Growth by insertion: The family of bacterial DDxP proteins

We have identified a variety of proteins in species of the Legionella, Aeromonas, Pseudomonas, Vibrio, Nitrosomonas, Nitrosospira, Variovorax, Halomonas, and Rhizobia genera, which feature repetitive modules of different length and composition, invariably ending at the COOH side with Asp–Asp–x–Pro (DDxP) motifs. DDxP proteins range in size from 900 to 6200 aa (amino acids), and contain 1 to 5 different module types, present in one or multiple copies. We hypothesize that DDxP proteins were modeled by the action of specific endonucleases inserting DNA segments into genes encoding DDxP motifs. Target site duplications (TSDs) formed upon repair of staggered ends generated by endonuclease cleavage would explain the DDxP motifs at repeat ends. TSDs acted eventually as targets for the insertion of more modules of the same or different types. Repeat clusters plausibly resulted from amplification of both repeat and flanking TSDs. The proposed growth shown by the insertion model is supported by the identification of homologous proteins lacking repeats in Pseudomonas and Rhizobium. The 85 DDxP repeats identified in this work vary in length, and can be sorted into short (136–215 aa) and long (243–304 aa) types. Conserved Asp–Gly–Asp–Gly–Asp motifs are located 11–19 aa from the terminal DDxP motifs in all repeats, and far upstream in most long repeats

ALS Yeast Models-Past Success Stories and New Opportunities

In the past two decades, yeast models have delivered profound insights into basic mechanisms of protein misfolding and the dysfunction of key cellular pathways associated with amyotrophic lateral sclerosis (ALS). Expressing ALS-associated proteins, such as superoxide dismutase (SOD1), TAR DNA binding protein 43 (TDP-43) and Fused in sarcoma (FUS), in yeast recapitulates major hallmarks of ALS pathology, including protein aggregation, mislocalization and cellular toxicity. Results from yeast have consistently been recapitulated in other model systems and even specimens from human patients, thus providing evidence for the power and validity of ALS yeast models. Focusing on impaired ribonucleic acid (RNA) metabolism and protein misfolding and their cytotoxic consequences in ALS, we summarize exemplary discoveries that originated from work in yeast. We also propose previously unexplored experimental strategies to modernize ALS yeast models, which will help to decipher the basic pathomechanisms underlying ALS and thus, possibly contribute to finding a cure

Are errors detected before they occur? Early error sensations revealed by metacognitive judgments on the timing of error awareness

Errors in choice tasks are not only detected fast and reliably, participants often report that they knew that an error occurred already before a response was produced. These early error sensations stand in contrast with evidence suggesting that the earliest neural correlates of error awareness emerge around 300 ms after erroneous responses. The present study aimed to investigate whether anecdotal evidence for early error sensations can be corroborated in a controlled study in which participants provide metacognitive judgments on the subjective timing of error awareness. In Experiment 1, participants had to report whether they became aware of their errors before or after the response. In Experiment 2, we measured confidence in these metacognitive judgments. Our data show that participants report early error sensations with high confidence in the majority of error trials across paradigms and experiments. These results provide first evidence for early error sensations, informing theories of error awareness

Politics and power in national REDD+ policy processes

National Strategy and Policy Options Maria Brockhaus Arild Angelsen ... depend on existing institutions and legal structures, current political and economic processes, the distribution of power and wealth, and the REDD+ actions appropriate to ..

Characterization of two new alleles at the goat CSN1S2 locus.

Two novel alleles at the goat CSN1S2 locus have been identified: CSN1S2(F) and CSN1S2(D). Sequence analyses revealed that the CSN1S2(F) allele is characterized by a G --> A transition at the 13th nucleotide in exon 3 changing the seventh amino acid of the mature protein from Val to Ile. The CSN1S2(D) allele, apparently associated with a decreased synthesis of alpha s2-casein, is characterized by a 106-bp deletion, involving the last 11 bp of the exon 11 and the first 95 bp of the following intron. Methods (PCR-RFLP and PCR) for identification of carriers of these alleles have been developed

Evolutionary changes in the notochord genetic toolkit: a comparative analysis of notochord genes in the ascidian Ciona and the larvacean Oikopleura

<p>Abstract</p> <p>Background</p> <p>The notochord is a defining feature of the chordate clade, and invertebrate chordates, such as tunicates, are uniquely suited for studies of this structure. Here we used a well-characterized set of 50 notochord genes known to be targets of the notochord-specific Brachyury transcription factor in one tunicate, <it>Ciona intestinalis </it>(Class Ascidiacea), to begin determining whether the same genetic toolkit is employed to build the notochord in another tunicate, <it>Oikopleura dioica </it>(Class Larvacea). We identified <it>Oikopleura </it>orthologs of the <it>Ciona </it>notochord genes, as well as lineage-specific duplicates for which we determined the phylogenetic relationships with related genes from other chordates, and we analyzed their expression patterns in <it>Oikopleura </it>embryos.</p> <p>Results</p> <p>Of the 50 <it>Ciona </it>notochord genes that were used as a reference, only 26 had clearly identifiable orthologs in <it>Oikopleura</it>. Two of these conserved genes appeared to have undergone <it>Oikopleura</it>- and/or tunicate-specific duplications, and one was present in three copies in <it>Oikopleura</it>, thus bringing the number of genes to test to 30. We were able to clone and test 28 of these genes. Thirteen of the 28 <it>Oikopleura </it>orthologs of <it>Ciona </it>notochord genes showed clear expression in all or in part of the <it>Oikopleura </it>notochord, seven were diffusely expressed throughout the tail, six were expressed in tissues other than the notochord, while two probes did not provide a detectable signal at any of the stages analyzed. One of the notochord genes identified, <it>Oikopleura netrin</it>, was found to be unevenly expressed in notochord cells, in a pattern reminiscent of that previously observed for one of the <it>Oikopleura </it><it>Hox </it>genes.</p> <p>Conclusions</p> <p>A surprisingly high number of <it>Ciona </it>notochord genes do not have apparent counterparts in <it>Oikopleura</it>, and only a fraction of the evolutionarily conserved genes show clear notochord expression. This suggests that <it>Ciona </it>and <it>Oikopleura</it>, despite the morphological similarities of their notochords, have developed rather divergent sets of notochord genes after their split from a common tunicate ancestor. This study demonstrates that comparisons between divergent tunicates can lead to insights into the basic complement of genes sufficient for notochord development, and elucidate the constraints that control its composition.</p

