitry, composed of a small set of important elements. It is still unclear how such a core circuit operates in the presence of many other regulatory molecules and in a crowded and noisy cellular environment...
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28289210/phosphorylation-induced-conformational-dynamics-in-an-intrinsically-disordered-protein-and-potential-role-in-phenotypic-heterogeneity
#6
Prakash Kulkarni, Mohit Kumar Jolly, Dongya Jia, Steven M Mooney, Ajay Bhargava, Luciane T Kagohara, Yihong Chen, Pengyu Hao, Yanan He, Robert W Veltri, Alexander Grishaev, Keith Weninger, Herbert Levine, John Orban
Intrinsically disordered proteins (IDPs) that lack a unique 3D structure and comprise a large fraction of the human proteome play important roles in numerous cellular functions. Prostate-Associated Gene 4 (PAGE4) is an IDP that acts as a potentiator of the Activator Protein-1 (AP-1) transcription factor. Homeodomain-Interacting Protein Kinase 1 (HIPK1) phosphorylates PAGE4 at S9 and T51, but only T51 is critical for its activity. Here, we identify a second kinase, CDC-Like Kinase 2 (CLK2), which acts on PAGE4 and hyperphosphorylates it at multiple S/T residues, including S9 and T51...
March 28, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28027310/m6a-driver-identifying-context-specific-mrna-m6a-methylation-driven-gene-interaction-networks
#7
Song-Yao Zhang, Shao-Wu Zhang, Lian Liu, Jia Meng, Yufei Huang
As the most prevalent mammalian mRNA epigenetic modification, N6-methyladenosine (m6A) has been shown to possess important post-transcriptional regulatory functions. However, the regulatory mechanisms and functional circuits of m6A are still largely elusive. To help unveil the regulatory circuitry mediated by mRNA m6A methylation, we develop here m6A-Driver, an algorithm for predicting m6A-driven genes and associated networks, whose functional interactions are likely to be actively modulated by m6A methylation under a specific condition...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/28018144/deciphering-the-epigenetic-code-in-embryonic-and-dental-pulp-stem-cells
#8
REVIEW
Dashzeveg Bayarsaihan
A close cooperation between chromatin states, transcriptional modulation, and epigenetic modifications is required for establishing appropriate regulatory circuits underlying self-renewal and differentiation of adult and embryonic stem cells. A growing body of research has established that the epigenome topology provides a structural framework for engaging genes in the non-random chromosomal interactions to orchestrate complex processes such as cell-matrix interactions, cell adhesion and cell migration during lineage commitment...
December 2016: Yale Journal of Biology and Medicine
https://www.readbyqxmd.com/read/27664398/efficacy-and-role-of-inulin-in-mitigation-of-enteric-sulfur-containing-odor-in-pigs
#9
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
#10
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
#11
Murray 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...
January 20, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/27508977/abnormal-blink-reflex-recovery-cycle-in-manifesting-and-nonmanifesting-carriers-of-the-dyt1-gene-mutation
#12
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
#13
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
#14
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
#15
REVIEW
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
#16
REVIEW
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
#17
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
#18
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
#19
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
#20
RANDOMIZED CONTROLLED TRIAL
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...
March 17, 2016: Trials
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