automatic identification of secondary structure in globular proteins

... bisphosphonates, such as tubulin cofactor B and ASK/DBF4 (Activator of S-phase kinase) The up-regulation of tubulin cofactor B may explain some previously unknown effects of nitrogen-containing bisphosphonates ... nitrogen-containing bisphosphonates induce extensive DNA damage, we also document the role of DBF4 as a key player in nitrogen-containing bisphosphonate-induced cytotoxicity, thus explaining the effects ... discovery rate of q < 0.001 for the haploinsufficient strains, and of q < 0.01 for the haploproficient ones since only a smaller number of strains displayed an increase in growth rate (see

Ngày tải lên: 09/08/2014, 20:20

... Additional data file 2 A table of the stability of mRNA secondary structures excluding the Gadd45a gene A table of the stability of mRNA secondary structures excluding the Gadd45a gene, where the ... lot of the sequence is base-paired Indeed, consistent with stems being under purifying selection to maintain secondary structure, while non-synony-mous rates are the same between codons in putative ... one mutation arising within a stem that has the knock-on effect of increasing substitution rates within stems would be most pronounced in genes with a high proportion of base-pairing Consequently,

Ngày tải lên: 14/08/2014, 14:22

... in a subset of human gliomas with distinct clinical and molecular features, including improved survival outcomes for those gliomas demonstrating CIMP [10] The gain of function mutations within ... Medicine and Department of Medical & Molecular Genetics, School of Clinical and Experimental Medicine, University of Birmingham College of Medical and Dental Sciences, Edgbaston, Birmingham, ... methylation profiling of 20 matched pairs of early and late gliomas using the Infinium HumanMethylation450 BeadChips to assess methylation at >485,000 cytosine positions within the human genome

Ngày tải lên: 14/10/2020, 17:38

... C-terminal part and the threadlike structure to N-terminal part of the protein [39] Small integrin-binding ligand N-linked glycoproteins (SIBLINGs), a family of five integrin binding glycopho-sphoproteins ... and con-tains an arginine-glycine-aspartic acid-binding (RGD) do-main as well as two heparin-binding sites, one thrombin cleavage site (RSK [arginine-serine-lysine]) and a calcium-binding site ... N-terminal GRGDS-containing osteopontin thrombin-cleavage fragment is highly active in promoting tumor cell migration [62] The N-terminal fragment contains two integrin binding sites These integrin

Ngày tải lên: 19/03/2023, 15:12

... sequences using machine learning? 2 What syntax infrastructure of secondary and tertiary motifs in DNA sequences can be determined using machine learning techniques? 3 What benefit is gained by using ... protocol used in the lab generally included the following steps: 1 Preprocessing and identification of protein domains, identification and removal of signal peptides, and protein secondary structure ... of functional/structural information of a prediction target through various database searches; 3 Protein triage and classification of target proteins into membrane proteins and soluble proteins,

Ngày tải lên: 02/10/2024, 01:33

... currently being developed in preclinical testing and clinical trials, including molecules targeting interleukin 12, interleukin 17, and endothelial integrins The efficacy of UC therapies in clinical ... symptom domain, the findings for the symp-tom domain stool mucus are presented in Figure 6 In this symptom domain, 48 of 60 individuals had a VAS rating greater than 50 mm for the first endpoint ("present ... for determining frequent and responsive symptom domains Figure 1 Flow diagram of 28 symptom domains in questionnaire and criteria for determining frequent and responsive symptom domains Sixteen

Ngày tải lên: 18/06/2014, 19:20

... ben-efits of additionally stimulating the plantarflexor muscles during the terminal double-support phase of gait, requiring the use of 2 footswitches in each shoe [14] In some systems a connecting ... that presented in this paper, they investigated the step-to-step variability in timing of maxima and minima in the sensor signals, suggesting these points could be used as the basis of a gait event ... collection, processing and in some aspects of the experimental design and EL and BF were involved in the development of the experimental set up including the design and manufacture of the instrumented