Majorana and the quasi-stationary states in Nuclear Physics

A complete theoretical model describing artificial disintegration of nuclei by bombardment with alpha-particles, developed by Majorana as early as in 1930, is discussed in detail alongside the basic experimental evidences that motivated it. By following the quantum dynamics of a state resulting from the superposition of a discrete state with a continuum one, whose interaction is described by a given potential term, Majorana obtained (among the other predictions) the explicit expression for the integrated cross section of the nuclear process, which is the direct measurable quantity of interest in the experiments. Though this is the first application of the concept of quasi-stationary states to a Nuclear Physics problem, it seems also that the unpublished Majorana's work anticipates by several years the related seminal paper by Fano on Atomic Physics.Comment: latex, amsart, 13 page

On random flights with non-uniformly distributed directions

This paper deals with a new class of random flights $\underline{\bf X}_d(t),t>0,$ defined in the real space $\mathbb{R}^d, d\geq 2,$ characterized by non-uniform probability distributions on the multidimensional sphere. These random motions differ from similar models appeared in literature which take directions according to the uniform law. The family of angular probability distributions introduced in this paper depends on a parameter $\nu\geq 0$ which gives the level of drift of the motion. Furthermore, we assume that the number of changes of direction performed by the random flight is fixed. The time lengths between two consecutive changes of orientation have joint probability distribution given by a Dirichlet density function. The analysis of $\underline{\bf X}_d(t),t>0,$ is not an easy task, because it involves the calculation of integrals which are not always solvable. Therefore, we analyze the random flight $\underline{\bf X}_m^d(t),t>0,$ obtained as projection onto the lower spaces $\mathbb{R}^m,m<d,$ of the original random motion in $\mathbb{R}^d$. Then we get the probability distribution of $\underline{\bf X}_m^d(t),t>0.$ Although, in its general framework, the analysis of $\underline{\bf X}_d(t),t>0,$ is very complicated, for some values of $\nu$, we can provide some results on the process. Indeed, for $\nu=1$, we obtain the characteristic function of the random flight moving in $\mathbb{R}^d$. Furthermore, by inverting the characteristic function, we are able to give the analytic form (up to some constants) of the probability distribution of $\underline{\bf X}_d(t),t>0.$Comment: 28 pages, 3 figure

Emerging role of metabolomics in ovarian cancer diagnosis

Ovarian cancer is considered a silent killer due to the lack of clear symptoms and efficient diagnostic tools that often lead to late diagnoses. Over recent years, the impelling need for proficient biomarkers has led researchers to consider metabolomics, an emerging omics science that deals with analyses of the entire set of small-molecules (≤1.5 kDa) present in biological systems. Metabolomics profiles, as a mirror of tumor–host interactions, have been found to be useful for the analysis and identification of specific cancer phenotypes. Cancer may cause significant metabolic alterations to sustain its growth, and metabolomics may highlight this, making it possible to detect cancer in an early phase of development. In the last decade, metabolomics has been widely applied to identify different metabolic signatures to improve ovarian cancer diagnosis. The aim of this review is to update the current status of the metabolomics research for the discovery of new diagnostic metabolomic biomarkers for ovarian cancer. The most promising metabolic alterations are discussed in view of their potential biological implications, underlying the issues that limit their effective clinical translation into ovarian cancer diagnostic tools

1H-NMR plasma lipoproteins profile analysis reveals lipid metabolism alterations in HER2-positive breast cancer patients

The lipid tumour demand may shape the host metabolism adapting the circulating lipids composition to its growth and progression needs. This study aims to exploit the straightforward 1 H-NMR lipoproteins analysis to investigate the alterations of the circulating lipoproteins’ fractions in HER2-positive breast cancer and their modulations induced by treatments. The baseline1H-NMR plasma lipoproteins profiles were measured in 43 HER2-positive breast cancer patients and compared with those of 28 healthy women. In a subset of 32 patients, longitudinal measurements were also performed along neoadjuvant chemotherapy, after surgery, adjuvant treatment, and during the two-year follow-up. Differences between groups were assessed by multivariate PLS-DA and by univariate analyses. The diagnostic power of lipoproteins subfractions was assessed by ROC curve, while lipoproteins time changes along interventions were investigated by ANOVA analysis. The PLS-DA model distinguished HER2-positive breast cancer patients from the control group with a sensitivity of 96.4% and specificity of 90.7%, mainly due to the differential levels of VLDLs subfractions that were significantly higher in the patients' group. Neoadjuvant chemotherapy-induced a significant drop in the HDLs after the first three months of treatment and a specific decrease in the HDL-3 and HDL-4 subfractions were found significantly associated with the pathological complete response achievement. These results indicate that HER2-positive breast cancer is characterized by a significant host lipid mobilization that could be useful for diagnostic purposes. Moreover, the lipoproteins profiles alterations induced by the therapeutic interventions could predict the clinical outcome supporting the application of1H-NMR lipoproteins profiles analysis for longitudinal monitoring of HER2-positive breast cancer in large clinical studies