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At least 145 records · Page 8Linked to original sources
PubMed1993

Cloning and sequencing of the Lactococcus lactis subsp. lactis groESL operon.

The operon (groESL) coding for the Lactococcus lactis subsp. lactis heat-shock proteins GroEL and GroES, has been isolated and its complete nucleotide (nt) sequence determined. A set of degenerate PCR primers, deduced from amino acids which are conserved in a number of prokaryotic GroELs, were synthesized and used to amplify a 957-bp fragment. This PCR fragment was used as a probe to isolate a 5.0-kb EcoRI chromosomally derived fragment. A region of this 5.0-kb EcoRI fragment was sequenced and revealed that the groES gene was located 5' to groEL. This sequence was then used to design a set of inverse PCR primers and a 2.5-kb HindIII fragment was cloned which contained the region 5' to groEL. The complete nt sequence of the groESL operon was determined from overlapping fragments. It revealed that the groESL operon was preceded by a stem-loop structure and the promoter appears similar to most L. lactis subsp. lactis and other Gram+ bacterial promoters. Northern analysis demonstrated that the groESL operon is under tight regulation and a dramatic induction of mRNA synthesis occurs within 15 min after heat shock.

Amino Acid Sequence↗
PubMed1994

Cloning and sequencing of the Lactococcus lactis subsp. lactis dnaK gene using a PCR-based approach.

The coding region for the dnaK gene from Lactococcus lactis subsp. lactis LM0230 was isolated and sequenced. An internal 789-bp fragment was amplified by the polymerase chain reaction (PCR) using a pair of degenerate oligodeoxyribonucleotide primers designed on the basis of amino acid (aa) sequences conserved in a number of DnaK. This PCR product was cloned, sequenced and used as a Southern hybridization probe to locate the flanking regions of the gene. The sequence of this central region from dnaK was also used to design two sets of inverse PCR primers to amplify, separately, the upstream and downstream regions. The inverse PCR products were then cloned and partially sequenced. The complete nucleotide sequence was obtained from overlapping cloned fragments of the gene and found to consist of a single 1824-bp open reading frame coding for a 602-aa protein. Alignment of the deduced aa sequence with those of other bacterial DnaK showed a high degree of homology and is most similar to the Bacillus megaterium DnaK.

Amino Acid Sequence↗
PubMed2001

Association between atopic dermatitis and insulin-dependent diabetes mellitus: a case-control study.

BACKGROUND: Up to two-thirds of children with atopic dermatitis have IgE-mediated allergic reactions and a Th2 immune reactivity pattern with low production of interferon gamma and high production of interleukin 4 after allergen stimulation of T lymphocytes. Insulin-dependent diabetes mellitus (IDDM) seems to be associated with a Th1 immune reactivity pattern. We therefore postulated that these diseases may be inversely associated. METHODS: We designed a case-control study including 920 children with IDDM, registered in the Danish Registry for Childhood Diabetes, and a sample of 9732 non-diabetic children registered in the Danish Medical Birth Registry. The children were aged 3-15 years. Information on atopic dermatitis was obtained by questionnaires. FINDINGS: The cumulative incidence of atopic dermatitis up to age 15 years was 13.1% among children with IDDM and 19.8% in non-diabetic children (p<0.0001). Among children who developed IDDM, the incidence of atopic dermatitis was significantly lower than in the controls before onset of IDDM (73 cases in 5314 person-months vs 1375 in 57432 person-months; odds ratio 0.49 [0.39-0.63]). After onset of IDDM, diabetic and non-diabetic groups did not differ in incidence of atopic dermatitis (1.36 [0.89-2.07]). INTERPRETATION: Our findings may be explained by different acquired or inherited reactivity patterns associated with atopic dermatitis (Th2) and IDDM (Th1). The results do not allow us to find out whether early development of atopic dermatitis reduces the risk of IDDM, or a propensity for IDDM reduces the risk of early-onset atopic dermatitis.

Adolescent↗
PubMed1992

Sequence-structure matching in globular proteins: application to supersecondary and tertiary structure determination.

