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Functional mapping

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https://www.readbyqxmd.com/read/28346745/emp10-encodes-a-mitochondrial-ppr-protein-that-affects-the-cis-splicing-of-nad2-intron-1-and-seed-development-in-maize
#1
Manjun Cai, L Shuzhen, Feng Sun, Qin Sun, Hailiang Zhao, Xuemei Ren, Yanxin Zhao, Baocai Tan, Zuxin Zhang, Fazhan Qiu
In higher plants, many mitochondrial genes contain group II-type introns that are removed from RNAs by splicing to produce mature transcripts that are then translated into functional proteins. However, the factors involved in the splicing of mitochondrial introns and their biological functions are not well understood in maize. Here, we isolated an empty pericarp 10 (emp10) mutant and identified the underlying gene by map-based cloning. Emp10 encodes a P-type mitochondria-targeted pentatricopeptide repeat (PPR) protein with 10 PPR motifs...
March 27, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28346710/the-arabidopsis-thiamin-deficient-mutant-pale-green1-lacks-thiamin-monophosphate-phosphatase-of-the-vitamin-b1-biosynthesis-pathway
#2
Wei-Yu Hsieh, Jo-Chien Liao, Hsin-Tzu Wang, Tzu-Huan Hung, Ching-Chih Tseng, Tsui-Yun Chung, Ming-Hsiun Hsieh
Thiamin diphosphate (TPP, vitamin B1) is an essential coenzyme present in all organisms. Animals obtain TPP from their diets, but plants synthesize TPP de novo. We isolated and characterized an Arabidopsis pale green1 (pale1) mutant that contained higher concentrations of thiamin monophosphate (TMP) and less thiamin and TPP than the wild type. Supplementation with thiamin, but not the thiazole and pyrimidine precursors, rescued the mutant phenotype, indicating that the pale1 mutant is a thiamin-deficient mutant...
March 27, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28346705/performance-of-a-polymer-coated-silicon-microarray-for-simultaneous-detection-of-food-allergen-specific-ige-and-igg4
#3
Steven Sievers, Marina Cretich, Paola Gagni, Birgit Ahrens, Galina Grishina, Hugh Sampson, Bodo Niggemann, Marcella Chiari, Kirsten Beyer
BACKGROUND: Microarray-based component-resolved diagnostics (CRD) has become an accepted tool to detect allergen specific IgE-sensitization towards hundreds of allergens in parallel from one drop of serum. Nevertheless specificity and sensitivity as well as a simultaneous detection of allergen specific IgG4, as a potential parameter for tolerance development, remain to be optimized. OBJECTIVE: We applied the recently introduced silicon chip coated with a functional polymer named copoly(DMA-NAS-MAPS) to the simultaneous detection of food allergen specific IgE and IgG4, and compared it with ImmunoCAP and ImmunoCAP ISAC...
March 27, 2017: Clinical and Experimental Allergy: Journal of the British Society for Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28346509/systematic-identification-of-phosphorylation-mediated-protein-interaction-switches
#4
Matthew J Betts, Oliver Wichmann, Mathias Utz, Timon Andre, Evangelia Petsalaki, Pablo Minguez, Luca Parca, Frederick P Roth, Anne-Claude Gavin, Peer Bork, Robert B Russell
Proteomics techniques can identify thousands of phosphorylation sites in a single experiment, the majority of which are new and lack precise information about function or molecular mechanism. Here we present a fast method to predict potential phosphorylation switches by mapping phosphorylation sites to protein-protein interactions of known structure and analysing the properties of the protein interface. We predict 1024 sites that could potentially enable or disable particular interactions. We tested a selection of these switches and showed that phosphomimetic mutations indeed affect interactions...
March 27, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28346356/microinjection-of-antibodies-targeting-the-lamin-a-c-histone-binding-site-blocks-mitotic-entry-and-reveals-separate-chromatin-interactions-with-hp1-cenpb-and-pml
#5
Charles R Dixon, Melpomeni Platani, Alexandr A Makarov, Eric C Schirmer
Lamins form a scaffold lining the nucleus that binds chromatin and contributes to spatial genome organization; however, due to the many other functions of lamins, studies knocking out or altering the lamin polymer cannot clearly distinguish between direct and indirect effects. To overcome this obstacle, we specifically targeted the mapped histone-binding site of A/C lamins by microinjecting antibodies specific to this region predicting that this would make the genome more mobile. No increase in chromatin mobility was observed; however, interestingly, injected cells failed to go through mitosis, while control antibody-injected cells did...
