Varying the number of telomere-bound proteins does not alter telomere length in tel1Δ cells

Yeast telomere DNA consists of a continuous, ≈330-bp tract of the heterogeneous repeat TG1-3 with irregularly spaced, high affinity sites for the protein Rap1p. Yeast monitor, or count, the number of telomeric Rap1p C termini in a negative feedback mechanism to modulate the length of the terminal TG1-3 repeats, and synthetic telomeres that tether Rap1p molecules adjacent to the TG1-3 tract cause wild-type cells to maintain a shorter TG1-3 tract. To identify trans-acting proteins required to count Rap1p molecules, these same synthetic telomeres were placed in two short telomere mutants: yku70Δ (which lack the yeast Ku70 protein) and tel1Δ (which lack the yeast ortholog of ATM). Although both mutants maintain telomeres with ≈100 bp of TG1-3, only yku70Δ cells maintained shorter TG1-3 repeats in response to internal Rap1p molecules. This distinct response to internal Rap1p molecules was not caused by a variation in Rap1p site density in the TG1-3 repeats as sequencing of tel1Δ and yku70Δ telomeres showed that both strains have only five to six Rap1p sites per 100-bp telomere. In addition, the tel1Δ short telomere phenotype was epistatic to the unregulated telomere length caused by deletion of the Rap1p C-terminal domain. Thus, the length of the TG1-3 repeats in tel1Δ cells was independent of the number of the Rap1p C termini at the telomere. These data indicate that tel1Δ cells use an alternative mechanism to regulate telomere length that is distinct from monitoring the number of telomere binding proteins.

A very limited number of keywords (main patterns) describes all sequences of the human variable heavy (VH) and κ (Vκ) domains

Sequences of the variable heavy (VH) and κ (Vκ) domains of Ig structures were divided into 21 fragments that correspond to strands, loops, or parts of these structural units of the variable domains. Amino acid sequences of fragments (termed “words”) were collected from the 1,172 human heavy and 668 human κ chains available in the Kabat database. Statistical analysis of words of 17 fragments was performed (fragments that comprise the complementary determining regions′ fragments will not be discussed in this paper). The number of different words (those with different residues in at least one position) ranged, for various fragments, from 11 to 75 in the κ chains, and from 23 to 189 in the heavy chains. The main result of this study is that very few keywords, or main patterns of words, were necessary to describe over 90% of the sequences (no more than two keywords per fragment in the κ and no more than five per fragment in the heavy chains). No identical keywords were found for different fragments of the variable domains. Keywords of aligned fragments of the VH and Vκ domains were different in all but two instances. Thus, knowing the keywords, one can determine whether any given small part of a sequence belongs to a heavy or κ chain and predict its precise localization in the sequence. In addition, by using all of the keywords obtained through analysis of the Kabat database, it was possible to describe completely the sequences of the human VH and Vκ germ-line segments.

The number of unidentified amacrine cells in the mammalian retina

The three largest known populations of amacrine cells in the rabbit retina were stained with fluorescent probes in whole mounts and counted at a series of retinal eccentricities. The retinas were counterstained using a fluorescent DNA-binding molecule and the total number of nuclei in the inner nuclear layer were counted in confocal sections. From the total number of inner nuclear layer cells and the known fraction of them occupied by amacrine cells, the fraction of amacrine cells made up by the stained populations could be calculated. Starburst cells made up 3%, indoleamine-accumulating cells made up 4%, and AII cells made up 11% of all amacrine cells. By referring four smaller populations of amacrine cells to the number of indoleamine-accumulating cells, they were estimated to make up 4% of all amacrine cells. Thus, 78% of all amacrine cells in the rabbit’s retina are known only from isolated examples, if at all. This proportion is similar in the retinas of the mouse, cat, and monkey. It is likely that a substantial fraction of the local circuit neurons present in other regions of the central nervous system are also invisible as populations to current techniques.

Heat effects on DNA repair after ionising radiation: hyperthermia commonly increases the number of non-repaired double-strand breaks and structural rearrangements

After ionising radiation double-strand breaks (dsb) are lethal if not repaired or misrepaired. Cell killing is greatly enhanced by hyperthermia and it is questioned here whether heat not only affects dsb repair capacity but also fidelity in a chromosomal context. dsb repair experiments were designed so as to mainly score non-homologous end joining, while homologous recombination was largely precluded. Human male G0 fibroblasts were either preheated (45°C, 20 min) or not before X-irradiation. dsb induction and repair were measured by conventional gel electrophoresis and an assay combining restriction digestion using a rare cutting enzyme (NotI) and Southern hybridisation, which detects large chromosomal rearrangements (>100 kb). dsb induction rate in an X-chromosomal NotI fragment was 4.8 × 10–3 dsb/Gy/Mb. Similar values were found for the genome overall and also when cells were preheated. After 50 Gy, fibroblasts were competent to largely restore the original restriction fragment size. Five per cent of dsb remained non-rejoined and 14% were misrejoined. Correct restitution of restriction fragments occurred preferably during the first hour but continued at a slow rate for 12–16 h. In addition, dsb appeared to misrejoin throughout the entire repair period. After hyperthermia the fractions of non-rejoined and misrejoined dsb were similarly increased to 13 and 51%, respectively. It is suggested that heat increases the probability of dsb being incorrectly rejoined but it is not likely to interfere with one dsb repair pathway in particular.

Multiplex genotype determination at a large number of gene loci.

