Experiments about the Generalization Ability of Common Vector based methods for Face Recognition

Abstract. This work presents some preliminary results about exploring and proposing new extensions of common vector based subspace methods that have been recently proposed to deal with very high dimensional classification problems. Both the common vector and the discriminant vector approaches are considered. The different dimensionalities of the subspaces that these methods use as intermediate step are considered in different situations and their relation to the generalization ability of each method is analyzed. Comparative experiments using different databases for the face recognition problem are performed to support the main conclusions of the paper

EXPERIMENTS ON AUTOMATIC DRUG ACTIVITY CHARACTERIZATION USING SUPPORT VECTOR CLASSIFICATION

ABSTRACT The characterization of pharmacological properties from their chemical structure has become a challenging and promising technique in computer aided drug design. The idea consists of finding appropriate representations of candidate compounds in terms of their chemical formulae and try to apply a particular machine learning method able to appropriately characterize certain desired properties or kinds of pharmacological activity. In this particular work antibacterial activity has been considered. Several classic pattern classification methods have already been applied to this problem with promising results. In this work, the support vector machine model is considered and compared to multilayer perceptrons in this particular context. The natural and unpredictable imbalance and the fact that only relatively small samples can be used for learning make this a challenging and interesting problem

Soil Bacterial Community Along an Altitudinal Gradient in the Sumaco, a Stratovolcano in the Amazon Region

Our study is a pioneering exploration of the microbiome in the soil of the Sumaco stratovolcano and an assessment of the effects of an elevational gradient and related physicochemical soil parameters on richness and community structure. The Sumaco, as an isolated Amazonian stratovolcano, may be among one of the least studied ecosystems in Ecuador and perhaps the Amazon region. Universal patterns remain unresolved or available information inconclusive to establish a supported consensus on general governing processes by which elevation and its associated environmental gradients may determine the microbial richness and community structure. We tested a recent proposal on how microbial diversity responds to montane gradients, placing a central role in soils as potentially independent of altitude along an elevational gradient. Correlations and effects among soil physicochemical parameters and altitude were contrasted against richness and community structure through quantitative ecology. The most informative physicochemical parameter in our assessment of bacterial community structure was neither pH nor altitude, but sulfur, which was mostly independent of the other tested parameters. We established a positive effect of richness by parameters associated with metallic cations such as Mn2+, and CEC, which were negatively correlated to altitude and pH. The possible relation between the significant role of sulfur on bacterial community structure with the unique geological origin of the Sumaco stratovolcano should be examined in the context of specialized sulfur metabolisms and additional information on community structure and environmental constraints. Our study establishes an initial baseline for further explorations of microbial diversity in this unexplored tropical stratovolcano

The microbiome of the ice-capped Cayambe Volcanic Complex in Ecuador

A major challenge in microbial ecology is to understand the principles and processes by which microbes associate and interact in community assemblages. Microbial communities in mountain glaciers are unique as first colonizers and nutrient enrichment drivers for downstream ecosystems. However, mountain glaciers have been distinctively sensitive to climate perturbations and have suffered a severe retreat over the past 40  years, compelling us to understand glacier ecosystems before their disappearance. This is the first study in an Andean glacier in Ecuador offering insights into the relationship of physicochemical variables and altitude on the diversity and structure of bacterial communities. Our study covered extreme Andean altitudes at the Cayambe Volcanic Complex, from 4,783 to 5,583 masl. Glacier soil and ice samples were used as the source for 16S rRNA gene amplicon libraries. We found (1) effects of altitude on diversity and community structure, (2) the presence of few significantly correlated nutrients to community structure, (3) sharp differences between glacier soil and glacier ice in diversity and community structure, where, as quantified by the Shannon γ-diversity distribution, the meta-community in glacier soil showed more diversity than in glacier ice; this pattern was related to the higher variability of the physicochemical distribution of variables in the former substrate, and (4) significantly abundant genera associated with either high or low altitudes that could serve as biomarkers for studies on climate change. Our results provide the first assessment of these unexplored communities, before their potential disappearance due to glacier retreat and climate change