A methodology designed to address the inverse globular protein-folding problem (the identification of which sequences are compatible with a given three-dimensional structure) is described. By using a library of protein finger-prints, defined by the side chain interaction pattern, it is possible to match each structure to its own sequence in an exhaustive data base search. It is shown that this is a permissive requirement for the validation of the methodology. To pass the more rigorous test of identifying proteins that are not close sequence homologs, but that have similar structure, the method has been extended to include insertions and deletions in the sequence, which is compared to the fingerprint. This allows for the identification of sequences having little or no sequence homology to the fingerprint. Examples include plastocyanin/azurin/pseudoazurin, the globin family, different families of proteases and cytochromes, including cytochromes c' and b-562, actinidin/papain, and lysozyme/alpha-lactalbumin. Turning to supersecondary structure prediction, we find that alpha/beta/alpha fragments possess sufficient specificity to identify their own and related sequences. By threading a beta-hairpin through a sequence, it is possible to predict the location of such hairpins and turns with remarkable fidelity. Thus, the method greatly extends existing techniques for the prediction of both global structural homology and local supersecondary structure.

Amino Acid Sequence↗
PubMed1995

A test of lattice protein folding algorithms.

We report a blind test of lattice-model-based search strategies for finding global minima of model protein chains. One of us (E.I.S.) selected 10 compact conformations of 48-mer chains on the three-dimensional cubic lattice and used their inverse folding algorithm to design HP (H, hydrophobic; P, polar) sequences that should fold to those "target" structures. The sequences, but not the structures, were sent to the UCSF group (K.Y., K.M.F., P.D.T., H.S.C., and K.A.D.), who used two methods to attempt to find the globally optimal conformations: "hydrophobic zippers" and a constraint-based hydrophobic core construction (CHCC) method. The CHCC method found global minima in all cases, and the hydrophobic zippers method found global minima in some cases, in minutes to hours on workstations. In 9 out of 10 sequences, the CHCC method found lower energy conformations than the 48-mers were designed to fold to. Thus the search strategies succeed for the HP model but the design strategy does not. For every sequence the global energy minimum was found to have multiple degeneracy with 10(3) to 10(6) conformations. We discuss the implications of these results for (i) searching conformational spaces of simple models of proteins and (ii) how these simple models relate to proteins.

Algorithms↗
PubMed1985

VLSI architectures for computing multiplications and inverses in GF(2m).

Finite field arithmetic logic is central in the implementation of Reed-Solomon coders and in some cryptographic algorithms. There is a need for good multiplication and inversion algorithms that can be easily realized on VLSI chips. Massey and Omura recently developed a new multiplication algorithm for Galois fields based on a normal basis representation. In this paper, a pipeline structure is developed to realize the Massey-Omura multiplier in the finite field GF(2m). With the simple squaring property of the normal basis representation used together with this multiplier, a pipeline architecture is developed for computing inverse elements in GF(2m). The designs developed for the Massey-Omura multiplier and the computation of inverse elements are regular, simple, expandable, and therefore, naturally suitable for VLSI implementation.

Algorithms↗
PubMed2004

Cloning and expression of afpA, a gene encoding an antifreeze protein from the arctic plant growth-promoting rhizobacterium Pseudomonas putida GR12-2.

The Arctic plant growth-promoting rhizobacterium Pseudomonas putida GR12-2 secretes an antifreeze protein (AFP) that promotes survival at subzero temperatures. The AFP is unusual in that it also exhibits a low level of ice nucleation activity. A DNA fragment with an open reading frame encoding 473 amino acids was cloned by PCR and inverse PCR using primers designed from partial amino acid sequences of the isolated AFP. The predicted gene product, AfpA, had a molecular mass of 47.3 kDa, a pI of 3.51, and no previously known function. Although AfpA is a secreted protein, it lacked an N-terminal signal peptide and was shown by sequence analysis to have two possible secretion systems: a hemolysin-like, calcium-binding secretion domain and a type V autotransporter domain found in gram-negative bacteria. Expression of afpA in Escherichia coli yielded an intracellular 72-kDa protein modified with both sugars and lipids that exhibited lower levels of antifreeze and ice nucleation activities than the native protein. The 164-kDa AFP previously purified from P. putida GR12-2 was a lipoglycoprotein, and the carbohydrate was required for ice nucleation activity. Therefore, the recombinant protein may not have been properly posttranslationally modified. The AfpA sequence was most similar to cell wall-associated proteins and less similar to ice nucleation proteins (INPs). Hydropathy plots revealed that the amino acid sequence of AfpA was more hydrophobic than those of the INPs in the domain that forms the ice template, thus suggesting that AFPs and INPs interact differently with ice. To our knowledge, this is the first gene encoding a protein with both antifreeze and ice nucleation activities to be isolated and characterized.

