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Functional mapping

Graham M Hughes, Emma M Boston, John A Finarelli, William J Murphy, Desmond G Higgins, Emma C Teeling
The olfactory receptor (OR) gene families, which govern mammalian olfaction, have undergone extensive expansion and contraction through duplication and pseudogenization. Previous studies have shown that broadly-defined environmental adaptations (e.g terrestrial vs aquatic) are correlated with the number of functional and non-functional OR genes retained. However, to date, no study has examined species-specific gene duplications in multiple phylogenetically divergent mammals to elucidate OR evolution and adaptation...
March 19, 2018: Molecular Biology and Evolution
R A Leo Elworth, Chabrielle Allen, Travis Benedict, Peter Dulworth, Luay Nakhleh
Summary: The evolutionary histories of individual regions across a genomic alignment - called 'local genealogies' - can differ from each other, due to processes such as recombination. Elucidating and analyzing these local genealogies are important for a large number of inference tasks, including those pertaining to species phylogenies, evolutionary processes, and trait mapping. In this paper, we present a toolkit for automated local phylogenomic analyses, or ALPHA. The purpose of this toolkit is to provide a wide array of functionalities for automated inference of local genealogies as well as analyses based on these local genealogies...
March 19, 2018: Bioinformatics
Wenhui Jiang, Tianxiang Liu, Wenzhi Nan, Diddugodage Chamila Jeewani, Yanlu Niu, Chunlian Li, Yong Wang, Xue Shi, Cong Wang, Jiahuan Wang, Yang Li, Xin Gao, Zhonghua Wang
The purple pericarp of bread wheat (Triticum aestivum L.) is a useful source of dietary anthocyanins. Previous mapping results indicated that the purple pericarp is controlled by two complementary genes located on chromosomes 7D and 2A. However, the related genes and their effects on regulating the purple pericarp are unknown. In this study, two transcription factors were characterised as anthocyanin activators in purple pericarp: TaPpm1 (purple pericarp-MYB 1) and TaPpb1 (purple pericarp-bHLH 1). Three nonfunctional variants were detected in the coding sequence of TaPpm1 from non-purple seed lines, in which the function of TaPpm1 was destroyed by insertion-caused frame shift or truncated peptides...
March 17, 2018: Journal of Experimental Botany
Subhasis Das, Manideepa Sengupta, Arijit Bag, Mumtaj Shah, Ankur Bordoloi
A synergistic approach was made to develop a highly stable and carbon resistant catalyst system based on cobalt and nickel supported over modified mesoporous silica for the dry reforming of methane (DRM). Modified mesoporous silica is prepared by a hydrothermal method, and the total Co & Ni composition is taken at around 5% by using the deposition-precipitation technique. CO2 reforming with methane was performed at 400-800 °C under atmospheric pressure as well as at a pressure of 1 MPa, keeping the CH4/CO2 ratio equal to unity...
March 21, 2018: Nanoscale
Lei Lei, Kesava Phaneendra Cherukuri, Uria Alcolombri, Diana Meltzer, Dan S Tawfik
Marine organisms release dimethylsulfide (DMS) via cleavage of dimethylsulfoniopropionate (DMSP). Different genes encoding proteins with DMSP lyase activity are known, yet these exhibit highly variable levels of activity. Most assigned bacterial DMSP lyases, including DddK, DddL, DddQ, DddW and DddY, appear to belong to one, cupin-like superfamily. Here, we attempted to define and map this superfamily dubbed Cupin-DLL: DMSP lyases and lyase-like. To this end, we have pursued the characterization of various recombinant DMSP lyases belonging to this superfamily of metallo-enzymes, and especially of DddY and DddL that seem to be the most active DMSP lyases in this superfamily...
March 21, 2018: Biochemistry
Ignacio Rebollo, Anne-Dominique Devauchelle, Benoît Béranger, Catherine Tallon-Baudry
Resting-state networks offer a unique window into the brain's functional architecture, but their characterization remains limited to instantaneous connectivity thus far. Here, we describe a novel resting-state network based on the delayed connectivity between the brain and the slow electrical rhythm (0.05 Hz) generated in the stomach. The gastric network cuts across classical resting-state networks with partial overlap with autonomic regulation areas. This network is composed of regions with convergent functional properties involved in mapping bodily space through touch, action or vision, as well as mapping external space in bodily coordinates...
March 21, 2018: ELife
Linlin Yang, Jun Zhao, Xinling Yu, Ruilong Zhang, Guangmei Han, Renyong Liu, Zhengjie Liu, Tingting Zhao, Ming-Yong Han, Zhongping Zhang
Hydrogen sulfide (H2S) is a key signaling molecule in the cytoprotection, vascular mediation and neurotransmission of living organisms. In-depth understanding of its production, trafficking, and transformation in cells is very important in the way H2S mediates cellular signal transductions and organism functions; it also motivates the development of H2S probes and imaging technologies. A fundamental challenge, however, is how to engineer probes with sensitivity and cellular penetrability that allow detection of spontaneous production of H2S in the entire cell space and live animals...