March 25, 2017: Cells
https://www.readbyqxmd.com/read/28346054/genomic-regions-in-local-endangered-sheep-encode-potentially-favorable-genes
#6
Bianca Moioli, Roberto Steri, Gennaro Catillo
The economic evaluation of farm animal genetic resources plays a key role in developing conservation programs. However, to date, the link between diversity as assessed by neutral genetic markers and the functional diversity is not yet understood. Two genome-wide comparisons, using over 44,000 Single Nucleotide Polymorphisms, identified the markers with the highest difference in allele frequency between the Alpago endangered breed and two clusters, composed of four specialized dairy sheep, and four meat breeds respectively...
March 27, 2017: Animal Biotechnology
https://www.readbyqxmd.com/read/28345642/dynamic-changes-in-amygdala-psychophysiological-connectivity-reveal-distinct-neural-networks-for-facial-expressions-of-basic-emotions
#7
Matteo Diano, Marco Tamietto, Alessia Celeghin, Lawrence Weiskrantz, Mona-Karina Tatu, Arianna Bagnis, Sergio Duca, Giuliano Geminiani, Franco Cauda, Tommaso Costa
The quest to characterize the neural signature distinctive of different basic emotions has recently come under renewed scrutiny. Here we investigated whether facial expressions of different basic emotions modulate the functional connectivity of the amygdala with the rest of the brain. To this end, we presented seventeen healthy participants (8 females) with facial expressions of anger, disgust, fear, happiness, sadness and emotional neutrality and analyzed amygdala's psychophysiological interaction (PPI). In fact, PPI can reveal how inter-regional amygdala communications change dynamically depending on perception of various emotional expressions to recruit different brain networks, compared to the functional interactions it entertains during perception of neutral expressions...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28345269/multi-task-diagnosis-for-autism-spectrum-disorders-using-multi-modality-features-a-multi-center-study
#8
Jun Wang, Qian Wang, Jialin Peng, Dong Nie, Feng Zhao, Minjeong Kim, Han Zhang, Chong-Yaw Wee, Shitong Wang, Dinggang Shen
Autism spectrum disorder (ASD) is a neurodevelopment disease characterized by impairment of social interaction, language, behavior, and cognitive functions. Up to now, many imaging-based methods for ASD diagnosis have been developed. For example, one may extract abundant features from multi-modality images and then derive a discriminant function to map the selected features toward the disease label. A lot of recent works, however, are limited to single imaging centers. To this end, we propose a novel multi-modality multi-center classification (M3CC) method for ASD diagnosis...
March 27, 2017: Human Brain Mapping
https://www.readbyqxmd.com/read/28344657/well-positioned-nucleosomes-punctuate-polycistronic-pol-ii-transcription-units-and-flank-silent-vsg-gene-arrays-in-trypanosoma-brucei
#9
Johannes Petrus Maree, Megan Lindsay Povelones, David Johannes Clark, Gloria Rudenko, Hugh-George Patterton
BACKGROUND: The compaction of DNA in chromatin in eukaryotes allowed the expansion of genome size and coincided with significant evolutionary diversification. However, chromatin generally represses DNA function, and mechanisms coevolved to regulate chromatin structure and its impact on DNA. This included the selection of specific nucleosome positions to modulate accessibility to the DNA molecule. Trypanosoma brucei, a member of the Excavates supergroup, falls in an ancient evolutionary branch of eukaryotes and provides valuable insight into the organization of chromatin in early genomes...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28344190/an-artificial-intelligence-approach-fit-for-trna-gene-studies-in-the-era-of-big-sequence-data
#10
Yuki Iwasaki, Takashi Abe, Kennosuke Wada, Yoshiko Wada, Toshimichi Ikemura
Unsupervised data mining capable of extracting a wide range of knowledge from big data without prior knowledge or particular models is a timely application in the era of big sequence data accumulation in genome research. By handling oligonucleotide compositions as high-dimensional data, we have previously modified the conventional self-organizing map (SOM) for genome informatics and established BLSOM, which can analyze more than ten million sequences simultaneously. Here, we develop BLSOM specialized for tRNA genes (tDNAs) that can cluster (self-organize) more than one million microbial tDNAs according to their cognate amino acid solely depending on tetra- and pentanucleotide compositions...
