On the interplay among ambient temperature basal metabolic rate and body mass

One of the most generalized conclusions arising from studies analyzing the ecological variation of energy metabolism in endotherms is the apparent negative correlation between ambient temperature and mass-independent basal metabolic rate (residual BMR). As a consequence, ambient temperature has been considered the most important external factor driving the evolution of residual BMR. It is not clear, however, whether this relationship is size dependent, and artifacts such as the biased sampling of body masses in physiological data sets could cause us to overstate the ubiquity of the relationship. Accordingly, here we used published data on body mass (mb), BMR, and annual mean temperature (Tmean) for 458 mammal species (and/or subspecies) to examine the size dependence of the relationship between temperature and BMR. We found a significant interaction between mb and Tmean as predictors of residual BMR, such that the effect of Tmean on residual BMR decreases as a function of mb. In line with this, the amount of residual variance in BMR explained by Tmean decreased with increasing mb, from 20%–30% at body sizes of less than 100 g to almost 0 at body sizes greater than 1,000 g. These data suggest that our current understanding of the importance of broad-scale variation in ambient temperature as a driver of metabolic evolution in endotherms probably is affected by the large number of small species in both nature and physiological data sets

First complete mitochondrial genome of the South American annual fish Austrolebias charrua (Cyprinodontiformes: Rivulidae): peculiar features among cyprinodontiforms mitogenomes

Selected nucleotide substitution models after the third codon positions were removed from the codon alignments. (PDF 7 kb

Mining of public sequencing databases supports a non-dietary origin for putative foreign miRNAs: underestimated effects of contamination in NGS

The report that exogenous plant miRNAs are able to cross the mammalian gastrointestinal tract and exert gene-regulation mechanism in mammalian tissues has yielded a lot of controversy, both in the public press and the scientific literature. Despite the initial enthusiasm, reproducibility of these results was recently questioned by several authors. To analyze the causes of this unease, we searched for diet-derived miRNAs in deep-sequencing libraries performed by ourselves and others. We found variable amounts of plant miRNAs in publicly available small RNA-seq data sets of human tissues. In human spermatozoa, exogenous RNAs reached extreme, biologically meaningless levels. On the contrary, plant miRNAs were not detected in our sequencing of human sperm cells, which was performed in the absence of any known sources of plant contamination. We designed an experiment to show that cross-contamination during library preparation is a source of exogenous RNAs. These contamination-derived exogenous sequences even resisted oxidation with sodium periodate. To test the assumption that diet-derived miRNAs were actually contamination-derived, we sought in the literature for previous sequencing reports performed by the same group which reported the initial finding. We analyzed the spectra of plant miRNAs in a small RNA sequencing study performed in amphioxus by this group in 2009 and we found a very strong correlation with the plant miRNAs which they later reported in human sera. Even though contamination with exogenous sequences may be easy to detect, cross-contamination between samples from the same organism can go completely unnoticed, possibly affecting conclusions derived from NGS transcriptomics

A comparison between Poisson and zero-inflated Poisson regression models with an application to number of black spots in Corriedale sheep

Dark spots in the fleece area are often associated with dark fibres in wool, which limits its competitiveness with other textile fibres. Field data from a sheep experiment in Uruguay revealed an excess number of zeros for dark spots. We compared the performance of four Poisson and zero-inflated Poisson (ZIP) models under four simulation scenarios. All models performed reasonably well under the same scenario for which the data were simulated. The deviance information criterion favoured a Poisson model with residual, while the ZIP model with a residual gave estimates closer to their true values under all simulation scenarios. Both Poisson and ZIP models with an error term at the regression level performed better than their counterparts without such an error. Field data from Corriedale sheep were analysed with Poisson and ZIP models with residuals. Parameter estimates were similar for both models. Although the posterior distribution of the sire variance was skewed due to a small number of rams in the dataset, the median of this variance suggested a scope for genetic selection. The main environmental factor was the age of the sheep at shearing. In summary, age related processes seem to drive the number of dark spots in this breed of sheep

Testing the existence of an unadmixed ancestor from a specific population t generations ago

Datos y códigos en: https://figshare.com/articles/dataset/Testing_the_existence_of_an_unadmixed_ancestor_from_a_specific_population_t_The ancestry of each locus of the genome can be estimated (local ancestry) based on sequencing or genotyping information together with reference panels of ancestral source populations. The length of those ancestry-specific genomic segments are commonly used to understand migration waves and admixture events. In short time scales, it is often of interest to determine the existence of the most recent unadmixed ancestor from a specific population t generations ago. We built a hypothesis test to determine if an individual has an ancestor belonging to a target ancestral population t generations ago based on these lengths of the ancestry-specific segments at an individual level. We applied this test on a data set that includes 20 Uruguayan admixed individuals to estimate for each one how many generations ago the most recent indigenous ancestor lived. As this method tests each individual separately, it is particularly suited to small sample sizes, such as our study or ancient genome samples

