Academic literature on the topic 'Protei chip'
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the lists of relevant articles, books, theses, conference reports, and other scholarly sources on the topic 'Protei chip.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Journal articles on the topic "Protei chip"
1
Tsujibo, Hiroshi, Hideyuki Orikoshi, Nao Baba, Masahiro Miyahara, Katsushiro Miyamoto, Masahide Yasuda, and Yoshihiko Inamori. "Identification and Characterization of the Gene Cluster Involved in Chitin Degradation in a Marine Bacterium, Alteromonas sp. Strain O-7." Applied and Environmental Microbiology 68, no. 1 (January 2002): 263–70. http://dx.doi.org/10.1128/aem.68.1.263-270.2002.
Full textAbstract:
ABSTRACT Alteromonas sp. strain O-7 secretes chitinase A (ChiA), chitinase B (ChiB), and chitinase C (ChiC) in the presence of chitin. A gene cluster involved in the chitinolytic system of the strain was cloned and sequenced upstream of and including the chiA gene. The gene cluster consisted of three different open reading frames organized in the order chiD, cbp1, and chiA. The chiD, cbp1, and chiA genes were closely linked and transcribed in the same direction. Sequence analysis indicated that Cbp1 (475 amino acids) was a chitin-binding protein composed of two discrete functional regions. ChiD (1,037 amino acids) showed sequence similarity to bacterial chitinases classified into family 18 of glycosyl hydrolases. The cbp1 and chiD genes were expressed in Escherichia coli, and the recombinant proteins were purified to homogeneity. The highest binding activities of Cbp1 and ChiD were observed when α-chitin was used as a substrate. Cbp1 and ChiD possessed a chitin-binding domain (ChtBD) belonging to ChtBD type 3. ChiD rapidly hydrolyzed chitin oligosaccharides in sizes from trimers to hexamers, but not chitin. However, after prolonged incubation with large amounts of ChiD, the enzyme produced a small amount of (GlcNAc)2 from chitin. The optimum temperature and pH of ChiD were 50°C and 7.0, respectively.
2
Orikoshi, Hideyuki, Nao Baba, Shigenari Nakayama, Hiroshi Kashu, Katsushiro Miyamoto, Masahide Yasuda, Yoshihiko Inamori, and Hiroshi Tsujibo. "Molecular Analysis of the Gene Encoding a Novel Cold-Adapted Chitinase (ChiB) from a Marine Bacterium, Alteromonas sp. Strain O-7." Journal of Bacteriology 185, no. 4 (February 15, 2003): 1153–60. http://dx.doi.org/10.1128/jb.185.4.1153-1160.2003.
Full textAbstract:
ABSTRACT The chitinase B (ChiB) secreted by Alteromonas sp. strain O-7 was purified, and the corresponding gene (chiB) was cloned and sequenced. The open reading frame of the chiB gene encodes a protein of 850 amino acids with a calculated molecular mass of 90,223 Da. ChiB is a modular enzyme consisting of two reiterated domains and a catalytic domain belonging to chitinase family 18. The reiterated domains are composed of chitin-binding domain (ChtBD) type 3 and two fibronectin type III (Fn3)-like domains. Expression plasmids coding for ChiB or deletion derivatives thereof were constructed in Escherichia coli. Deletion analysis showed that the ChtBD of ChiB plays an important role in efficient hydrolysis of insoluble chitin. The optimum pH and temperature of ChiB were 6.0 and 30°C, respectively. The enzyme showed relatively high catalysis, even at low temperatures close to 0°C, and remarkable thermal lability compared to ChiA and ChiC, which are the mesophilic chitinases of the same strain. The k cat/K m value for the ChiB reaction at 10°C was about 4.7 times higher than that of ChiC. These results suggest that ChiB is a cold-adapted enzyme. The RNA transcript of chiB was induced by 1% GlcNAc, and along with a rise in temperature, the RNA transcript showed a tendency to decrease. Thus, among the ChiA, ChiB, and ChiC chitinases, production of ChiB may be advantageous for the strain, allowing it to easily acquire nutrients from chitin and to survive in cold environments.
3
Kim, Yeon-Ki, Zhi-Mei Liu, Daoxin Li, and Pappachan E. Kolattukudy. "Two Novel Genes Induced by Hard-Surface Contact ofColletotrichum gloeosporioides Conidia." Journal of Bacteriology 182, no. 17 (September 1, 2000): 4688–95. http://dx.doi.org/10.1128/jb.182.17.4688-4695.2000.
Full textAbstract:
ABSTRACT Germinating conidia of many phytopathogenic fungi must differentiate into an infection structure called the appressorium in order to penetrate into their hosts. This differentiation is known to require contact with a hard surface. However, the molecular basis for this requirement is not known. Induction of this differentiation in the avocado pathogen, Colletotrichum gloeosporioides, by chemical signals such as the host's surface wax or the fruit-ripening hormone, ethylene, requires contact of the conidia with a hard surface for about 2 h. To study molecular events triggered by hard-surface contact, we isolated several genes expressed during the early stage of hard-surface treatment by a differential-display method. The genes that encode Colletotrichum hard-surface induced proteins are designated chip genes. In this study, we report the characterization of CHIP2 and CHIP3 genes that would encode proteins with molecular masses of 65 and 64 kDa, respectively, that have no homology to any known proteins. TheCHIP2 product would contain a putative nuclear localization signal, a leucine zipper motif, and a heptad repeat region which might dimerize into coiled-coil structure. The CHIP3 product would be a nine-transmembrane-domain-containing protein. RNA blots showed that CHIP2 and CHIP3 are induced by a 2-h hard-surface contact. However, disruption of these genes did not affect the appressorium-forming ability and did not cause a significant decrease in virulence on avocado or tomato fruits suggesting thatC. gloeosporioides might have genes functionally redundant to CHIP2 and CHIP3 or that these genes induced by hard-surface contact control processes not directly involved in pathogenesis.
4
Hamilton, Jaeger J., Victoria L. Marlow, Richard A. Owen, Marília de Assis Alcoforado Costa, Manman Guo, Grant Buchanan, Govind Chandra, et al. "A holin and an endopeptidase are essential for chitinolytic protein secretion in Serratia marcescens." Journal of Cell Biology 207, no. 5 (December 8, 2014): 615–26. http://dx.doi.org/10.1083/jcb.201404127.
Full textAbstract:
Pathogenic bacteria adapt to their environment and manipulate the biochemistry of hosts by secretion of effector molecules. Serratia marcescens is an opportunistic pathogen associated with healthcare-acquired infections and is a prolific secretor of proteins, including three chitinases (ChiA, ChiB, and ChiC) and a chitin binding protein (Cbp21). In this work, genetic, biochemical, and proteomic approaches identified genes that were required for secretion of all three chitinases and Cbp21. A genetic screen identified a holin-like protein (ChiW) and a putative l-alanyl-d-glutamate endopeptidase (ChiX), and subsequent biochemical analyses established that both were required for nonlytic secretion of the entire chitinolytic machinery, with chitinase secretion being blocked at a late stage in the mutants. In addition, live-cell imaging experiments demonstrated bimodal and coordinated expression of chiX and chiA and revealed that cells expressing chiA remained viable. It is proposed that ChiW and ChiX operate in tandem as components of a protein secretion system used by gram-negative bacteria.
5
Coorey, Ranil, Alexandra Grant, and Vijay Jayasena. "Effects of Chia Flour Incorporation on the Nutritive Quality and Consumer Acceptance of Chips." Journal of Food Research 1, no. 4 (October 25, 2012): 85. http://dx.doi.org/10.5539/jfr.v1n4p85.
Full textAbstract:
<p>Gluten free, antioxidant, calcium and dietary fibre rich, chia is known to contain the highest level of omega-3 available in any cultivated plant source. The objective of this research was to develop a high protein, high dietary fibre, gluten free and omega-3 fatty acid rich chips. Four different levels of whole chia flour (5%, 10%, 12%, and 15%) were incorporated to produce chia chip. There were no significant differences in appearance, colour, flavour and overall liking between a commercial chip sample and the 5% chia chips. The chemical analysis indicated that all four trial chips are excellent sources of omega-3 and the baking process has a limited impact on their nutritional profile. For optimal consumer acceptance and nutritional benefits, the incorporation of 5% chia is recommended. With limited chia based food products currently available, a chia chip would be a well-accepted and healthy alternative to the common unhealthy chips.</p>
6
Folders, Jindra, Jon Algra, Marc S. Roelofs, Leendert C. van Loon, Jan Tommassen, and Wilbert Bitter. "Characterization of Pseudomonas aeruginosa Chitinase, a Gradually Secreted Protein." Journal of Bacteriology 183, no. 24 (December 15, 2001): 7044–52. http://dx.doi.org/10.1128/jb.183.24.7044-7052.2001.
