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Computation gene circuits

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https://www.readbyqxmd.com/read/29437890/brain-transcriptome-databases-a-user-s-guide
#1
Jason M Keil, Adel Qalieh, Kenneth Y Kwan
Transcriptional programs instruct the generation and maintenance of diverse subtypes of neural cells, establishment of distinct brain regions, formation and function of neural circuits, and ultimately behavior. Spatiotemporal and cell type-specific analyses of the transcriptome, the sum total of all RNA transcripts in a cell or an organ, can provide insights into the role of genes in brain development and function, and their potential contribution to disorders of the brain. In the previous decade, advances in sequencing technology and funding from the National Institutes of Health and private foundations for large-scale genomics projects have led to a growing collection of brain transcriptome databases...
February 7, 2018: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/29401445/simulating-genetic-circuits-in-bacterial-populations-with-growth-heterogeneity
#2
Anjan Roy, Stefan Klumpp
We computationally study genetic circuits in bacterial populations with heterogeneities in the growth rate. To that end, we present a stochastic simulation method for gene circuits in populations of cells and propose an efficient implementation that we call the "Next Family Method". Within this approach, we implement different population setups, specifically Chemostat-type growth and growth in an ideal Mother Machine and show that the population structure and its statistics are different for the different setups whenever there is growth heterogeneity...
January 23, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29371263/tulsa-1000-a-naturalistic-study-protocol-for-multilevel-assessment-and-outcome-prediction-in-a-large-psychiatric-sample
#3
Teresa A Victor, Sahib S Khalsa, W Kyle Simmons, Justin S Feinstein, Jonathan Savitz, Robin L Aupperle, Hung-Wen Yeh, Jerzy Bodurka, Martin P Paulus
INTRODUCTION: Although neuroscience has made tremendous progress towards understanding the basic neural circuitry underlying important processes such as attention, memory and emotion, little progress has been made in applying these insights to psychiatric populations to make clinically meaningful treatment predictions. The overall aim of the Tulsa 1000 (T-1000) study is to use the NIMH Research Domain Criteria framework in order to establish a robust and reliable dimensional set of variables that quantifies the positive and negative valence, cognition and arousal domains, including interoception, to generate clinically useful treatment predictions...
January 24, 2018: BMJ Open
https://www.readbyqxmd.com/read/29258623/dynamic-modeling-of-folliculogenesis-signaling-pathways-in-the-presence-of-mirnas-expression
#4
Abolfazl Bahrami, Seyed Reza Miraie-Ashtiani, Mostafa Sadeghi, Ali Najafi, Reza Ranjbar
BACKGROUND: TEK signaling plays a very important role in folliculogenesis. It activates Ras/ERK/MYC, PI3K/AKT/mTORC1 and ovarian steroidogenesis activation pathways. These are the main pathways for cell growth, differentiation, migration, adhesion, proliferation, survival and protein synthesis. RESULTS: TEK signaling on each of the two important pathways where levels of pERK, pMYC, pAkt, pMCL1 and pEIF4EBP1 are increased in dominant follicles and pMYC is decreased in dominant follicles...
December 19, 2017: Journal of Ovarian Research
https://www.readbyqxmd.com/read/29227103/a-robust-molecular-network-motif-for-period-doubling-devices
#5
Christian Cuba Samaniego, Elisa Franco
Life is sustained by a variety of cyclic processes such as cell division, muscle contraction, and neuron firing. The periodic signals powering these processes often direct a variety of other downstream systems, which operate at different time scales and must have the capacity to divide or multiply the period of the master clock. Period modulation is also an important challenge in synthetic molecular systems, where slow and fast components may have to be coordinated simultaneously by a single oscillator whose frequency is often difficult to tune...
December 11, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29200199/programmable-full-adder-computations-in-communicating-three-dimensional-cell-cultures
#6
David Ausländer, Simon Ausländer, Xavier Pierrat, Leon Hellmann, Leila Rachid, Martin Fussenegger
Synthetic biologists have advanced the design of trigger-inducible gene switches and their assembly into input-programmable circuits that enable engineered human cells to perform arithmetic calculations reminiscent of electronic circuits. By designing a versatile plug-and-play molecular-computation platform, we have engineered nine different cell populations with genetic programs, each of which encodes a defined computational instruction. When assembled into 3D cultures, these engineered cell consortia execute programmable multicellular full-adder logics in response to three trigger compounds...
