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https://www.readbyqxmd.com/read/28220420/identification-of-mapk-substrates-using-quantitative-phosphoproteomics
#1
Tong Zhang, Jacqueline D Schneider, Ning Zhu, Sixue Chen
Activation of mitogen-activated protein kinases (MAPKs) under diverse biotic and abiotic factors and identification of an array of downstream MAPK target proteins are hot topics in plant signal transduction. Through interactions with a plethora of substrate proteins, MAPK cascades regulate many physiological processes in the course of plant growth, development, and response to environmental factors. Identification and quantification of potential MAPK substrates are essential, but have been technically challenging...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28197189/does-a-combined-intervention-program-of-repetitive-transcranial-magnetic-stimulation-and-intensive-occupational-therapy-affect-cognitive-function-in-patients-with-post-stroke-upper-limb-hemiparesis
#2
Takatoshi Hara, Masahiro Abo, Kiyohito Kakita, Takeshi Masuda, Ryunosuke Yamazaki
Low-frequency repetitive transcranial magnetic stimulation (LF-rTMS) to the contralesional hemisphere and intensive occupational therapy (iOT) have been shown to contribute to a significant improvement in upper limb hemiparesis in patients with chronic stroke. However, the effect of the combined intervention program of LF-rTMS and iOT on cognitive function is unknown. We retrospectively investigated whether the combined treatment influence patient's Trail-Making Test part B (TMT-B) performance, which is a group of easy and inexpensive neuropsychological tests that evaluate several cognitive functions...
December 2016: Neural Regeneration Research
https://www.readbyqxmd.com/read/28196536/community-engagement-and-the-social-context-of-targeted-malaria-treatment-a-qualitative-study-in-kayin-karen-state-myanmar
#3
Kate Sahan, Christopher Pell, Frank Smithuis, Aung Kyaw Phyo, Sai Maung Maung, Chanida Indrasuta, Arjen M Dondorp, Nicholas J White, Nicholas P J Day, Lorenz von Seidlein, Phaik Yeong Cheah
BACKGROUND: The spread of artemisinin-resistance in Plasmodium falciparum is a threat to current global malaria control initiatives. Targeted malaria treatment (TMT), which combines mass anti-malarial administration with conventional malaria prevention and control measures, has been proposed as a strategy to tackle this problem. The effectiveness of TMT depends on high levels of population coverage and is influenced by accompanying community engagement activities and the local social context...
February 14, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28195392/relative-protein-quantification-and-accessible-biology-in-lung-tumor-proteomes-from-four-lc-ms-ms-discovery-platforms
#4
Paul A Stewart, Bin Fang, Robbert J C Slebos, Guolin Zhang, Adam L Borne, Katherine Fellows, Jamie K Teer, Y Ann Chen, Eric Welsh, Steven A Eschrich, Eric B Haura, John M Koomen
Discovery proteomics experiments include many options for sample preparation and mass spectrometry data acquisition, which are capable of creating datasets for quantifying thousands of proteins. To define a strategy that would produce a dataset with sufficient content while optimizing required resources, we compared 1) single sample liquid chromatography-tandem mass spectrometry (LC-MS/MS) with data dependent acquisition (DDA) to single sample LC-MS/MS with data independent acquisition (DIA) and 2) peptide fractionation with label-free quantification (LF) to isobaric labeling followed by peptide fractionation (TMT 6-plex)...
February 14, 2017: Proteomics
https://www.readbyqxmd.com/read/28194965/extensive-peptide-fractionation-and-y1-ion-based-interference-detection-method-for-enabling-accurate-quantification-by-isobaric-labeling-and-mass-spectrometry
#5
Mingming Niu, Ji-Hoon Cho, Kiran Kodali, Vishwajeeth Pagala, Anthony A High, Hong Wang, Zhiping Wu, Yuxin Li, Wenjian Bi, Hui Zhang, Xusheng Wang, Wei Zou, Junmin Peng
Isobaric labeling quantification by mass spectrometry (MS) has emerged as a powerful technology for multiplexed large-scale protein profiling, but measurement accuracy in complex mixtures is confounded by the interference from coisolated ions, resulting in ratio compression. Here we report that the ratio compression can be essentially resolved by the combination of pre-MS peptide fractionation, MS2-based interference detection, and post-MS computational interference correction. To recapitulate the complexity of biological samples, we pooled tandem mass tag (TMT)-labeled Escherichia coli peptides at 1:3:10 ratios and added in ∼20-fold more rat peptides as background, followed by the analysis of two-dimensional liquid chromatography (LC)-MS/MS...
