A new methodology for kerogen maturity estimation based on Raman spectroscopy and chemometric analysis.

Diverse criteria or parameters have been cited as tools to determine the maturity of carbonaceous matter (CM) found in geologic samples using Raman spectroscopy. However, these approaches involve the mathematical decomposition of Raman bands which can vary with the specific method, the software employed, or even the individual user. Data should be treated spectrum by spectrum and a similar spectroscopic pre-treatment should be applied to the whole dataset. All these factors affect the final result and can introduce a wide uncertainty and bias. We propose an alternative chemometric method that avoids these sources of uncertainty by considering the entire spectrum, not just certain regions, while allowing specific regions of interest to be defined. Moreover, spectra pre-treatment is not required. We employ principal component analysis (PCA) across the whole range of spectra. While the method does not provide an absolute maturity value, it allows comparison of different CM in terms of maturity or H:C ratio. In the analysis of coal standards, samples were grouped by maturity.

Approximations for expected generation number.

A deterministic formula is commonly used to approximate the expected generation number of a population of growing cells. However, this can give misleading results because it does not allow for natural variation in the times that individual cells take to reproduce. Here we present more accurate approximations for both symmetric and asymmetric cell division. Based on the first two moments of the generation time distribution, these approximations are also robust. We illustrate the improved approximations using data that arise from monitoring individual yeast cells under a microscope and also demonstrate how the approximations can be used when such detailed data are not available.

New approximations to the Malthusian parameter.

Approximations to the Malthusian parameter of an age-dependent branching process are obtained in terms of the moments of the lifetime distribution, by exploiting a link with renewal theory. In several examples, the new approximations are more accurate than those currently in use, even when based on only the first two moments. The new approximations are extended to include a form of asymmetric cell division that occurs in some species of yeast. When used for inference, the new approximations are shown to have high efficiency.

Estimating the number of prions in yeast cells.

Certain yeast cells contain proteins that behave like the mammalian prion PrP and are called yeast prions. The yeast prion protein Sup35p can exist in one of two stable forms, giving rise to phenotypes [PSI(+)] and [psi(-)]. If the chemical guanidine hydrochloride (GdnHCl) is added to a culture of growing [PSI(+)] cells, the proportion of [PSI(+)] cells decreases over time. This process is called curing and is due to a failure to propagate the prion form of Sup35p. We describe how curing can be modelled, and improve upon previous models for the underlying processes of cell division and prion segregation; the new model allows for asymmetric cell division and unequal prion segregation. We conclude by outlining plans for future experimentation and modelling.

The Candida albicans gene encoding the cytoplasmic leucyl-tRNA synthetase: implications for the evolution of CUG codon reassignment.

In a number of Candida species the 'universal' leucine codon CUG is decoded as serine. To help understand the evolution of such a codon reassignment we have analyzed the Candida albicans leucyl-tRNA synthetase (CaLeuRS) gene (CaCDC60). The predicted CaLeuRS sequence shows a significant level of amino acid identity to LeuRS from other organisms. A mitochondrial LeuRS (ScNAM2) homologue, which shared low identity with the CaLeuRS, was also identified in C. albicans. Antigenically-related LeuRSs were identified in a range of Candida species decoding the CUG codon as both serine and leucine, using an antibody raised against the N-terminal 15 amino acids of the CaLeuRS. Complementation experiments demonstrated that the CaLeuRS was able to functionally complement a Saccharomyces cerevisiae cdc60::kanMX null mutation. We conclude that there is no alteration in tRNA recognition and aminoacylation by the C. albicans LeuRS, which argues against it having a role in codon reassignment. The nucleotide sequences of the CaCDC60 and CaNAM2 genes were deposited at GenBank under Accession numbers AF293346 and AF352020, respectively.

The elimination of the yeast [PSI+] prion by guanidine hydrochloride is the result of Hsp104 inactivation.

