To the knowledge of the genus Pseudospora Cienkowski [Translation from: Archiv fur Protistenkunde 59, 350-368, 1927]

Morphological observations on the two types of Pseudospora are given. The two Pseudospora whic are described are Pseudospora eudorini and Pseudospora volvocis. The systematic classification of the genus Pseudospora is discussed

National Interest: From Abstraction to Strategy

Because the national interest is the foundation for both the National Security Strategy and its supporting National Military Strategy, it is essential that military leaders understand the political context from which the details of the national interest emerge. The guiding concept of national interest is more often assumed than analyzed in the dynamic context of domestic and international politics. For these reasons, Dr. Michael Roskin, Visiting Professor of Foreign Policy, was asked to synthesize the academic literature, focusing on those works that had greatest value and relevance to members of the national security community who must apply as well as serve the national interest.https://press.armywarcollege.edu/monographs/1897/thumbnail.jp

Origin of the Sinai-Negev erg, Egypt and Israel: mineralogical and geochemical evidence for the importance of the Nile and sea level history

The Sinai-Negev erg occupies an area of 13,000 km2 in the deserts of Egypt and Israel. Aeolian sand of this erg has been proposed to be derived from the Nile Delta, but empirical data supporting this view are lacking. An alternative source sediment is sand from the large Wadi El Arish drainage system in central and northern Sinai. Mineralogy of the Negev and Sinai dunes shows that they are high in quartz, with much smaller amounts of K-feldspar and plagioclase. Both Nile Delta sands and Sinai wadi sands, upstream of the dunes, also have high amounts of quartz relative to K-feldspar and plagioclase. However, Sinai wadi sands have abundant calcite, whereas Nile Delta sands have little or no calcite. Overall, the mineralogical data suggest that the dunes are derived dominantly from the Nile Delta, with Sinai wadi sands being a minor contributor. Geochemical data that proxy for both the light mineral fraction (SiO2/10-Al2O3 + Na2O + K2O-CaO) and heavy mineral fraction (Fe2O3-MgO-TiO2) also indicate a dominant Nile Delta source for the dunes. Thus, we report here the first empirical evidence that the Sinai-Negev dunes are derived dominantly from the Nile Delta. Linkage of the Sinai-Negev erg to the Nile Delta as a source is consistent with the distribution of OSL ages of Negev dunes in recent studies. Stratigraphic studies show that during the Last Glacial period, when dune incursions in the Sinai-Negev erg began, what is now the Nile Delta area was characterized by a broad, sandy, minimally vegetated plain, with seasonally dry anastomosing channels. Such conditions were ideal for providing a ready source of sand for aeolian transport under what were probably much stronger glacial-age winds. With the post-glacial rise in sea level, the Nile River began to aggrade. Post-glacial sedimentation has been dominated by fine-grained silts and clays. Thus, sea level, along with favorable climatic conditions, emerges as a major influence on the timing of dune activity in the Sinai-Negev erg, through its control on the supply of sand from the Nile Delta. The mineralogy of the Sinai-Negev dunes is also consistent with a proposed hypothesis that these sediments are an important source of loess in Israel

Meta-Alignment with Crumble and Prune: Partitioning very large alignment problems for performance and parallelization

<p>Abstract</p> <p>Background</p> <p>Continuing research into the global multiple sequence alignment problem has resulted in more sophisticated and principled alignment methods. Unfortunately these new algorithms often require large amounts of time and memory to run, making it nearly impossible to run these algorithms on large datasets. As a solution, we present two general methods, Crumble and Prune, for breaking a phylogenetic alignment problem into smaller, more tractable sub-problems. We call Crumble and Prune <it>meta-alignment </it>methods because they use existing alignment algorithms and can be used with many current alignment programs. Crumble breaks long alignment problems into shorter sub-problems. Prune divides the phylogenetic tree into a collection of smaller trees to reduce the number of sequences in each alignment problem. These methods are orthogonal: they can be applied together to provide better scaling in terms of sequence length and in sequence depth. Both methods partition the problem such that many of the sub-problems can be solved independently. The results are then combined to form a solution to the full alignment problem.</p> <p>Results</p> <p>Crumble and Prune each provide a significant performance improvement with little loss of accuracy. In some cases, a gain in accuracy was observed. Crumble and Prune were tested on real and simulated data. Furthermore, we have implemented a system called Job-tree that allows hierarchical sub-problems to be solved in parallel on a compute cluster, significantly shortening the run-time.</p> <p>Conclusions</p> <p>These methods enabled us to solve gigabase alignment problems. These methods could enable a new generation of biologically realistic alignment algorithms to be applied to real world, large scale alignment problems.</p

Impact of somatic and germline mutations on the outcome of systemic mastocytosis

[EN]Systemic mastocytosis (SM) is a highly heterogeneous disease with indolent and aggressive forms, with the mechanisms leading to malignant transformation still remaining to be elucidated. Here, we investigated the presence and frequency of genetic variants in 34 SM patients with multilineal KIT D816V mutations. Initial screening was performed by targeted sequencing of 410 genes in DNA extracted from purified bone marrow cells and hair from 12 patients with nonadvanced SM and 8 patients with advanced SM, followed by whole-genome sequencing (WGS) in 4 cases. Somatic mutations were further investigated in another 14 patients with advanced SM. Despite the fact that no common mutation other than KIT D816V was found in WGS analyses, targeted next-generation sequencing identified 67 nonsynonymous genetic variants involving 39 genes. Half of the mutations were somatic (mostly multilineal), whereas the other half were germline variants. The presence of ≥1 multilineal somatic mutation involving genes other than KIT D816V, ≥3 germline variants, and ≥1 multilineal mutation in the SRSF2, ASXL1, RUNX1, and/or EZH2 genes (S/A/R/E genes), in addition to skin lesions, splenomegaly, thrombocytopenia, low hemoglobin levels, and increased alkaline phosphatase and β2-microglobulin serum levels, were associated with a poorer patient outcome. However, the presence of ≥1 multilineal mutation, particularly involving S/A/R/E genes, was the only independent predictor for progression-free survival and overall survival in our cohort

Identification and Classification of Conserved RNA Secondary Structures in the Human Genome

The discoveries of microRNAs and riboswitches, among others, have shown functional RNAs to be biologically more important and genomically more prevalent than previously anticipated. We have developed a general comparative genomics method based on phylogenetic stochastic context-free grammars for identifying functional RNAs encoded in the human genome and used it to survey an eight-way genome-wide alignment of the human, chimpanzee, mouse, rat, dog, chicken, zebra-fish, and puffer-fish genomes for deeply conserved functional RNAs. At a loose threshold for acceptance, this search resulted in a set of 48,479 candidate RNA structures. This screen finds a large number of known functional RNAs, including 195 miRNAs, 62 histone 3′UTR stem loops, and various types of known genetic recoding elements. Among the highest-scoring new predictions are 169 new miRNA candidates, as well as new candidate selenocysteine insertion sites, RNA editing hairpins, RNAs involved in transcript auto regulation, and many folds that form singletons or small functional RNA families of completely unknown function. While the rate of false positives in the overall set is difficult to estimate and is likely to be substantial, the results nevertheless provide evidence for many new human functional RNAs and present specific predictions to facilitate their further characterization

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead