keyword
MENU ▼
Read by QxMD icon Read
search

Walhout

keyword
https://www.readbyqxmd.com/read/28088694/metabolic-network-modeling-with-model-organisms
#1
REVIEW
L Safak Yilmaz, Albertha Jm Walhout
Flux balance analysis (FBA) with genome-scale metabolic network models (GSMNM) allows systems level predictions of metabolism in a variety of organisms. Different types of predictions with different accuracy levels can be made depending on the applied experimental constraints ranging from measurement of exchange fluxes to the integration of gene expression data. Metabolic network modeling with model organisms has pioneered method development in this field. In addition, model organism GSMNMs are useful for basic understanding of metabolism, and in the case of animal models, for the study of metabolic human diseases...
January 12, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/27934693/gene-centered-yeast-one-hybrid-assays
#2
Juan I Fuxman Bass, John S Reece-Hoyes, Albertha J M Walhout
An important question when studying gene regulation is which transcription factors (TFs) interact with which cis-regulatory elements, such as promoters and enhancers. Addressing this issue in complex multicellular organisms is challenging as several hundreds of TFs and thousands of regulatory elements must be considered in the context of different tissues and physiological conditions. Yeast one-hybrid (Y1H) assays provide a powerful "gene-centered" method to identify the TFs that can bind a DNA sequence of interest...
December 1, 2016: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/27934686/zymolyase-treatment-and-polymerase-chain-reaction-amplification-from-genomic-and-plasmid-templates-from-yeast
#3
Juan I Fuxman Bass, John S Reece-Hoyes, Albertha J M Walhout
Here, we present a protocol for amplifying DNA fragments from the genome of, or plasmids transformed into, yeast strains that require the use of the lytic enzyme zymolyase to break open the yeast cells by digesting the cell wall. Yeast strains requiring such treatment include YM4271 and Y1HaS2, whereas other yeast strains (e.g., MaV103) might not require treatment with Zymolyase.
December 1, 2016: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/27934685/colony-lift-colorimetric-assay-for-%C3%AE-galactosidase-activity
#4
Juan I Fuxman Bass, John S Reece-Hoyes, Albertha J M Walhout
In this protocol, we present a qualitative assay for monitoring the level of expression of β-galactosidase, an enzyme encoded by the LacZ gene, in yeast. This is useful both for determining autoactivity of LacZ expression in yeast DNA "bait" strains and for assessing LacZ reporter gene activation mediated by a transcription factor "prey" interaction with a DNA bait of interest in yeast one-hybrid (Y1H) assays. In this colorimetric assay, yeast are lysed in liquid nitrogen and then assayed for β-galactosidase expression using the colorless compound X-gal, which turns blue in the presence of this enzyme...
December 1, 2016: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/27934684/performing-yeast-one-hybrid-library-screens
#5
Juan I Fuxman Bass, John S Reece-Hoyes, Albertha J M Walhout
Yeast one-hybrid (Y1H) assays are used to identify which transcription factor (TF) "prey" molecules can bind a DNA fragment of interest that is used as "bait". Y1H assays involve introducing plasmids that encode TFs into a yeast "bait strain" in which the DNA fragment of interest is integrated upstream of one or more reporters, and activation of these reporters indicates that a TF-DNA interaction has occurred. These plasmids express each TF as a hybrid protein (hence the "one-hybrid" name) fused to the activation domain (AD) of the yeast TF Gal4...
December 1, 2016: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/27934683/generating-bait-strains-for-yeast-one-hybrid-assays
#6
Juan I Fuxman Bass, John S Reece-Hoyes, Albertha J M Walhout
Yeast one-hybrid (Y1H) assays are used to identify which transcription factor (TF) "preys" can bind a DNA fragment of interest that is used as the "bait." Undertaking Y1H assays requires the generation of a yeast "bait strain" for each DNA fragment of interest that features the DNA bait coupled to a reporter(s). Plasmids encoding TFs fused to the Gal4 activation domain (AD) are then introduced into the bait strain, and activation of the reporter(s) indicates that a TF-DNA interaction has occurred. Here, we present a protocol for the first part of the strategy-the generation of a bait strain for Y1H assays...