December 4, 2017: Nature Methods
https://www.readbyqxmd.com/read/29163022/the-insula-and-taste-learning
#7
REVIEW
Adonis Yiannakas, Kobi Rosenblum
The sense of taste is a key component of the sensory machinery, enabling the evaluation of both the safety as well as forming associations regarding the nutritional value of ingestible substances. Indicative of the salience of the modality, taste conditioning can be achieved in rodents upon a single pairing of a tastant with a chemical stimulus inducing malaise. This robust associative learning paradigm has been heavily linked with activity within the insular cortex (IC), among other regions, such as the amygdala and medial prefrontal cortex...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/29142298/shaping-bacterial-population-behavior-through-computer-interfaced-control-of-individual-cells
#8
Remy Chait, Jakob Ruess, Tobias Bergmiller, Gašper Tkačik, Călin C Guet
Bacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29133926/genetic-programs-can-be-compressed-and-autonomously-decompressed-in-live-cells
#9
Nicolas Lapique, Yaakov Benenson
Fundamental computer science concepts have inspired novel information-processing molecular systems in test tubes 1-13 and genetically encoded circuits in live cells 14-21 . Recent research has shown that digital information storage in DNA, implemented using deep sequencing and conventional software, can approach the maximum Shannon information capacity 22 of two bits per nucleotide 23 . In nature, DNA is used to store genetic programs, but the information content of the encoding rarely approaches this maximum 24 ...
November 13, 2017: Nature Nanotechnology
https://www.readbyqxmd.com/read/29122925/genetic-circuit-characterization-and-debugging-using-rna-seq
#10
Thomas E Gorochowski, Amin Espah Borujeni, Yongjin Park, Alec Ak Nielsen, Jing Zhang, Bryan S Der, D Benjamin Gordon, Christopher A Voigt
Genetic circuits implement computational operations within a cell. Debugging them is difficult because their function is defined by multiple states (e.g., combinations of inputs) that vary in time. Here, we develop RNA-seq methods that enable the simultaneous measurement of: (i) the states of internal gates, (ii) part performance (promoters, insulators, terminators), and (iii) impact on host gene expression. This is applied to a three-input one-output circuit consisting of three sensors, five NOR/NOT gates, and 46 genetic parts...
November 9, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/29100073/synaptic-neurexin-complexes-a-molecular-code-for-the-logic-of-neural-circuits
#11
REVIEW
Thomas C Südhof
Synapses are specialized junctions between neurons in brain that transmit and compute information, thereby connecting neurons into millions of overlapping and interdigitated neural circuits. Here, we posit that the establishment, properties, and dynamics of synapses are governed by a molecular logic that is controlled by diverse trans-synaptic signaling molecules. Neurexins, expressed in thousands of alternatively spliced isoforms, are central components of this dynamic code. Presynaptic neurexins regulate synapse properties via differential binding to multifarious postsynaptic ligands, such as neuroligins, cerebellin/GluD complexes, and latrophilins, thereby shaping the input/output relations of their resident neural circuits...
November 2, 2017: Cell
https://www.readbyqxmd.com/read/29054289/cross-talk-between-the-epigenome-and-neural-circuits-in-drug-addiction
#12
Philipp Mews, Erin S Calipari
Drug addiction is a behavioral disorder characterized by dysregulated learning about drugs and associated cues that result in compulsive drug seeking and relapse. Learning about drug rewards and predictive cues is a complex process controlled by a computational network of neural connections interacting with transcriptional and molecular mechanisms within each cell to precisely guide behavior. The interplay between rapid, temporally specific neuronal activation, and longer-term changes in transcription is of critical importance in the expression of appropriate, or in the case of drug addiction, inappropriate behaviors...
2017: Progress in Brain Research
https://www.readbyqxmd.com/read/29052539/engineering-diagnostic-and-therapeutic-gut-bacteria
#13
Brian P Landry, Jeffrey J Tabor
Genetically engineered bacteria have the potential to diagnose and treat a wide range of diseases linked to the gastrointestinal tract, or gut. Such engineered microbes will be less expensive and invasive than current diagnostics and more effective and safe than current therapeutics. Recent advances in synthetic biology have dramatically improved the reliability with which bacteria can be engineered with the sensors, genetic circuits, and output (actuator) genes necessary for diagnostic and therapeutic functions...
October 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/29040384/selansi-a-toolbox-for-simulation-of-stochastic-gene-regulatory-networks
#14
Manuel Pájaro, Irene Otero-Muras, Carlos Vázquez, Antonio A Alonso
Motivation: Gene regulation is inherently stochastic. In many applications concerning Systems and Synthetic Biology such as the reverse engineering and the de novo design of genetic circuits, stochastic effects (yet potentially crucial) are often neglected due to the high computational cost of stochastic simulations. With advances in these fields there is an increasing need of tools providing accurate approximations of the stochastic dynamics of gene regulatory networks (GRNs) with reduced computational effort...