Full textAbstract:
ABSTRACT The gram-negative bacterium Pseudomonas aeruginosasecretes many proteins into its extracellular environment via the type I, II, and III secretion systems. In this study, a gene,chiC, coding for an extracellular chitinolytic enzyme, was identified. The chiC gene encodes a polypeptide of 483 amino acid residues, without a typical N-terminal signal sequence. Nevertheless, an N-terminal segment of 11 residues was found to be cleaved off in the secreted protein. The protein shows sequence similarity to the secreted chitinases ChiC of Serratia marcescens, ChiA of Vibrio harveyi, and ChiD ofBacillus circulans and consists of an activity domain and a chitin-binding domain, which are separated by a fibronectin type III domain. ChiC was able to bind and degrade colloidal chitin and was active on the artificial substrates carboxymethyl-chitin-Remazol Brilliant Violet andp-nitrophenyl-β-d-N,N′,N"-triacetylchitotriose, but not onp-nitrophenyl-β-d-N-acetylglucosamine, indicating that it is an endochitinase. Expression of thechiC gene appears to be regulated by the quorum-sensing system of P. aeruginosa, since this gene was not expressed in a lasIR vsmI mutant. After overnight growth, the majority of the ChiC produced was found intracellularly, whereas only small amounts were detected in the culture medium. However, after several days, the cellular pool of ChiC was largely depleted, and the protein was found in the culture medium. This release could not be ascribed to cell lysis. Since ChiC did not appear to be secreted via any of the known secretion systems, a novel secretion pathway seems to be involved.
7
Tsujibo, Hiroshi, Takahiro Kubota, Mitsugu Yamamoto, Katsushiro Miyamoto, and Yoshihiko Inamori. "Characterization of Chitinase Genes from an Alkaliphilic Actinomycete, Nocardiopsis prasina OPC-131." Applied and Environmental Microbiology 69, no. 2 (February 2003): 894–900. http://dx.doi.org/10.1128/aem.69.2.894-900.2003.
Full textAbstract:
ABSTRACT An alkaliphilic actinomycete, Nocardiopsis prasina OPC-131, secretes chitinases, ChiA, ChiB, and ChiBΔ, in the presence of chitin. The genes encoding ChiA and ChiB were cloned and sequenced. The open reading frame (ORF) of chiA encoded a protein of 336 amino acids with a calculated molecular mass of 35,257 Da. ChiA consisted of only a catalytic domain and showed a significant homology with family 18 chitinases. The chiB ORF encoded a protein of 296 amino acids with a calculated molecular mass of 31,500 Da. ChiB is a modular enzyme consisting of a chitin-binding domain type 3 (ChtBD type 3) and a catalytic domain. The catalytic domain of ChiB showed significant similarity to Streptomyces family 19 chitinases. ChiBΔ was the truncated form of ChiB lacking ChtBD type 3. Expression plasmids coding for ChiA, ChiB, and ChiBΔ were constructed to investigate the biochemical properties of these recombinant proteins. These enzymes showed pHs and temperature optima similar to those of native enzymes. ChiB showed more efficient hydrolysis of chitin and stronger antifungal activity than ChiBΔ, indicating that the ChtBD type 3 of ChiB plays an important role in the efficient hydrolysis of chitin and in antifungal activity. Furthermore, the finding of family 19 chitinase in N. prasina OPC-131 suggests that family 19 chitinases are distributed widely in actinomycetes other than the genus Streptomyces.
8
Lee, Yoonsuk, Dong-Ku Kang, Soo-Ik Chang, Moon Hi Han, and In-Cheol Kang. "High-Throughput Screening of Novel Peptide Inhibitors of an Integrin Receptor from the Hexapeptide Library by Using a Protein Microarray Chip." Journal of Biomolecular Screening 9, no. 8 (December 2004): 687–94. http://dx.doi.org/10.1177/1087057104268125.
Full textAbstract:
Protein microarray is an emerging technology that makes high-throughput analysis possible for protein-protein interactions and analysis of proteome and biomarkers in parallel. The authors investigated the application of a novel protein microarray chip, Proteo Chip, in new drug discovery. Integrin αvβ3 microarray immobilized on the Proteo Chip was employed to screen new active peptides against the integrin from multiple hexapeptide sublibraries of a positional scanning synthetic peptide combinatorial library (PS-SPCL). The integrin αvβ3-vitronectin interaction was successfully demonstrated on the integrin microarray in a dose-dependent manner andwas inhibited not only by the syntheticRGDpeptide but also by various integrin antagonists on the integrin microarray chip. Novel peptide ligands with high affinity to the integrin were also identified from the peptide libraries with this chip-based screening system by a competitive inhibition assay in a simultaneous and highthroughput fashion. The authors have confirmed antiangiogenic functions of the novel peptides thus screened through an in vitro and in vivo angiogenesis assay. These results provide evidence that the Proteo Chip is a promising tool for highthroughput screening of lead molecules in new drug development.
9
Zhu, Heng, and Michael Snyder. "Protein chip technology." Current Opinion in Chemical Biology 7, no. 1 (February 2003): 55–63. http://dx.doi.org/10.1016/s1367-5931(02)00005-4.
Full text
10
Howard, Michael B., Nathan A. Ekborg, Larry E. Taylor, Ronald M. Weiner, and Steven W. Hutcheson. "Genomic Analysis and Initial Characterization of the Chitinolytic System of Microbulbifer degradans Strain 2-40." Journal of Bacteriology 185, no. 11 (June 1, 2003): 3352–60. http://dx.doi.org/10.1128/jb.185.11.3352-3360.2003.
Full textAbstract:
ABSTRACT The marine bacterium Microbulbifer degradans strain 2-40 produces at least 10 enzyme systems for degrading insoluble complex polysaccharides (ICP). The draft sequence of the 2-40 genome allowed a genome-wide analysis of the chitinolytic system of strain 2-40. The chitinolytic system includes three secreted chitin depolymerases (ChiA, ChiB, and ChiC), a secreted chitin-binding protein (CbpA), periplasmic chitooligosaccharide-modifying enzymes, putative sugar transporters, and a cluster of genes encoding cytoplasmic proteins involved in N-acetyl-d-glucosamine (GlcNAc) metabolism. Each chitin depolymerase was detected in culture supernatants of chitin-grown strain 2-40 and was active against chitin and glycol chitin. The chitin depolymerases also had a specific pattern of activity toward the chitin analogs 4-methylumbelliferyl-β-d-N,N′-diacetylchitobioside (MUF-diNAG) and 4-methylumbelliferyl-β-d-N,N′,N"-triacetylchitotrioside (MUF-triNAG). The depolymerases were modular in nature and contained glycosyl hydrolase family 18 domains, chitin-binding domains, and polycystic kidney disease domains. ChiA and ChiB each possessed polyserine linkers of up to 32 consecutive serine residues. In addition, ChiB and CbpA contained glutamic acid-rich domains. At 1,271 amino acids, ChiB is the largest bacterial chitinase reported to date. A chitodextrinase (CdxA) with activity against chitooligosaccharides (degree of polymerization of 5 to 7) was identified. The activities of two apparent periplasmic (HexA and HexB) N-acetyl-β-d-glucosaminidases and one cytoplasmic (HexC) N-acetyl-β-d-glucosaminidase were demonstrated. Genes involved in GlcNAc metabolism, similar to those of the Escherichia coli K-12 NAG utilization operon, were identified. NagA from strain 2-40, a GlcNAc deacetylase, was shown to complement a nagA mutation in E. coli K-12. Except for the GlcNAc utilization cluster, genes for all other components of the chitinolytic system were dispersed throughout the genome. Further examination of this system may provide additional insight into the mechanisms by which marine bacteria degrade chitin and provide a basis for future research on the ICP-degrading systems of strain 2-40.
Dissertations / Theses on the topic "Protei chip"
1
Yang, Zhugen. "3D-Microstructured Protein Chip for Cancer Diagnosis." Phd thesis, Ecole Centrale de Lyon, 2012. http://tel.archives-ouvertes.fr/tel-00780192.