December 1, 2016: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/27777270/a-gene-centered-c-%C3%A2-elegans-protein-dna-interaction-network-provides-a-framework-for-functional-predictions
#7
Juan I Fuxman Bass, Carles Pons, Lucie Kozlowski, John S Reece-Hoyes, Shaleen Shrestha, Amy D Holdorf, Akihiro Mori, Chad L Myers, Albertha Jm Walhout
Transcription factors (TFs) play a central role in controlling spatiotemporal gene expression and the response to environmental cues. A comprehensive understanding of gene regulation requires integrating physical protein-DNA interactions (PDIs) with TF regulatory activity, expression patterns, and phenotypic data. Although great progress has been made in mapping PDIs using chromatin immunoprecipitation, these studies have only characterized ~10% of TFs in any metazoan species. The nematode C. elegans has been widely used to study gene regulation due to its compact genome with short regulatory sequences...
October 24, 2016: Molecular Systems Biology
https://www.readbyqxmd.com/read/27756805/widespread-structural-brain-involvement-in-als-is-not-limited-to-the-c9orf72-repeat-expansion
#8
Henk-Jan Westeneng, Renée Walhout, Milou Straathof, Ruben Schmidt, Jeroen Hendrikse, Jan H Veldink, Martijn P van den Heuvel, Leonard H van den Berg
BACKGROUND: In patients with a C9orf72 repeat expansion (C9+), a neuroimaging phenotype with widespread structural cerebral changes has been found. We aimed to investigate the specificity of this neuroimaging phenotype in patients with amyotrophic lateral sclerosis (ALS). METHODS: 156 C9- and 14 C9+ patients with ALS underwent high-resolution T1-weighted MRI; a subset (n=126) underwent diffusion-weighted imaging. Cortical thickness, subcortical volumes and white matter integrity were compared between C9+ and C9- patients...
October 18, 2016: Journal of Neurology, Neurosurgery, and Psychiatry
https://www.readbyqxmd.com/read/27383050/metabolic-network-rewiring-of-propionate-flux-compensates-vitamin-b12-deficiency-in-c-elegans
#9
Emma Watson, Viridiana Olin-Sandoval, Michael J Hoy, Chi-Hua Li, Timo Louisse, Victoria Yao, Akihiro Mori, Amy D Holdorf, Olga G Troyanskaya, Markus Ralser, Albertha Jm Walhout
Metabolic network rewiring is the rerouting of metabolism through the use of alternate enzymes to adjust pathway flux and accomplish specific anabolic or catabolic objectives. Here, we report the first characterization of two parallel pathways for the breakdown of the short chain fatty acid propionate in Caenorhabditis elegans. Using genetic interaction mapping, gene co-expression analysis, pathway intermediate quantification and carbon tracing, we uncover a vitamin B12-independent propionate breakdown shunt that is transcriptionally activated on vitamin B12 deficient diets, or under genetic conditions mimicking the human diseases propionic- and methylmalonic acidemia, in which the canonical B12-dependent propionate breakdown pathway is blocked...
2016: ELife
https://www.readbyqxmd.com/read/27227390/scanning-tunneling-spectroscopy-study-of-the-dirac-spectrum-of-germanene
#10
C J Walhout, A Acun, L Zhang, M Ezawa, H J W Zandvliet
The temperature dependence of the density of states of germanene, synthesized on Ge/Pt crystals, has been investigated with scanning tunneling spectroscopy. After correction for thermal broadening, a virtually perfect V-shaped density of states, which is a hallmark of a two-dimensional Dirac system, has been found. In an attempt to directly measure the energy dispersion relation via quasiparticle interference we have recorded spatial maps of the differential conductivity near the edges and defects of germanene...
July 20, 2016: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/27211857/a-caenorhabditis-elegans-genome-scale-metabolic-network-model
#11
L Safak Yilmaz, Albertha J M Walhout
Caenorhabditis elegans is a powerful model to study metabolism and how it relates to nutrition, gene expression, and life history traits. However, while numerous experimental techniques that enable perturbation of its diet and gene function are available, a high-quality metabolic network model has been lacking. Here, we reconstruct an initial version of the C. elegans metabolic network. This network model contains 1,273 genes, 623 enzymes, and 1,985 metabolic reactions and is referred to as iCEL1273. Using flux balance analysis, we show that iCEL1273 is capable of representing the conversion of bacterial biomass into C...
