Region Signature Research Articles

Ferritin from the Pacific abalone Haliotis discus hannai: Analysis of cDNA sequence, expression, and activity.

Ferritin plays an important role in iron homeostasis due to its ability to bind and sequester large amounts of iron. In this study, the gene encoding a ferritin (HdhFer2) was cloned from Pacific abalone (Haliotis discus hannai). The full-length cDNA of HdhFer2 contains a 5'-UTR of 121bp, an ORF of 516bp, and a 3'-UTR of 252bp with a polyadenylation signal sequence of AATAAA and a poly(A) tail. It also contains a 31bp iron-responsive element (IRE) in the 5'-UTR position, which is conserved in many ferritins. HdhFer2 consists of 171 amino acid residues with a predicted molecular weight (MW) ∼19.8kDa and a theoretical isoelectric point (PI) of 4.84. The deduced amino acid sequence of HdhFer2 contains two ferritin iron-binding region signatures (IBRSs). HdhFer2 mRNA was detected in a wide range of tissues and was dominantly expressed in the gill. Infection with the bacterial pathogen Vibrio anguillarum significantly upregulated HdhFer2 expression in a time-dependent manner. Recombinant HdhFer2 (rHdhFer2) purified from Escherichia coli was able to bind ferrous iron in a concentration-dependent manner. In summary, these results suggest that HdhFer2 is a crucial protein in the iron-withholding defense system, and plays an important role in the innate immune response of abalone.

EVIDENCE FOR A TRANSITION REGION RESPONSE TO PENUMBRAL MICROJETS IN SUNSPOTS

Penumbral microjets are short-lived, fine-structured and bright jets that are generally observed in chromospheric imaging of the penumbra of sunspots. Here we investigate their potential transition region signature, by combining observations with the Swedish 1-m Solar Telescope (SST) in the Ca II H and Ca II 8542{\AA} lines with ultraviolet imaging and spectroscopy obtained with the Interface Region Imaging Spectrograph (IRIS), which includes the C II 1334/1335{\AA}, Si IV 1394/1403{\AA} and Mg II h & k 2803/2796{\AA} lines. We find a clear corresponding signal in the IRIS Mg II k, C II and Si IV slit-jaw images, typically offset spatially from the Ca II signature in the direction along the jets: from base to top, the penumbral microjets are predominantly visible in Ca II, Mg II k and C II/Si IV, suggesting progressive heating to transition region temperatures along the jet extent. Hence, these results support the suggestion from earlier studies that penumbral microjets may heat to transition region temperatures.

What Can We Learn about Magnetotail Reconnection from 2D PIC Harris-Sheet Simulations?

The Magnetosphere Multiscale Mission (MMS) will provide the first opportunity to probe electron-scale physics during magnetic reconnection in Earth’s magnetopause and magnetotail. This article will address only tail reconnection—as a non-steady-state process in which the first reconnected field lines advance away from the $x$ -point in flux pile-up fronts directed Earthward and anti-Earthward. An up-to-date microscopic physical picture of electron and ion-scale collisionless tail reconnection processes is presented based on 2-D Particle-In-Cell (PIC) simulations initiated from a Harris current sheet and on Cluster and Themis measurements of tail reconnection. The successes and limitations of simulations when compared to measured reconnection are addressed in detail. The main focus is on particle and field diffusion region signatures in the tail reconnection geometry. The interpretation of these signatures is vital to enable spacecraft to identify physically significant reconnection events, to trigger meaningful data transfer from MMS to Earth and to construct a useful overall physical picture of tail reconnection. New simulation results and theoretical interpretations are presented for energy transport of particles and fields, for the size and shape of electron and ion diffusion regions, for processes occurring near the fronts and for the $\mathbf{j} \times \mathbf{B}$ (Hall) electric field.

