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461.
Costa FF Bischof JM Vanin EF Lulla RR Wang M Sredni ST Rajaram V Bonaldo Mde F Wang D Goldman S Tomita T Soares MB 《PloS one》2011,6(10):e25114
Introduction
We have examined expression of microRNAs (miRNAs) in ependymomas to identify molecular markers of value for clinical management. miRNAs are non-coding RNAs that can block mRNA translation and affect mRNA stability. Changes in the expression of miRNAs have been correlated with many human cancers.Materials and Methods
We have utilized TaqMan Low Density Arrays to evaluate the expression of 365 miRNAs in ependymomas and normal brain tissue. We first demonstrated the similarity of expression profiles of paired frozen tissue (FT) and paraffin-embedded specimens (FFPE). We compared the miRNA expression profiles of 34 FFPE ependymoma samples with 8 microdissected normal brain tissue specimens enriched for ependymal cells. miRNA expression profiles were then correlated with tumor location, histology and other clinicopathological features.Results
We have identified miRNAs that are over-expressed in ependymomas, such as miR-135a and miR-17-5p, and down-regulated, such as miR-383 and miR-485-5p. We have also uncovered associations between expression of specific miRNAs which portend a worse prognosis. For example, we have identified a cluster of miRNAs on human chromosome 14q32 that is associated with time to relapse. We also found that miR-203 is an independent marker for relapse compared to the parameters that are currently used. Additionally, we have identified three miRNAs (let-7d, miR-596 and miR-367) that strongly correlate to overall survival.Conclusion
We have identified miRNAs that are differentially expressed in ependymomas compared with normal ependymal tissue. We have also uncovered significant associations of miRNAs with clinical behavior. This is the first report of clinically relevant miRNAs in ependymomas. 相似文献462.
Aruna Jangid Yogesh Kumar Narayan Rishi 《Archives Of Phytopathology And Plant Protection》2017,50(7-8):341-348
Velvet bean severe mosaic virus (VbSMV) is a bipartite DNA virus infecting Mucuna pruriens (Velvet bean), belongs to the genus Begomovirus in the family Geminiviridae. Velvet bean is a medicinal plant of enormous medicinal value. In the present study, it was delineated that proteins encoded by VbSMV viz. AV2 (pre-coat protein), AC2 (TrAP), AV1 (coat protein) are suppressors of RNA silencing as identified through Agrobacterium co-infiltration assays using Nicotiana benthamiana as a host plant. AV2 showed strong suppressor activity whereas AC1 and AV1 were found to be weak suppressors. To the best of our knowledge, this is the first report on identification of suppressor of RNA silencing encoded by VbSMV infecting a medicinal plant. 相似文献
463.
Rishi Kishore Vishwakarma Krunal Arvind Patel Prashant Sonawane Somesh Singh Ruby Uma Kumari Dinesh Chandra Agrawal Bashir Mohammad Khan 《Bioinformation》2012,8(22):1075-1081
Farnesyl pyrophosphate synthase (FPS; EC 2.5.1.10) is a key enzyme in isoprenoid biosynthetic pathway and provides precursors
for the biosynthesis of various pharmaceutically important metabolites. It catalyzes head to tail condensation of two isopentenyl
pyrophosphate molecules with dimethylallyl pyrophosphate to form C15 compound farnesyl pyrophosphate. Recent studies have
confirmed FPS as a molecular target of bisphosphonates for drug development against bone diseases as well as pathogens.
Although large numbers of FPSs from different sources are known, very few protein structures have been reported till date. In the
present study, FPS gene from medicinal plant Bacopa monniera (BmFPS) was characterized by comparative modeling and docking.
Multiple sequence alignment showed two highly conserved aspartate rich motifs FARM and SARM (DDXXD). The 3-D model of
BmFPS was generated based on structurally resolved FPS crystal information of Gallus gallus. The generated models were validated
by various bioinformatics tools and the final model contained only α-helices and coils. Further, docking studies of modeled BmFPS
with substrates and inhibitors were performed to understand the protein ligand interactions. The two Asp residues from FARM
(Asp100 and Asp104) as well as Asp171, Lys197 and Lys262 were found to be important for catalytic activity. Interaction of
nitrogen containing bisphosphonates (risedronate, alendronate, zoledronate and pamidronate) with modeled BmFPS showed
competitive inhibition; where, apart from Asp (100, 104 and 171), Thr175 played an important role. The results presented here
could be useful for designing of mutants for isoprenoid biosynthetic pathway engineering well as more effective drugs against
osteoporosis and human pathogens.
