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Proceedings of the International Symposium on Room Acoustics : 15 to 17 September 2019 in Amsterdam, Netherlands : ISRA 2019 Amsterdam / proceedings editor: Margriet Lautenbach, Ingo Witew, Diemer de Vries, Maarten Hornikx International Symposium on Room Acoustics, ISRA 2019, Amsterdam, Netherlands, 15 Sep 2019 - 17 Sep 2019; Heerde : Nederlands Akoestisch Genootschap (2019). doi:10.18154/RWTH-CONV-240102, Published by Nederlands Akoestisch Genootschap, Heerde

Wepresent the high-quality genome sequence of a 45,000-year-old modern human male from Siberia. This individual derives from a population that lived before¿or simultaneously with¿the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000¿13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 x 10-9 to 0.6x10-9 per site per year, a Y chromosomal mutation rate of 0.7x10-9 to 0.9x10-9 per site per year based on the additional substitutions that have occurred in present-day non- Africans compared to this genome, and a mitochondrial mutation rate of 1.8x10-8 to 3.2x10-8 per site per year based on the age of the bone.

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Background Genome-wide expression, sequence and association studies typically yield large sets of gene candidates, which must then be further analysed and interpreted. Information about these genes is increasingly being captured and organized in ontologies, such as the Gene Ontology. Relationships between the gene sets identified by experimental methods and biological knowledge can be made explicit and used in the interpretation of results. However, it is often difficult to assess the statistical significance of such analyses since many inter-dependent categories are tested simultaneously. Results We developed the program package FUNC that includes and expands on currently available methods to identify significant associations between gene sets and ontological annotations. Implemented are several tests in particular well suited for genome wide sequence comparisons, estimates of the family-wise error rate, the false discovery rate, a sensitive estimator of the global significance of the results and an algorithm to reduce the complexity of the results. Conclusion FUNC is a versatile and useful tool for the analysis of genome-wide data. It is freely available under the GPL license and also accessible via a web service.

Acacia glomerosa, Acacia tortuosa, Acacia macracantha, Samanea samán y Enterolobium cyclocarpum, especies Mimosaceae venezolanas, tiene la capacidad de exudar goma, después de un estímulo apropiado. Datos de estas gomas, determinados por métodos analíticos clásicos, son muy interesantes. Las gomas de Acacia tortuosa y Acacia macracantha son muy solubles en agua; las gomas de Enterolobium cyclocarpum y Samanea samán mostraron alto valor de la viscosidad intrínseca. La composición de azúcares de las gomas estudiadas demostró contener galactosa, arabinosa, ramnosa, ácido glucuronico y su 4-0-methyl derivado. Los datos obtenidos mostraron algunas similitudes con los reportados para la goma de Acacia senegal, la cual tiene amplia aplicación industrial; por lo tanto, seria muy interesante ensayar el comportamiento de esas gomas en la industria alimentaría y en otras aplicaciones industriales. Acacia glomerosa, Acacia tortuosa, Acacia macracantha, Samanea saman and Enterolobium cyclocarpum, Venezuelan Mimosaceae species, are able to exudate gum, after appropriate stimulation. Data on these gums, determined by classical analytical methods, are very interesting. Acacia tortuosa and Acacia macracantha gums are very soluble, in water; Enterolobium cyclocarpum and Samanea saman gums showed high intrinsic viscosity. Sugar composition of the gums studied showed them to contain galactose, arabinose, rhamnose, glucuronic acid and its 4-0-methyl derivative. The data obtained showed some similarities with that reported for Acacia senegal gum, which has wide industrial application; therefore, it would be very interesting to test the behavior of those gums in the food industry and other industrial applications.

The influence of 9-beta-D-arabinofuranosyladenine (ara-A) and its 5'-triphosphate derivative on programmed synthesis was tested with an intact cell system as well as with isolated enzyme systems. The effect of ara-A was tested in mouse lymphoma cells (L5178Y). The compound reduces cell proliferation in low concentration by cytostasis; under high ara-A concentration of radioactive precursors into DNA, RNA, and protein showed that ara-A selectively inhibits DNA synthesis. Formation of a polysome complex is not affected by ara-A. [3H]ara-A is incorporated into DNA in an intact cell system; 1 molecule of ara-A is incorporated per 8000 molecules of deoxyadenosine. Most of the ara-A molecules appeared to be in internucleotide linkages. Incorporation of ara-A into RNA could not be detected. 9-BETA-D-Arabinofuranosyladenine 5'-triphosphate (ara-ATP) does not reduce the incorporation rate of the following enzymes, isolated from quail oviducts: DNA-dependent RNA polymerases I and II, polyadenylic acid polymerase, and poly(adenosine diphosphate ribose) polymerase. The compound was found to inhibit DNA synthesis catalyzed by DNA polymerases isolated from quail oviducts and from oncogenic RNA viruses (Rous sarcoma viruses). All the enzymes tested were inhibited by ara-ATP in a competitive way with respect to deoxyadenosine 5'-triphosphate. The highest affinity of ara-ATP, i.e., the highest inhibitory potency of the drug, was found in the assays with the eukaryotic low-molecular DNA-dependent DNA polymerase. The influence on the eukaryotic high-molecular DNA-dependent Dna polymerase was a litte less. Compared to the eukaryotic DNA polymerases, the viral enzymes (RNA-directed DNA polymerase and DNA-directed DNA polymerase) are affected to a smaller extent by ara-ATP. No effects of ara-A and ara-ATP are observed in a protein-synthesizing, cell-free system isolated from L5178Y cells.

Formycin B inhibited growth of L5178Y mouse leukemia cells in concentrations of less than twice the concentration that inhibits cell proliferation at 50% by cytostasis; at higher concentrations (more than twice the 50% concentration mentioned), the cells were killed. In cells treated with the concentration that inhibits cell proliferation at 50%, the average cell volume did not change. The formycin B inhibitory effect on cell proliferation was reduced by coincubation with nicotinamide adenine diphosphate or adenosine. The biosyntheses of DNA,RNA, and protein in whole cells were sensitively inhibited by formycin B as checked by incorporation studies with radioactive precursors. In addition, the formation of polyadenosine diphosphoribose was reduced even with higher sensitivity; in particular the extent of adenosine diphosphate ribosylation of histone subfraction H1 was reduced. Formycin B has been shown to be an inhibitor for the polyadenosine diphosphoribose polymerase, isolated from oviduct nuclei of quails. Both the chromatin-bound and the soluble enzyme are inhibited competitively; the relative affinity (Ki/Km) of formycin B to the polyadenosine diphosphoribose polymerase is 1.5.

Background Hybridization differences caused by target sequence differences can be a confounding factor in analyzing gene expression on microarrays, lead to false positives and reduce power to detect real expression differences. We prepared an R Bioconductor compatible package to detect, characterize and remove such probes in Affymetrix 3’IVT and exon-based arrays on the basis of correlation of signal intensities from probes within probe sets. Results Using completely mouse genomes we determined type 1 (false negatives) and type 2 (false positives) errors with high accuracy and we show that our method routinely outperforms previous methods. When detecting 76.2% of known SNP/indels in mouse expression data, we obtain at most 5.5% false positives. At the same level of false positives, best previous method detected 72.6%. We also show that probes with differing binding affinity both hinder differential expression detection and introduce artifacts in cancer-healthy tissue comparison. Conclusions Detection and removal of such probes should be a routine step in Affymetrix data preprocessing. We prepared a user friendly R package, compatible with Bioconductor, that allows the filtering and improving of data from Affymetrix microarrays experiments.