Molecular profile and functional characterization of the ferritin H subunit from rock bream (Oplegnathus fasciatus), revealing its putative role in host antioxidant and immune defense

Ferritins are iron binding proteins made out of 24 subunits, involved in iron homeostasis and metabolism in cellular environments. Here, we sought to identify and functionally characterize a one type of subunits of ferritin (ferritin H-like subunit) from rock bream (Oplegnathus fasciatus; RbFerH). The complete coding sequence of RbFerH was 531bp in length, encoding a 177-amino acid protein with a predicted molecular mass of 20.8kDa. The deduced protein structure possessed the domain architecture characteristic of known ferritin H subunits, including metal ligands for iron binding, a ferroxidase center, and two iron-binding region signatures. As expected, the 5′ untranslated region of the RbFerH cDNA sequence contained a putative iron response element region, a characteristic regulatory element involved in its translation. The RbFerH gene comprised 5 exons and 4 introns spanning a 4195bp region. Overexpressed recombinant RbFerH protein demonstrated prominent Fe(II) ion depriving activity, bacteriostatic properties, and protective effects against oxidative double-stranded DNA damage. Using quantitative polymerase chain reaction (qPCR), we found that RbFerH was expressed ubiquitously in the majority of physiologically important tissues in rock bream. A greater abundance of the mRNA transcripts were detected in blood and liver tissues. Upon administering different microbial pathogens and pathogen-derived mitogens, RbFerH transcription was markedly elevated in the blood of rock bream. Taken together, our findings suggest that RbFerH acts as a potent iron sequestrator in rock bream and may actively participate in antimicrobial as well as antioxidative defense.

Molecular cloning and expression analysis of ferritin, heavy polypeptide 1 gene from duck (Anas platyrhynchos).

H-ferritin is a core subunit of the iron storage protein ferritin, and is related to the pathogenesis of malignant diseases. A differential expressed sequence tag of the ferritin, heavy polypeptide 1 gene (FTH1) was obtained from our previously constructed suppression subtractive cDNA library from 3-day-old ducklings challenged with duck hepatitis virus type I (DHV-1). The expression and function of FTH1 in immune defense against infection remains largely unknown in ducks. In this study, the full-length duFTH1 cDNA was obtained using reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends. It consisted of 153 basepairs (bp) 5'untranslated region (UTR), 183 bp 3'UTR, and 546 bp open reading frame that encodes a single protein of 181 amino acid residues. duFTH1 shares high similarity with FTH1 genes from other vertebrates. The amino acid sequence possesses the conserved domain of typical ferritin H subunits, including seven metal ligands in the ferroxidase center, one iron binding region signature, and a potential bio-mineralization residue (Thy(29)). Moreover, in agreement with a previously reported ferritin H subunit, we identified an iron response element in the 5'UTR. RT-PCR analyses revealed duFTH1 mRNA is widely expressed in various tissues. Real-time quantitative polymerase chain reaction analyses suggested that duFTH1 mRNA is significantly up-regulated in the liver after DHV-1 injection or polyriboinosinic polyribocytidylic acid (polyI:C) treatment, reaching a peak 4 h post-infection, and dropping progressively and returning to normal after 24 h. Our findings suggest that duFTH1 functions as an iron chelating protein subunit in duck and contributes to the innate immune responses against viral infections.

Molecular cloning, characterisation and expression of the translationally controlled tumor protein gene in rock bream (Oplegnathus fasciatus)

Translationally controlled tumor protein (TCTP) is an important immune regulator that has been implicated in a number of cellular processes, including cell growth, cell cycle progression, apoptosis regulation and protection of cells against various environmental stresses. In this study, we cloned and characterised TCTP from rock bream (Oplegnathus fasciatus), which is an economically important species in the Korean aquaculture industry. The full-length rock bream TCTP (RbTCTP) cDNA was of 1,041 bp and contained an open reading frame of 513 bp, which encoded 170 amino acids. The 5′ untranslated region (UTR) was 90 bp, while the 3′ UTR was 438 bp, containing a polyadenylation signal. RbTCTP showed 76, 75 and 74 % amino acid sequence identities to those of tilapia (Oreochromis niloticus), orange-spotted grouper (Epinephelus coioides) and Japanese sea perch (Lateolabrax japonicus), respectively. The positions of microtubule binding region, Ca+ binding region and TCTP signature regions in RbTCTP were similar to other fish species and mammals. RbTCTP mRNA expression level was highest in the gill compared to other tissues. The level of RbTCTP mRNA expression was significantly regulated by injection of red seabream iridovirus, Streptococcus iniae and Edwardsiella tarda.