Amino Acid Motifs↗
PubMed1986

Herpes simplex virus 1 recombinants with noninverting genomes frozen in different isomeric arrangements are capable of independent replication.

Herpes simplex virus 1 genome consists of two covalently linked components, L and S, that invert relative to each other to yield four equimolar isomeric populations designated P (prototype), Is (inversion of S component), Il (inversion of L component), and Ils (inversion of L and S components) differing in the orientation of the two components. Previous studies have yielded recombinant genomes frozen in the P isomeric arrangement, reinforcing suggestions that the four isomers may not be functionally equivalent. We report the isolation of recombinants produced by insertional mutagenesis with alpha TK mini-Mu that are frozen in Is and Ils arrangements. Thus, all isomeric forms of herpes simplex virus DNA appear to be capable of independent replication and must be considered as functionally equivalent.

Base Sequence↗
PubMed1991

Alzheimer disease: measuring loss of cerebral gray matter with MR imaging.

The distributions of the cerebral gray matter, the white matter, and the intracranial cerebrospinal fluid (CSF) were measured in 14 patients with Alzheimer disease (AD) and in 14 healthy control subjects. The measurements, derived from two specifically designed magnetic resonance inversion-recovery sequences, compensate for partial signal averaging. The percentage of the gray matter in the brains of AD patients (44.9% +/- 4.4) was significantly lower than in control subjects (50.2% +/- 3.2). The most significant reduction (P less than .001) occurred in the temporal lobes (13.8%) and a central region (12.8); the reduction in frontal lobe (11.2%) and occipital lobe (9.2%) was also statistically significant (P less than .01). There was an increase in the CSF volume in the temporal, occipital, and frontal regions; no region showed a significant difference in the white matter content. The findings of diffuse changes and temporal lobe involvement in AD are consistent with pathologic observations of cortical cell loss.

Aged↗
PubMed2001

An improved MR imaging technique for the visualization of myocardial infarction.

PURPOSE: To design a segmented inversion-recovery turbo fast low-angle shot (turboFLASH) magnetic resonance (MR) imaging pulse sequence for the visualization of myocardial infarction, compare this technique with other MR imaging approaches in a canine model of ischemic injury, and evaluate its utility in patients with coronary artery disease. MATERIALS AND METHODS: Six dogs and 18 patients were examined. In dogs, infarction was produced and images were acquired by using 10 different pulse sequences. In patients, the segmented turboFLASH technique was used to acquire contrast material-enhanced images 19 days +/- 7 (SD) after myocardial infarction. RESULTS: Myocardial regions of increased signal intensity were observed in all animals and patients at imaging. With the postcontrast segmented turboFLASH sequence, the signal intensity of the infarcted myocardium was 1,080% +/- 214 higher than that of the normal myocardium in dogs-nearly twice that of the next best sequence tested and approximately 10-fold greater than that in previous reports. All 18 patients with myocardial infarction demonstrated high signal intensity at imaging. On average, the signal intensity of the high-signal-intensity regions in patients was 485% +/- 43 higher than that of the normal myocardium. CONCLUSION: The segmented inversion-recovery turboFLASH sequence produced the greatest differences in regional myocardial signal intensity in animals. Application of this technique in patients with infarction substantially improved differentiation between injured and normal regions.

Adult↗
PubMed1994

Comparative study of ankle support devices.