Inference of the life cycle of environmental phages from genomic signature distances to their hosts

The environmental impact of uncultured phages is shaped by their preferred life cycle (lytic or lysogenic). However, our ability to predict it is very limited. We aimed to discriminate between lytic and lysogenic phages by comparing the similarity of their genomic signatures to those of their hosts, reflecting their co-evolution. We tested two approaches: (1) similarities of tetramer relative frequencies, (2) alignment-free comparisons based on exact k = 14 oligonucleotide matches. First, we explored 5126 reference bacterial host strains and 284 associated phages and found an approximate threshold for distinguishing lysogenic and lytic phages using both oligonucleotide-based methods. The analysis of 6482 plasmids revealed the potential for horizontal gene transfer between different host genera and, in some cases, distant bacterial taxa. Subsequently, we experimentally analyzed combinations of 138 Klebsiella pneumoniae strains and their 41 phages and found that the phages with the largest number of interactions with these strains in the laboratory had the shortest genomic distances to K. pneumoniae. We then applied our methods to 24 single-cells from a hot spring biofilm containing 41 uncultured phage-host pairs, and the results were compatible with the lysogenic life cycle of phages detected in this environment. In conclusion, oligonucleotide-based genome analysis methods can be used for predictions of (1) life cycles of environmental phages, (2) phages with the broadest host range in culture collections, and (3) potential horizontal gene transfer by plasmids

Driven progressive evolution of genome sequence complexity in Cyanobacteria

Progressive evolution, or the tendency towards increasing complexity, is a controversial issue in biology, which resolution entails a proper measurement of complexity. Genomes are the best entities to address this challenge, as they encode the historical information of a species’ biotic and environmental interactions. As a case study, we have measured genome sequence complexity in the ancient phylum Cyanobacteria. To arrive at an appropriate measure of genome sequence complexity, we have chosen metrics that do not decipher biological functionality but that show strong phylogenetic signal. Using a ridge regression of those metrics against root-to-tip distance, we detected positive trends towards higher complexity in three of them. Lastly, we applied three standard tests to detect if progressive evolution is passive or driven—the minimum, ancestor– descendant, and sub-clade tests. These results provide evidence for driven progressive evolution at the genome-level in the phylum Cyanobacteria.Generalitat Valenciana Prometeo/2018/A/133European Union (EU)Fulbright fellowship (Spanish Minister of Science, Innovation and Universities)SAF2015-65878-RAGL2017-88702-C2-2-RPGC2018-099344-B-I0

Progressive genome evolution in Cyanobacteria

Resumen del trabajo presentado a la VII Biennial Congress of Sociedad Española de Biología Evolutiva (SEBE), celebrada en Sevilla (España) del 5 al 7 de febrero de 2020.Progressive evolution, the tendency towards increasing complexity, is a controversial issue in Biology, whose resolution requires the proper measurement of complexity. To address this challenge, we consider that genomes are the best entities to measure complexity because they record the history and information gain of organisms in their ongoing biotic and environmental interactions. By recurring to six metrics that measure genome complexity, which are not primarily associated to functionality, we report the existence of progressive evolution towards higher genome complexity in the evolution of the Cyanobacteria phylum. We show that these complexity metrics plus three additional genome parameters present statistically significant phylogenetic signal in Cyanobacteria. Moreover, a ridge regression of genome complexity metrics against evolutionary age shows that three out of six present a positively driven evolutionary trend towards higher complexity. These findings support the existence of progressive genome evolution in this ancient and diverse group of organisms.Peer reviewe

Synthase-selected sorting approach identifies a beta-lactone synthase in a nudibranch symbiotic bacterium