Molecular cloning and tissue distribution of peroxisome proliferator-activated receptor-alpha (PPARα) and gamma (PPARγ) in the pigeon (Columba livia domestica)

1. Peroxisome proliferator-activated receptors (PPAR) are involved in lipid metabolism through transcriptional regulation of target gene expression. The objective of the current study was to clone and characterise the PPARα and PPARγ genes in pigeon.2. The full-length of 1941-bp PPARα and 1653-bp PPARγ were cloned from pigeons. The two genes were predicted to encode 468 and 475 amino acids, respectively. Both proteins contained two C4-type zinc fingers, a nuclear hormone receptor DNA-binding region signature and a HOLI domain (ligand binding domain of hormone receptors), and had high identities with other corresponding avian genes.3. Using quantitative real-time PCR, pigeon PPARα gene expression was shown to be high in kidney, liver, gizzard and duodenum whereas PPARγ was predominantly expressed in adipose tissue.

Ferritin H-like subunit from Manila clam (Ruditapes philippinarum): Molecular insights as a potent player in host antibacterial defense

Ferritins are iron chelating proteins, which involve in iron metabolism and sequestration, contributing to the iron homeostasis in living organisms. In the present study, one ferritin subunit which was identified as H-like subunit was completely characterized in cDNA and protein levels from Manila clam (Ruditapes philippinarum); (RpFeH). The full length cDNA of RpFeH was 776 bp and it consisted of open reading frame of 513 bp, encoding a 171 amino acid peptide with a calculated molecular mass of 19.6 kDa and isoelectric point of 5.23. The amino acid sequence resembled the characteristic features of typical ferritin H subunits, including seven metal ligands in ferroxidase center, two iron binding region signatures and potential bio-mineralization residue (Thy27). Moreover, it was possible to identify an iron response element in 5′ untranslated region, showing an agreement with previously reported ferritin H like subunits. The generated 3 dimensional tertiary structure of RpFeH showed a substantial consistency with the human ferritin H subunit, reinforcing its validity. Recombinant RpFeH was overexpressed in Escherichia coli BL21 (DE3) and purified. The recombinant protein showed a detectable iron binding activity according to the results obtained in our iron chelating activity assay. Furthermore it showed a noticeable anti-bacterial activity through suppressing the growth of Vibrio tapetis bacteria. The quantitative real time PCR detected ubiquitous RpFeH expression in tissues examined. However expression was found to be elevated in hemocyte and gill tissues. Transcriptional profile of Manila clam gill tissue, challenged with V. tapetis demonstrated a prolonged significant (P < 0.05) transcriptional up-regulations from 12 h post injection to 48 h post injection. Our findings suggest that RpFeH functions as an iron chelating protein subunit in Manila clam while contributing to the innate immune responses against bacterial infections, via its iron withholding function.

Cloning, sequencing, and in silico characterization of Omp 28 of Salmonella Typhi (strain MTCC 733) to develop r-DNA vaccine for typhoid fever.

