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Lynex CN Carr IM Leek JP Achuthan R Mitchell S Maher ER Woods CG Bonthon DT Markham AF 《BMC neurology》2004,4(1):20
Background
Cerebral palsy (CP) is an heterogeneous group of neurological disorders of movement and/or posture, with an estimated incidence of 1 in 1000 live births. Non-progressive forms of symmetrical, spastic CP have been identified, which show a Mendelian autosomal recessive pattern of inheritance. We recently described the mapping of a recessive spastic CP locus to a 5 cM chromosomal region located at 2q24-31.1, in rare consanguineous families. 相似文献2.
KiYoung Lee David Thorneycroft Premanand Achuthan Henning Hermjakob Trey Ideker 《The Plant cell》2010,22(4):997-1005
Most cellular processes are enabled by cohorts of interacting proteins that form dynamic networks within the plant proteome. The study of these networks can provide insight into protein function and provide new avenues for research. This article informs the plant science community of the currently available sources of protein interaction data and discusses how they can be useful to researchers. Using our recently curated IntAct Arabidopsis thaliana protein–protein interaction data set as an example, we discuss potentials and limitations of the plant interactomes generated to date. In addition, we present our efforts to add value to the interaction data by using them to seed a proteome-wide map of predicted protein subcellular locations.For well over two decades, plant scientists have studied protein interactions within plants using many different and evolving approaches. Their findings are represented by a large and growing corpus of peer-reviewed literature reflecting the increasing activity in this area of plant proteomic research. More recently, a number of predicted interactomes have been reported in plants and, while these predictions remain largely untested, they could act as a useful guide for future research. These studies have allowed researchers to better understand the function of protein complexes and to refine our understanding of protein function within the cell (Uhrig, 2006; Morsy et al., 2008). The extraction of protein interaction data from the literature and its standardized deposition and representation within publicly available databases remains a challenging task. Aggregating the data in databases allows researchers to leverage visualization, data mining, and integrative approaches to produce new insights that would be unachievable when the data are dispersed within largely inaccessible formats (Rodriguez et al., 2009).Currently, there are three databases that act as repositories of plant protein interaction data. These are IntAct (http://www.ebi.ac.uk/intact/; Aranda et al., 2010), The Arabidopsis Information Resource (TAIR; http://www.Arabidopsis.org/; Poole, 2007), and BioGRID (http://www.thebiogrid.org/; Breitkreutz et al., 2008). These databases curate experimentally established interactions available from the peer-reviewed literature (as opposed to predicted interactions, which will be discussed below). Each repository takes its own approach to the capture, storage, and representation of protein interaction data. TAIR focuses on Arabidopsis thaliana protein–protein interaction data exclusively; BioGRID currently focuses on the plant species Arabidopsis and rice (Oryza sativa), while IntAct attempts to capture protein interaction data from any plant species. Unlike the other repositories, IntAct follows a deep curation strategy that captures detailed experimental and biophysical details, such as binding regions and subcellular locations of interactions using controlled vocabularies (Aranda et al., 2010). While the majority of plant interaction data held by IntAct concern protein–protein interaction data in Arabidopsis, there is a small but growing content of interaction data relating to protein–DNA, protein–RNA, and protein–small molecule interactions, as well as interaction data from other plant species.Using the IntAct Arabidopsis data set as an example, we outline how the accumulating knowledge captured in these repositories can be used to further our understanding of the plant proteome. We compare the characteristics of predicted interactomes with the IntAct protein–protein interaction data set, which consists entirely of experimentally measured protein interactions, to gauge the predictive accuracy of these