The purpose of this study was to compare the ability of four commonly used ankle support devices (Active Ankle, Aircast Sport Stirrup, DonJoy Ankle Ligament Protector and Malleoloc) to restrict active inversion range of motion before and after exercise. The subjects also compared the devices on subjective characteristics, including stability, comfort, and ease of application and removal. Eighteen subjects had both ankles tested for maximum inversion on a specially designed measuring apparatus during three sessions: 1) before application, 2) before exercise with the support device, and 3) after exercise with the support device.

Adult↗
PubMed1986

[Inversion of the metE-oriC-rpsE chromosome segment in Escherichia coli K12].

We have described recently a large inversion of the Escherichia coli chromosome (designated udpPf1), including region of the chromosomal replication region (oriC). The udpPf1 inversion was induced by Tn10 transposon (metE::Tn10). It results in increased expression of the uridine phosphorylase gene (udp) which is closely linked to the metE gene. The data of conjugational and transductional experiments presented in this report demonstrate that the udpPf1 inversion covers a chromosomal segment extending over 12 min of the E. coli genetic map and including the rpsE, crp and metE::Tn5 markers. The results are presented indicating that the increased uridine phosphorylase activity is due to fusion of the udp gene to a more strong promoter located, probably, in the operon for ribosomal proteins cluster, near 73 min on the E. coli chromosome.

Chromosome Inversion↗
PubMed1996

Infection of human papillomavirus (HPV) and p53 over-expression in human female genital tract carcinoma.

Inactivation of p53 gene products either by mutation or by complex formation with E6 oncoprotein encoded by high risk HPV appears to be a common event in cervical carcinogenesis. This study was designed to clarify this association in 41 primary cervical, 15 endometrial, 3 ovarian and one rectal carcinomas. Polymerase chain reaction analysis revealed presence of high risk HPV in 36 (88%) cervical, 5 (33%) endometrial and none of ovarian and rectal carcinomas. HPV 16 was found in 14 cervical carcinomas, HPV 18 in 19 cervical and 2 endometrial carcinomas and HPV 33 in 28 cervical and 5 endometrial carcinomas. Expression of tumor suppressor protein p53 by using polyclonal antibody CM-1, was detected in 28 (68%) cervical, 7 (47%) endometrial, 2 (66%) ovarian and one (100%) rectal carcinoma. Twenty six cervical and 3 endometrial carcinoma cases were positive for both high risk HPV and p53. We conclude that beside cervical carcinoma HPV infection is not uncommon in endometrial carcinoma and in our experimental design there is no inverse correlation between HPV infection and p53 over-expression in a variety of the tumors analysed in the present study.

Adult↗
PubMed1998

Design of solenoidal microcoils for high-resolution 13C NMR spectroscopy.

Typical high-resolution natural-abundance 13C NMR experiments require milligrams of material. In this study, solenoidal microcoil direct and inverse detection probes have been designed to explore improvements in the limits of detection (LOD) for 13C NMR at 11.7 T. A direct-detection radio frequency probe with an observe volume (Vobs) of 1 microL has been developed with carbon observe, deuterium lock, and proton decouple channels. The nonspinning line width of a decoupled [3-13C]-L-alanine (99%) peak achieved is 1.3 Hz. The natural-abundance 13C3 sigma LOD for sucrose for a 90-min acquisition time is 18 micrograms (52 nmol). The 3 sigma LOD for [3-13C]-L-alanine (99%) is 375 ng (4.2 nmol) for an acquisition time less than 30 s. The inverse detection probe has proton observe and carbon decouple channels and a Vobs of 550 nL. The 3 sigma LOD for sucrose from a 1 D 13C decoupled HMQC spectrum is 1.6 micrograms (4.5 nmol) for a 14-min acquisition time.

Alanine↗
PubMedDate not supplied

Imaging pancreatic cancer with a peptide-nanoparticle conjugate targeted to normal pancreas.