In the yeast Saccharomyces cerevisiae, Sup35p (eRF3), a subunit of the translation termination complex, can take up a prion-like, self-propagating conformation giving rise to the non-Mendelian [PSI+] determinant. The replication of [PSI+] prion seeds can be readily blocked by growth in the presence of low concentrations of guanidine hydrochloride (GdnHCl), leading to the generation of prion-free [psi-] cells. Here, we provide evidence that GdnHCl blocks seed replication in vivo by inactivation of the molecular chaperone Hsp104. Although growth in the presence of GdnHCl causes a modest increase in HSP104 expression (20-90%), this is not sufficient to explain prion curing. Rather, we show that GdnHCl inhibits two different Hsp104-dependent cellular processes, namely the acquisition of thermotolerance and the refolding of thermally denatured luciferase. The inhibitory effects of GdnHCl protein refolding are partially suppressed by elevating the endogenous cellular levels of Hsp104 using a constitutive promoter. The kinetics of GdnHCl-induced [PSI+] curing could be mimicked by co-expression of an ATPase-negative dominant HSP104 mutant in an otherwise wild-type [PSI+] strain. We suggest that GdnHCl inactivates the ATPase activity of Hsp104, leading to a block in the replication of [PSI+] seeds.

Angled oblique sagittal MR imaging of rotator cuff tears: comparison with standard oblique sagittal images.

OBJECTIVE: To compare the accuracy for diagnosing rotator cuff tears of oblique coronal images supplemented with standard oblique sagittal images versus thinner-section angled oblique sagittal images. DESIGN AND PATIENTS: The study included 75 consecutive patients who had a shoulder MR scan followed by arthroscopy. MR images included oblique coronal, oblique sagittal (4 mm thick, 1 mm interslice gap), and angled oblique sagittal (3 mm/0.2 mm) images perpendicular to the lateral cuff. A musculoskeletal staff radiologist and fellow separately evaluated the cuff for tears on the oblique coronal images supplemented with either the oblique sagittal or the angled sagittal images. RESULTS: For distinguishing a cuff tear from no tear, the staff radiologist had an accuracy of 0.76 (95% confidence interval: 0.67, 0.85) with the standard sagittal set, and 0.88 (0.80, 0.95) with the angled set (P=0.04). There was a nonsignificant improvement in accuracy for the fellow, calculated as 0.73 (0.63, 0.83) on the standard sagittal set and 0.76 (0.67, 0.85) on the angled set. Both readers also improved their diagnostic accuracy for partial-thickness tears with the angled set, although the improvement was statistically significant only for the staff radiologist. CONCLUSION: There is a slight improvement in accuracy for diagnosing rotator cuff tears, particularly partial-thickness tears, for the more experienced radiologist using thinner-section angled oblique sagittal images. These images may be useful as a supplemental sequence in patients where it is important to identify partial-thickness tears accurately.

Oligopeptide repeats in the yeast protein Sup35p stabilize intermolecular prion interactions.

The nuclear-encoded Sup35p protein is responsible for the prion-like [PSI(+)] determinant of yeast, with Sup35p existing largely as a high molecular weight aggregate in [PSI(+)] strains. Here we show that the five oligopeptide repeats present at the N-terminus of Sup35p are responsible for stabilizing aggregation of Sup35p in vivo. Sequential deletion of the oligopeptide repeats prevented the maintenance of [PSI(+)] by the truncated Sup35p, although deletants containing only two repeats could be incorporated into pre-existing aggregates of wild-type Sup35p. The mammalian prion protein PrP also contains similar oligopeptide repeats and we show here that a human PrP repeat (PHGGGWGQ) is able functionally to replace a Sup35p oligopeptide repeat to allow stable [PSI(+)] propagation in vivo. Our data suggest a model in which the oligopeptide repeats in Sup35p stabilize intermolecular interactions between Sup35p proteins that initiate establishment of the aggregated state. Modulating repeat number therefore alters the rate of yeast prion conversion in vivo. Furthermore, there appears to be evolutionary conservation of function of the N-terminally located oligopeptide repeats in prion propagation.

Seryl-tRNA synthetase is not responsible for the evolution of CUG codon reassignment in Candida albicans.