Full textAbstract:
Protein microarrays are becoming powerful tools to screen and identify tumor markers for cancer diagnosis, because of the multiplex detection and minute volume of sample requirement. Due to the diversity and variation in different cancers, no single tumor marker is sensitive and specific enough to meet strict diagnostic criteria. Therefore, a combination of tumor markers is required to increase sensitivity and to establish distinct patterns to increase specificity. To obtain reliable tests, the development of reproducible surface chemistry and immobilization procedure are crucial steps in the elaboration of efficient protein microarrays. In this thesis, 3D micro-structured glass slides were functionalized with various surface chemistries like silane monolayer (amino, epoxy and carboxy), and polymer layers of Jeff amine, chitosan, carboxymethyl dextran (CMD), maleic anhydride-alt-methyl vinyl ether copolymer (MAMVE) for physical adsorption or covalent binding with proteins. Surface characterizations, such as X-ray photoelectron spectroscopy (XPS) and Attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), confirmed the monolayer/polymer grafting on the glass slides. Colorimetric assay for determining amine density of three aminated surfaces demonstrated that APDMES had more grafting density than Jeffamine and chitosan. Contact angle measurements show that polymer surfaces were more hydrophilic than monolayer surfaces due to the increasing dosages of polar functional groups. Moreover, the parameters such as additives and pH of spotting buffer, probe concentration, blocking procedures etc, were optimized for tumor marker detection. Under the optimized conditions, antibody microarrays were validated with purified tumor antigens. The best analytical performances obtained for each tumor antigen tested were strongly dependent on functionalized surfaces, e.g. MAMVE exhibited best analytical performances for CEA andHsp60 while NHS leads to best results for PDI and CA19-9. Besides, the implemented antibody microarrays were applied to tumor marker detection from colorectal cancer sera. This evaluation shows the interest to combine several tumor markers on the same surface and the combination of tumor markers on their specific surface lead to remarkably increase the positive responses of tested cancer sera (even up to 100 %). A second type of microarrays (tumor-associated antigens - TAA microarrays) was designed to discriminate breast cancer patients from healthy donors through the detection of tumor autoantibodies. This study included a cohort of 29 breast cancer patients' and 28 healthy donors' sera. A panel of fiveTAAs (Hsp60, p53, Her2, NY-ESO-1 and Hsp70) immobilized on their respective optimized surface chemistry allowed to specifically detect over 82% of breast cancer patients.
2
Robinson, David Edward. "Investigating glycosaminoglycan-protein interactions : the 'sugar chip'." Thesis, University of Sheffield, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.505339.
Full textAbstract:
The aim of these studies is to investigate the production of plasma polymer modified surfaces for the non-covalent binding of glycosaminoglycans (GAGs). These surfaces are designed to aid the investigation of GAG-protein interactions, and enable the elucidation of the important biological processes they may be involved in. It is also hoped that the discoveries in this thesis will translate into the production of new technology for studying GAG-protein interactions for example a sugar plate array that can be utilised in probe GAGprotein interactions and gycomics in a high-throughput platform. In this work investigations have been carried out on binding of heparin, heparin sulphate, chondroitin sulphate, dermatan sulphate and the unsulphated hyaluronic acid. Allylamine can be plasma-polymerised (PpAA) on to surfaces to provide a positivelycharged surface to which sulphated glycosaminoglycans (GAGs) such as heparin can bind. A range of plasma polymer chemistries were investigated, for the elucidation of the requirements for efficient binding of biologically active GAGs, initially using heparin as the . . model ligand. The influence of heparin concentration, solution ionic strength and incubation time were all explored as variables in the immobilization of heparin to ppAA modified microtitre plates. Gradients of surface chemistry were produced by mixing of allylamine with a hydrocarbon monomer octadiene to elucidate the optimal surface chemistry for the binding of heparin. The amount of heparin bound to the plates was monitored by X-ray photoelectron spectroscopy (XPS), using the S2p from heparin on the surface and radio-labelled esS] heparin. The biological activity of the surface immobilised GAGs were investigated using a range of protein binding assays. These systems involved using GAGs to capture proteins on the allylamine modified surfaces in a modified sandwich ELISA approach. Readout systems such as antibody specific binding to the proteins retained on the surface was utilised with a colourimetric change being read as an absorbance readout. The results showed that there are differences in binding by the GAGs for the different binding proteins. OPG protein appeared to be dependent on sulphation levels with higher sulphated GAGs binding more protein. Link _ TSG-6 protein showed the opposite, with less sulphated GAGs binding better in general. While TIMP-3 showed no correlation with sulphation levels, as heparan sulphates containing different sulphation levels bound equally well. This suggests a specific molecular binding moiety for binding may be utilised by TIMP- 3, meaning the protein structure for GAG interactions may be more specific. However, more research to elucidate these specific moieties is required. These results clearly demonstrate that if scaled down to a micro array format, these surfaces could act as a platform for a high-throughput sugar chip for the investigation of GAG-protein interactions. These could have some advantages over current assay formats that are widely used so far as they are inexpensive to produce and can bind native GAGs with no modifications. This allows avoidance of expensive and time consuming synthesis procedures for GAG production containing modified regions. As well as the risks involved in modifying a GAG such as altering its affinities for its binding proteins.
3
Klenkar, Goran. "Protein Microarray Chips." Doctoral thesis, Linköping : Univ, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-8904.
Full text
4
Gunnarsson, Ida. "Deriving Protein Networks by Combining Gene Expression and Protein Chip Analysis." Thesis, University of Skövde, Department of Computer Science, 2002. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-706.
Full textAbstract:
In order to derive reliable protein networks it has recently been suggested that the combination of information from both gene and protein level is required. In this thesis a combination of gene expression and protein chip analysis was performed when constructing protein networks. Proteins with high affinity to the same substrates and encoded by genes with high correlation is here thought to constitute reliable protein networks. The protein networks derived are unfortunately not as reliable as were hoped for. According to the tests performed, the method derived in this thesis does not perform more than slightly better than chance. However, the poor results can depend on the data used, since mismatching and shortage of data has been evident.
5
Ning, Jia. "Allosteric effects of TPR domain-mediated protein-protein interactions." Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/31145.
Full textAbstract:
The tetratricopeptide repeat (TPR) motif contains 34 amino acids forming a helix-turn-helix structure. Different numbers of tandem TPR motifs assemble to form a TPR domain, thereby generating a polypeptide-binding interaction surface. The TPR domain provides a scaffold for mediating protein-protein interactions. Proteins that contain TPR domains exist in a broad range of organisms. These proteins have various functions. Cyclophilin 40 (Cyp40) and C-terminal Hsc70 interaction protein (CHIP) are two typical members of the family of TPR-containing proteins. Both proteins have the ability to bind the molecular chaperones Hsp70 and Hsp90. In most cases, TPR domains act as a scaffold to link chaperone and substrate or multi-protein complexes. Recent evidence suggests that Hsp90 binding to TPR domains can change the overall protein conformation but the allosteric mechanism triggered by ligand binding to the TPR domain remained unknown. This study focuses on using biophysical methods on the two TPR domain containing proteins Cyp40 and CHIP. In particular, this study reveals how the binding of the molecular chaperones Hsp70/90 to the TPR domains of Cyp40 and CHIP influences protein conformation and function. Here we show how conformational changes of the TPR domains affect structure and activity of Cyp40 and CHIP. By using biophysical methods, including thermal denaturation assay (TDA), differential scanning calorimetry (DSC), hydrogen deuterium exchange with mass spectrometry (HDX-MS) and small angle X-ray scattering (SAXS), together with enzymatic assays, we showed that (1) heat shock proteins allosterically affect the enzyme activity of both Cyp40 and CHIP, (2) heat shock proteins bind to the TPR domains of both Cyp40 and CHIP; (3) the binding increases the thermostability of both proteins. Further, by mutating an essential lysine in the TPR1 domain of both proteins (K30 for CHIP, and K227 for Cyp40) to alanine, the thermostability was significantly affected. The SAXS data showed in addition of the SRMEEVD peptide reduced the flexibility of CHIP. HDX-MS experiments suggest that the dynamic alteration due to binding with the Hsp90 peptide or the mutations further reduce the flexibility of the catalytic domains of both proteins. The results imply that the allosteric effects on the enzymatic activity are consequences of dynamic changes of the TPR domains. Hsp70 was also found to bind less tightly to CHIP-K30A than to wild-type CHIP, and thus showed less inhibition of enzymatic activity. These results further confirmed the discovery, that the dynamics of TPR domains allosterically affect enzymatic activity.
6
NDONI, ENEA. "Characterization of the immune response and cross protection activity elicited by the Neisserial Heparin Binding Antigen (NHBA), a component of the 4CMenB vaccine." Doctoral thesis, Università di Siena, 2017. http://hdl.handle.net/11365/1011542.