February 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28188956/the-neural-substrate-of-gait-and-executive-function-relationship-in-elderly-women-a-pet-study
#6
Ryota Sakurai, Kenji Ishii, Masashi Yasunaga, Rumi Takeuchi, Yoh Murayama, Naoko Sakuma, Muneyuki Sakata, Keiichi Oda, Kenji Ishibashi, Kiichi Ishiwata, Yoshinori Fujiwara, Manuel Montero-Odasso
AIM: Understanding the relationship between age-related gait impairment, such as slow gait, and executive functioning in seniors may help identify individuals at higher risk of mobility decline, falls, and progression to dementia at earlier stages. We aim to identify brain regions concomitantly associated with poor gait and executive functioning in a cohort of well-functioning elderly women. METHODS: In total, 149 well-functioning women aged 70.1 ± 6.2 years underwent FDG-PET to evaluate regional cerebral metabolic rates of glucose normalized in reference to cerebellar glucose metabolic value (normalized-rCMRglc) in 16 brain areas...
February 11, 2017: Geriatrics & Gerontology International
https://www.readbyqxmd.com/read/28188531/relative-protein-quantification-using-tandem-mass-tag-mass-spectrometry
#7
Lichao Zhang, Joshua E Elias
Measuring protein changes over time or following stimuli is one of the important tasks of proteomics. In the past decade, several strategies have been developed for the relative quantification of proteins using mass spectrometry (MS). Isobaric labeling strategies for relative quantitative proteomics allow for parallel multiplexing of quantitative experiments. With this technique, multiple peptide samples are chemically labeled with isobaric chemical tag variants and each variant has the same molecular structure and mass...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28188525/high-ph-reversed-phase-micro-columns-for-simple-sensitive-and-efficient-fractionation-of-proteome-and-tmt-labeled-phosphoproteome-digests
#8
Benjamin Ruprecht, Jana Zecha, Daniel P Zolg, Bernhard Kuster
Despite recent advances in mass spectrometric sequencing speed and improved sensitivity, the in-depth analysis of proteomes still widely relies on off-line peptide separation and fractionation to deal with the enormous molecular complexity of shotgun digested proteomes. While a multitude of methods has been established for off-line peptide separation using HPLC columns, their use can be limited particularly when sample quantities are scarce. In this protocol, we describe an approach which combines high pH reversed-phase peptide separation into few fractions in StageTip micro-columns...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28183337/the-added-value-of-kinematic-evaluation-of-the-timed-finger-to-nose-test-in-persons-post-stroke
#9
Gudrun M Johansson, Helena Grip, Mindy F Levin, Charlotte K Häger
BACKGROUND: Upper limb coordination in persons post-stroke may be estimated by the commonly used Finger-to-Nose Test (FNT), which is also part of the Fugl-Meyer Assessment. The total movement time (TMT) is used as a clinical outcome measure, while kinematic evaluation also enables an objective quantification of movement quality and motor performance. Our aims were to kinematically characterize FNT performance in persons post-stroke and controls and to investigate the construct validity of the test in persons with varying levels of impairment post-stroke...
February 10, 2017: Journal of Neuroengineering and Rehabilitation
https://www.readbyqxmd.com/read/28176443/quantitative-phosphoproteomic-analysis-reveals-system-wide-signaling-pathways-regulated-by-site-specific-phosphorylation-on-keratin-8-in-skin-squamous-cell-carcinoma-derived-cell-line
#10
Richa Tiwari, Indrajit Sahu, Bihari Lal Soni, Gajanan J Sathe, Keshava K Datta, Pankaj Thapa, Shruti Sinha, Chella Krishna Vadivel, Bharti Dhaka, Harsha Gowda, Milind M Vaidya
Keratin 8/18, a simple epithelia specific keratin pair, is often aberrantly expressed in squamous cell carcinomas (SCC) where its expression is correlated with increased invasion and poor prognosis. Majority of Keratin 8 (K8) functions are governed by its phosphorylation at Serine(73) (head-domain) and Serine(431) (tail-domain) residues. Although, deregulation of K8 phosphorylation is associated with progression of different carcinomas, its role in skin-SCC and the underlying mechanism is obscure. In this direction, we performed TMT-based quantitative phosphoproteomics by expressing K8 wild type, phosphodead and phosphomimetic mutants in K8-deficient A431 cells...
