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(1/16923) A computational screen for methylation guide snoRNAs in yeast.

Small nucleolar RNAs (snoRNAs) are required for ribose 2'-O-methylation of eukaryotic ribosomal RNA. Many of the genes for this snoRNA family have remained unidentified in Saccharomyces cerevisiae, despite the availability of a complete genome sequence. Probabilistic modeling methods akin to those used in speech recognition and computational linguistics were used to computationally screen the yeast genome and identify 22 methylation guide snoRNAs, snR50 to snR71. Gene disruptions and other experimental characterization confirmed their methylation guide function. In total, 51 of the 55 ribose methylated sites in yeast ribosomal RNA were assigned to 41 different guide snoRNAs.  (+info)

(2/16923) Influence of sampling on estimates of clustering and recent transmission of Mycobacterium tuberculosis derived from DNA fingerprinting techniques.

The availability of DNA fingerprinting techniques for Mycobacterium tuberculosis has led to attempts to estimate the extent of recent transmission in populations, using the assumption that groups of tuberculosis patients with identical isolates ("clusters") are likely to reflect recently acquired infections. It is never possible to include all cases of tuberculosis in a given population in a study, and the proportion of isolates found to be clustered will depend on the completeness of the sampling. Using stochastic simulation models based on real and hypothetical populations, the authors demonstrate the influence of incomplete sampling on the estimates of clustering obtained. The results show that as the sampling fraction increases, the proportion of isolates identified as clustered also increases and the variance of the estimated proportion clustered decreases. Cluster size is also important: the underestimation of clustering for any given sampling fraction is greater, and the variability in the results obtained is larger, for populations with small clusters than for those with the same number of individuals arranged in large clusters. A considerable amount of caution should be used in interpreting the results of studies on clustering of M. tuberculosis isolates, particularly when sampling fractions are small.  (+info)

(3/16923) Capture-recapture models including covariate effects.

Capture-recapture methods are used to estimate the incidence of a disease, using a multiple-source registry. Usually, log-linear methods are used to estimate population size, assuming that not all sources of notification are dependent. Where there are categorical covariates, a stratified analysis can be performed. The multinomial logit model has occasionally been used. In this paper, the authors compare log-linear and logit models with and without covariates, and use simulated data to compare estimates from different models. The crude estimate of population size is biased when the sources are not independent. Analyses adjusting for covariates produce less biased estimates. In the absence of covariates, or where all covariates are categorical, the log-linear model and the logit model are equivalent. The log-linear model cannot include continuous variables. To minimize potential bias in estimating incidence, covariates should be included in the design and analysis of multiple-source disease registries.  (+info)

(4/16923) Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of beta-sheet formation in proteins.

A statistical analysis of a representative data set of 169 known protein structures was used to analyze the specificity of residue interactions between spatial neighboring strands in beta-sheets. Pairwise potentials were derived from the frequency of residue pairs in nearest contact, second nearest and third nearest contacts across neighboring beta-strands compared to the expected frequency of residue pairs in a random model. A pseudo-energy function based on these statistical pairwise potentials recognized native beta-sheets among possible alternative pairings. The native pairing was found within the three lowest energies in 73% of the cases in the training data set and in 63% of beta-sheets in a test data set of 67 proteins, which were not part of the training set. The energy function was also used to detect tripeptides, which occur frequently in beta-sheets of native proteins. The majority of native partners of tripeptides were distributed in a low energy range. Self-correcting distance geometry (SECODG) calculations using distance constraints sets derived from possible low energy pairing of beta-strands uniquely identified the native pairing of the beta-sheet in pancreatic trypsin inhibitor (BPTI). These results will be useful for predicting the structure of proteins from their amino acid sequence as well as for the design of proteins containing beta-sheets.  (+info)

(5/16923) Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes.

We examine the similarities and differences between two widely used knowledge-based potentials, which are expressed as contact matrices (consisting of 210 elements) that gives a scale for interaction energies between the naturally occurring amino acid residues. These are the Miyazawa-Jernigan contact interaction matrix M and the potential matrix S derived by Skolnick J et al., 1997, Protein Sci 6:676-688. Although the correlation between the two matrices is good, there is a relatively large dispersion between the elements. We show that when Thr is chosen as a reference solvent within the Miyazawa and Jernigan scheme, the dispersion between the M and S matrices is reduced. The resulting interaction matrix B gives hydrophobicities that are in very good agreement with experiment. The small dispersion between the S and B matrices, which arises due to differing reference states, is shown to have dramatic effect on the predicted native states of lattice models of proteins. These findings and other arguments are used to suggest that for reliable predictions of protein structures, pairwise additive potentials are not sufficient. We also establish that optimized protein sequences can tolerate relatively large random errors in the pair potentials. We conjecture that three body interaction may be needed to predict the folds of proteins in a reliable manner.  (+info)

(6/16923) Cloning, overexpression, purification, and physicochemical characterization of a cold shock protein homolog from the hyperthermophilic bacterium Thermotoga maritima.