A number of Candida species translate the standard leucine-CUG codon as serine using a novel ser-tRNA(CAG). This tRNA, which has an unusual anticodon stem-loop structure, has been implicated in the evolution of this codon reassignment. However, such a sense codon reassignment might also require a change in the specificity of the cognate aminoacyl tRNA-synthetase, in this case the ser-tRNA synthetase. Here we describe the cloning and sequence analysis of the C. albicans seryl aminoacyl-tRNA synthetase (CaSerRS) gene (CaSES1). The predicted CaSerRS sequence shows a significant level of amino acid identity to SerRs from other organisms and fully complements a S. cerevisiae SerRS null strain without any apparent defect in growth rate. This suggests that the SerRS recognizes and charges S. cerevisiae ser-tRNAs with similar efficiency to that of the S. cerevisiae SerRS. Using an antibody raised against CaSerRS, we also demonstrate the presence of SerRS in a range of Candida spp. showing CUG codon reassignment. We conclude that the key element in CUG reassigment in Candida spp. is the tRNA that decodes the CUG codon rather than a SerRS structural change. The nucleotide sequence of the CaSES1 gene has been deposited at GenBank under Accession No. AF290915.

Codon reassignment and the evolving genetic code: problems and pitfalls in post-genome analysis.

The in silico translation of open reading frames, using the 'universal genetic code', must be approached with caution. The uncovering of a number of codon reassignments in nuclear and organellar genomes highlights the importance of experimentally confirming the assignments of all 64 codons for the species whose genome is under investigation. Such alterations to codon meaning also suggest that the genetic code is not 'frozen' and continues to evolve.

Cell biology. Sowing the protein seeds of prion propagation.

Ever since Prusiner first proposed his radical "protein-only" hypothesis to explain how certain infectious proteins (prions) are transmitted from one mammal to another in the absence of DNA or RNA, scientists have been trying to prove him right (or wrong). The study of mammalian prions, such as those causing Creutzfeldt-Jakob disease in humans, scrapie in sheep and mad cow disease in cattle, has been slow to yield answers. However, as Tuite discusses in his Perspective, the Sup35p and Ure2p proteins of yeast that exist in both normal and infectious forms are providing evidence that the "protein-only" hypothesis may be right (Sparrer et al.).

Superior labrum anterior-posterior (SLAP) tears: evaluation of three MR signs on T2-weighted images.

PURPOSE: To compare the sensitivity and specificity of three magnetic resonance (MR) imaging signs for the diagnosis of superior labrum anterior-posterior (SLAP) tears. MATERIALS AND METHODS: The study involved 23 consecutive patients with a type 2, 3, or 4 SLAP tear at arthroscopy and 31 age-matched control patients with an arthroscopically normal or type 1 SLAP lesion. The superior labrum was evaluated on MR images for high signal intensity extending to the articular surface in the posterior third of the labrum, an irregular or laterally curved area of high signal intensity, or two high-signal-intensity lines. RESULTS: The sensitivity, specificity, and accuracy of posterior high signal intensity for a type 2, 3, or 4 SLAP tear were 48%, 94%, and 74%, respectively, for observer 1 and 61%, 81%, and 72%, respectively, for observer 2. For laterally curved area of high signal intensity, these values were 65%, 84%, and 76%, respectively, and 56%, 84%, and 72%, respectively. For two high-signal-intensity lines, these values were 17%, 94%, and 61%, respectively, and 13%, 94%, and 59%, respectively. For the presence of either posterior or laterally curved high signal intensity, the sensitivity was 65% for both observers, whereas the specificity was 84% for observer 1 and 74% for observer 2. The kappa values for interobserver agreement were 0.60 for posterior high signal intensity and 0.58 for laterally curved high signal intensity. CONCLUSION: Laterally curved and posterior high signal intensities are specific signs for distinguishing a SLAP tear from a normal-variant superior sublabral recess.

"Dem bones": osteochondral injuries of the knee.

MR imaging plays a valuable role in the diagnosis and staging of osteochondral injuries of the femorotibial joint. Bone contusions may be the source of a patient's pain, and MR imaging characteristics of certain types may help to predict which contusions might progress to more serious osteochondral lesions. MR imaging also is vital in the diagnosis of occult osteochondral fractures and in accurately classifying displaced intra-articular fractures. Although osteochondral dissecans usually is diagnosed radiographically, MR imaging is the best noninvasive test for determining if an osteochondral fragment is unstable. Unstable lesions are a treatable cause of knee pain.

The crystal structure of human eukaryotic release factor eRF1--mechanism of stop codon recognition and peptidyl-tRNA hydrolysis.

The release factor eRF1 terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase center. The crystal structure of human eRF1 to 2.8 A resolution, combined with mutagenesis analyses of the universal GGQ motif, reveals the molecular mechanism of release factor activity. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase center. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site.