February 7, 2017: Proteomics
https://www.readbyqxmd.com/read/28165663/interrogating-the-hidden-phosphoproteome
#11
Un-Beom Kang, William M Alexander, Jarrod A Marto
Post-genomic studies continue to highlight the potential clinical importance of protein phosphorylation signaling pathways in drug discovery. Unfortunately the dynamic range and variable stoichiometry of protein phosphorylation continues to stymie efforts to achieve comprehensive characterization of the human phosphoproteome. In this study, we develop a complementary, two-stage method for enrichment of cysteine-containing phosphopeptides combined with TMT multiplex labeling for relative quantification. Use of this approach with multi-dimension fractionation in mammalian cells yielded more than 7,000 unique cys-phosphopeptide sequences, comprising 15%-20% novel phosphorylation sites...
February 6, 2017: Proteomics
https://www.readbyqxmd.com/read/28156249/utility-of-mri-based-disproportionately-enlarged-subarachnoid-space-hydrocephalus-scoring-for-predicting-prognosis-after-surgery-for-idiopathic-normal-pressure-hydrocephalus-clinical-research
#12
Narihide Shinoda, Osamu Hirai, Shinya Hori, Kazuyuki Mikami, Toshiaki Bando, Daisuke Shimo, Takahiro Kuroyama, Yoji Kuramoto, Masato Matsumoto, Yasushi Ueno
OBJECTIVE The presence of disproportionately enlarged subarachnoid space hydrocephalus (DESH) on brain imaging is a recognized finding of idiopathic normal pressure hydrocephalus (iNPH), but the features of DESH can vary across patients. The aim of this study was to evaluate the utility of MRI-based DESH scoring for predicting prognosis after surgery. METHODS In this single-center, retrospective cohort study, the DESH score was determined by consensus between a group of neurosurgeons, neurologists, and a neuroradiologist based on the preoperative MRI findings of the patients with suspected iNPH...
February 3, 2017: Journal of Neurosurgery
https://www.readbyqxmd.com/read/28152591/analysis-of-reproducibility-of-proteome-coverage-and-quantitation-using-isobaric-mass-tags-itraq-and-tmt
#13
Tammy M Casey, Javed M Khan, Scott D Bringans, Tomas Koudelka, Pari S Takle, Rachael A Downs, Andreja Livk, Robert A Syme, Kar-Chun Tan, Richard J Lipscombe
This study aimed to compare the depth and reproducibility of total proteome and differentially expressed protein coverage in technical duplicates and triplicates using iTRAQ 4-plex, iTRAQ 8-plex, and TMT 6-plex reagents. The analysis was undertaken because comprehensive comparisons of isobaric mass tag reproducibility have not been widely reported in the literature. The highest number of proteins was identified with 4-plex, followed by 8-plex and then 6-plex reagents. Quantitative analyses revealed that more differentially expressed proteins were identified with 4-plex reagents than 8-plex reagents and 6-plex reagents...
February 3, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28152536/convergent-results-from-neuropsychology-and-from-neuroimaging-in-patients-with-mild-cognitive-impairment
#14
Carl Fredrik Eliassen, Ivar Reinvang, Per Selnes, Tormod Fladby, Erik Hessen
BACKGROUND/AIMS: To investigate the correspondence between neuropsychological single measures and variation in fludeoxyglucose positron emission tomography (FDG PET) glucose metabolism and magnetic resonance imaging (MRI) cortical thickness in mild cognitive impairment (MCI) patients. METHODS: Forty-two elderly controls and 73 MCI subjects underwent FDG PET and MRI scanning. Backward regression analyses with PET and MRI regions were used as dependent variables, while Rey Auditory Verbal Memory Test (RAVLT) recall, Trail Making Test B (TMT B), and a composite test score (RAVLT learning and immediate recall, TMT A, COWAT, and letter-number sequencing) were used as predictor variables...
February 3, 2017: Dementia and Geriatric Cognitive Disorders
https://www.readbyqxmd.com/read/28145956/evaluation-of-first-ray-mobility-in-patients-with-hallux-valgus-using-weight-bearing-ct-and-a-3-d-analysis-system-a-comparison-with-normal-feet
#15
Tadashi Kimura, Makoto Kubota, Tetsuya Taguchi, Naoki Suzuki, Asaki Hattori, Keishi Marumo
BACKGROUND: Some physicians report that patients with hallux valgus have hypermobility at the tarsometatarsal (TMT) joint of the first ray and 3-dimensional (3-D) deformity. With use of non-weight-bearing and weight-bearing computed tomography (CT), we evaluated the 3-D mobility of each joint of the first ray in feet with hallux valgus compared with normal feet. METHODS: Ten feet of 10 patients with hallux valgus and 10 feet of 10 healthy volunteers with no foot disorders were examined...