Ngày tải lên: 19/06/2014, 08:20

... and in drafting of the manuscript YNL is the co-supervisor who participated in the data analysis and drafting of the manuscript XDS contributed in the planning of the experimental program and in ... approximately 5 nm in size To further examine Trang 5the interior structure of the carbon spheres, the carbon sphere powders were cast into epoxy and then sliced for examination of their cross sections ... furanic species The continued growth in size of the cross-linked furanic species eventually results in the precipitation of the molecular clusters out of the solution into the primary carbonaceous

Ngày tải lên: 20/06/2014, 23:20

... found in the larger set Figure 2 Distribution of domain gain events according to the position of domain insertion and number of exons gained Gains at amino and carboxyl termini and in the middle of ... domain gain in animals and there are also indications of the importance of adjacent gene join-ing [11] and NAHR [43] in the formation of chimeric genes in the Drosophila lineage Terminal gains of ... domain has lost the introns present in the original sequence and the pre-SET domain has an intron containing repeat elements in a position not present in the original domain, suggesting it was inserted

Ngày tải lên: 09/08/2014, 20:22

... reported to interact with Bcl-xL, and Ras in T-cells, resulting in the inhibition of apoptosis [29,30] IKZF3 is located at the ERBB2-amplicon [31] Interestingly, our preliminary analysis of clinical ... most of the fusions (23 of 27) were predicted to be in-frame (Table 1), assuming that the splicing pattern of the rest of the transcript is retained Should the reading frame not be retained across ... membrane protein-associated protein B and C) and the carboxy-terminal part of IKZF3, which harbors two Zn-finger domains.IKZF3 was only detected as a fusion transcript, indicating activation of a quiescent

Ngày tải lên: 09/08/2014, 22:23

... Department of Applied Biology, PO Box 27, FIN-00014 University of Helsinki, Helsinki, Finland, 2 Finnish Graduate School in Plant Biology, PO Box 56, FIN-00014 University of Helsinki, Helsinki, Finland, ... School in Biosciences, PO Box 56, FIN-00014 University of Helsinki, Helsinki, Finland, 4 Horticultural Sciences Department, University of Florida, Gainesville, FL, USA and 5 Institute of Biotechnology, ... Biotechnology, PO Box 56, FIN-00014 University of Helsinki, Helsinki, Finland Email: Katriina Mouhu - katriina.mouhu@helsinki.fi; Timo Hytönen* - timo.hytonen@helsinki.fi; Kevin Folta - kfolta@ifas.ufl.edu;

Ngày tải lên: 12/08/2014, 03:21

... hyponastic leaves (HYL1), a double-stranded RNA-binding domain (dsRBD)-containing protein, and SERRATE, a C2H2 zinc finger protein, assists DCL1 in releasing the miRNA duplex [5-7] Then HEN1, a methyl ... only in Arabidopsis thus far, are also conserved in Brassica spp These findings will be useful for tracing the evolution of small RNAs by examining their expression in common ancestors of the ... These findings will be useful for tracing the evolution of small RNAs by exam-ining their expression in common ancestors of the Arabi-dopsis-Brassica lineage. Methods Blast search against NCBI

Ngày tải lên: 12/08/2014, 05:20

... said to be realized by a cyclic ordering of X if the straight line connecting a and b and the straight line connecting c and d do not intersect in the interior of the circle There is a circular ... cutoff value of q depends on the tree topology and in particular on the number of taxa It pays to determine the maximum of the gain as a function of q and to use the corresponding optimal cutoff ... rescaled consistency index and the scaled log-likelihood values increases with increasing values of q cut-off While the tree-stability indices improve consistently indicating that the reconstructions

Ngày tải lên: 12/08/2014, 17:20

... respiratory tract infection [1-3] The aerial part of A paniculata is commonly used in Chinese medicine. According to Chinese medicine theory, A paniculata 'cools' and relieves internal heat, inflammation ... in treating acute upper respira-tory tract infections and relieving the inflammarespira-tory symptoms of sinusitis [85]. The migratory response of leukocytes to chemokines forms the first line ... macrophages LPS-induced acute inflammation in mice (orally 0.78~3.12 mg/kg BW, 7d) [5,39] aqueous extract protect nicotine-induced toxicity in brain (i.p 250 mg/kg BW, 7d) nicotine induced DNA

