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Functional mapping

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https://www.readbyqxmd.com/read/28454383/fam53b-truncation-caused-by-t-10-19-q26-q13-chromosome-translocation-in-acute-lymphoblastic-leukemia
#1
Ioannis Panagopoulos, Ludmila Gorunova, Synne Torkildsen, Anne Tierens, Sverre Heim, Francesca Micci
RNA-sequencing of the patient's bone marrow detected fusion transcripts in which the coding sequence of the FAM53B gene (from 10q26) was fused to a genomic sequence (from 19q13) that mapped upstream of the SLC7A10 locus. Reverse transcription-polymerase chain reaction together with Sanger sequencing verified the presence of this fusion transcript. The FAM53B fusion transcript is not expected to produce any chimeric protein. However, it may code for a truncated FAM53B protein consisting of the first 302 amino acids of FAM53B together with amino acids from the 19q13 sequence...
April 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454066/direct-measurement-of-igm-antigen-interaction-energy-on-individual-red-blood-cells
#2
Natasha Yeow, Rico F Tabor, Gil Garnier
Most blood grouping tests rely on the principle of red blood cells (RBCs) agglutination. Agglutination is triggered by the binding of specific blood grouping antibodies to the corresponding RBC surface antigen on multiple cells. The interaction energies between blood grouping antibodies and antigens have been poorly defined in immunohaematology. Here for the first time, we functionalized atomic force microscope (AFM) cantilevers with the IgM form of blood grouping antibodies to probe populations of individual RBCs of different groups under physiological conditions...
April 21, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28454042/cortical-plasticity-and-levodopa-induced-dyskinesias-in-parkinson-s-disease-connecting-the-dots-in-a-multicomponent-network
#3
REVIEW
Roopa Rajan, Traian Popa, Angelo Quartarone, Maria Felice Ghilardi, Asha Kishore
Levodopa-induced dyskinesias are motor complications following long term dopaminergic therapy in Parkinson's disease (PD). Impaired brain plasticity resulting in the creation of aberrant motor maps intended to encode normal voluntary movement is proposed to result in the development of dyskinesias. Traditionally, the various nodes in the motor network like the striato-cortical and the cerebello-thalamic loops were thought to function independent of each other with little communication among them. Anatomical evidence from primates revealed the existence of reciprocal loops between the basal ganglia and the cerebellum providing an anatomical basis for communication between the motor network loops...
April 10, 2017: Clinical Neurophysiology: Official Journal of the International Federation of Clinical Neurophysiology
https://www.readbyqxmd.com/read/28453673/vexor-an-integrative-environment-for-prioritization-of-functional-variants-in-fine-mapping-analysis
#4
Audrey Lemaçon, Charles Joly Beauparlant, Penny Soucy, Jamie Allen, Douglas Easton, Peter Kraft, Jacques Simard, Arnaud Droit
Motivation: The identification of the functional variants responsible for observed genome-wide association studies (GWAS) signals is one of the most challenging tasks of the post-GWAS research era. Several tools have been developed to annotate genetic variants by their genomic location and potential functional implications. Each of these tools has its own requirements and internal logic, which forces the user to become acquainted with each interface. Results: From an awareness of the amount of work needed to analyze a single locus, we have built a flexible, versatile and easy-to-use web interface designed to help in prioritizing variants and predicting their potential functional implications...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453668/a-mass-graph-based-approach-for-the-identification-of-modified-proteoforms-using-top-down-tandem-mass-spectra
#5
Qiang Kou, Si Wu, Nikola Tolic, Ljiljana Paša-Tolic, Yunlong Liu, Xiaowen Liu
Motivation: Although proteomics has rapidly developed in the past decade, researchers are still in the early stage of exploring the world of complex proteoforms, which are protein products with various primary structure alterations resulting from gene mutations, alternative splicing, post-translational modifications, and other biological processes. Proteoform identification is essential to mapping proteoforms to their biological functions as well as discovering novel proteoforms and new protein functions...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453662/mglur5-tunes-ngf-trka-signaling-to-orient-spiny-stellate-neuron-dendrites-toward-thalamocortical-axons-during-whisker-barrel-map-formation
#6
Jui-Yen Huang, Hui-Chen Lu
Neurons receive and integrate synaptic inputs at their dendrites, thus dendritic patterning shapes neural connectivity and behavior. Aberrant dendritogenesis is present in neurodevelopmental disorders such as Down's syndrome and autism. Abnormal glutamatergic signaling has been observed in these diseases, as has dysfunction of the metabotropic glutamate receptor 5 (mGluR5). Deleting mGluR5 in cortical glutamatergic neurons disrupted their coordinated dendritic outgrowth toward thalamocortical axons and perturbed somatosensory circuits...
April 27, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/28449477/continuous-administration-of-recombinant-human-b-type-natriuretic-peptide-can-improve-heart-and-renal-function-in-patients-after-cardiopulmonary-bypass-surgery
#7
Shiguan Le, Jian Xiao, Wei Li, Jing Wang, Qing Wang, Wang Xi, Jibin Xu, Zhinong Wang
BACKGROUND: Any cardiac surgery under cardiopulmonary bypass (CPB) will induce ischemia-reperfusion injury and systematic inflammatory response, which may lead to exacerbation. Conventional therapy strategy is to use inotropes, diuretics and vasodilator drugs, yet, the therapeutic effects of which need to be improved. Recombinant human B-type natriuretic peptide (rhBNP) has been shown to be efficacious in the treatment of acute decompensated heart failure and acute myocardial infarction...
March 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/28449397/differential-proteome-profiling-in-the-hippocampus-of-amnesic-mice
#8
Meghraj Singh Baghel, Mahendra Kumar Thakur
Amnesia or memory loss is associated with brain aging and several neurodegenerative pathologies including Alzheimer's disease (AD). This can be induced by a cholinergic antagonist scopolamine, but the underlying molecular mechanism is poorly understood. The present study of proteome profiling in the hippocampus could provide conceptual insights into the molecular mechanisms involved in amnesia. To reveal this, mice were administered scopolamine to induce amnesia and memory impairment was validated by novel object recognition test...
April 27, 2017: Hippocampus
https://www.readbyqxmd.com/read/28449077/executive-network-activation-is-linked-to-walking-speed-in-older-adults-functional-mri-and-tcd-ultrasound-evidence-from-the-mobilize-boston-study
#9
Azizah J Jor'dan, Victoria N Poole, Ikechukwu Iloputaife, William Milberg, Brad Manor, Michael Esterman, Lewis A Lipsitz
Background: Changes in cerebral blood flow velocity (CBF) in response to a cognitive task (task-related ΔCBF) have been shown by Transcranial Doppler ultrasonography (TCD) to be reduced in slow walkers. However, it is unknown whether reduced task-related ΔCBF is associated with reduced neural activity in specific brain regions, as measured by blood-oxygen-level dependent (BOLD) functional magnetic resonance imaging (fMRI). Methods: We assessed the regional changes in neural activity associated with reduced middle cerebral artery (MCA) task-related ΔCBF to an executive task and slow walking speed in 67 community-dwelling older adults from the MOBILIZE Boston Study...
April 26, 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/28449067/using-high-throughput-barcode-sequencing-to-efficiently-map-connectomes
#10
Ian D Peikon, Justus M Kebschull, Vasily V Vagin, Diana I Ravens, Yu-Chi Sun, Eric Brouzes, Ivan R Corrêa, Dario Bressan, Anthony M Zador
The function of a neural circuit is determined by the details of its synaptic connections. At present, the only available method for determining a neural wiring diagram with single synapse precision-a 'connectome'-is based on imaging methods that are slow, labor-intensive and expensive. Here, we present SYNseq, a method for converting the connectome into a form that can exploit the speed and low cost of modern high-throughput DNA sequencing. In SYNseq, each neuron is labeled with a unique random nucleotide sequence-an RNA 'barcode'-which is targeted to the synapse using engineered proteins...
April 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28448657/association-between-slc16a5-genetic-variation-and-cisplatin-induced-ototoxic-effects-in-adult-patients-with-testicular-cancer
#11
Britt I Drögemöller, Jose G Monzon, Amit P Bhavsar, Adrienne E Borrie, Beth Brooks, Galen E B Wright, Geoffrey Liu, Daniel J Renouf, Christian K Kollmannsberger, Philippe L Bedard, Folefac Aminkeng, Ursula Amstutz, Claudette A Hildebrand, Erandika P Gunaretnam, Carol Critchley, Zhuo Chen, Liam R Brunham, Michael R Hayden, Colin J D Ross, Karen A Gelmon, Bruce C Carleton
Importance: Cisplatin-induced ototoxic effects are an important complication that affects testicular cancer survivors as a consequence of treatment. The identification of genetic variants associated with this adverse drug reaction will further our mechanistic understanding of its development and potentially lead to strategies to prevent ototoxic effects. Objective: To identify the genetic variants associated with cisplatin-induced ototoxic effects in adult testicular cancer patients...
April 27, 2017: JAMA Oncology
https://www.readbyqxmd.com/read/28448640/mapping-of-the-lassa-virus-lamp1-binding-site-reveals-unique-determinants-not-shared-by-other-old-world-arenaviruses
#12
Hadar Israeli, Hadas Cohen-Dvashi, Anastasiya Shulman, Amir Shimon, Ron Diskin
Cell entry of many enveloped viruses occurs by engagement with cellular receptors, followed by internalization into endocytic compartments and pH-induced membrane fusion. A previously unnoticed step of receptor switching was found to be critical during cell entry of two devastating human pathogens: Ebola and Lassa viruses. Our recent studies revealed the functional role of receptor switching to LAMP1 for triggering membrane fusion by Lassa virus and showed the involvement of conserved histidines in this switching, suggesting that other viruses from this family may also switch to LAMP1...
April 27, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28448616/abundance-profiling-of-specific-gene-groups-using-precomputed-gut-metagenomes-yields-novel-biological-hypotheses
#13
Konstantin Yarygin, Alexander Tyakht, Andrey Larin, Elena Kostryukova, Sergei Kolchenko, Vilgelm Bitner, Dmitry Alexeev
The gut microbiota is essentially a multifunctional bioreactor within a human being. The exploration of its enormous metabolic potential provides insights into the mechanisms underlying microbial ecology and interactions with the host. The data obtained using "shotgun" metagenomics capture information about the whole spectrum of microbial functions. However, each new study presenting new sequencing data tends to extract only a little of the information concerning the metabolic potential and often omits specific functions...
2017: PloS One
https://www.readbyqxmd.com/read/28448538/combined-lipidomic-and-proteomic-analysis-of-isolated-human-islets-exposed-to-palmitate-reveals-time-dependent-changes-in-insulin-secretion-and-lipid-metabolism
#14
Kirsten Roomp, Hjalti Kristinsson, Domitille Schvartz, Kumari Ubhayasekera, Ernest Sargsyan, Levon Manukyan, Azazul Chowdhury, Hannes Manell, Venkata Satagopam, Karlfried Groebe, Reinhard Schneider, Jonas Bergquist, Jean-Charles Sanchez, Peter Bergsten
Studies on the pathophysiology of type 2 diabetes mellitus (T2DM) have linked the accumulation of lipid metabolites to the development of beta-cell dysfunction and impaired insulin secretion. In most in vitro models of T2DM, rodent islets or beta-cell lines are used and typically focus is on specific cellular pathways or organs. Our aim was to, firstly, develop a combined lipidomics and proteomics approach for lipotoxicity in isolated human islets and, secondly, investigate if the approach could delineate novel and/ or confirm reported mechanisms of lipotoxicity...
2017: PloS One
https://www.readbyqxmd.com/read/28448523/semaphorin-1a-prevents-drosophila-olfactory-projection-neuron-dendrites-from-mis-targeting-into-select-antennal-lobe-regions
#15
Hung-Chang Shen, Sao-Yu Chu, Tsai-Chi Hsu, Chun-Han Wang, I-Ya Lin, Hung-Hsiang Yu
Elucidating how appropriate neurite patterns are generated in neurons of the olfactory system is crucial for comprehending the construction of the olfactory map. In the Drosophila olfactory system, projection neurons (PNs), primarily derived from four neural stem cells (called neuroblasts), populate their cell bodies surrounding to and distribute their dendrites in distinct but overlapping patterns within the primary olfactory center of the brain, the antennal lobe (AL). However, it remains unclear whether the same molecular mechanisms are employed to generate the appropriate dendritic patterns in discrete AL glomeruli among PNs produced from different neuroblasts...