Full textAbstract:
Invasive disease caused by capsular group B Neisseria meningitidis (MenB) is life threating disease causing hundred thousands of deaths every year, still remaining an unmet medical need in many countries. Although disease can be observed at all age groups, infants and adolescents are the most at risk populations showing the highest incidence in case numbers. Since the MenB capsule was not-immunogenic the development of a MenB vaccine which makes the use of other antigens becomes necessary. 4CMenB is a multicomponent vaccine against serogroup B N. meningitidis composed by three major protein antigens, factor H-binding protein (fHbp), Neisserial Heparin-Binding Antigen (NHBA) and Neisserial adhesin A (NadA), combined with outer membrane vesicles (OMVs) from the New-Zealand epidemic strain (NZ98/254). Neisserial Heparin Binding Antigen (NHBA) is a surface-exposed lipoprotein expressed by all N. meningitidis strains analyzed so far and is composed of two major domains, a highly variable amino-terminal (N-term) domain which anchors the protein on the bacterial outer membrane through the lipobox motif, and a highly conserved carboxyl-terminal (C-term) domain. These domains are separated by a short and quite conserved Arginine-rich (Arg-rich) motif which has been reported to be involved in different mechanisms that mediate meningococci adhesion, infection and survival within the host’s blood stream. NHBA is susceptible to cleavage by NalP, a bacterial protease which has its cleavage site upstream of the arginine region. Moreover human proteases such as human lactoferrin (hLf) and kallikrein are able to process NHBA downstream the the Arg-rich region. Both bacterial and human proteases-mediated cleavage releases the C-term of NHBA in the supernatant, while the N-term of the protein remains anchored on the bacterial surface. NalP cleavage did not impact SBA titers elicited by anti-NHBA antibodies but little is known about the impact that host’s proteases have on bactericidal titers. Based on sequence analysis it has been reported that NHBA has two major alleles, the so called “short” and “long” variants, which differentiate by the presence or absence of a 190 bp long fragment. Despite its sequence variability, NHBA is able to induce a robust and broad immune response against meningococcal strains expressing vaccine homologous and heterologous variants. Although anti-NHBA antibodies are able to induce bacterial killing when tested in serum bactericidal activity assay (SBA), the regions involved in eliciting cross protective immune response remain still unknown. Aims of this study were to use monoclonal antibodies (mAbs) raised against the NHBA vaccine variant peptide 2 (NHBAp2) to (i) map the NHBA regions involved in eliciting the functional response, (ii) test their ability to induce cross protection against strains expressing epidemiologically relevant homologous and heterologous NHBA variants, and (iii) investigate the molecular mechanism of NHBA-mediated bactericidal activity. To this end we used a panel of anti-NHBA mAbs selected to recognize different regions of the protein. Our results showed that only anti-N-term mAbs were able to induce killing of bacterial strains expressing the homologous NHBAp2 and closely related heterologous NHBA variants. Synergy between monoclonal antibodies targeting the N-term and the C-term of NHBA resulted in a significant increase of bactericidal titers but cross protection remained restricted to closely phylogenetic NHBA variants. Anti C-term mAbs were not able to induce SBA activity when tested individually, but surprisingly they became bactericidal when tested in combination. Moreover they were able to induce full cross protection against a panel of strains expressing phylogenetically distant heterologous NHBA variants.
Our results suggest that the partial release of the NHBA C-terminal portion upon NalP and serum proteases could explain why anti-C-term mAbs are not able to induce complement mediated bactericidal killing when tested individually. However, the simultaneous binding of C-term mapping mAbs on the same NHBA molecule can induce the formation of a very stable ternary complex that probably allows a more efficient C1q engagement and C3 deposition, thus leading to the observed co-operative bactericidal activity. These results suggest that synergy between anti-NHBA antibodies is at the basis of the mechanism of NHBA-induced bactericidal activity, which could explain the robust and cross-protective immune response elicited by anti-NHBA polyclonal antibodies following immunization. Collectively, the body of experimental data suggests that both domains of NHBA are required to elicit complement mediated bactericidal activity against strains expressing the vaccine homologous and heterologous NHBA variants.
7
Dai, Qian Patterson Cam. "The cochaperone and ubiquitin ligase CHIP in protein quality control." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2006. http://dc.lib.unc.edu/u?/etd,285.
Full textAbstract:
Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2006.Title from electronic title page (viewed Oct. 10, 2007). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Pharmacology." Discipline: Pharmacology; Department/School: Medicine.
8
Katira, Parag. "Characterizing and modeling protein-surface interactions in lab-on-chip devices." [Gainesville, Fla.] : University of Florida, 2009. http://purl.fcla.edu/fcla/etd/UFE0024702.
Full text
9
Vangone, Anna. "In silico study of protein-protein interactions." Doctoral thesis, Universita degli studi di Salerno, 2013. http://hdl.handle.net/10556/1164.
Full textAbstract:
2011 - 2012Protein-protein interactions are at the basis of many of the most important molecular processes in the cell, which explains the constantly growing interest within the scientific community for the structural characterization of protein complexes.1 However, experimental knowledge of the 3D structure of the great majority of such complexes is missing, and this spurred their accurate prediction through molecular docking simulations, one of the major challenges in the field of structural computational biology and bioinformatics.2,3 My PhD work aims to contribute to the field, by providing novel computational instruments and giving useful insight on specific case studies in the field. In particular, in the first part of my PhD thesis, I present novel methods I developed: i) for analysing and comparing the 3D structure of protein complexes, to immediately extract useful information on the interaction based on a contact map visualization (COCOMAPS4 web tool, Chapter 2), and ii) for analysing a set of multiple docking solutions, to single out the key inter-residue contacts and to distinguish native-like solutions from the incorrect ones (CONS-COCOMAPS5 web tool and CONS-RANK program, Chapter 3 and 4, respectively). In the second part of the thesis, these methods have been applied, in combination with classical state-of-art computational biology techniques, to predict and analyse the binding mode in real biological systems, related to particular diseases. This part of the work has been afforded in collaboration with experimental groups, to take advantage of specific biological information on the systems under study. In particular, the interaction between proteins involved in the autoimmune response in celiac disease6,7 (Chapters 5 and 6) has been studied in collaboration with the group directed by Prof. Sblattero, University of Piemonte Orientale (Italy) and the group directed by Prof. Esposito, University of Salerno (Italy). In addition, recognition properties of 3 the FXa enzymatic system8 has been studied through dynamic characterization of a FXa pathogenic mutant that causes problems in the blood coagulation cascade (Chapter 7). This study has been performed in collaboration with the group directed by Prof. De Cristofaro, Catholic University School of Medicine, Rome (Italy) and the group directed by Prof. Peyvandi, Ospedale Maggiore Policlinico and Università degli Studi di Milano (Italy)... [edited by author]
XI n.s.
10
Hlatshwayo, Nkosikhona Rejoyce. "Comparison of protein binding microarray derived and ChIP-seq derived transcription factor binding DNA motifs." Thesis, Rhodes University, 2015. http://hdl.handle.net/10962/d1017907.
Full textAbstract:
Transcription factors (TFs) are biologically important proteins that interact with transcription machinery and bind DNA regulatory sequences to regulate gene expression by modulating the synthesis of the messenger RNA. The regulatory sequences comprise of short conserved regions of a specific length called motifs . TFs have very diverse roles in different cells and play a very significant role in development. TFs have been associated with carcinogenesis in various tissue types, as well as developmental and hormone response disorders. They may be responsible for the regulation of oncogenes and can be oncogenic. Consequently, understanding TF binding and knowing the motifs to which they bind is worthy of attention and research focus. Various projects have made the study of TF binding their main focus; nevertheless, much about TF binding remains confounding. Chromatin immunoprecipitation in conjunction with deep sequencing (ChIP-seq) techniques are a popular method used to investigate DNA-TF interactions in vivo. This procedure is followed by motif discovery and motif enrichment analysis using relevant tools. Protein Binding Microarrays (PBMs) are an in vitro method for investigating DNA-TF interactions. We use a motif enrichment analysis tools (CentriMo and AME) and an empirical quality assessment tool (Area under the ROC curve) to investigate which method yields motifs that are a true representation of in vivo binding. Motif enrichment analysis: On average, ChIP-seq derived motifs from the JASPAR Core database outperformed PBM derived ones from the UniPROBE mouse database. However, the performance of motifs derived using these two methods is not much different from each other when using CentriMo and AME. The E-values from Motif enrichment analysis were not too different from each other or 0. CentriMo showed that in 35 cases JASPAR Core ChIP-seq derived motifs outperformed UniPROBE mouse PBM derived motifs, while it was only in 11 cases that PBM derived motifs outperformed ChIP-seq derived motifs. AME showed that in 18 cases JASPAR Core ChIP-seq derived motifs did better, while only it was only in 3 cases that UniPROBE motifs outperformed ChIP-seq derived motifs. We could not distinguish the performance in 25 cases. Empirical quality assessment: Area under the ROC curve values computations followed by a two-sided t-test showed that there is no significant difference in the average performances of the motifs from the two databases (with 95% confidence, mean of differences=0.0088125 p-value= 0.4874, DF=47) .