Ngày tải lên: 13/08/2014, 15:21

... non-specific binding of peptides to the resin despite stringent wash conditions, and in the case of the cysteine-containing peptides, from a small amount of hydrolysis of the alkyldisulfide linkage during ... functions of cyc-lin A-CDK2 and cyccyc-lin B-CDK1 For example, we found nine proteins involved in protein translation and/or ribosome function, but none of these proteins were found with cyclin B-CDK1, ... Classification of proteins by functional category Figure 3 Classification of proteins by functional category Numbers indicate identified proteins in each category. Chromatin packaging and remodeling (12)

Ngày tải lên: 14/08/2014, 21:20

... University LGR5 Leucine-rich repeat containing G protein-coupled receptor 5 LRRC59 Leucine rich repeat containing 59 MAPK Mitogen-activated protein kinase MCM2 Minichromosome maintenance complex ... genes that are involved in the maintenance of genome integrity Thus, inheritance of a mutation in these genes dramatically elevates lifetime risk of ovarian cancer from a baseline of 1.0% to 39% ... Zinc finger E-box binding homeobox 1 β-catenin Catenin (cadherin-associated protein), beta 1, 88kDa γTuRC gamma-tubulin ring complex γTuSC gamma-tubulin sub-complex Trang 21LIST OF PUBLICATION1

Ngày tải lên: 09/09/2015, 11:09

... Supplementing Lefty2 RNAi cultures with recombinant Lefty1 protein was able to block reduction in level of alkaline phosphatase staining induced by Lefty2 RNAi Alkalline phosphatase staining was ... in maintaining the undifferentiated cell state (Figure 2) One interesting factor identified from the screen is Lefty2, a secreted protein well known for its role in regulating Nodal signaling ... homology of 97%, excluding the four carboxyl terminal amino acid residues which are variable In comparison, the proprotein region is less conserved between the two Lefty proteins, with an identity of

Ngày tải lên: 11/09/2015, 16:02

... primers contained a V5 tag fused at the C-terminal of Lefty2 for detection in western blots A V5 tag at the C-terminus of Lefty2 was chosen instead of the N-terminus because tagging at N-terminus may ... the fourth day of selection 4.9 Alkaline phosphatase staining Detection of alkaline phosphatase, which is indicative of the nondifferentiated state of ES cells, was carried out using a commercial ... blotting To obtain protein extracts, cells were trypsinized from culture dishes harvested in chilled PBS, centrifuged at 10,000g for 4 min at 4 °C, washed again in PBS and incubated for 30 min

Ngày tải lên: 11/09/2015, 16:02

... M T., King, C C., and Hayek, A (2005) Activin A maintains pluripotency of human embryonic stem cells in the absence of feeder layers Stem Cells 23, 489-495 Besser, D (2004) Expression of nodal, ... defects and results in perinatal death Development 121, 1283-1299 Goldin, S N., and Papaioannou, V E (2003) Paracrine action of FGF4 during periimplantation development maintains trophectoderm ... The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells Cell 113, 631-642 Moffat, J., and Sabatini, D M (2006) Building mammalian signalling pathways

Ngày tải lên: 11/09/2015, 16:02

... differentiation even in the presence of LIF (Niwa et al., 1998) Also, point mutation of the tyrosine residue of gp130 responsible for STAT3 binding abrogated the ability of LIF to maintain self renewal ... from the C terminus of mature proteins Active dimerized TGF-ß ligands are linked by the formation of disulfide bonds between the fourth cysteine residues at the C terminus of the proteins LEFTY and ... plethora of differentiated cell types of the three germ layers in culture Another defining feature of ES cells is their acquired capacity to proliferate indefinitely in vitro without undergoing senescence

Ngày tải lên: 11/09/2015, 16:02