May 25, 2016: Cell Systems
https://www.readbyqxmd.com/read/27127907/intramolecular-hydrogen-bonding-effects-on-the-fluorescence-of-prodan-derivatives
#12
Isaac G Alty, Douglas W Cheek, Tao Chen, David B Smith, Emma Q Walhout, Christopher J Abelt
The effects of intramolecular hydrogen-bonding on the fluorescence behavior of three derivatives of 6-propionyl-2-dimethylaminonaphthalene are reported. The H-bonding effects are revealed through comparisons with corresponding reference compounds in which the H-bond-donating hydroxyl groups are replaced with methoxy groups. In toluene, intramolecular H bonding gives rise to a dramatic increase in the fluorescence intensity but only a slight red shift in the position. This behavior is attributed to decreased efficiency in intersystem crossing due to an increase in the energy of the n → π* triplet state...
May 26, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/26631516/understanding-metabolic-regulation-at-a-systems-level-metabolite-sensing-mathematical-predictions-and-model-organisms
#13
REVIEW
Emma Watson, L Safak Yilmaz, Albertha J M Walhout
Metabolic networks are extensively regulated to facilitate tissue-specific metabolic programs and robustly maintain homeostasis in response to dietary changes. Homeostatic metabolic regulation is achieved through metabolite sensing coupled to feedback regulation of metabolic enzyme activity or expression. With a wealth of transcriptomic, proteomic, and metabolomic data available for different cell types across various conditions, we are challenged with understanding global metabolic network regulation and the resulting metabolic outputs...
2015: Annual Review of Genetics
https://www.readbyqxmd.com/read/25910213/human-gene-centered-transcription-factor-networks-for-enhancers-and-disease-variants
#14
Juan I Fuxman Bass, Nidhi Sahni, Shaleen Shrestha, Aurian Garcia-Gonzalez, Akihiro Mori, Numana Bhat, Song Yi, David E Hill, Marc Vidal, Albertha J M Walhout
Gene regulatory networks (GRNs) comprising interactions between transcription factors (TFs) and regulatory loci control development and physiology. Numerous disease-associated mutations have been identified, the vast majority residing in non-coding regions of the genome. As current GRN mapping methods test one TF at a time and require the use of cells harboring the mutation(s) of interest, they are not suitable to identify TFs that bind to wild-type and mutant loci. Here, we use gene-centered yeast one-hybrid (eY1H) assays to interrogate binding of 1,086 human TFs to 246 enhancers, as well as to 109 non-coding disease mutations...
April 23, 2015: Cell
https://www.readbyqxmd.com/read/25910212/widespread-macromolecular-interaction-perturbations-in-human-genetic-disorders
#15
Nidhi Sahni, Song Yi, Mikko Taipale, Juan I Fuxman Bass, Jasmin Coulombe-Huntington, Fan Yang, Jian Peng, Jochen Weile, Georgios I Karras, Yang Wang, István A Kovács, Atanas Kamburov, Irina Krykbaeva, Mandy H Lam, George Tucker, Vikram Khurana, Amitabh Sharma, Yang-Yu Liu, Nozomu Yachie, Quan Zhong, Yun Shen, Alexandre Palagi, Adriana San-Miguel, Changyu Fan, Dawit Balcha, Amelie Dricot, Daniel M Jordan, Jennifer M Walsh, Akash A Shah, Xinping Yang, Ani K Stoyanova, Alex Leighton, Michael A Calderwood, Yves Jacob, Michael E Cusick, Kourosh Salehi-Ashtiani, Luke J Whitesell, Shamil Sunyaev, Bonnie Berger, Albert-László Barabási, Benoit Charloteaux, David E Hill, Tong Hao, Frederick P Roth, Yu Xia, Albertha J M Walhout, Susan Lindquist, Marc Vidal
How disease-associated mutations impair protein activities in the context of biological networks remains mostly undetermined. Although a few renowned alleles are well characterized, functional information is missing for over 100,000 disease-associated variants. Here we functionally profile several thousand missense mutations across a spectrum of Mendelian disorders using various interaction assays. The majority of disease-associated alleles exhibit wild-type chaperone binding profiles, suggesting they preserve protein folding or stability...