Books on the topic "Protei chip"
1
Blazek, Matthias. Analysis of fast protein phosphorylation kinetics in single cells on a microfluidic chip. Freiburg: Universität, 2015.
Find full text
2
Bisutti, Francesca, and Elisabetta Molteni. La corte della Niobe. Venice: Edizioni Ca' Foscari, 2018. http://dx.doi.org/10.30687/978-88-6969-281-9.
Full textAbstract:
La coincidenza delle ricorrenze – l’Università Ca’ Foscari compie 150 anni dalla fondazione e sono passati 100 anni dalla fine della Grande guerra – invita a ricordare la coraggiosa, allora ancora giovane, Scuola Superiore di Commercio, che, alla fine del primo conflitto, è costretta a contare i suoi allievi caduti. Dopo due decenni, nel 1943, il Regio Istituto di Economia e Commercio stabilisce di dedicare la corte minore del palazzo Giustinian dei Vescovi alla memoria di tutti gli studenti, i docenti e i dipendenti caduti nei conflitti che fino ad allora avevano insanguinato il secolo. Monumenti, memorie e lapidi sono, in senso figurato, ricomposti nella statua di Niobe, Mater Studiorum che piange la morte violenta dei propri allievi. La corte della Niobe è abitata dalla potente scultura di Napoleone Martinuzzi, suo fulcro visivo ed emotivo, e da tanti, tanti nomi. Il tentativo è stato quindi di cominciare a restituire non solo la storia di quello spazio ma anche delle esistenze e del pensiero di coloro i cui nomi hanno qui trovato dimora. Questi aspetti della memoria sono stati al centro del lavoro di molti e sottotraccia nel lavoro di tutti: di chi si è occupato di delineare un profilo esistenziale dei caduti, di chi ha studiato le ideologie e le politiche che hanno animato i periodi tribolati delle guerre e dei dopoguerra o ha analizzato i processi istituzionali e la mentalità in tempo di guerra, di chi ha indagato sull’assetto e le trasformazioni architettoniche della corte. Ma il problema del tempo passato, delle tracce che lascia e di come conservarle si è posto anche a chi ha compiuto ricerche sui documenti e a chi ha studiato le pietre del sacrario e ne ha avuto cura.
3
Graham, Louise. Can I Have Chips?: Fill up, Lose Weight, Feel Great. Troubador Publishing Limited, 2014.
Find full text
4
Graham, Louise. Can I Have Chips?: Fill up, Lose Weight, Feel Great. Troubador Publishing Limited, 2014.
Find full text
5
Co, Business Communications. Protein Chips: Where To? (Business Opportunity Report). Business Communications Company, 2003.
Find full text
6
Parker, Philip M. The 2007-2012 World Outlook for Proteomic Protein Chips. ICON Group International, Inc., 2006.
Find full text
7
Mifsud, Borbala, Kathi Zarnack, and Anaïs F. Bardet. Practical Guide to ChIP-Seq Data Analysis. Taylor & Francis Group, 2018.
Find full text
8
Mifsud, Borbala, Kathi Zarnack, and Anais Bardet. Practical Guide to Chip-Seq Data Analysis. Taylor & Francis Group, 2021.
Find full text
9
Mifsud, Borbala, Kathi Zarnack, and Anaïs F. Bardet. Practical Guide to ChIP-Seq Data Analysis. Taylor & Francis Group, 2018.
Find full text
10
Mifsud, Borbala, and Anais Bardet. Practical Guide to Chip-Seq Data Analysis. Taylor & Francis Group, 2018.
Find full textBook chapters on the topic "Protei chip"
1
Zhu, Yonggang, and Barbara E. Power. "Lab-on-a-chip in Vitro Compartmentalization Technologies for Protein Studies." In Protein – Protein Interaction, 81–114. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/10_2008_098.
Full text
2
Tong, Yunguang, and Jeff Falk. "Genome-Wide Analysis for Protein−DNA Interaction: ChIP-Chip." In Methods in Molecular Biology, 235–51. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-378-7_15.
Full text
3
Kaledhonkar, Sandip, Ziao Fu, Howard White, and Joachim Frank. "Time-Resolved Cryo-electron Microscopy Using a Microfluidic Chip." In Protein Complex Assembly, 59–71. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7759-8_4.
Full text
4
Jain, Ritu, Tiffany Devine, Ajish D. George, Sridar V. Chittur, Timothy E. Baroni, Luiz O. Penalva, and Scott A. Tenenbaum. "RIP-Chip Analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling." In RNA, 247–63. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-59745-248-9_17.
Full text
5
Tuteja, Geetu. "DNA–Protein Interaction Analysis (ChIP-Seq)." In Bioinformatics for High Throughput Sequencing, 127–49. New York, NY: Springer New York, 2011. http://dx.doi.org/10.1007/978-1-4614-0782-9_8.
Full text
6
Stevenson, Clare E. M., and David M. Lawson. "Analysis of Protein–DNA Interactions Using Surface Plasmon Resonance and a ReDCaT Chip." In Protein-Ligand Interactions, 369–79. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1197-5_17.
Full text
7
Panda, Siddhartha, and Saiju Pyarajan. "Lab-on-Chip Devices for Protein Analysis." In Encyclopedia of Microfluidics and Nanofluidics, 1562–70. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4614-5491-5_777.
Full text
8
Zhang, Xian-En, and Li-Jun Bi. "Protein Chip for Detection of DNA Mutations." In Methods in Molecular Biology, 163–76. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-304-2_11.
Full text
9
Massie, Charles E., and Ian G. Mills. "Mapping Protein–DNA Interactions Using ChIP-Sequencing." In Methods in Molecular Biology, 157–73. New York, NY: Springer New York, 2011. http://dx.doi.org/10.1007/978-1-61779-376-9_11.
Full text
10
Panda, Siddhartha, and Saiju Pyarajan. "Lab-on-Chip Devices for Protein Analysis." In Encyclopedia of Microfluidics and Nanofluidics, 1–11. Boston, MA: Springer US, 2014. http://dx.doi.org/10.1007/978-3-642-27758-0_777-2.
Full textConference papers on the topic "Protei chip"
1
Li, Shifeng, David Fozdar, Dongbing Shao, Shaochen Chen, Pierre N. Floriano, Nicolaos Christodoulides, Mehnaaz F. Ali, Priya Dharshan, John T. McDevitt, and Dean Neikirk. "Disposable Polydimethylsiloxane/Silicon Hybrid Chips for Protein Detection." In ASME 2004 International Mechanical Engineering Congress and Exposition. ASMEDC, 2004. http://dx.doi.org/10.1115/imece2004-62170.
Full textAbstract:
This paper presents disposable protein analysis chips with single and multiple chambers - constructed from poly (dimethylsiloxane) (PDMS) and silicon. The chips are composed of a multilayer stack of PDMS layers that sandwich a silicon microchip. This inner silicon chip features an etched array of microcavities hosting agarose beads. The sample is introduced into the fluid network in the top PDMS layer where it is directed to the bead chamber. After reaction of the analyte with the probe beads, signal generated on the beads is captured with a CCD camera, digitally processed, and analyzed. An established bead-based fluorescent assay for C-reactive protein (CRP) was used here to characterize these hybrid chips. The detection limit of the single chamber protein chip was found to be 1ng/mL. Additionally, using the back pressure compensation method, the signals from each of the four-chamber chip were found to be within 10% of each other. Moreover, the fabrication of the multiple-chamber chip may increase throughput and multiplex assay capacity.
2
Kim, Joonwan, Yutaka Yamagata, Kozo Inoue, and Toshiro Higuchi. "A Device for Fabricating Protein Chips Using Surface Acoustic Wave Atomizer and Electrostatic Deposition." In ASME 2001 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2001. http://dx.doi.org/10.1115/imece2001/mems-23910.
Full textAbstract:
Abstract To fabricate protein chips from solution, we propose an advanced system by utilizing the surface acoustic wave atomizer and electrostatic deposition. The system mainly consists of three components: the protein solution supply system, the piezo-SAW atomizer, and the electrostatic particle collector. Protein chips are successfully formed by the device and the particle diameter ranged from 0.2 to 1μm using BSA. The chip of luciferase from firefly was formed by the device and was dissolved in reaction mixture to show strong luminescence. Chips of Anti-mouse IgG was also formed and cross-linked and their activity as immuno globulin was verified by fluorescence method. By utilizing insulation mask, protein chips with desired shapes like rectangular or circular are formed with relatively uniform thickness. Though there are rooms for improvements in terms of deposition efficiency, the device proved to be very effective in forming biochemical active protein chips.