March 21, 2018: Analyst
David T Chau, Phoebe Fogelman, Pia Nordanskog, Wayne C Drevets, J Paul Hamilton
BACKGROUND: Functional neuroimaging studies have examined the neural substrates of treatments for major depressive disorder (MDD). Low sample size and methodological heterogeneity, however, undermine the generalizability of findings from individual studies. We conducted a meta-analysis to identify reliable neural changes resulting from different modes of treatment for MDD and compared them with each other and with reliable neural functional abnormalities observed in depressed versus control samples...
May 2017: Biological Psychiatry: Cognitive Neuroscience and Neuroimaging
Delphine Masschaele, Joris Wauman, Giel Vandemoortele, Delphine De Sutter, Leentje De Ceuninck, Sven Eyckerman, Jan Tavernier
Ring finger protein 41 (RNF41) is an E3 ubiquitin ligase involved in the ubiquitination and degradation of many proteins including ErbB3 receptors, BRUCE and parkin. Next to this, RNF41 regulates the intracellular trafficking of certain JAK2-associated cytokine receptors by ubiquitinating and suppressing USP8 which in turn destabilizes the ESCRT-0 complex. To further elucidate the function of RNF41 we used different orthogonal approaches to reveal the RNF41 protein complex: Affinity Purification-Mass Spectrometry, BioID and Virotrap...
March 21, 2018: Journal of Proteome Research
Shabnam Sadeghi Esfahlani, Tommy Thompson, Ali Davod Parsa, Ian Brown, Silvia Cirstea
This paper proposes the use of a non-immersive virtual reality rehabilitation system "ReHabgame" developed using Microsoft Kinect™ and the Thalmic™ Labs Myo gesture control armband. The ReHabgame was developed based on two third-person video games that provide a feasible possibility of assessing postural control and functional reach tests. It accurately quantifies specific postural control mechanisms including timed standing balance, functional reach tests using real-time anatomical landmark orientation, joint velocity, and acceleration while end trajectories were calculated using an inverse kinematics algorithm...
February 2018: Heliyon
Yang Dong, Dan Yang, Yuchi Han, Wei Cheng, Jiayu Sun, Ke Wan, Hong Liu, Andreas Greiser, Xiaoyue Zhou, Yucheng Chen
Background: Diffuse myocardial fibrosis is a common pathological process in many cardiovascular diseases. In order to determine disease, we must have standard normal imaging values. We investigated myocardial interstitial fibrosis of the left ventricle (LV) in a healthy population of Chinese adults and explored the impact of gender, age, and other physiological factors using a T1 mapping technique of cardiac magnetic resonance imaging (CMR). Materials and Methods: We recruited 69 healthy adult Chinese subjects (35 males; age 18-76)...
2018: Frontiers in Physiology
Ana Luisa Duarte, João Lopes Dias, Teresa Margarida Cunha
Diffusion-weighted imaging (DWI) is widely used in protocols for magnetic resonance imaging (MRI) of the female pelvis. It provides functional and structural information about biological tissues, without the use of ionizing radiation or intravenous administration of contrast medium. High signal intensity on DWI with simultaneous low signal intensity on apparent diffusion coefficient maps is usually associated with malignancy. However, that pattern can also be seen in many benign lesions, a fact that should be recognized by radiologists...
January 2018: Radiologia Brasileira
Jenna M Reinen, Oliver Y Chén, R Matthew Hutchison, B T Thomas Yeo, Kevin M Anderson, Mert R Sabuncu, Dost Öngür, Joshua L Roffman, Jordan W Smoller, Justin T Baker, Avram J Holmes
Higher-order cognition emerges through the flexible interactions of large-scale brain networks, an aspect of temporal coordination that may be impaired in psychosis. Here, we map the dynamic functional architecture of the cerebral cortex in healthy young adults, leveraging this atlas of transient network configurations (states), to identify state- and network-specific disruptions in patients with schizophrenia and psychotic bipolar disorder. We demonstrate that dynamic connectivity profiles are reliable within participants, and can act as a fingerprint, identifying specific individuals within a larger group...
March 20, 2018: Nature Communications
Carlos E Cardenas, Rachel E McCarroll, Laurence E Court, Baher A Elgohari, Hesham Elhalawani, Clifton D Fuller, Mona J Kamal, Mohamed A M Meheissen, Abdallah S R Mohamed, Arvind Rao, Bowman Williams, Andrew Wong, Jinzhong Yang, Michalis Aristophanous
PURPOSE: Automating and standardizing the contouring of clinical target volumes (CTVs) can reduce interphysician variability, which is one of the largest sources of uncertainty in head and neck radiation therapy. In addition to using uniform margin expansions to auto-delineate high-risk CTVs, very little work has been performed to provide patient- and disease-specific high-risk CTVs. The aim of the present study was to develop a deep neural network for the auto-delineation of high-risk CTVs...