Designing molecules that bind to targets that become upregulated or overexpressed as normal cells become cancerous is an important strategy for both therapeutic and diagnostic drug design. We hypothesized that pancreatic ductal adenocarcinoma (PDAC) might be imaged with the inverse strategy, that is by the design of a nanoparticle-conjugate targeted to bombesin (BN) receptors present on normal acinar cells of the pancreas. Using the fluorescein hapten visualization method to assess the presence of bombesin (BN) receptors, we first demonstrated BN receptors in the normal mouse and human pancreas, but then the lack of BN binding receptors in 13 out of 13 specimens of PDAC. The BN peptide-nanoparticle conjugate, BN-CLIO(Cy5.5), was synthesized and accumulated in the mouse pancreas in receptor dependent fashion, but not in a receptor dependent fashion in other tissues, based on tissue fluorescence measurements. The BN-CLIO(Cy5.5) nanoparticle decreased the T2 of normal pancreas and enhanced the ability to visualize tumor in a model of pancreatic cancer by MRI. The use of BN-CLIO(Cy5.5) nanoparticle as a normal tissue-targeted, T2-reducing contrast agent offers a promising approach to imaging PDAC.

Adenocarcinoma↗
PubMedDate not supplied

Snowboarder's talus fractures experimentally produced by eversion and dorsiflexion.

BACKGROUND: Fracture of the lateral process of the talus is an unusual injury that has received heightened attention in recent years because of its association with snowboarding. The diagnosis is often confused with that of lateral ankle sprain. If left untreated, it can cause long-term impairment, including osteoarthritis and subtalar joint degeneration. It is generally thought to result from dorsiflexion and inversion. However, few experimental studies have been conducted to investigate the injury mechanism. HYPOTHESIS: Eversion of a dorsiflexed ankle is more likely to fracture the lateral process of the talus than inversion of a dorsiflexed ankle. STUDY DESIGN: Controlled laboratory study. METHODS: Ten cadaveric leg specimens were subjected to dynamic inversion or eversion of an axially loaded and dorsiflexed ankle. RESULTS: Inversion failed to produce any fractures in three injured specimens. However, all six specimens subjected to eversion sustained a fracture of the lateral process of the talus. CONCLUSIONS: The incidence of fracture of the lateral process of the talus was significantly higher in the eversion group compared with the inversion group. CLINICAL RELEVANCE: Eversion of an axially loaded and dorsiflexed ankle may be an important injury mechanism for fracture of the lateral process of the talus among snowboarders.

Aged↗
PubMed2002

Rigorous uncertainty assessment in contaminant transport inverse modelling: a case study of fluoride diffusion through clay liners.

Inverse methods used in assessing landfill liner design have not yet taken advantage of current developments in inverse procedures. Here, a method for inverting contaminant transport models is presented including a general error model and procedures for differentially weighted multiple response regression. General error models are employed in cases where the residuals are heteroscedastic and correlated, and lead to valid inference on model parameter and predictive uncertainty. The Shuffled Complex Evolution algorithm is used to optimise model parameters. Model parameter uncertainty is assessed by exploring the posterior probability distribution with the Metropolis algorithm, a Markov chain Monte Carlo sampling method. The inverse method is applied to simultaneously determine the sorption and diffusion parameters from laboratory diffusion cell experiments. In these experiments, fluoride migration through kaolin clays was measured by sampling the source and collector cells over time. To uniquely determine the transport model parameters, it was necessary to simultaneously fit the observed data from two independent diffusion cell experiments with different initial concentrations. The jointly fitted transport model parameters compared well with those fitted to independent batch experiments.

Aluminum Silicates↗
PubMed2002

Design and plasma deposition of dispersion-corrected multiband rugate filters.

Inverse Fourier transform method has been commonly used for designing complex inhomogeneous optical coatings. Since it assumes dispersion-free optical constants, introducing real optical materials induces shifts in the position of reflectance bands in multiband inhomogeneous minus (rugate) filters. We propose a simple method for considering optical dispersion in the synthesis of multiband rugate filter designs. Model filters designed with this method were fabricated on glass and polycarbonate substrates by plasma-enhanced chemical vapor deposition of silicon oxynitrides and SiO2/TiO2 mixtures with precisely controlled composition gradients.

Journal Article↗