studies. Finally, we show how the IntAct data set can be used together with a recently developed Divide and Conquer k-Nearest Neighbors Method (DC-kNN; K. Lee et al., 2008) to predict the subcellular locations for most Arabidopsis proteins. This data set predicts high confidence subcellular locations for many unannotated Arabidopsis proteins and should act as a useful resource for future studies of protein function. Although this article focuses on the IntAct Arabidopsis protein–protein interaction data set, readers are also encouraged to explore the resources offered by our colleagues at TAIR and BioGRID.Each database employs its own system to report molecular interactions, as represented in the referenced source publications, and each avoids making judgments on interaction reliability or whether two participants in a complex have a direct interaction. Thus, the user should carefully filter these data sets for their specific purpose based on the full annotation of the data sets. In particular, the user should consider the experimental methods and independent observation of the same interaction in different publications when assessing the reliability and type of interaction of the proteins (e.g., direct or indirect). Confidence scoring schemes for interaction data are discussed widely in the literature (Yu and Finley, 2009). 相似文献
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Achuthan A Masendycz P Lopez JA Nguyen T James DE Sweet MJ Hamilton JA Scholz GM 《Molecular and cellular biology》2008,28(20):6149-6159
Colony-stimulating factor 1 (CSF-1) is the main growth factor controlling the development of macrophages from myeloid progenitor cells. However, CSF-1 also regulates some of the key effector functions of macrophages (e.g., phagocytosis and cytokine secretion). The endosomal SNARE protein syntaxin 7 (Stx7) regulates vesicle trafficking events involved in phagocytosis and cytokine secretion. Therefore, we investigated the ability of CSF-1 to regulate Stx7. CSF-1 upregulated Stx7 expression in primary mouse macrophages; it also upregulated expression of its SNARE partners Vti1b and VAMP8 but not Stx8. Additionally, CSF-1 induced the rapid serine phosphorylation of Stx7 and enhanced its binding to Vti1b, Stx8, and VAMP8. Bioinformatics analysis and results from experiments with kinase inhibitors suggested the CSF-1-induced phosphorylation of Stx7 was mediated by protein kinase C and Akt in response to phosphatidylinositol 3-kinase activation. Based on mutagenesis studies, CSF-1 appeared to increase the binding of Stx7 to its SNARE partners by inducing the phosphorylation of serine residues in the Habc domain and/or “linker” region of Stx7. Thus, CSF-1 is a key regulator of Stx7 expression and function in macrophages. Furthermore, the effects of CSF-1 on Stx7 may provide a mechanism for the regulation of macrophage effector functions by CSF-1. 相似文献
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V. J. Rejish Kumar Cini Achuthan N. J. Manju Rosamma Philip I. S. Bright Singh 《World journal of microbiology & biotechnology》2009,25(3):407-414
Two distinct nitrifying bacterial consortia, namely an ammonia oxidizing non-penaeid culture (AMONPCU-1) and an ammonia oxidizing
penaeid culture (AMOPCU-1), have been mass produced in a nitrifying bacterial consortia production unit (NBCPU). The consortia,
maintained at 4°C were activated and cultured in a 2 l fermentor initially. At this stage the net biomass (0.105 and 0.112 g/l),
maximum specific growth rate (0.112 and 0.105/h) and yield coefficients (1.315 and 2.08) were calculated respectively, for
AMONPCU-1 and AMOPCU-1 on attaining stationary growth phase. Subsequently on mass production in a 200 l NBCPU under optimized
culture conditions, the total amounts of NH4
+–N removed by AMONPCU-1 and AMOPCU-1 were 1.948 and 1.242 g/l within 160 and 270 days, respectively. Total alkalinity reduction
of 11.7–14.4 and 7.5–9.1 g/l were observed which led to the consumption of 78 and 62 g Na2CO3. The yield coefficient and biomass of AMONPCU-1 were 0.67 and 125.3 g/l and those of AMOPCU-1 were 1.23 and 165 g/l. The
higher yield coefficient and growth rate of AMOPCU-1 suggest better energy conversion efficiency and higher CO2 fixation potential. Both of the consortia were dominated by Nitrosomonas-like organisms. The consortia may find application in the establishment of nitrification within marine and brackish water
culture systems. 相似文献
8.