February 7, 2018: International Journal of Radiation Oncology, Biology, Physics
Jiabin Liu, Guangyuan Wang, Qi Lin, Wenxing Liang, Zhiqiang Gao, Ping Mu, Guiquan Li, Limin Song
BACKGROUND: Protein lysine malonylation, a newly discovered post-translational modification (PTM), plays an important role in diverse metabolic processes in both eukaryotes and prokaryotes. Common wheat is a major global cereal crop. However, the functions of lysine malonylation are relatively unknown in this crop. Here, a global analysis of lysine malonylation was performed in wheat. RESULTS: In total, 342 lysine malonylated sites were identified in 233 proteins...
March 20, 2018: BMC Genomics
Zsolt Zador, Andrew T King, Nophar Geifman
BACKGROUND: Atypical meningiomas are common central nervous system neoplasms with high recurrence rate and poorer prognosis compared to their grade I counterparts. Surgical excision and radiotherapy remains the mainstay therapy but medical treatments are limited. We explore new drug candidates using computational drug repurposing based on the gene expression signature of atypical meningioma tissue with subsequent analysis of drug-generated expression profiles. We further explore possible mechanisms of action for the identified drug candidates using ingenuity pathway analysis (IPA)...
2018: PloS One
Xiaofen Zhang, Guoyun Wang, Bin Chen, Heshan Du, Fenglan Zhang, Haiying Zhang, Qian Wang, Sansheng Geng
First flower node (FFN) is an important trait for evaluating fruit earliness in pepper (Capsicum annuum L.), but the genetic mechanisms that control FFN are still poorly understood. In the present study, we developed 249 F2 plants derived from an intraspecific cross between the inbred pepper lines Z4 and Z5. Thirty plants with the highest FFN and 30 plants with the lowest FFN were chosen and their DNAs were pooled according to phenotype to construct two bulked DNA pools. Specific-locus amplified fragment sequencing (SLAF-seq) was combined with bulked segregant analysis (BSA) to identify candidate regions related to FFN...
2018: PloS One
Stephen Ashford, Heather Williams, Ajoy Nair, Samantha Orridge, Lynne Turner-Stokes
BACKGROUND: Goal-classification of person-centred goals, using Goal Attainment Scaling for leg spasticity treatment. METHODS: The study was conducted in two phases: phase I, a retrospective review to evaluate categories of goal set in routine clinical practice. Findings were used to design a goal classification system. Phase II, a multi-centre study to confirm the goal categories. Goals set (n = 270) were analysed from data collected at three centres in the UK (one centre for phase I)...
March 20, 2018: Disability and Rehabilitation
Yun-Ting Su, Meng-Yang Gu, Xi Chu, Xiang Feng, Yan-Qin Yu
The GABAergic neurons in the parafacial zone (PZ) play an important role in sleep-wake regulation and have been identified as part of a sleep-promoting center in the brainstem, but the long-range connections mediating this function remain poorly characterized. Here, we performed whole-brain mapping of both the inputs and outputs of the GABAergic neurons in the PZ of the mouse brain. We used the modified rabies virus EnvA-ΔG-DsRed combined with a Cre/loxP gene-expression strategy to map the direct monosynaptic inputs to the GABAergic neurons in the PZ, and found that they receive inputs mainly from the hypothalamic area, zona incerta, and parasubthalamic nucleus in the hypothalamus; the substantia nigra, pars reticulata and deep mesencephalic nucleus in the midbrain; and the intermediate reticular nucleus and medial vestibular nucleus (parvocellular part) in the pons and medulla...
March 20, 2018: Neuroscience Bulletin
Yeong Ran Jeong, Rae Ung Jeong, Jeong Hyun Son, Joon Cheol Kwon, Saem Jung, Mi A Song, Jin Ah Hwang, Gyun Min Lee
BACKGROUND: For regulatory approval, the comparability of a biosimilar product to an originator product should be ensured through thorough physicochemical and biological characterization. OBJECTIVE: To evaluate the biosimilarity between LBDE, the proposed biosimilar darbepoetin alfa, and NESP® , its originator, we performed a comprehensive physicochemical and biological characterization study. METHODS: Primary and higher-order protein structures were analyzed using Lys-C peptide mapping with liquid chromatography-mass spectrometry (LC-MS), disulfide bond identification, circular dichroism, and fluorescence spectroscopy...
March 19, 2018: BioDrugs: Clinical Immunotherapeutics, Biopharmaceuticals and Gene Therapy
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