[Background] Nudibranchs comprise a group of > 6000 marine soft-bodied mollusk species known to use secondary metabolites (natural products) for chemical defense. The full diversity of these metabolites and whether symbiotic microbes are responsible for their synthesis remains unexplored. Another issue in searching for undiscovered natural products is that computational analysis of genomes of uncultured microbes can result in detection of novel biosynthetic gene clusters; however, their in vivo functionality is not guaranteed which limits further exploration of their pharmaceutical or industrial potential. To overcome these challenges, we used a fluorescent pantetheine probe, which produces a fluorescent CoA-analog employed in biosynthesis of secondary metabolites, to label and capture bacterial symbionts actively producing these compounds in the mantle of the nudibranch Doriopsilla fulva.[Results] We recovered the genome of Candidatus Doriopsillibacter californiensis from the Ca. Tethybacterales order, an uncultured lineage of sponge symbionts not found in nudibranchs previously. It forms part of the core skin microbiome of D. fulva and is nearly absent in its internal organs. We showed that crude extracts of D. fulva contained secondary metabolites that were consistent with the presence of a beta-lactone encoded in Ca. D. californiensis genome. Beta-lactones represent an underexplored group of secondary metabolites with pharmaceutical potential that have not been reported in nudibranchs previously.[Conclusions] Altogether, this study shows how probe-based, targeted sorting approaches can capture bacterial symbionts producing secondary metabolites in vivo.The work (proposal: 10.46936/10.25585/60000940) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231. RS, MB, JL, and TW are supported by NIH grant R01AI168993. The John Templeton Foundation (grant nos. 51250 and 60973) supported TT and SVD, and the Gordon and Betty Moore Foundation grants (GBMF7617 and GBMF9340) supported SVD. MD is supported by the Generalitat Valenciana program GenT grant number CDEIGENT/2021/008. SPE is supported by a FPU grant from the Spanish Ministry of Universities (Reference: FPU20/05756).Peer reviewe

Complexity metrics trend analysis through endosymbiosis evolution

Resumen del póster presentado al XLII Congreso de la Sociedad Española de Genética, celebrado de forma virtual del 14 al 18 de junio de 2021.The existence in biological evolution of a trend towards greater complexity is an open question that has generated much debate. This is mostly due to the existence of multiple definitions of complexity and their measures. Moya et al. (2020), assuming that the genome is a good record of the evolutionary history of the species in their interaction with the physical and biotic environment (Adami, 2002), carried out a study of the evolution of cyanobacteria, measuring in their genomes several metrics and genomic parameters. Through phylogenomic analysis, they estimated the values of these metrics in the internal nodes, detected a phylogenetic signal in all of them and showed that some of them presented a positive trend, that is: the genomes of the most recent species were more complex than the older species. This hypothesis can be tested by the investigation of the evolution of an opposite case, that of endosymbionts, intracellular bacteria of eukaryotes whose genomes have undergone with respect to their free-living ancestors a drastic process of reduction and degeneration, as well as loss of metabolic diversity. These organisms should present metrics of decreasing complexity with respect to the organisms from which they are derived and, therefore, the trend should be negative. In this communication, we study a set of 192 genomes where 102 organisms are endosymbionts that belong to 13 different phyla. All the complexity metrics studied and proposed in the study of cyanobacteria were applied to the endosymbiont genomes. We derived a phylogenomic tree based on a matrix of 31 proteins to reconstruct the ancestral states of the metrics and, subsequently, we carried out the trend analysis. The metrics surprisingly show a positive slope, indicating an unexplained increase in the complexity of recent endosymbiont genomes relative to ancestral free-living bacterial genomes. The only connection point that we found between the positive trend metrics in cyanobacteria and endosymbionts is the greater evolutionary acceleration with respect to their values in the corresponding ancestors. These results highlight the need to work on improving the metrics, or new ones, that be independent of the evolutionary acceleration, in such a way as to find those that really measure the evolution towards greater complexity, if it exists.Peer reviewe