March 24, 2017: Genes & Genetic Systems
https://www.readbyqxmd.com/read/28343986/the-hemodynamic-signal-as-a-first-order-low-pass-temporal-filter-evidence-and-implications-for-neuroimaging-studies
#11
Antoine Sauvage, Guillaume Hubert, Jonathan Touboul, Jérôme Ribot
Neuronal activation triggers local changes in blood flow and hemoglobin oxygenation. These hemodynamic signals can be recorded through functional magnetic resonance imaging or intrinsic optical imaging, and allows inferring neural activity in response to stimuli. These techniques are widely used to uncover functional brain architectures. However, their accuracy suffers from distortions inherent to hemodynamic responses and noise. The analysis of these signals currently relies on models of impulse hemodynamic responses to brief stimuli...
March 23, 2017: NeuroImage
https://www.readbyqxmd.com/read/28343628/functional-architectures-of-local-and-distal-regulation-of-gene-expression-in-multiple-human-tissues
#12
Xuanyao Liu, Hilary K Finucane, Alexander Gusev, Gaurav Bhatia, Steven Gazal, Luke O'Connor, Brendan Bulik-Sullivan, Fred A Wright, Patrick F Sullivan, Benjamin M Neale, Alkes L Price
Genetic variants that modulate gene expression levels play an important role in the etiology of human diseases and complex traits. Although large-scale eQTL mapping studies routinely identify many local eQTLs, the molecular mechanisms by which genetic variants regulate expression remain unclear, particularly for distal eQTLs, which these studies are not well powered to detect. Here, we leveraged all variants (not just those that pass stringent significance thresholds) to analyze the functional architecture of local and distal regulation of gene expression in 15 human tissues by employing an extension of stratified LD-score regression that produces robust results in simulations...
March 18, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28343082/lateralizing-language-function-with-pre-operative-functional-magnetic-resonance-imaging-in-early-proficient-bilingual-patients
#13
Monika M Połczyńska, Kevin Japardi, Susan Y Bookheimer
Research on bilinguals with brain lesions is complicated by high patient variability, making it difficult to find well-matched controls. We benefitted from a database of over 700 patients and conducted an analysis of pre-operative functional magnetic resonance imaging data to assess language dominance in 25 early, highly proficient Spanish-English bilinguals, and 25 carefully matched monolingual controls. Our results showed that early bilingualism is associated with greater bilateral hemispheric involvement, and monolingualism is associated with stronger left hemisphere lateralization (p=0...
March 23, 2017: Brain and Language
https://www.readbyqxmd.com/read/28342886/using-genetic-data-to-improve-species-distribution-models
#14
Jérémy Bouyer, Renaud Lancelota
Tsetse flies (Diptera, Glossinidae) transmit human and animal trypanosomoses in Africa, respectively a neglected human disease (sleeping sickness) and the most important constraint to cattle production in infested countries (nagana). We recently developed a methodology to map landscape friction (i.e. resistance to movement) for tsetse in West Africa. The goal was to identify natural barriers to tsetse dispersal, and potentially isolated tsetse populations for targeting elimination programmes. Most species distribution models neglect landscape functional connectivity whereas environmental factors affecting suitability or abundance are not necessarily the same as those influencing gene flows...
March 22, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28342751/reproducibility-of-four-frequently-used-local-heating-protocols-to-assess-cutaneous-microvascular-function
#15
Kirsty A Roberts, Thijs van Gent, Nicola D Hopkins, Helen Jones, Ellen A Dawson, Richard Draijer, Howard H Carter, Ceri L Atkinson, Daniel J Green, Dick H J Thijssen, David A Low
BACKGROUND: Skin microvascular responses to local heating are frequently used to assess microvascular function. Several local heating protocols have been developed, all varying slightly in execution. The aim of this study was to determine the inter-day reproducibility of the four most commonly used local heating protocols in healthy young subjects. METHODS: Fifteen, healthy males (28±5yrs, BMI 25±2kg/m(2)) attended two experimental trials 2-7days apart. During each trial, baseline and maximal thermally stimulated forearm skin responses were examined simultaneously at four sites on the dominant forearm using laser Doppler flowmetry (LDF)...