February 1, 2017: Journal of Bone and Joint Surgery. American Volume
https://www.readbyqxmd.com/read/28135715/peptidomic-analysis-of-cultured-cardiomyocytes-exposed-to-acute-ischemic-hypoxia
#16
Lijie Wu, Hua Li, Xing Li, Yumei Chen, Qijun Zhang, Zijie Cheng, Yi Fan, Guixian Song, Lingmei Qian
BACKGROUND: Acute Myocardial Infarction (AMI) is a life-threatening cardiovascular disease involving disruption of blood flow to the heart, consequent tissue damage, and sometimes death. Peptidomics, an emerging branch of proteomics, has attracted wide attention. METHODS: A comparative peptidomic profiling was used to explore changes induced by acute ischemic-hypoxia in primary cultured neonatal rat myocardial cells. Analysis of six-plex tandem mass tag (TMT) labelled peptides was performed using nanoflow liquid chromatography coupled online with an LTQ-Orbitrap Velos mass spectrometer...
26, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28132846/a-90-day-toxicity-study-of-gmtmt-transgenic-maize-in-sprague-dawley-rats
#17
Jin Fang, Yongquan Feng, Yuan Zhi, Lan Zhang, Zhou Yu, Xudong Jia
GmTMT transgenic maize is a genetically modified maize plant that overexpresses the γ-tocopherol methyltransferase (γ-TMT) from Glycine max (Gm). The γ-TMT gene was introduced into maize line Zhen58 to encode the GmTMT2a protein which can convert γ-tocopherol into α-tocopherol. Overexpression of GmTMT2a significantly increased the α-tocopherol content in transgenic maize. The present study was designed to investigate any potential effects of GmTMT maize grain in a 90-day subchronic rodent feeding study...
January 27, 2017: Regulatory Toxicology and Pharmacology: RTP
https://www.readbyqxmd.com/read/28121007/nanotubes-impregnated-human-olfactory-bulb-neural-stem-cells-promote-neuronal-differentiation-in-trimethyltin-induced-neurodegeneration-rat-model
#18
H E Marei, A A Elnegiry, A Zaghloul, A Althani, N Afifi, A Abd-Elmaksoud, A Farag, S Lashen, S Rezk, Z Shouman, C Cenciarelli, Anwarul Hasan
Neural stem cells (NSCs) are multipotent self-renewing cells that could be used in cellular-based therapy for a wide variety of neurodegenerative diseases including Alzheimer's diseases (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), and multiple sclerosis (MS). Being multipotent in nature, they are practically capable of giving rise to major cell types of the nervous tissue including neurons, astrocytes and oligodendrocytes. This is in marked contrast to neural progenitor cells which are committed to a specific lineage fate...
January 25, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/28109439/deep-profiling-of-proteome-and-phosphoproteome-by-isobaric-labeling-extensive-liquid-chromatography-and-mass-spectrometry
#19
B Bai, H Tan, V R Pagala, A A High, V P Ichhaporia, L Hendershot, J Peng
Mass spectrometry-based proteomics has experienced an unprecedented advance in comprehensive analysis of proteins and posttranslational modifications, with particular technical progress in liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) and isobaric labeling multiplexing capacity. Here, we introduce a deep proteomics profiling protocol that combines 10-plex tandem mass tag (TMT) labeling with an optimized LC-MS/MS platform to quantitate whole proteome and phosphoproteome. The major steps include protein extraction and digestion, TMT labeling, two-dimensional liquid chromatography, TiO2-mediated phosphopeptide enrichment, high-resolution mass spectrometry, and computational data processing...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28106925/clinical-study-evaluating-the-accuracy-of-injecting-the-distal-tarsal-joints-in-the-horse
#20
K A Seabaugh, K T Selberg, P O E Mueller, R B Eggleston, J F Peroni, K M Claunch, H J Markwell, G M Baxter
BACKGROUND: Osteoarthritis (OA) of the centrodistal (CD) and tarsometatarsal (TMT) joints is a common cause of lameness in horses. Intra-articular diagnostic anaesthesia and/or therapeutic injection are relied upon to help diagnose and treat many horses with OA of these joints. OBJECTIVES: The objective of this study was to determine the accuracy of arthrocentesis of the CD and TMT joints using a sample population of equine surgeons and surgery residents. STUDY DESIGN: Randomised experimental study...
January 20, 2017: Equine Veterinary Journal
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