April 23, 2015: Cell
https://www.readbyqxmd.com/read/25905672/mapping-and-analysis-of-caenorhabditis-elegans-transcription-factor-sequence-specificities
#16
Kamesh Narasimhan, Samuel A Lambert, Ally W H Yang, Jeremy Riddell, Sanie Mnaimneh, Hong Zheng, Mihai Albu, Hamed S Najafabadi, John S Reece-Hoyes, Juan I Fuxman Bass, Albertha J M Walhout, Matthew T Weirauch, Timothy R Hughes
Caenorhabditis elegans is a powerful model for studying gene regulation, as it has a compact genome and a wealth of genomic tools. However, identification of regulatory elements has been limited, as DNA-binding motifs are known for only 71 of the estimated 763 sequence-specific transcription factors (TFs). To address this problem, we performed protein binding microarray experiments on representatives of canonical TF families in C. elegans, obtaining motifs for 129 TFs. Additionally, we predict motifs for many TFs that have DNA-binding domains similar to those already characterized, increasing coverage of binding specificities to 292 C...
2015: ELife
https://www.readbyqxmd.com/read/25559107/rna-interference-in-caenorhabditis-elegans
#17
Darryl Conte, Lesley T MacNeil, Albertha J M Walhout, Craig C Mello
RNAi has become an essential tool in C. elegans research. This unit describes procedures for RNAi in C. elegans by microinjecting with dsRNA, feeding with bacteria expressing dsRNA, and soaking in dsRNA solution, as well as high-throughput methods for RNAi-based screens.
2015: Current Protocols in Molecular Biology
https://www.readbyqxmd.com/read/25281019/subcortical-structures-in-amyotrophic-lateral-sclerosis
#18
Henk-Jan Westeneng, Esther Verstraete, Renée Walhout, Ruben Schmidt, Jeroen Hendrikse, Jan H Veldink, Martijn P van den Heuvel, Leonard H van den Berg
The aim of this study was to assess the involvement of deep gray matter, hippocampal subfields, and ventricular changes in patients with amyotrophic lateral sclerosis (ALS). A total of 112 ALS patients and 60 healthy subjects participated. High-resolution T1-weighted images were acquired using a 3T MRI scanner. Thirty-nine patients underwent a follow-up scan. Volumetric and shape analyses of subcortical structures were performed, measures were correlated with clinical parameters, and longitudinal changes were assessed...
February 2015: Neurobiology of Aging
https://www.readbyqxmd.com/read/25215497/determination-and-inference-of-eukaryotic-transcription-factor-sequence-specificity
#19
Matthew T Weirauch, Ally Yang, Mihai Albu, Atina G Cote, Alejandro Montenegro-Montero, Philipp Drewe, Hamed S Najafabadi, Samuel A Lambert, Ishminder Mann, Kate Cook, Hong Zheng, Alejandra Goity, Harm van Bakel, Jean-Claude Lozano, Mary Galli, Mathew G Lewsey, Eryong Huang, Tuhin Mukherjee, Xiaoting Chen, John S Reece-Hoyes, Sridhar Govindarajan, Gad Shaulsky, Albertha J M Walhout, François-Yves Bouget, Gunnar Ratsch, Luis F Larrondo, Joseph R Ecker, Timothy R Hughes
Transcription factor (TF) DNA sequence preferences direct their regulatory activity, but are currently known for only ∼1% of eukaryotic TFs. Broadly sampling DNA-binding domain (DBD) types from multiple eukaryotic clades, we determined DNA sequence preferences for >1,000 TFs encompassing 54 different DBD classes from 131 diverse eukaryotes. We find that closely related DBDs almost always have very similar DNA sequence preferences, enabling inference of motifs for ∼34% of the ∼170,000 known or predicted eukaryotic TFs...
September 11, 2014: Cell
https://www.readbyqxmd.com/read/25172020/worms-bacteria-and-micronutrients-an-elegant-model-of-our-diet
#20
REVIEW
Lutfu Safak Yilmaz, Albertha J M Walhout
Micronutrients are required in small proportions in a diet to carry out key metabolic roles for biomass and energy production. Humans receive micronutrients either directly from their diet or from gut microbiota that metabolize other nutrients. The nematode Caenorhabditis elegans and its bacterial diet provide a relatively simple and genetically tractable model to study both direct and microbe-mediated effects of micronutrients. Recently, this model has been used to gain insight into the relationship between micronutrients, physiology, and metabolism...
November 2014: Trends in Genetics: TIG
keyword
keyword
24963
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"