Laura Laynes Achuthan C. Raghavamenon Oswald D’Auvergne Vinitha Achuthan Rao M. Uppu 《Biochemical and biophysical research communications》2011,(1):90
3β-Hydroxy-5,6-secocholestan-6-al (cholesterol secoaldehyde or ChSeco), an oxysterol known to be formed in ozone- and singlet oxygen-mediated oxidations of cholesterol, has been detected in the atherosclerotic plaque and in the brain of patients suffering from Alzheimer’s disease and Lewy body dementia. Previously, we have shown that, in H9c2 cardiomyoblasts, ChSeco induces oxidative stress followed by apoptosis involving both intrinsic and extrinsic signaling pathways. In the present study, we investigated the nature of reactive oxygen species (ROS) and its associated redox signaling in H9c2 cells upon treatment with ChSeco. Both catalase and deferoxamine, which lowered intracellular ROS, were found to alleviate the ChSeco-induced cytotoxicity. ChSeco-treated H9c2 cells showed a significant decrease in the intracellular catalase activity, suggesting the involvement of H2O2 in the associated cytotoxicity. Additionally, in ChSeco-exposed cells, there was a marked increase in lipid peroxidation and pre-treatment with SB 203580 (p38 MAPK inhibitor) and MEK1/2 inhibitor (ERK1/2 and JNK inhibitor) rendered protection against the cytotoxicity. An early increase in the expression of p-SAPK/JNK or delayed p38 MAPK did not alter ATF-2 but decreased c-Jun expression in these cells. Overall, these findings are consistent with MAPK signaling resulting from increased cellular H2O2 in ChSeco-induced cytotoxicity in cardiomyoblasts. 相似文献
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Achuthan S Santhoshkumar TR Prabhakar J Nair SA Pillai MR 《The Journal of biological chemistry》2011,286(43):37813-37829
Tumor recurrence after chemotherapy or radiation remains a major obstacle to successful cancer treatment. A subset of cancer cells, termed cancer stem cells, can elude conventional treatments and eventually regenerate a tumor that is more aggressive. Despite the large number of studies, molecular events that govern the emergence of aggressive therapy-resistant cells with stem cell properties after chemotherapy are poorly defined. The present study provides evidence for the rare escape of tumor cells from drug-induced cell death, after an intermediate stay in a non-cycling senescent stage followed by unstable multiplication characterized by spontaneous cell death. However, some cells appear to escape and generate stable colonies with an aggressive tumor stem cell-like phenotype. These cells displayed higher CD133 and Oct-4 expression. Notably, the drug-selected cells that contained low levels of reactive oxygen species (ROS) also showed an increase in antioxidant enzymes. Consistent with this in vitro experimental data, we observed lower levels of ROS in breast tumors obtained after neoadjuvant chemotherapy compared with samples that did not receive preoperative chemotherapy. These latter tissues also expressed enhanced levels of ROS defenses with enhanced expression of superoxide dismutase. Higher levels of Oct-4 and CD133 were also observed in tumors obtained after neoadjuvant chemotherapy. Further studies provided evidence for the stabilization of Nrf2 due to reduced 26 S proteasome activity and increased p21 association as the driving signaling event that contributes to the transition from a high ROS quiescent state to a low ROS proliferating stage in drug-induced tumor stem cell enrichment. 相似文献
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Neeraj Raizada Kuldeep Singh Sachdeva Sreenivas Achuthan Nair Shubhangi Kulsange Radhey Shayam Gupta Rahul Thakur Malik Parmar Christen Gray Ranjani Ramachandran Bhavin Vadera Shobha Ekka Shikha Dhawan Ameet Babre Mayank Ghedia Umesh Alavadi Puneet Dewan Mini Khetrapal Ashwini Khanna Catharina Boehme Chinnambedu Nainarappan Paramsivan 《PloS one》2014,9(8)