Background:Typhoid is one of the most important diseases of human beings caused by Salmonella Typhi. There are many vaccine reported against Salmonella Typhi, but search for new candidate vaccine antigens is still going on because presently available vaccines have several limitations such as short-term immunity, high cost, and allergic reaction. Several approaches such as subunit vaccines, Vi polysaccharide, mutant vaccines, and r-DNA vaccines have been tested. r- DNA vaccines have shown some promising potential (targeted Omp). Omp 28 had shown very promising results and suggests that it should be used in further studies of animal protection against the disease.Objective:Cloning, Sequencing and In silico analysis of Omp 28 gene to develop r-DNA vaccine of S. Typhi.Materials and Methods:Omp 28 is made up of three identical subunits of 9.6 kDa showing PCR amplicon of 330 bp which has been cloned in the pJET vector. Recombinant clones has been sequenced, and data submitted to NCBI. Secondary structure was deduced by the Chou Fasman and Garnier method. The sequence of Omp 28 was studied for antigenic indexing, epitope mapping, and MHC mapping using various bioinformatics tool.Results and Conclusion:The sequence of Omp 28 has been assigned accession no GQ 907044.1 by NCBI. Secondary structure has shown it has more alpha region. Hydrophobic plot and surface probability plot shows most amino acids are surface exposed which is a requirement to develop a r-DNA vaccine. Antigenic sites are located within surface exposed regions and eight antigenic determinants are present in Omp 28. On Prosite analysis of Protein shown two motifs i.e. anaphylatoxin domain signature motif at position 219-252 and other one was iron sulphur binding region signature motif at position 36-44. On epitope analysis total six major B cell epitopes were observed which can provoke humoral immunity. On T cell epitope mapping several major epitopes has been found in case of MHC class I and MHC class II. It indicates that Omp 28 can provoke cell mediated as well as humoral immunity and can be proven a promising candidates of Salmonella Typhi.

Cloning and pharmaceutical analysis of CaMK gene of Botrytis cinerea

Using a PCR homology approach, DNA and cDNA sequences of calcium/calmodulin-dependent protein kinase (CaMK) gene of Botrytis cinerea were obtained. Southern blotting result displayed that CaMK was single copy in the genome of B. cinerea. The cDNA sequence of CaMK revealed an open reading frame of 2190 nucleotides encoding a 730 amino acid protein with predicted molecular weight of 81.8748 kDa. The genomic sequence of CaMK revealed the same ORF interrupted by six introns. Bioinformatics analysis showed that this protein had the distinctive features that characterize CaMK ATP binding region signature and serine/threonine protein kinase active-site signature. Pharmaceutical analysis displayed that the CaMK specific inhibitor, KN-62, could inhibit conidial germination, pathogenicity and herbicidal activity of B. cinerea BC4 strain. It was suggested that CaMK played an important role in regulating conidial germination, pathogenicity and herbicidal activity of B. cinerea.

Molecular Cloning and Copy Number Variation of a Ferritin Subunit (Fth1) and Its Association with Growth in Freshwater Pearl Mussel Hyriopsis cumingii

Iron is one of the most important minor elements in the shells of bivalves. This study was designed to investigate the involvement of ferritin, the principal protein for iron storage, in shell growth. A novel ferritin subunit (Fth1) cDNA from the freshwater pearl mussel (Hyriopsis cumingii) was isolated and characterized. The complete cDNA contained 822 bp, with an open reading frame (ORF) of 525 bp, a 153 bp 5′ untranslated region (UTR) and a 144 bp 3′ UTR. The complete genomic DNA was 4125 bp, containing four exons and three introns. The ORF encoded a protein of 174 amino acids without a signal sequence. The deduced ferritin contained a highly conserved motif for the ferroxidase center comprising seven residues of a typical vertebrate heavy-chain ferritin. It contained one conserved iron associated residue (Try27) and iron-binding region signature 1 residues. The mRNA contained a 27 bp iron-responsive element with a typical stem-loop structure in the 5′-UTR position. Copy number variants (CNVs) of Fth1 in two populations (PY and JH) were detected using quantitative real-time PCR. Associations between CNVs and growth were also analyzed. The results showed that the copy number of the ferritin gene of in the diploid genome ranged from two to 12 in PY, and from two to six in JH. The copy number variation in PY was higher than that in JH. In terms of shell length, mussels with four copies of the ferritin gene grew faster than those with three copies (P<0.05), suggesting that CNVs in the ferritin gene are associated with growth in shell length and might be a useful molecular marker in selective breeding of H. cumingii.

