Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment

Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult to assess in those analyses. To compare the performance of different aligners and help detect systematic errors in alignments, a number of benchmarking strategies have been pursued. Here we present an overview of the main strategies--based on simulation, consistency, protein structure, and phylogeny--and discuss their different advantages and associated risks. We outline a set of desirable characteristics for effective benchmarking, and evaluate each strategy in light of them. We conclude that there is currently no universally applicable means of benchmarking MSA, and that developers and users of alignment tools should base their choice of benchmark depending on the context of application--with a keen awareness of the assumptions underlying each benchmarking strategy.Comment: Revie

T cell lineage choice and differentiation in the absence of the RNase III enzyme dicer

The ribonuclease III enzyme Dicer is essential for the processing of micro-RNAs (miRNAs) and small interfering RNAs (siRNAs) from double-stranded RNA precursors. miRNAs and siRNAs regulate chromatin structure, gene transcription, mRNA stability, and translation in a wide range of organisms. To provide a model system to explore the role of Dicer-generated RNAs in the differentiation of mammalian cells in vivo, we have generated a conditional Dicer allele. Deletion of Dicer at an early stage of T cell development compromised the survival of alphabeta lineage cells, whereas the numbers of gammadelta-expressing thymocytes were not affected. In developing thymocytes, Dicer was not required for the maintenance of transcriptional silencing at pericentromeric satellite sequences (constitutive heterochromatin), the maintenance of DNA methylation and X chromosome inactivation in female cells (facultative heterochromatin), and the stable shutdown of a developmentally regulated gene (developmentally regulated gene silencing). Most remarkably, given that one third of mammalian mRNAs are putative miRNA targets, Dicer seems to be dispensable for CD4/8 lineage commitment, a process in which epigenetic regulation of lineage choice has been well documented. Thus, although Dicer seems to be critical for the development of the early embryo, it may have limited impact on the implementation of some lineage-specific gene expression programs

Diverse immunotherapies can effectively treat syngeneic brainstem tumors in the absence of overt toxicity

Background: Immunotherapy has shown remarkable clinical promise in the treatment of various types of cancers. However, clinical benefits derive from a highly inflammatory mechanism of action. This presents unique challenges for use in pediatric brainstem tumors including diffuse intrinsic pontine glioma (DIPG), since treatment-related inflammation could cause catastrophic toxicity. Therefore, the goal of this study was to investigate whether inflammatory, immune-based therapies are likely to be too dangerous to pursue for the treatment of pediatric brainstem tumors. Methods: To complement previous immunotherapy studies using patient-derived xenografts in immunodeficient mice, we developed fully immunocompetent models of immunotherapy using transplantable, syngeneic tumors. These four models – HSVtk/GCV suicide gene immunotherapy, oncolytic viroimmunotherapy, adoptive T cell transfer, and CAR T cell therapy – have been optimized to treat tumors outside of the CNS and induce a broad spectrum of inflammatory profiles, maximizing the chances of observing brainstem toxicity. Results: All four models achieved anti-tumor efficacy in the absence of toxicity, with the exception of recombinant vaccinia virus expressing GMCSF, which demonstrated inflammatory toxicity. Histology, imaging, and flow cytometry confirmed the presence of brainstem inflammation in all models. Where used, the addition of immune checkpoint blockade did not introduce toxicity. Conclusions: It remains imperative to regard the brainstem with caution for immunotherapeutic intervention. Nonetheless, we show that further careful development of immunotherapies for pediatric brainstem tumors is warranted to harness the potential potency of anti-tumor immune responses, despite their possible toxicity within this anatomically sensitive location

Stabilization of monodomain polarization in ultrathin PbTiO3 films

Using in situ high-resolution synchrotron x-ray scattering, the Curie temperature T-C has been determined for ultrathin c-axis epitaxial PbTiO3 films on conducting substrates (SrRuO3 on SrTiO3), with surfaces exposed to a controlled vapor environment. The suppression of T-C was relatively small, even for the thinnest film (1.2 nm). We observe that 180 degrees stripe domains do not form, indicating that the depolarizing field is compensated by free charge at both interfaces. This is confirmed by ab initio calculations that find polar ground states in the presence of ionic adsorbates.open15511

Accreting Neutron Stars in Low-Mass X-Ray Binary Systems

Using the Rossi X-ray Timing Explorer (RossiXTE), astronomers have discovered that disk-accreting neutron stars with weak magnetic fields produce three distinct types of high-frequency X-ray oscillations. These oscillations are powered by release of the binding energy of matter falling into the strong gravitational field of the star or by the sudden nuclear burning of matter that has accumulated in the outermost layers of the star. The frequencies of the oscillations reflect the orbital frequencies of gas deep in the gravitational field of the star and/or the spin frequency of the star. These oscillations can therefore be used to explore fundamental physics, such as strong-field gravity and the properties of matter under extreme conditions, and important astrophysical questions, such as the formation and evolution of millisecond pulsars. Observations using RossiXTE have shown that some two dozen neutron stars in low-mass X-ray binary systems have the spin rates and magnetic fields required to become millisecond radio-emitting pulsars when accretion ceases, but that few have spin rates above about 600 Hz. The properties of these stars show that the paucity of spin rates greater than 600 Hz is due in part to the magnetic braking component of the accretion torque and to the limited amount of angular momentum that can be accreted in such systems. Further study will show whether braking by gravitational radiation is also a factor. Analysis of the kilohertz oscillations has provided the first evidence for the existence of the innermost stable circular orbit around dense relativistic stars that is predicted by strong-field general relativity. It has also greatly narrowed the possible descriptions of ultradense matter.Comment: 22 pages, 7 figures, updated list of sources and references, to appear in "Short-period Binary Stars: Observation, Analyses, and Results", eds. E.F. Milone, D.A. Leahy, and D. Hobill (Dordrecht: Springer, http://www.springerlink.com

State of the art: refinement of multiple sequence alignments

BACKGROUND: Accurate multiple sequence alignments of proteins are very important in computational biology today. Despite the numerous efforts made in this field, all alignment strategies have certain shortcomings resulting in alignments that are not always correct. Refinement of existing alignment can prove to be an intelligent choice considering the increasing importance of high quality alignments in large scale high-throughput analysis. RESULTS: We provide an extensive comparison of the performance of the alignment refinement algorithms. The accuracy and efficiency of the refinement programs are compared using the 3D structure-based alignments in the BAliBASE benchmark database as well as manually curated high quality alignments from Conserved Domain Database (CDD). CONCLUSION: Comparison of performance for refined alignments revealed that despite the absence of dramatic improvements, our refinement method, REFINER, which uses conserved regions as constraints performs better in improving the alignments generated by different alignment algorithms. In most cases REFINER produces a higher-scoring, modestly improved alignment that does not deteriorate the well-conserved regions of the original alignment