3
Woody, Bethany A., K. Scott Smith, David J. Adams, and William E. Barkman. "Assessment of the Process Parameters and Their Effect on the Chip Length When Using CNC Toolpaths to Provide Chip Breaking in Turning Operations." In ASME 2008 International Manufacturing Science and Engineering Conference collocated with the 3rd JSME/ASME International Conference on Materials and Processing. ASMEDC, 2008. http://dx.doi.org/10.1115/msec_icmp2008-72468.
Full textAbstract:
Past work at UNC Charlotte has demonstrated that the use of oscillating CNC toolpaths provides a reliable chip breaking alternative to conventional methods such as the use of cutting inserts with special geometries and/or adjusting machining parameters. The specific toolpath geometry and the selection of the oscillating parameters is an important step to reliably and constantly create broken chips using this new method. This paper builds on the past work and discusses the proper selection of oscillation amplitude and its effect on the ability to break chips and to achieve desired chip lengths.
4
Saiki, Naoya, Kazuaki Inaba, Kikuo Kishimoto, and Hideo Senoo. "Evaluation of the Reliability of Film Adhesives Under Hygrothermal Condition." In ASME 2011 Pacific Rim Technical Conference and Exhibition on Packaging and Integration of Electronic and Photonic Systems. ASMEDC, 2011. http://dx.doi.org/10.1115/ipack2011-52096.
Full textAbstract:
Mechanical evaluation method of adhesive strength for bonding IC chips in chip-stacked packages is investigated. These film adhesives are required to bond IC chips securely under JEDEC moisture/reflow test. The stress condition of film adhesives under the moisture/reflow test is analyzed by FEM to clarify proper stress condition for the adhesive test. Thermal strain, moisture expansion and strain induced by vapor pressure is considered. It is found that the shear stress is the main loading factor on reflow process in the analysis. A shear test using chevron-shaped chip is proposed as the adhesive test, which apply shear load to the film adhesive at the corner of a chip. The specimen is fabricated by the same process of actual semiconductor manufacturing. The evaluation method is conducted without any problem. The proposed method is thought to be suitable for film adhesives of chip bonding.
5
Horiuchi, Keisuke, Prashanta Dutta, Huanchun Cui, and Cornelius F. Ivory. "High Resolution Separation of Proteins in a Polymeric Micro-Fluidic Chip." In ASME 2003 International Mechanical Engineering Congress and Exposition. ASMEDC, 2003. http://dx.doi.org/10.1115/imece2003-41206.
Full textAbstract:
An integrated micro-fluidic chip has been developed using Poly-di-methyl siloxane (PDMS) to separate proteins by isoelectric focusing (IEF). Soft lithography techniques, which offer rapid prototyping, easy multilayer fabrication, mass production capability and biocompatibility, were utilized to fabricate various parts of the micro-fluidic chip. Separately molded PDMS layers were bonded together to form three-dimensional microfluidic chips. The microfluidic chips were prepared for IEF by conditioning the channel with 1 M NaOH and then loading it with a solution of fluorescent proteins made using 0.4% MC, 4% broad-range ampholyte and 0.018 mg/ml protein in 18 MOhm water. Relatively large reservoirs on the acidic and basic ends of the channel were filled with anolyte (50 mM phosphoric acid) and catholyte (50 mM sodium hydroxide), respectively, and then current was applied along the axis of the channel until one or more bands of protein focused, usually in just a few minutes even at relatively low voltages. The focused bands were generally well-formed with sharp edges and were less than 100 microns across yielding a putative peak capacity in excess of 100 peaks in a 2-cm long channel.
6
Trinkle, Christine A., Christopher J. Morgan, and Luke P. Lee. "High Precision Assembly of Soft-Polymer Microfluidic Circuits." In ASME 2006 International Mechanical Engineering Congress and Exposition. ASMEDC, 2006. http://dx.doi.org/10.1115/imece2006-14631.
Full textAbstract:
Microfluidic chips have made it possible to manipulate biological fluidic samples in increasingly smaller volumes—even enabling multiplexed study of individual cells. Performing biological assays using microfluidic technology not only makes them more portable when compared to their traditional counterparts, but also decreases testing time and cost. These biofluidic circuits vary widely in design and function: multiplexed cell electroporation, on-chip cell culturing, cell-cell communication monitoring, protein crystallization, and small volume sample analysis are only a few examples of potential applications. The rapid rate of growth and change in this field creates a need for inexpensive and flexible rapid prototyping of microfluidic chips.
7
Lin, Shih-Chang, Fangang Tseng, and Ching-Chang Chieng. "Numerical Simulation of Protein Stamping Process Driven by Capillary Force." In ASME 2002 International Mechanical Engineering Congress and Exposition. ASMEDC, 2002. http://dx.doi.org/10.1115/imece2002-33070.
Full textAbstract:
“Microstamping” is one of patterning techniques [1] developed to deliver thousands of samples in parallel onto a surface for use in biosensors and medical diagnostics and the inexpensive production of micropatterned arrays of active proteins is of interest. Successful print of these protein island arrays includes conformal contact between an inked patterned stamp and the surface of a substrate and the full control over the amount and distribution of protein solution transferred from the impregnated stamps. In most common design, stamper is made of a solid material and proper inking method is required. Martin et al [2] have created a microstamper constructed by forming the hydrogel in sequence within the narrow ends of machine-pulled capillary tubes. This paper studies the protein-filling (inking)/stamping/printing process by numerical computations for a proposed Array-Stamper Chip with embedded microchannels. (Fig. 1) The array chip consists of thousands of microchannels with their own stampers to deliver thousands of fixed size/shape liquid samples to a bottom chip by capillary force simultaneously. The transfer process and physics are analyzed by solving first principle equations, i.e. conservation laws of mass, momentum. Due to the symmetry design of the array chip, the analysis is performed for a representative stamp only (Fig. 1b). Stable and robust numerical approaches as volume-of-Fluid (VOF) method [3] for two phase homogenous flow model and the interface tracking technique in cooperation with Continuum Surface tension Force (CSF) Model [4] are employed to determine the shape of liquid/gas interface as well as the fluid flowing pattern. Figure 2 shows the entire protein transfer during stamping/printing process, the Stamper Chip is moved toward/touch/away bio reaction chip starting at a distance of 50 μm away. The process consists of (a) The liquid fluid forms a meniscus and tends to reach out at the tip of the microchannel from the Stamping Chip (Fig. 2a), (b) The droplet meniscus is formed and the Stamper Chip starts to be moved toward the bottom chip (Fig. 2b), (c) The Stamper Chip is touched down and then is pulled up from the Bio-Reaction Chip, the liquid flows horizontally via the horizontal microchannels (Fig. 2c) and reaches the bottom chip, (d) part of the liquid is pushed upward and formed a small waist (Fig. 2d), (e) The Stamper Chip is moved further upwards with liquid slug of narrower waist (Fig. 2e), and (f) Stamper Chip is back to the original position with part of liquid broken at some point and left on the Bio-reaction Chip successfully. The controlling of the spot size left on bio-chip can be manipulated by physical properties of the filling protein, the inner/outer diameter of the microchannel, moving speed of the Stamper Chip, and the hydrophilic nature of the outer edge surface of the stamper. Two sets of physical properties are employed for computations (1) protein of low concentration with physical properties as water (2) 2mg/ml BSA concentration according to Fig. 3. Degree of hydrophilic nature with different liquid/gas/solid contact angle on stamper edge surface AB and the stamping speed do play significant role on the printing spot formation and size as shown in Table 1. Figure 4 shows that the size of printing size decreases with outer diameter of the microchannel. The detailed flowing process illustrate that the formations of the printing spot are resulted from forces interactions between the capillary flow formation process and stamper moving speed. In summary, numerical simulations not only give the suggestions for the array-stamper design with precise control of printing spot but also provide the physics and detailed information of the spot formation.
8
Kao, Nicholas, Jeng Yuan Lai, Jase Jiang, Yu Po Wang, and C. S. Hsiao. "Underfill Assessments and Validations for Low-k FCBGA." In ASME 2006 International Mechanical Engineering Congress and Exposition. ASMEDC, 2006. http://dx.doi.org/10.1115/imece2006-15432.