Molecular cloning and expression of interleukin-1 receptor-associated kinase 4, an important mediator of Toll-like receptor signal pathway, from small abalone Haliotis diversicolor

Mammal interleukin-1 receptor-associated kinases (IRAKs) have been demonstrated to play important functions in TLRs (Toll-like receptor) signal pathway and T cell proliferation, but there is less knowledge available on mollusc IRAKs. In this study, a molluscan IRAK-4 gene, saIRAK-4, was cloned for the first time from the small abalone ( Haliotis diversicolor). Its full-length cDNA sequence was 2062 bp, with a 1548 bp open reading frame encoding a protein of 516 aa. The molecular mass of the deduced protein was approximately 57.8 kDa with an estimated pI of 5.23, and showed highest identity (47%) to acorn worm Saccoglossus kowalevskii. Amino acid sequence analysis revealed saIRAK-4 shares conserved signature motifs with other IRAK-4 proteins, including the death domain (DD), serine/threonine/tyrosine protein kinase domain (STYKc), protein kinases ATP-binding region signature, serine/threonine protein kinases active-site signature and prokaryotic membrane lipoprotein lipid attachment site. Quantitative real-time PCR was employed to investigate the tissue distribution of saIRAK-4 mRNA, and its expression in abalone under bacteria challenge and larvae at different developmental stages. The saIRAK-4 mRNA could be detected in all examined tissues, with the highest expression level in gills, and was up-regulated in hemocytes and gills after bacteria injection. Additionally, saIRAK-4 was constitutively expressed at all examined developmental stages. These results indicate that saIRAK-4 could respond to pathogenic infection and may play an important role in the adult abalone immune system and early innate immunity in the process of abalone larval development.

AIP56: a novel bacterial apoptogenic toxin.

Photobacterium damselae subsp. piscicida (Phdp) is a Gram-negative pathogen agent of an important fish septicemia. The key virulence factor of Phdp is the plasmid-encoded exotoxin AIP56, which is secreted by exponentially growing pathogenic strains. AIP56 has 520 amino acids including an N-terminal cleavable signal peptide of 23 amino acid residues, two cysteine residues and a zinc-binding region signature HEXXH that is typical of most zinc metallopeptidases. AIP56 induces in vitro and in vivo selective apoptosis of fish macrophages and neutrophils through a caspase-3 dependent mechanism that also involves caspase-8 and -9. In vivo, the AIP56-induced phagocyte apoptosis progresses to secondary necrosis with release of cytotoxic phagocyte molecules including neutrophil elastase. Fish injected with recombinant AIP56 die with a pathology similar to that seen in the natural infection.

Template matching of freeform surfaces based on orthogonal distance fitting for precision metrology

Freeform surfaces are widely used in advanced optical and mechanical devices. In order to assess the form quality of a freeform surface, it is required to match the measurement surface with the design template. To improve the matching efficiency and accuracy, the whole procedure is divided into two stages: rough matching and final fitting. A new rough matching method, called the structured region signature, is proposed. The structured region signature is a generalized global feature which represents the surface shape by a one-dimensional function. The template location occupying the best matching signature is considered to be the correct rough position of the measurement surface. After that the motion parameters are updated iteratively based on the orthogonal distance fitting. The dependence between the foot-point parameters of the projection points and the motion parameters is derived from the closest-distance relationship between correspondence point pairs. Numerical experiments are given to demonstrate the validity of this approach.