Thermotoga maritima (Tm) expresses a 7 kDa monomeric protein whose 18 N-terminal amino acids show 81% identity to N-terminal sequences of cold shock proteins (Csps) from Bacillus caldolyticus and Bacillus stearothermophilus. There were only trace amounts of the protein in Thermotoga cells grown at 80 degrees C. Therefore, to perform physicochemical experiments, the gene was cloned in Escherichia coli. A DNA probe was produced by PCR from genomic Tm DNA with degenerated primers developed from the known N-terminus of TmCsp and the known C-terminus of CspB from Bacillus subtilis. Southern blot analysis of genomic Tm DNA allowed to produce a partial gene library, which was used as a template for PCRs with gene- and vector-specific primers to identify the complete DNA sequence. As reported for other csp genes, the 5' untranslated region of the mRNA was anomalously long; it contained the putative Shine-Dalgarno sequence. The coding part of the gene contained 198 bp, i.e., 66 amino acids. The sequence showed 61% identity to CspB from B. caldolyticus and high similarity to all other known Csps. Computer-based homology modeling allowed the conclusion that TmCsp represents a beta-barrel similar to CspB from B. subtilis and CspA from E. coli. As indicated by spectroscopic analysis, analytical gel permeation chromatography, and mass spectrometry, overexpression of the recombinant protein yielded authentic TmCsp with a molecular weight of 7,474 Da. This was in agreement with the results of analytical ultracentrifugation confirming the monomeric state of the protein. The temperature-induced equilibrium transition at 87 degrees C exceeds the maximum growth temperature of Tm and represents the maximal Tm-value reported for Csps so far.  (+info)

(7/16923) pKa calculations for class A beta-lactamases: influence of substrate binding.

Beta-Lactamases are responsible for bacterial resistance to beta-lactams and are thus of major clinical importance. However, the identity of the general base involved in their mechanism of action is still unclear. Two candidate residues, Glu166 and Lys73, have been proposed to fulfill this role. Previous studies support the proposal that Glu166 acts during the deacylation, but there is no consensus on the possible role of this residue in the acylation step. Recent experimental data and theoretical considerations indicate that Lys73 is protonated in the free beta-lactamases, showing that this residue is unlikely to act as a proton abstractor. On the other hand, it has been proposed that the pKa of Lys73 would be dramatically reduced upon substrate binding and would thus be able to act as a base. To check this hypothesis, we performed continuum electrostatic calculations for five wild-type and three beta-lactamase mutants to estimate the pKa of Lys73 in the presence of substrates, both in the Henri-Michaelis complex and in the tetrahedral intermediate. In all cases, the pKa of Lys73 was computed to be above 10, showing that it is unlikely to act as a proton abstractor, even when a beta-lactam substrate is bound in the enzyme active site. The pKa of Lys234 is also raised in the tetrahedral intermediate, thus confirming a probable role of this residue in the stabilization of the tetrahedral intermediate. The influence of the beta-lactam carboxylate on the pKa values of the active-site lysines is also discussed.  (+info)

(8/16923) Simplified methods for pKa and acid pH-dependent stability estimation in proteins: removing dielectric and counterion boundaries.

Much computational research aimed at understanding ionizable group interactions in proteins has focused on numerical solutions of the Poisson-Boltzmann (PB) equation, incorporating protein exclusion zones for solvent and counterions in a continuum model. Poor agreement with measured pKas and pH-dependent stabilities for a (protein, solvent) relative dielectric boundary of (4,80) has lead to the adoption of an intermediate (20,80) boundary. It is now shown that a simple Debye-Huckel (DH) calculation, removing both the low dielectric and counterion exclusion regions associated with protein, is equally effective in general pKa calculations. However, a broad-based discrepancy to measured pH-dependent stabilities is maintained in the absence of ionizable group interactions in the unfolded state. A simple model is introduced for these interactions, with a significantly improved match to experiment that suggests a potential utility in predicting and analyzing the acid pH-dependence of protein stability. The methods are applied to the relative pH-dependent stabilities of the pore-forming domains of colicins A and N. The results relate generally to the well-known preponderance of surface ionizable groups with solvent-mediated interactions. Although numerical PB solutions do not currently have a significant advantage for overall pKa estimations, development based on consideration of microscopic solvation energetics in tandem with the continuum model could combine the large deltapKas of a subset of ionizable groups with the overall robustness of the DH model.  (+info)

What kind of modeling agencies accept glamour models?