March 22, 2017: Microvascular Research
https://www.readbyqxmd.com/read/28342743/measurement-of-ion-fluxes-across-epithelia
#16
REVIEW
Miroslaw Zajac, Krzysztof Dolowy
Epithelial tissues line all wet surfaces of vertebrate bodies. Their major function is directional transport of ions and water. Cells forming an epithelial layer are bound together by a tight junction that forms a barrier to ion flux. Ions and water are transported via specialized molecules. The presence of a defect in a single ion channel molecule leads to cystic fibrosis - the most common, fatal, human genetic disease. The paper describes ion transport data obtained by means of different experimental techniques...
March 22, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28342400/using-gene-expression-database-to-uncover-biology-functions-of-1-4-disubstituted-1-2-3-triazole-analogues-synthesized-via-a-copper-i-catalyzed-reaction
#17
Chun-Li Su, Chia-Ling Tseng, Chintakunta Ramesh, Hsiao-Sheng Liu, Chi-Ying F Huang, Ching-Fa Yao
We have synthesized bioactive 1,4-disubstituted 1,2,3-triazole analogues containing 2H-1,4-benzoxazin-3-(4H)-one derivatives via 1,3-dipolar cycloaddition in the presence of CuI. All the reactions proceeded smoothly and afforded its desired products in excellent yields. Among these analogues, 3y exhibited a better cytotoxic effect on human hepatocellular carcinoma (HCC) Hep 3B cells and displayed less cytotoxicity on normal human umbilical vein endothelial cells, compared with Sorafenib, a targeted therapy for advanced HCC...
March 18, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28342325/development-of-a-rapid-matrix-digestion-technique-for-ultrastructural-analysis-of-elastic-fibers-in-the-intervertebral-disc
#18
Javad Tavakoli, John J Costi
Collagen and elastic fibers are two major fibrous constituents of the annulus fibrosus (AF) in the disc that contribute to its mechanical and viscoelastic properties. It was thought that elastic fibers play no substantial role in the function and properties of the disc as these fibers were irregularly distributed. Studies that have revealed highly organized elastic fibers with different regional orientation and distribution, while being strongly crosslinked with matrix, suggesting their contribution to disc structure-function properties...
March 21, 2017: Journal of the Mechanical Behavior of Biomedical Materials
https://www.readbyqxmd.com/read/28342191/exploiting-multicompartment-effects-in-triple-echo-steady-state-t2-mapping-for-fat-fraction-quantification
#19
Dian Liu, Andreas Steingoetter, Jelena Curcic, Sebastian Kozerke
PURPOSE: To investigate and exploit the effect of intravoxel off-resonance compartments in the triple-echo steady-state (TESS) sequence without fat suppression for T2 mapping and to leverage the results for fat fraction quantification. METHODS: In multicompartment tissue, where at least one compartment is excited off-resonance, the total signal exhibits periodic modulations as a function of echo time (TE). Simulated multicompartment TESS signals were synthesized at various TEs...
March 25, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28341866/mapping-brain-structure-and-function-cellular-resolution-global-perspective
#20
REVIEW
Günther K H Zupanc
A comprehensive understanding of the brain requires analysis, although from a global perspective, with cellular, and even subcellular, resolution. An important step towards this goal involves the establishment of three-dimensional high-resolution brain maps, incorporating brain-wide information about the cells and their connections, as well as the chemical architecture. The progress made in such anatomical brain mapping in recent years has been paralleled by the development of physiological techniques that enable investigators to generate global neural activity maps, also with cellular resolution, while simultaneously recording the organism's behavioral activity...
March 24, 2017: Journal of Comparative Physiology. A, Neuroethology, Sensory, Neural, and Behavioral Physiology
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