Identifying meteorite source regions through near-Earth object spectroscopy

By virtue of their landing on Earth, meteorites reside in near-Earth object (NEO) orbits prior to their arrival. Thus the population of observable NEOs, in principle, gives important representation of meteorite source bodies. By linking meteorites to NEOs, and linking NEOs to their most likely main-belt source locations, we seek to gain insight into the original Solar System formation locations for different meteorite classes. To forge possible links between meteorites and NEOs, we have developed a three dimensional method for quantitative comparisons between laboratory measurements of meteorites and telescopic measurements of near-Earth objects. We utilize meteorite spectra from the Reflectance Experiment Laboratory (RELAB) database and NEO data from the SpeX instrument on the NASA Infrared Telescope Facility (IRTF). Using the Modified Gaussian Model (MGM) as a mathematical tool, we treat asteroid and meteorite spectra identically in the calculation of 1-μm and 2-μm Geometric Band Centers and their Band Area Ratios (BARs). Using these identical numerical parameters we quantitatively compare the spectral properties of S-, Sq-, Q- and V-type NEOs with the spectral properties of the meteorites in four classes: H, L, LL and HED. For each NEO spectrum, we assign a set of probabilities for it being related to each of these four meteorite classes. Our NEO-meteorite correlation probabilities are then convolved with NEO-source region probabilities to yield a final set of meteorite-source region correlations. While the ν6 resonance dominates the delivery for all four meteorite classes, an excess (significant at the 2.1-sigma level) source region signature is found for the H chondrites through the 3:1 mean motion resonance. This results suggest an H chondrite source with a higher than average delivery preference through the 3:1 resonance. A 3:1 resonance H chondrite source region is consistent with the short cosmic ray exposure ages known for H chondrites.

Concurrent genotyping of Helicobacter pylorivirulence genes and human cytokine SNP sites using whole genome amplified DNA derived from minute amounts of gastric biopsy specimen DNA

BackgroundBacterial and cellular genotyping is becoming increasingly important in the diagnosis of infectious diseases. However, difficulties in obtaining sufficient amount of bacterial and cellular DNA extracted from the same human biopsy specimens is often a limiting factor. In this study, total DNA (host and bacterial DNA) was isolated from minute amounts of gastric biopsy specimens and amplified by means of whole genome amplification using the multiple displacement amplification (MDA) technique. Subsequently, MDA-DNA was used for concurrent Helicobacter pylori and human host cellular DNA genotyping analysis using PCR-based methods.ResultsTotal DNA was isolated from gastric biopsy specimens of 12 subjects with gastritis and 16 control subjects having a normal mucosa. The DNA was amplified using a multiple displacement amplification (MDA) kit. Next, concurrent genotyping was performed using H. pylori-specific virulence gene PCR amplification assays, pyrosequencing of bacterial 16S rDNA and PCR characterisation of various host genes. This includes Interleukin 1-beta (IL1B) and Interferon-gamma receptor (IFNGR1) SNP analysis, and Interleukin-1 receptor antagonist (IL1RN) variable tandem repeats (VNTR) in intron 2. Finally, regions of the vacA-gene were PCR amplified using M13-sequence tagged primers which allowed for direct DNA sequencing, omitting cloning of PCR amplicons. H. pylori specific multiplex PCR assays revealed the presence of H. pylori cagA and vacA genotypic variations in 11 of 12 gastritis biopsy specimens. Using pyrosequencing, 16S rDNA variable V3 region signatures of H. pylori were found in 11 of 12 individuals with gastritis, but in none of the control subjects. Similarly, IL1B and IFNGR1-SNP and IL1RN-VNTR patterns could be established in all individuals. Furthermore, sequencing of M13-sequence tagged vacA-PCR amplicons revealed the presence of highly diverse H. pylori vacA-s/i/m regions.ConclusionThe PCR-based molecular typing methods applied, using MDA-amplified DNA derived from small amounts of gastric biopsy specimens, enabled a rapid and concurrent molecular analysis of bacterial and host genes in the same biopsy specimen. The principles and technologies used in this study could also be applied to any situation in which human host and microbial genes of interest in microbial-host interactions would need to be sequenced.