Guanidine hydrochloride blocks a critical step in the propagation of the prion-like determinant [PSI(+)] of Saccharomyces cerevisiae.

The cytoplasmic heritable determinant [PSI(+)] of the yeast Saccharomyces cerevisiae reflects the prion-like properties of the chromosome-encoded protein Sup35p. This protein is known to be an essential eukaryote polypeptide release factor, namely eRF3. In a [PSI(+)] background, the prion conformer of Sup35p forms large oligomers, which results in the intracellular depletion of functional release factor and hence inefficient translation termination. We have investigated the process by which the [PSI(+)] determinant can be efficiently eliminated from strains, by growth in the presence of the protein denaturant guanidine hydrochloride (GuHCl). Strains are "cured" of [PSI(+)] by millimolar concentrations of GuHCl, well below that normally required for protein denaturation. Here we provide evidence indicating that the elimination of the [PSI(+)] determinant is not derived from the direct dissolution of self-replicating [PSI(+)] seeds by GuHCl. Although GuHCl does elicit a moderate stress response, the elimination of [PSI(+)] is not enhanced by stress, and furthermore, exhibits an absolute requirement for continued cell division. We propose that GuHCl inhibits a critical event in the propagation of the prion conformer and demonstrate that the kinetics of curing by GuHCl fit a random segregation model whereby the heritable [PSI(+)] element is diluted from a culture, after the total inhibition of prion replication by GuHCl.

The Candida albicans CUG-decoding ser-tRNA has an atypical anticodon stem-loop structure.

In many Candida species, the leucine CUG codon is decoded by a tRNA with two unusual properties: it is a ser-tRNA and, uniquely, has guanosine at position 33 (G33). Using a combination of enzymatic (V1 RNase, RnI nuclease) and chemical (Pb(2+), imidazole) probing of the native Candida albicans ser-tRNACAG, we demonstrate that the overall tertiary structure of this tRNA resembles that of a ser-tRNA rather than a leu-tRNA, except within the anticodon arm where there is considerable disruption of the anticodon stem. Using non-modified in vitro transcripts of the C. albicans ser-tRNACAG carrying G, C, U or A at position 33, we demonstrate that it is specifically a G residue at this position that induces the atypical anticodon stem structure. Further quantitative evidence for an unusual structure in the anticodon arm of the G33-tRNA is provided by the observed change in kinetics of methylation of the G at position 37, by purified Escherichia coli m(1)G37 methyltransferase. We conclude that the anticodon arm distortion, induced by a guanosine base at position 33 in the anticodon loop of this novel tRNA, results in reduced decoding ability which has facilitated the evolution of this tRNA without extinction of the species encoding it.

The C-terminus of eRF1 defines a functionally important domain for translation termination in Saccharomyces cerevisiae.

Translation termination in eukaryotes is mediated by two release factors, eRF1 and eRF3, which interact to form a heterodimer that mediates termination at all three stop codons. By C-terminal deletion analysis of eRF1 from the yeast Saccharomyces cerevisiae, we show that the extreme C-terminus of this 437-amino-acid protein defines a functionally important domain for translation termination. A strain encoding eRF1 lacking the C-terminal 32 amino acids is not viable, whereas deletion of the C-terminal 19 amino acids is viable but shows a termination defect in vivo causing an enhancement of nonsense suppression. Using a combination of two-hybrid analysis and in vitro binding studies, we demonstrate that deletions encompassing the C-terminus of eRF1 cause a significant reduction in eRF3 binding to eRF1. All of the C-terminally truncated eRF1 still bind the ribosome, suggesting that the C-terminus does not constitute a ribosome-binding domain and eRF1 does not need to form a stable complex with eRF3 in order to bind the ribosome. These data, together with previously published data, suggest that the region between amino acids 411 and 418 of yeast eRF1 defines an essential functional domain that is part of the major site of interaction with eRF3. However, a stable eRF1:eRF3 complex does not have to be formed to maintain viability or efficient translation termination. Alignment of the seven known eukaryotic eRF1 sequences indicates that a highly conserved motif, GFGGIGG/A is present within the region of the C-terminus, although our deletion studies suggest that it is sequences C-terminal to this region that are functionally important.