Full textAbstract:
With the trend of electronic consumer product toward more functionality, high performance and miniaturization, IC chip is required to deliver more I/Os signals and better electrical characteristics under same package form factor. Thus, Flip Chip BGA (FCBGA) package was developed to meet those requirements offering better electrical performance, more I/O pins accommodation and high transmission speed. For high-speed application, the low dielectric constant (low-k) material that can effectively reduce the signal delays is extensively used in IC chips. However, the low-k material possesses fragile mechanical property and high coefficient of thermal expansion (CTE) compared with silicon chip, which raises the reliability concerns of low-k material integrated into IC chip. The typical reliability failure modes are low-k layer delamination and bump crack under temperature loading during assembly and reliability test. Delamination is occurred in the interface between low-k dielectric layers and underfill material at chip corner. Bump crack is at Under Bump Metallization (UBM) corner. Thus, the adequate underfill material selection becomes very important for both solder bump and low-k chips [1]. This paper mainly characterized FCBGA underfill materials to guide the adequate candidates to prevent failures on low-k chip and solder bump. Firstly, test vehicle was a FCBGA package with heat spreader and was investigated the thermal stress by finite element models. In order to analyze localized low-k structures, sub-modeling technique is used for underfill characterizations. Then, the proper underfill candidates picked from modeling results were experimentally validated by reliability tests. Finally, various low-k FCBGA package structures were also studied with same finite element technique.
9
Fengchun Zhang, Xia Chen, Ping Sun, and Su Luo. "The development of slides protein detection chip." In 2011 International Conference on Remote Sensing, Environment and Transportation Engineering (RSETE). IEEE, 2011. http://dx.doi.org/10.1109/rsete.2011.5966290.
Full text
10
Stuffer, Anton, Peter Egger, Helmut Pohl, and Antje Moffat. "Laser-Voltage-Prober Measurements on Bipolar Devices." In ISTFA 2002. ASM International, 2002. http://dx.doi.org/10.31399/asm.cp.istfa2002p0177.
Full textAbstract:
Abstract Modern package technologies like flip-chip, require measurements of transient signals from the chip backside [1], [2]. This is because frontside access is not possible while running a test pattern. This is an established method for CMOS devices and commercial equipment is available. This paper demonstrates the usefulness of a Laser- Voltage-Prober for transient signal measurements from the backside on bipolar-devices.
Reports on the topic "Protei chip"
1
Watkins, Nicholas. Protein Factory on a Chip for Rapid Therapeutics. Office of Scientific and Technical Information (OSTI), April 2020. http://dx.doi.org/10.2172/1615568.
Full text
2
Lev, Benjamin L. Atom chip microscopy: A novel probe for strongly correlated materials. Office of Scientific and Technical Information (OSTI), November 2011. http://dx.doi.org/10.2172/1028620.
Full text
3
Demina, Regina. J/Ψ from chi Production in proton-antiproton Collisions at √s = 1.8 TeV. Office of Scientific and Technical Information (OSTI), January 1994. http://dx.doi.org/10.2172/1372374.
Full text
4
Harman, Gary E., and Ilan Chet. Enhancement of plant disease resistance and productivity through use of root symbiotic fungi. United States Department of Agriculture, July 2008. http://dx.doi.org/10.32747/2008.7695588.bard.
Full textAbstract:
The objectives of the project were to (a) compare effects ofT22 and T-203 on growth promotion and induced resistance of maize inbred line Mol7; (b) follow induced resistance of pathogenesis-related proteins through changes in gene expression with a root and foliar pathogen in the presence or absence of T22 or T-203 and (c) to follow changes in the proteome of Mol? over time in roots and leaves in the presence or absence of T22 or T-203. The research built changes in our concepts regarding the effects of Trichoderma on plants; we hypothesized that there would be major changes in the physiology of plants and these would be reflected in changes in the plant proteome as a consequence of root infection by Trichoderma spp. Further, Trichoderma spp. differ in their effects on plants and these changes are largely a consequence of the production of different elicitors of elicitor mixtures that are produced in the zone of communication that is established by root infection by Trichoderma spp. In this work, we demonstrated that both T22 and T-203 increase growth and induce resistance to pathogens in maize. In Israel, it was shown that a hydrophobin is critical for root colonization by Trichoderma strains, and that peptaibols and an expansin-like protein from Ttrichoderma probably act as elicitors of induced resistance in plants. Further, this fungus induces the jasmonate/ethylene pathway of disease resistance and a specific cucumber MAPK is required for transduction of the resistance signal. This is the first such gene known to be induced by fungal systems. In the USA, extensive proteomic analyses of maize demonstrated a number of proteins are differentially regulated by T. harzianum strain T22. The pattern of up-regulation strongly supports the contention that this fungus induces increases in plant disease resistance, respiratory rates and photosynthesis. These are all very consistent with the observations of effects of the fungus on plants in the greenhouse and field. In addition, the chitinolytic complex of maize was examined. The numbers of maize genes encoding these enzymes was increased about 3-fold and their locations on maize chromosomes determined by sequence identification in specific BAC libraries on the web. One of the chitinolytic enzymes was determined to be a heterodimer between a specific exochitinase and different endochitinases dependent upon tissue differences (shoot or root) and the presence or absence of T. harzianum. These heterodimers, which were discovered in this work, are very strongly antifungal, especially the one from shoots in the presence of the biocontrol fungus. Finally, RNA was isolated from plants at Cornell and sent to Israel for transcriptome assessment using Affymetrix chips (the chips became available for maize at the end of the project). The data was sent back to Cornell for bioinformatic analyses and found, in large sense, to be consistent with the proteomic data. The final assessment of this data is just now possible since the full annotation of the sequences in the maize Affy chips is just now available. This work is already being used to discover more effective strains of Trichoderma. It also is expected to elucidate how we may be able to manipulate and breed plants for greater disease resistance, enhanced growth and yield and similar goals. This will be possible since the changes in gene and protein expression that lead to better plant performance can be elucidated by following changes induced by Trichoderma strains. The work was in, some parts, collaborative but in others, most specifically transcriptome analyses, fully synergistic.
5
Rumerio, Paolo Giuseppe. Interference measurement of the chi c0 (1 P-3 0) in proton anti-proton annihilation into two neutral pseudoscalar mesons. Office of Scientific and Technical Information (OSTI), January 2003. http://dx.doi.org/10.2172/1419220.
Full text
6
Boswell, Christopher Mark. Chi Meson Production in Proton - Antiproton Interactions at the Center-of-Mass Energy of 1.8-TeV. Office of Scientific and Technical Information (OSTI), November 1993. http://dx.doi.org/10.2172/1372842.
Full text
7
Casey, Therese, Sameer J. Mabjeesh, Avi Shamay, and Karen Plaut. Photoperiod effects on milk production in goats: Are they mediated by the molecular clock in the mammary gland? United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7598164.bard.
Full textAbstract:
US scientists, Dr. Theresa Casey and Dr. Karen Plaut, collaborated with Israeli scientists, Dr. SameerMabjeesh and Dr. AviShamay to conduct studies proposed in the BARD Project No. US-4715-14 Photoperiod effects on milk production in goats: Are they mediated by the molecular clock in the mammary gland over the last 3 years. CLOCK and BMAL1 are core components of the circadian clock and as heterodimers function as a transcription factor to drive circadian-rhythms of gene expression. Studies of CLOCK-mutant mice found impaired mammary development in late pregnancy was related to poor lactation performance post-partum. To gain a better understanding of role of clock in regulation of mammary development studies were conducted with the mammary epithelial cell line HC11. Decreasing CLOCK protein levels using shRNA resulted in increased mammary epithelial cell growth rate and impaired differentiation, with lower expression of differentiation markers including ad herens junction protein and fatty acid synthesis genes. When BMAL1 was knocked out using CRISPR-CAS mammary epithelial cells had greater growth rate, but reached stationary phase at a lower density, with FACS indicating cells were growing and dying at a faster rate. Beta-casein milk protein levels were significantly decreased in BMAL1 knockout cells. ChIP-seq analysis was conducted to identify BMAL1 target genes in mammary epithelial cells. Studies conducted in goats found that photoperiod duration and physiological state affected the dynamics of the mammary clock. Effects were likely independent of the photoperiod effects on prolactin levels. Interestingly, circadian rhythms of core body temperature, which functions as a key synchronizing cue sent out by the central clock in the hypothalamus, were profoundly affected by photoperiod and physiological state. Data support that the clock in the mammary gland regulates genes important to development of the gland and milk synthesis. We also found the clock in the mammary is responsive to changes in physiological state and photoperiod, and thus may serve as a mechanism to establish milk production levels in response to environmental cues.
8
Lane, Lerose, R. Gary Hicks, DingXin Cheng, and Erik Updyke. Manual for Thin Asphalt Overlays. Mineta Transportation Institute, October 2020. http://dx.doi.org/10.31979/mti.2020.1906.