April 27, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28448275/multi-band-decomposition-analysis-application-to-cardiac-alternans-as-a-function-of-temperature
#16
A Gizzi, A Loppini, E M Cherry, C Cherubini, F H Fenton, S Filippi
OBJECTIVE: It has long been known that variations in temperature can facilitate the development of cardiac arrhythmias. Here, we aim to quantify the effects of temperature on cardiac alternans properties. APPROACH: in this work, we use optical mapping recordings of canine ventricular epicardial preparations to demonstrate that hypothermia can promote the formation of alternans, which is an important precursor to potentially lethal arrhythmias like fibrillation. We then present a novel quantification of alternans properties for a broad range of cycle lengths under different thermal states...
May 2017: Physiological Measurement
https://www.readbyqxmd.com/read/28448253/a-map-of-abstract-relational-knowledge-in-the-human-hippocampal-entorhinal-cortex
#17
Mona M Garvert, Raymond J Dolan, Timothy Ej Behrens
The hippocampal-entorhinal system encodes a map of space that guides spatial navigation. Goal-directed behaviour outside of spatial navigation similarly requires a representation of abstract forms of relational knowledge. This information relies on the same neural system, but it is not known whether the organisational principles governing continuous maps may extend to the implicit encoding of discrete, non-spatial graphs. Here, we show that the human hippocampal-entorhinal system can represent relationships between objects using a metric that depends on associative strength...
April 27, 2017: ELife
https://www.readbyqxmd.com/read/28448233/t1-and-t2-mapping-in-recognition-of-early-cardiac-involvement-in-systemic-sarcoidosis
#18
Valentina O Puntmann, Alexander Isted, Rocio Hinojar, Lucy Foote, Gerald Carr-White, Eike Nagel
Purpose To determine whether quantitative tissue characterization with T1 and T2 mapping supports recognition of myocardial involvement in patients with systemic sarcoidosis. Materials and Methods Fifty-three consecutive patients with a biopsy-proven extracardiac diagnosis of systemic sarcoidosis (21 men; median age, 45 years; interquartile range, 22 years) and 36 normotensive previously healthy control subjects (14 men; median age, 43 years; interquartile range, 18 years) underwent cardiovascular magnetic resonance imaging, which was performed to assess cardiac function and late gadolinium enhancement, and T1 and T2 mapping...
April 27, 2017: Radiology
https://www.readbyqxmd.com/read/28448074/simultaneous-electrical-recording-of-cardiac-electrophysiology-and-contraction-on-chip
#19
Fang Qian, Chao Huang, Yi-Dong Lin, Anna N Ivanovskaya, Thomas J O'Hara, Ross H Booth, Cameron J Creek, Heather A Enright, David A Soscia, Anna M Belle, Ronglih Liao, Felice C Lightstone, Kristen S Kulp, Elizabeth K Wheeler
Prevailing commercialized cardiac platforms for in vitro drug development utilize planar microelectrode arrays to map action potentials, or impedance sensing to record contraction in real time, but cannot record both functions on the same chip with high spatial resolution. Here we report a novel cardiac platform that can record cardiac tissue adhesion, electrophysiology, and contractility on the same chip. The platform integrates two independent yet interpenetrating sensor arrays: a microelectrode array for field potential readouts and an interdigitated electrode array for impedance readouts...
April 27, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28447979/reconstitution-of-nucleosomes-with-differentially-isotope-labeled-sister-histones
#20
Stamatios Liokatis
Asymmetrically modified nucleosomes contain the two copies of a histone (sister histones) decorated with distinct sets of Post-translational Modifications (PTMs). They are newly identified species with unknown means of establishment and functional implications. Current analytical methods are inadequate to detect the copy-specific occurrence of PTMs on the nucleosomal sister histones. This protocol presents a biochemical method for the in vitro reconstitution of nucleosomes containing differentially isotope-labeled sister histones...
March 26, 2017: Journal of Visualized Experiments: JoVE
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