October 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29020745/transcriptional-mapping-of-the-primary-somatosensory-cortex-upon-sensory-deprivation
#15
Koen Kole, Yutaro Komuro, Jan Provaznik, Jelena Pistolic, Vladimir Benes, Paul Tiesinga, Tansu Celikel
Experience-dependent plasticity (EDP) is essential for anatomical and functional maturation of sensory circuits during development. Although the principal synaptic and circuit mechanisms of EDP are increasingly well studied experimentally and computationally, its molecular mechanisms remain largely elusive. EDP can be readily studied in the rodent barrel cortex, where each "barrel column" preferentially represents deflections of its own principal whisker. Depriving select whiskers while sparing their neighbours introduces competition between barrel columns, ultimately leading to weakening of intracortical, translaminar (i...
October 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28942923/transcriptional-architecture-of-synaptic-communication-delineates-gabaergic-neuron-identity
#16
Anirban Paul, Megan Crow, Ricardo Raudales, Miao He, Jesse Gillis, Z Josh Huang
Understanding the organizational logic of neural circuits requires deciphering the biological basis of neuronal diversity and identity, but there is no consensus on how neuron types should be defined. We analyzed single-cell transcriptomes of a set of anatomically and physiologically characterized cortical GABAergic neurons and conducted a computational genomic screen for transcriptional profiles that distinguish them from one another. We discovered that cardinal GABAergic neuron types are delineated by a transcriptional architecture that encodes their synaptic communication patterns...
October 19, 2017: Cell
https://www.readbyqxmd.com/read/28934501/model-based-design-of-rna-hybridization-networks-implemented-in-living-cells
#17
Guillermo Rodrigo, Satya Prakash, Shensi Shen, Eszter Majer, José-Antonio Daròs, Alfonso Jaramillo
Synthetic gene circuits allow the behavior of living cells to be reprogrammed, and non-coding small RNAs (sRNAs) are increasingly being used as programmable regulators of gene expression. However, sRNAs (natural or synthetic) are generally used to regulate single target genes, while complex dynamic behaviors would require networks of sRNAs regulating each other. Here, we report a strategy for implementing such networks that exploits hybridization reactions carried out exclusively by multifaceted sRNAs that are both targets of and triggers for other sRNAs...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28928941/computational-design-of-molecular-motors-as-nanocircuits-in-leishmaniasis
#18
Dipali Kosey, Shailza Singh
Cutaneous leishmaniasis is the most common form of lesihmaniasis, caused by Leishmania major and is spread by the bite of a sandfly .This species infects the macrophages and dendritic cells Due to multi-drug resistance, there is a need for a new therapeutic technique. Recently, a novel molecular motor of Leishmania, Myosin XXI, was classified and characterized. In addition, the drug resistance in this organism has been linked with the overexpression of ABC transporters. Systems biology aims to study the simulation and modeling of natural biological systems whereas synthetic biology deals with building novel and artificial biological parts and devices  Together they have contributed enormously to drug discovery, vaccine design and development, infectious disease detection and diagnostics...
2017: F1000Research
https://www.readbyqxmd.com/read/28864344/understanding-and-engineering-plant-form
#19
REVIEW
Jennifer A N Brophy, Therese LaRue, José R Dinneny
A plant's form is often an important determinant of its fitness and economic value. Historically, the process of changing a plant's form has been slow, requiring iterative rounds of growth and selection. Here, we review strategies for producing plants with altered forms. We discuss techniques for identifying genes involved in plant form development and the tools that will be needed to design and engineer plants with altered forms. Synthetic genetic circuits are highlighted for their potential to generate novel plant forms...
August 29, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28801912/computational-sequence-design-with-r2odna-designer
#20
James T MacDonald, Velia Siciliano
Recently developed DNA assembly methods have enabled the rapid and simultaneous assembly of multiple parts to create complex synthetic gene circuits. A number of groups have proposed the use of computationally designed orthogonal spacer sequences to guide the ordered assembly of parts using overlap-directed or homologous recombination-based methods. This approach is particularly useful for assembling multiple parts with repetitive elements. Orthogonal spacer sequences (sometimes called UNSs-unique nucleotide sequences) also have a number of other potential uses including in the design of synthetic promoters regulated by novel regulatory elements...
2017: Methods in Molecular Biology
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