A new free-form surface fitting method for precision coordinate metrology

Free-form surfaces are widely used in advanced optical and mechanical devices. In order to assess the form accuracy of free-form surfaces, it is needed to fit the measurement surface with the design template. To improve the fitting efficiency and accuracy, the fitting procedure is divided into two stages, rough fitting and final fitting. A new rough fitting method, called structured region signature is proposed. Structured region signature is a generalised global feature which represents the surface shape by a one-dimensional function. The template location occupying the best fitting signature is considered to be the correct initial position of the measurement surface. In the final fitting, the motion parameters are calculated iteratively using the Levenberg-Marquardt algorithm. Simulation and experiments are given to identify the validity of this method. It is demonstrated that the fitting accuracy is as high as 1:10 6.

Two ferritin subunits from disk abalone ( Haliotis discus discus): Cloning, characterization and expression analysis

Ferritin plays a key role in cellular iron metabolism, which includes iron storage and detoxification. From disk abalone, Haliotis discus discus, the cDNA that encodes the two ferritin subunits abalone ferritin subunit 1 (Abf1) and abalone ferritin subunit 2 (Abf2) were cloned. The complete cDNA coding sequences for Abf1 and Abf2 contained 621 and 549 bp, encoding for 207 and 183 amino acid residues, respectively. The H. discus discus Abf2 subunit contained a highly conserved motif for the ferroxidase center, which consists of seven residues of a typical vertebrate heavy-chain ferritin with a typical stem–loop structure. Abf2 mRNA contains a 27 bp iron-responsive element (IRE) in the 5′UTR position. This IRE exhibited 96% similarity with pearl and Pacific oyster and 67% similarity with human H type IREs. However, the Abf1 subunit had neither ferroxidase center residues nor the IRE motif sequence; instead, it contained iron-binding region signature 2 (IBRS) residues. Recombinant Abf1 and Abf2 proteins were purified and the respective sizes were about 24 and 21 kDa. Abf1 and Abf2 exhibited iron-chelating activity 44.2% and 22.0%, respectively, at protein concentration of 6 μg/ml. Analysis of tissue-specific expression by RT-PCR revealed that Abf1 and Abf2 ferritin mRNAs were expressed in various abalone tissues, such as gill, mantle, gonad, foot and digestive tract in a wide distribution profile, but Abf2 expression was more prominent than Abf1.

Scatterometry-based metrology with feature region signatures matching

Scatterometry takes advantage of the sensitivity exhibited by optical diffraction from periodic structures, and hence is an efficient technique for lithographic process monitoring. A feature region measurement algorithm has been developed to extract accurately and quickly the relevant constitutive parameters from diffraction data. It is a method for efficiently determining grating structure by seeking the reflectance at some angles contains more information about the structure of the surface relief profile than the reflectance at other angles in a library data match process. The number of measurements and size of signature matching library will be reduced in a great percentage by performing the feature region algorithm.

Control of glucose- and NaCl-induced biofilm formation by rbf in Staphylococcus aureus.

Both Staphylococcus aureus and S. epidermidis are capable of forming biofilm on biomaterials. We used Tn917 mutagenesis to identify a gene, rbf, affecting biofilm formation in S. aureus NCTC8325-4. Sequencing revealed that Rbf contained a consensus region signature of the AraC/XylS family of regulators, suggesting that Rbf is a transcriptional regulator. Insertional duplication inactivation of the rbf gene confirmed that the gene was involved in biofilm formation on polystyrene and glass. Phenotypic analysis of the wild type and the mutant suggested that the rbf gene mediates the biofilm formation of S. aureus at the multicellular aggregation stage rather than at initial attachment. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis demonstrated that the mutation resulted in the loss of an approximately 190-kDa protein. Biofilm production by the mutant could be restored by complementation with a 2.5-kb DNA fragment containing the rbf gene. The rbf-specific mutation affected the induction of biofilm formation by glucose and a high concentration of NaCl but not by ethanol. The mutation did not affect the transcription of the ica genes previously shown to be required for biofilm formation. Taken together, our results suggest that the rbf gene is involved in the regulation of the multicellular aggregation step of S. aureus biofilm formation in response to glucose and salt and that this regulation may be mediated through the 190-kDa protein.