To facilitate large-scale genotype analysis, an efficient PCR-based multiplex approach has been developed. For simultaneously amplifying the target sequences at a large number of genetic loci, locus-specific primers containing 5' universal tails are used. Attaching the universal tails to the target sequences in the initial PCR steps allows replacement of all specific primers with a pair of primers identical to the universal tails and converts the multiplex amplification into "uniplex." Simultaneous amplification of 26 genetic loci with this approach is described. The multiplex amplification can be coupled with genotype determination. By incorporating a single-base mismatch between a primer and the template into the target sequences, a polymorphic site can be converted into a desirable restriction fragment length polymorphism when it is necessary. In this way, the allelic PCR products for the polymorphic loci can be discriminated by gel electrophoresis after restriction enzyme digestion. In this study, 32 loci were typed in such a multiplex way.

On the time to reach a critical number of infections in epidemic models with infective and susceptible immigrants.

In this paper we examine the time T to reach a critical number K0 of infections during an outbreak in an epidemic model with infective and susceptible immigrants. The underlying process X, which was first introduced by Ridler-Rowe (1967), is related to recurrent diseases and it appears to be analytically intractable. We present an approximating model inspired from the use of extreme values, and we derive formulae for the Laplace-Stieltjes transform of T and its moments, which are evaluated by using an iterative procedure. Numerical examples are presented to illustrate the effects of the contact and removal rates on the expected values of T and the threshold K0, when the initial time instant corresponds to an invasion time. We also study the exact reproduction number Rexact,0 and the population transmission number Rp, which are random versions of the basic reproduction number R0.

Number of discernible colors for color-deficient observers estimated from the MacAdam limits

We estimated the number of colors perceived by color normal and color-deficient observers when looking at the theoretic limits of object-color stimuli. These limits, the optimal color stimuli, were computed for a color normal observer and CIE standard illuminant D65, and the resultant colors were expressed in the CIELAB and DIN99d color spaces. The corresponding color volumes for abnormal color vision were computed using models simulating for normal trichromatic observers the appearance for dichromats and anomalous trichomats. The number of colors perceived in each case was then computed from the color volumes enclosed by the optimal colors also known as MacAdam limits. It was estimated that dichromats perceive less than 1% of the colors perceived by normal trichromats and that anomalous trichromats perceive 50%–60% for anomalies in the medium-wavelength-sensitive and 60%–70% for anomalies in the long-wavelength-sensitive cones. Complementary estimates obtained similarly for the spectral locus of monochromatic stimuli suggest less impairment for color-deficient observers, a fact that is explained by the two-dimensional nature of the locus.

Evidence-based editing: factors influencing the number of citations in a national journal

Purpose: Citations received by papers published within a journal serve to increase its bibliometric impact. The objective of this paper was to assess the influence of publication language, article type, number of authors, and year of publication on the citations received by papers published in Gaceta Sanitaria, a Spanish-language journal of public health. Methods: The information sources were the journal website and the Web of Knowledge, of the Institute of Scientific Information. The period analyzed was from 2007 to 2010. We included original articles, brief original articles, and reviews published within that period. We extracted manually information regarding the variables analyzed and we also differentiated among total citations and self-citations. We constructed logistic regression models to analyze the probability of a Gaceta Sanitaria paper to be cited or not, taking into account the aforementioned independent variables. We also analyzed the probability of receiving citations from non-Spanish authors. Results: Two hundred forty papers fulfilled the inclusion criteria. The included papers received a total of 287 citations, which became 202 when excluding self-citations. The only variable influencing the probability of being cited was the publication year. After excluding never cited papers, time since publication and review papers had the highest probabilities of being cited. Papers in English and review articles had a higher probability of citation from non-Spanish authors. Conclusions: Publication language has no influence on the citations received by a national, non-English journal. Reviews in English have the highest probability of citation from abroad. Editors should decide how to manage this information when deciding policies to raise the bibliometric impact factor of their journals.

Optimizing the number of stations in arrays measurements: experimental outcomes for different array geometries and the f-k method

Array measurements have become a valuable tool for site response characterization in a non-invasive way. The array design, i.e. size, geometry and number of stations, has a great influence in the quality of the obtained results. From the previous parameters, the number of available stations uses to be the main limitation for the field experiments, because of the economical and logistical constraints that it involves. Sometimes, from the initially planned array layout, carefully designed before the fieldwork campaign, one or more stations do not work properly, modifying the prearranged geometry. Whereas other times, there is not possible to set up the desired array layout, because of the lack of stations. Therefore, for a planned array layout, the number of operative stations and their arrangement in the array become a crucial point in the acquisition stage and subsequently in the dispersion curve estimation. In this paper we carry out an experimental work to analyze which is the minimum number of stations that would provide reliable dispersion curves for three prearranged array configurations (triangular, circular with central station and polygonal geometries). For the optimization study, we analyze together the theoretical array responses and the experimental dispersion curves obtained through the f-k method. In the case of the f-k method, we compare the dispersion curves obtained for the original or prearranged arrays with the ones obtained for the modified arrays, i.e. the dispersion curves obtained when a certain number of stations n is removed, each time, from the original layout of X geophones. The comparison is evaluated by means of a misfit function, which helps us to determine how constrained are the studied geometries by stations removing and which station or combination of stations affect more to the array capability when they are not available. All this information might be crucial to improve future array designs, determining when it is possible to optimize the number of arranged stations without losing the reliability of the obtained results.