Full textAbstract:
This manual presents best practices on project selection, mix design, and construction to ensure a superior product when constructing thin asphalt overlays. Experience shows these treatments provide excellent performance when placed on pavements in fair to good condition using proper construction techniques. Though sometime referred to by other names, thin asphalt overlays have been widely used for pavement preservation throughout the world for over 50 years. Limited infrastructure funding at the local, state, and federal levels has resulted in greater emphasis on the use of pavement preservation techniques to extend pavement life and reduce maintenance costs. Thin asphalt overlays are one of many preventative maintenance treatments. Thin asphalt overlays are placed directly on existing pavement and can range from 1/2 inch to 1 1/2 inches in thickness. Thin asphalt overlays have proven to be an economical means for maintaining and improving the functional condition of an existing pavement since the 1960s. Specifically, this manual provides guidance for engineers regarding where and when to use thin asphalt overlays including: (1) Types and variations of thin overlays; (2) Materials and the design process; (3) Construction; (4) Quality Assurance; and (5) Troubleshooting. This chapter by chapter guidance enables an Agency’s engineers to design and construct a successful thin asphalt overlay project to completion. This manual is one of four new manuals prepared by the California Pavement Preservation Center (CP2Center) using funding from California Senate Bill 1 (SB-1), passed in April 2017. The other three manuals provide detailed design and construction information for (1) chip seals, (2) slurry surfacing, and (3) Cape seals. The creation of these manuals was a task funded entirely from SB-1 monies for the purpose of disseminating training and technical information on highway pavement preservation to local agencies throughout California.
9
Barg, Rivka, Erich Grotewold, and Yechiam Salts. Regulation of Tomato Fruit Development by Interacting MYB Proteins. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7592647.bard.
Full textAbstract:
Background to the topic: Early tomato fruit development is executed via extensive cell divisions followed by cell expansion concomitantly with endoreduplication. The signals involved in activating the different modes of growth during fruit development are still inadequately understood. Addressing this developmental process, we identified SlFSM1 as a gene expressed specifically during the cell-division dependent stages of fruit development. SlFSM1 is the founder of a class of small plant specific proteins containing a divergent SANT/MYB domain (Barg et al 2005). Before initiating this project, we found that low ectopic over-expression (OEX) of SlFSM1 leads to a significant decrease in the final size of the cells in mature leaves and fruits, and the outer pericarp is substantially narrower, suggesting a role in determining cell size and shape. We also found the interacting partners of the Arabidopsis homologs of FSM1 (two, belonging to the same family), and cloned their tomato single homolog, which we named SlFSB1 (Fruit SANT/MYB–Binding1). SlFSB1 is a novel plant specific single MYB-like protein, which function was unknown. The present project aimed at elucidating the function and mode of action of these two single MYB proteins in regulating tomato fruit development. The specific objectives were: 1. Functional analysis of SlFSM1 and its interacting protein SlFSB1 in relation to fruit development. 2. Identification of the SlFSM1 and/or SlFSB1 cellular targets. The plan of work included: 1) Detailed phenotypic, histological and cellular analyses of plants ectopically expressing FSM1, and plants either ectopically over-expressing or silenced for FSB1. 2) Extensive SELEX analysis, which did not reveal any specific DNA target of SlFSM1 binding, hence the originally offered ChIP analysis was omitted. 3) Genome-wide transcriptional impact of gain- and loss- of SlFSM1 and SlFSB1 function by Affymetrix microarray analyses. This part is still in progress and therefore results are not reported, 4) Search for additional candidate partners of SlFSB1 revealed SlMYBI to be an alternative partner of FSB1, and 5) Study of the physical basis of the interaction between SlFSM1 and SlFSB1 and between FSB1 and MYBI. Major conclusions, solutions, achievements: We established that FSM1 negatively affects cell expansion, particularly of those cells with the highest potential to expand, such as the ones residing inner to the vascular bundles in the fruit pericarp. On the other hand, FSB1 which is expressed throughout fruit development acts as a positive regulator of cell expansion. It was also established that besides interacting with FSM1, FSB1 interacts also with the transcription factor MYBI, and that the formation of the FSB1-MYBI complex is competed by FSM1, which recognizes in FSB1 the same region as MYBI does. Based on these findings a model was developed explaining the role of this novel network of the three different MYB containing proteins FSM1/FSB1/MYBI in the control of tomato cell expansion, particularly during fruit development. In short, during early stages of fruit development (Phase II), the formation of the FSM1-FSB1 complex serves to restrict the expansion of the cells with the greatest expansion potential, those non-dividing cells residing in the inner mesocarp layers of the pericarp. Alternatively, during growth phase III, after transcription of FSM1 sharply declines, FSB1, possibly through complexing with the transcription factor MYBI serves as a positive regulator of the differential cell expansion which drives fruit enlargement during this phase. Additionally, a novel mechanism was revealed by which competing MYB-MYB interactions could participate in the control of gene expression. Implications, both scientific and agricultural: The demonstrated role of the FSM1/FSB1/MYBI complex in controlling differential cell growth in the developing tomato fruit highlights potential exploitations of these genes for improving fruit quality characteristics. Modulation of expression of these genes or their paralogs in other organs could serve to modify leaf and canopy architecture in various crops.
10
Droby, Samir, Michael Wisniewski, Ron Porat, and Dumitru Macarisin. Role of Reactive Oxygen Species (ROS) in Tritrophic Interactions in Postharvest Biocontrol Systems. United States Department of Agriculture, December 2012. http://dx.doi.org/10.32747/2012.7594390.bard.
Full textAbstract:
To elucidate the role of ROS in the tri-trophic interactions in postharvest biocontrol systems a detailed molecular and biochemical investigation was undertaken. The application of the yeast biocontrol agent Metschnikowia fructicola, microarray analysis was performed on grapefruit surface wounds using an Affymetrix Citrus GeneChip. the data indicated that 1007 putative unigenes showed significant expression changes following wounding and yeast application relative to wounded controls. The expression of the genes encoding Respiratory burst oxidase (Rbo), mitogen-activated protein kinase (MAPK) and mitogen-activated protein kinase kinase (MAPKK), G-proteins, chitinase (CHI), phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS) and 4-coumarate-CoA ligase (4CL). In contrast, three genes, peroxidase (POD), superoxide dismutase (SOD) and catalase (CAT), were down-regulated in grapefruit peel tissue treated with yeast cells. The yeast antagonists, Metschnikowia fructicola (strain 277) and Candida oleophila (strain 182) generate relatively high levels of super oxide anion (O2−) following its interaction with wounded fruit surface. Using laser scanning confocal microscopy we observed that the application of M. fructicola and C. oleophila into citrus and apple fruit wounds correlated with an increase in H2O2 accumulation in host tissue. The present data, together with our earlier discovery of the importance of H₂O₂ production in the defense response of citrus flavedo to postharvest pathogens, indicate that the yeast-induced oxidative response in fruit exocarp may be associated with the ability of specific yeast species to serve as biocontrol agents for the management of postharvest diseases. Effect of ROS on yeast cells was also studied. Pretreatment of the yeast, Candida oleophila, with 5 mM H₂O₂ for 30 min (sublethal) increased yeast tolerance to subsequent lethal levels of oxidative stress (50 mM H₂O₂), high temperature (40 °C), and low pH (pH 4). Suppression subtractive hybridization analysis was used to identify genes expressed in yeast in response to sublethal oxidative stress. Transcript levels were confirmed using semi quantitative reverse transcription-PCR. Seven antioxidant genes were up regulated. Pretreatment of the yeast antagonist Candida oleophila with glycine betaine (GB) increases oxidative stress tolerance in the microenvironment of apple wounds. ROS production is greater when yeast antagonists used as biocontrol agents are applied in the wounds. Compared to untreated control yeast cells, GB-treated cells recovered from the oxidative stress environment of apple wounds exhibited less accumulation of ROS and lower levels of oxidative damage to cellular proteins and lipids. Additionally, GB-treated yeast exhibited greater biocontrol activity against Penicillium expansum and Botrytis cinerea, and faster growth in wounds of apple fruits compared to untreated yeast. The expression of major antioxidant genes, including peroxisomal catalase, peroxiredoxin TSA1, and glutathione peroxidase was elevated in the yeast by GB treatment. A mild heat shock (HS) pretreatment (30 min at 40 1C) improved the tolerance of M. fructicola to subsequent high temperature (45 1C, 20–30 min) and oxidative stress (0.4 mol-¹) hydrogen peroxide, 20–60 min). HS-treated yeast cells showed less accumulation of reactive oxygen species (ROS) than non-treated cells in response to both stresses. Additionally, HS-treated yeast exhibited significantly greater (P≥0.0001) biocontrol activity against Penicillium expansum and a significantly faster (Po0.0001) growth rate in wounds of apple fruits stored at 25 1C compared with the performance of untreated yeast cells. Transcription of a trehalose-6-phosphate synthase gene (TPS1) was up regulated in response to HS and trehalose content also increased.