SynBlast: Assisting the Analysis of Conserved Synteny Information

Motivation: In the last years more than 20 vertebrate genomes have been sequenced, and the rate at which genomic DNA information becomes available is rapidly accelerating. Gene duplication and gene loss events inherently limit the accuracy of orthology detection based on sequence similarity alone. Fully automated methods for orthology annotation do exist but often fail to identify individual members in cases of large gene families, or to distinguish missing data from traceable gene losses. This situation can be improved in many cases by including conserved synteny information. Results: Here we present the SynBlast pipeline that is designed to construct and evaluate local synteny information. SynBlast uses the genomic region around a focal reference gene to retrieve candidates for homologous regions from a collection of target genomes and ranks them in accord with the available evidence for homology. The pipeline is intended as a tool to aid high quality manual annotation in particular in those cases where automatic procedures fail. We demonstrate how SynBlast is applied to retrieving orthologous and paralogous clusters using the vertebrate Hox and ParaHox clusters as examples

Exclusion of repetitive DNA elements from gnathostome Hox clusters

Despite their homology and analogous function, the Hox gene clusters of vertebrates and invertebrates are subject to different constraints on their structural organization. This is demonstrated by a drastically different distribution of repetitive DNA elements in the Hox cluster regions. While gnathostomes have a strong tendency to exclude repetitive DNA elements from the inside of their Hox clusters, no such trend can be detected in the Hox gene clusters of protostomes. Repeats “invade” the gnathostome Hox clusters from the 5′ and 3′ ends while the core of the clusters remains virtually free of repetitive DNA. This invasion appears to be correlated with relaxed constraints associated with gene loss after cluster duplications

Independent Hox‐cluster duplications in lampreys

The analysis of the publicly available Hox gene sequences from the sea lamprey Petromyzon marinus provides evidence that the Hox clusters in lampreys and other vertebrate species arose from independent duplications. In particular, our analysis supports the hypothesis that the last common ancestor of agnathans and gnathostomes had only a single Hox cluster which was subsequently duplicated independently in the two lineages

Factores advectivos en el clima de la Puna Argentina

Advective factors in tbe climate o f tbe argentine Altiplano. The dimate of the argentine Altiplano, predominantly autoctonous, is modified in its northeastern part by the advection of air-masses of tropical origin during the summer season, caused by the general atmospheric circulation. The mean wind direction is Northeast during the summer months (Nov.-March) and west and south in winter. In both seasons the gradient wind has approximately the same direction as the local thermal wind system, from the plains towards the mountains in summer and the other way round in winter. This advection introduces tropical characteristics in the typical subtropical climate of the frontier — zone between Bolivia and Argentina of the Altiplano as exemplified by the observations of the Geophysical Observatory of La Quiaca (22’06’S; 65"36’W ; 3.-Í60 m) : high atmospheric humidity, low clouds, precipitations, inestability of the air-masses and thunderstorms; all these meteorological elements are influencing the radiation balance of short and Iong wave lengths and thereby also the temperature and its variation (aperiodic, periodic, interdiurnal, etc.). This transpon of air-masses from the tropical zones to the Cordillera produces a great uniformity in the climatic conditions on the entire eastern slope of the Andes, from Perú to the extrem north of Argentine during the summertime.Fil: Prohaska, Federico J.. Instituto Nacional de Tecnología Agropecuaria (Argentina

Algunos aspectos del clima de la Alta Coordillera y de la Puna Argentina

Fil: Prohaska, Federico J.. Instituto Nacional de Tecnología Agropecuaria (Argentina

Validation of Different Combination of Three Reversing Half-Hitches Alternating Posts (RHAPs) Effects on Arthroscopic Knot Integrity

Introduction. With arthroscopic techniques being used, the importanceof knot tying has been examined. Previous literaturehas examined the use of reversing half-hitches on alternatingposts (RHAPs) on knot security. Separately, there has been researchregarding different suture materials commonly used inthe operating room. The specific aim of this study was to validatethe effect of different stacked half-hitch configuration anddifferent braided suture materials on arthroscopic knot integrity. Methods. Three different suture materials tied withfive different RHAPs in arthroscopic knots were compared.A single load-to-failure test was performed andthe mean ultimate clinical failure load was obtained. Results. Significant knot holding strength improvement wasfound when one half-hitch was reversed as compared to baselineknot. When two of the half-hitches were reversed, therewas a greater improvement with all knots having a mean ultimateclinical failure load greater than 150 newtons (N). Comparisonof the suture materials demonstrated a higher meanultimate clinical failure load when Force Fiber® was used andat least one half-hitch was reversed. Knots tied with eitherForce Fiber® or Orthocord® showed 0% chance of knot slippagewhile knots tied with FiberWire® or braided fishing linehad about 10 and 30% knot slippage chances, respectively. Conclusion. A significant effect was observed in regards to bothstacked half-hitch configuration and suture materials used onknot loop and knot security. Caution should be used with tyingthree RHAPs in arthroscopic surgery, particularly witha standard knot pusher and arthroscopic cannulas. The findingsof this study indicated the importance of three RHAPsin performing arthroscopic knot tying and provided evidenceregarding discrepancies of maximum clinical failure loads observedbetween orthopaedic surgeons, thereby leading to bettersurgical outcomes in the future. KS J Med 2017;10(2):35-39

Divergence of Conserved Non-Coding Sequences: Rate Estimate and Relative Rate Tests

In many eukaryotic genomes only a small fraction of the DNA codes for proteins, but the non-protein coding DNA harbors important genetic elements directing the development and the physiology of the organisms, like promoters, enhancers, insulators, and micro-RNA genes. The molecular evolution of these genetic elements is difficult to study because their functional significance is hard to deduce from sequence information alone. Here we propose an approach to the study of the rate of evolution of functional non-coding sequences at a macro-evolutionary scale. We identify functionally important non-coding sequences as Conserved Non-Coding Nucleotide (CNCN) sequences from the comparison of two outgroup species. The CNCN sequences so identified are then compared to their homologous sequences in a pair of ingroup species, and we monitor the degree of modification these sequences suffered in the two ingroup lineages. We propose a method to test for rate differences in the modification of CNCN sequences among the two ingroup lineages, as well as a method to estimate their rate of modification. We apply this method to the full sequences of the HoxA clusters from six gnathostome species: a shark, Heterodontus francisci; a basal ray finned fish, Polypterus senegalus; the amphibian, Xenopus tropicalis; as well as three mammalian species, human, rat and mouse. The results show that the evolutionary rate of CNCN sequences is not distinguishable among the three mammalian lineages, while the Xenopus lineage has a significantly increased rate of evolution. Furthermore the estimates of the rate parameters suggest that in the stem lineage of mammals the rate of CNCN sequence evolution was more than twice the rate observed within the placental amniotes clade, suggesting a high rate of evolution of cis-regulatory elements during the origin of amniotes and mammals. We conclude that the proposed methods can be used for testing hypotheses about the rate and pattern of evolution of putative cis-regulatory elements