Abbreviations
IPP - Isopentenyl Pyrophosphate, DMAPP - Dimethylallyl Pyrophosphate, GPP - Geranyl Pyrophosphate, FPP - FPPFarnesyl Pyrophosphate, DOPE - Discrete Optimized Protein Energy, BmFPS - Bacopa monniera Farnesyl Pyrophosphate Synthase, RMSD - Root Mean square Deviation, OPLS-AA - Optimized Potentials for Liquid Simulations- All Atom, FARM - First Aspartate Rich Motif, SARM - Second Aspartate Rich Motif. 相似文献464.
Thermotogae species are currently identified mainly on the basis of their unique toga and distinct branching in the rRNA and
other phylogenetic trees. No biochemical or molecular markers are known that clearly distinguish the species from this phylum
from all other bacteria. The taxonomic/evolutionary relationships within this phylum, which consists of a single family, are
also unclear. We report detailed phylogenetic analyses on Thermotogae species based on concatenated sequences for many ribosomal
as well as other conserved proteins that identify a number of distinct clades within this phylum. Additionally, comprehensive
analyses of protein sequences from Thermotogae genomes have identified >60 Conserved Signature Indels (CSI) that are specific
for the Thermotogae phylum or its different subgroups. Eighteen CSIs in important proteins such as PolI, RecA, TrpRS and ribosomal
proteins L4, L7/L12, S8, S9, etc. are uniquely present in various Thermotogae species and provide molecular markers for the
phylum. Many CSIs were specific for a number of Thermotogae subgroups. Twelve of these CSIs were specific for a clade consisting
of various Thermotoga species except Tt. lettingae, which was separated from other Thermotoga species by a long branch in phylogenetic trees; Fourteen CSIs were specific for a clade consisting of the Fervidobacterium and Thermosipho genera and eight additional CSIs were specific for the genus Thermosipho. In addition, the existence of a clade consisting of the deep branching species Petrotoga mobilis,
Kosmotoga olearia and Thermotogales bacterium mesG1 was supported by seven CSIs. The deep branching of this clade was also supported by a number of CSIs that were present in
various Thermotogae species, but absent in this clade and all other bacteria. Most of these clades were strongly supported
by phylogenetic analyses based on two datasets of protein sequences and they identify potential higher taxonomic grouping
(viz. families) within this phylum. We also report 16 CSIs that are shared by either some or all Thermotogae species and some
species from other taxa such as Archaea, Aquificae, Firmicutes, Proteobacteria, Deinococcus, Fusobacteria, Dictyoglomus, Chloroflexi
and eukaryotes. The shared presence of some of these CSIs could be due to lateral gene transfers between these groups. However,
no clear preference for any particular group was observed in this regard. The molecular probes based on different genes/proteins,
which contain these Thermotogae-specific CSIs, provide novel and highly specific means for identification of both known as
well as previously unknown Thermotogae species in different environments. Additionally, these CSIs also provide valuable tools
for genetic and biochemical studies that could lead to discovery of novel properties that are unique to these bacteria. 相似文献
465.
Shalabh Dixit Anshuman Singh Nitika Sandhu Aditi Bhandari Prashant Vikram Arvind Kumar 《Molecular breeding : new strategies in plant improvement》2017,37(12):143
TDK1 is a popular rice variety from the Lao PDR. Originally developed for irrigated conditions, this variety suffers a high decline in yield under drought conditions. Studies have identified three quantitative trait loci (QTLs) for grain yield under drought conditions, qDTY 3.1 , qDTY 6.1 , and qDTY 6.2 , that show a high effect in the background of this variety. We report here the pyramiding of these three QTLs with SUB1 that provides 2–3 weeks of tolerance to complete submergence, with the aim to develop drought- and submergence-tolerant near-isogenic lines (NILs) of TDK1. We used a tandem approach that combined marker-assisted backcross breeding with phenotypic selection to develop NILs with high yield under drought stress and non-stress conditions and preferred grain quality. The effect of different QTL combinations on yield and yield-related traits under drought stress and non-stress conditions is also reported. Our results show qDTY 3.1 to be the largest and most consistent QTL affecting yield under drought conditions, followed by qDTY 6.1 and qDTY 6.2 , respectively. QTL class analysis also showed that lines with a combination of qDTY 3.1 and qDTY 6.1 consistently showed a higher tolerance to drought than those in which one of these QTLs was missing. In countries such as Lao PDR, where large areas under rice cultivation suffer vegetative-stage submergence and reproductive-stage drought, these lines could ensure yield stability. These lines can also serve as valuable genetic material to be used for further breeding of high-yielding, drought- and submergence-tolerant varieties in local breeding programs. 相似文献
466.
467.
Scrophularia himalensis has anab initio cellular endosperm. A transverse division separates a micropylar chamber from a chalazal chamber. The second division is vertical in both, the third is also vertical but at right angles to the second and restricted to the micropylar chamber just as the fourth transverse division. The four-celled micropylar haustorium is branched, highly aggressive, and persists for a long time during seed development. The bicelled chalazal haustorium is non-aggressive and is relatively short-lived. The endosperm proper is ruminate. Variation in the early ontogeny of the endosperm and the structure of endosperm haustoria in the tribeScrophularieae are evaluated. 相似文献
468.
In the present study, mineralization of an aromaticN-heterocyclic molecule, indole, by microorganisms present in anaerobically digested sewage sludge was examined. The first
step in indole mineralization was the formation of a hydroxylated intermediate, oxindole. The rate of transformation of indole
to oxindole and its subsequent disappearance was dependent on the concentration of inoculum and indole and the incubation
temperature. Methanogenesis appeared to be the dominant process in the mineralization of indole in 10% digested sludge even
in the presence of high concentrations of sulfate. Enrichment of the digested sludge with sulfate as an electron acceptor
allowed the isolation of a metabolically stable mixed culture of anaerobic bacteria which transformed indole to oxindole and
acetate, and ultimately to methane and carbon dioxide. This mixed culture exhibited a predominance of sulfate-reducers over
methanogens with more than 75% of the substrate mineralized to carbon dioxide. The investigation demonstrates that indole
can be transformed by both methanogenic and sulfate-reducing microbial populations. 相似文献
469.
Huanxing Sun Rayman Choo-Wing Angara Sureshbabu Juan Fan Lin Leng Shuang Yu Dianhua Jiang Paul Noble Robert J. Homer Richard Bucala Vineet Bhandari 《PloS one》2013,8(4)
Background
The role and mechanism of action of MIF in hyperoxia-induced acute lung injury (HALI) in the newborn lung are not known. We hypothesized that MIF is a critical regulatory molecule in HALI in the developing lung.Methodology
We studied newborn wild type (WT), MIF knockout (MIFKO), and MIF lung transgenic (MIFTG) mice in room air and hyperoxia exposure for 7 postnatal (PN) days. Lung morphometry was performed and mRNA and protein expression of vascular mediators were analyzed.Results
MIF mRNA and protein expression were significantly increased in WT lungs at PN7 of hyperoxia exposure. The pattern of expression of Angiopoietin 2 protein (in MIFKO>WT>MIFTG) was similar to the mortality pattern (MIFKO>WT>MIFTG) in hyperoxia at PN7. In room air, MIFKO and MIFTG had modest but significant increases in chord length, compared to WT. This was associated with decreased expression of Angiopoietin 1 and Tie 2 proteins in the MIFKO and MIFTG, as compared to the WT control lungs in room air. However, on hyperoxia exposure, while the chord length was increased from their respective room air controls, there were no differences between the 3 genotypes.Conclusion
These data point to the potential roles of Angiopoietins 1, 2 and their receptor Tie2 in the MIF-regulated response in room air and upon hyperoxia exposure in the neonatal lung. 相似文献470.
Emily Chen Krystle Reiss Dilip Shah Ramu Manjula Brandon Allen Eva L. Murphy James W. Murphy Victor S. Batista Vineet Bhandari Elias J. Lolis George P. Lisi 《The Journal of biological chemistry》2021,297(3)
The macrophage migration inhibitory factor (MIF) family of cytokines contains multiple ligand-binding sites and mediates immunomodulatory processes through an undefined mechanism(s). Previously, we reported a dynamic relay connecting the MIF catalytic site to an allosteric site at its solvent channel. Despite structural and functional similarity, the MIF homolog D-dopachrome tautomerase (also called MIF-2) has low sequence identity (35%), prompting the question of whether this dynamic regulatory network is conserved. Here, we establish the structural basis of an allosteric site in MIF-2, showing with solution NMR that dynamic communication is preserved in MIF-2 despite differences in the primary sequence. X-ray crystallography and NMR detail the structural consequences of perturbing residues in this pathway, which include conformational changes surrounding the allosteric site, despite global preservation of the MIF-2 fold. Molecular simulations reveal MIF-2 to contain a comparable hydrogen bond network to that of MIF, which was previously hypothesized to influence catalytic activity by modulating the strength of allosteric coupling. Disruption of the allosteric relay by mutagenesis also attenuates MIF-2 enzymatic activity in vitro and the activation of the cluster of differentiation 74 receptor in vivo, highlighting a conserved point of control for nonoverlapping functions in the MIF superfamily. 相似文献