What I mean is, when I look at playboy models and video models, they don't look like fashion models.  What kind of agency accepts glamour models that are shorter than the high fashion model?

From what ive seen there isnt a particular big glam agency, you more so try to make direct contact with a publication and send them pics.  Glam models arent your usual fashion models like you said they are shorter then most models.  Start off by finding a photographer you are comfortable with and get a portofolio together.  Once you have a variety of poses you are willing to take use that to shop yourself around with any magazines in the area.

What is modeling,who is a model and how do models make money?What do modeling agents do?

What is modeling,who is a model and how do models make money?What do modeling agents do?

A model is a person who appears in magazines, ad campaigns, catalogues, fashion shows, billboards, etc often selling a product or representing a designer. The agent is the one who finds the work for models. Models get paid by the clients who book them and the agent takes a 10-15% commission

So Vogue magazine needs models to wear the clothes on the page, They call various agencies and have a bunch of models come to the office and decide which one they want for the shoot. Then they pay the agency, and the agency takes their commission and pays the model

What is the link between atheletes/models/etc and binge-eating disorders?

I read somewhere that atheletes and models- or any other professionals whose bodies are on "public display on a frequent basis"- notably struggle with binge-eating disorders where they rapidly and excessively consume foods at certain periods of time, usually due to depression, anxiety, boredom, etc. 

It seems sort of odd to me that this is the case, considering atheletes and models are usually very slender. 

What do you guys think are some of the links?

You are asking about two very different groups of people. 

When it comes to elite level athletes, yes, there are certain sports where eating disorders are a big problem. It has less to do with "bodies on display" than with "if I lose 5 kg I'll shave 5 seconds off my time" or similar. You can, for example, look into ski jumping, where a minimum BMI has been set due to  jumpers losing as much weight as they can - to unhealthy low lovels - to be able to fly further on their jumps. 

Models are on public display, but they also have to maintain a certain body type as their role is a living hanger for the clothes. Unlike with (most) athletes, models can and do use illicit drugs to keep their weight down.

Now there will be binging and purging in both groups, but I do not know to what extent it exists.

What are the names of the abercrombie and fitch models in Hawaii?

Recently while shopping, I saw some male models at the front of both the womens and mens store at the Ala Moana Shopping centre in Hawaii. Are they workers or models?


What do modeling agencies look at in models?

When a model applies to a modeling agency, do they care about the colour of the eyes and hair? I've noticed that the majority of models are either blonde with blue eyes or brown hair with blue or green eyes. Also, for runway models, is the body more important than the looks?

No, however say an agency has mainly blonde/blue eyed models, then they will likely be looking for brown/black eyed/hair models to expand their selection. In general, the modeling industry doesn't really favor a specific eye or hair color. (Eastern Europeans are very popular, they have light eyes and hair but to balance that Brazilians are also very popular who mainly have dark eyes and hair)!

What is the difference between centerfolds and fashion models?

Are centerfolds considered to be models? I say no because they model for lust, whereas fashion models are used to sell or market clothes through campaigns, runways, and magazines. Can anyone provide a clear explanation between these professions?

They are both considered models.

One models for the fashion industry to sell clothes. The other models for the adult entertainment industry to sell its products.They both model to sell some sort of product. Although the fashion model usually has clothes on, and the other models nude usually, but sometimes the roles are reversed and the fashion model can sometimes model nude, but they are still selling some sort of fashion item. 

I think the main different is the fashion model, models to sell a fashion item. While the centerfold model, models to sell nude images of themselves which is the actual product, and not usually an item outside of that (at least most of the time).

What kind of a diet do male models and actors have?

I'm talking about male movie stars, male models, and male adult film stars.  I know they spend a lot of time in the gym, but what about their diet?

Can they never eat any fatty foods or just limit the bad food they eat?

Or do they only work out a lot when they have an upcoming movie or photoshoot and just kind of let themselves go a little when they are not working?

Sex, Alchol and Parties. I have a male model friend - he's all about that. I keep annoying him with "stop, you are harming yourself" comments! ==>>Don't do it!

Whats the difference between Sonicare models?

For the Sonicare Flexicare toothbrush, i'm seeing models like R910, R940, R980, but the toothbrushes look the same. Only difference is the box they come in. Is there any differences between them or does the model number just signify when the item came out in stores? Which model is the newest?

They are constantly changing their model numbers.  Go to their web site for a comparison between models or call a customer service rep to answer your questions.  They make a great product.  Good luck.