HPLC-MS/MS Oxylipin Analysis of Plasma from Amyotrophic Lateral Sclerosis Patients

Oxylipins play a critical role in regulating the onset and resolution phase of inflammation. Despite inflammation is a pathological hallmark in amyotrophic lateral sclerosis (ALS), the plasma oxylipin profile of ALS patients has not been assessed yet. Herein, we develop an oxylipin profile-targeted analysis of plasma from 74 ALS patients and controls. We found a significant decrease in linoleic acid-derived oxylipins in ALS patients, including 9-hydroxy-octadecadienoic acid (9-HODE) and 13-HODE. These derivatives have been reported as important regulators of inflammation on different cell systems. In addition, some 5-lipoxygenase metabolites, such as 5-hydroxy- eicosatetraenoic acid also showed a significant decrease in ALS plasma samples. Isoprostanes of the F2 alpha family were detected only in ALS patients but not in control samples, while the hydroxylated metabolite 11-HETE significantly decreased. Despite our effort to analyze specialized pro-resolving mediators, they were not detected in plasma samples. However, we found the levels of 14-hydroxy-docosahexaenoic acid, a marker pathway of the Maresin biosynthesis, were also reduced in ALS patients, suggesting a defective activation in the resolution programs of inflammation in ALS. We further analyze oxylipin concentration levels in plasma from ALS patients to detect correlations between these metabolites and some clinical parameters. Interestingly, we found that plasmatic levels of 13-HODE and 9-HODE positively correlate with disease duration, expressed as days since onset. In summary, we developed a method to analyze (oxy)lipidomics in ALS human plasma and found new profiles of metabolites and novel lipid derivatives with unknown biological activities as potential footprints of disease onset

Transcriptome Sequencing Reveals Wide Expression Reprogramming of Basal and Unknown Genes in Leptospira biflexa Biofilms

The genus Leptospira is composed of pathogenic and saprophytic spirochetes. Pathogenic Leptospira is the etiological agent of leptospirosis, a globally spread neglected disease. A key ecological feature of some pathogenic species is their ability to survive both within and outside the host. For most leptospires, the ability to persist outside the host is associated with biofilm formation, a most important bacterial strategy to face and overcome hostile environmental conditions. The architecture and biochemistry of leptospiral biofilms are rather well understood; however, the genetic program underpinning biofilm formation remains mostly unknown. In this work, we used the saprophyte Leptospira biflexa as a model organism to assess over- and underrepresented transcripts during the biofilm state, using transcriptome sequencing (RNA-seq) technology. Our results showed that some basal biological processes like DNA replication and cell division are downregulated in the mature biofilm. Additionally, we identified significant expression reprogramming for genes involved in motility, sugar/lipid metabolism, and iron scavenging, as well as for outer membrane-encoding genes. A careful manual annotation process allowed us to assign molecular functions to many previously uncharacterized genes that are probably involved in biofilm metabolism. We also provided evidence for the presence of small regulatory RNAs in this species. Finally, coexpression networks were reconstructed to pinpoint functionally related gene clusters that may explain how biofilm maintenance is regulated. Beyond elucidating some genetic aspects of biofilm formation, this work reveals a number of pathways whose functional dissection may impact our understanding of leptospiral biology, in particular how these organisms adapt to environmental changes.Agencia Nacional de Investigación e Innovació

Complete genome sequence of Campylobacter fetus subsp. venerealis biovar Intermedius, isolated from the prepuce of a bull

Campylobacter fetus subsp. venerealis is the causative agent of bovine genital campylobacteriosis, a sexually transmitted disease distributed worldwide. Campylobacter fetus subsp. venerealis biovar Intermedius strains differ in their biochemical behavior and are prevalent in some countries. We report the first genome sequence for this biovar, isolated from bull prepuce.Fil: Iraola, Gregorio. Instituto Pasteur de Montevideo; Uruguay. Facultad de Ciencias; UruguayFil: Pérez, Ruben. Facultad de Ciencias; UruguayFil: Naya, Hugo. Universidad de la República; Uruguay. Instituto Pasteur de Montevideo; Uruguay. Universidad de la República; UruguayFil: Paolicchi, Fernando Alberto. Universidad Nacional de Mar del Plata; Argentina. Instituto Nacional de Tecnología Agropecuaria; ArgentinaFil: Harris, David. Wellcome Trust; Reino UnidoFil: Lawley, Trevor D.. Wellcome Trust; Reino UnidoFil: Rego, Natalia. Instituto Pasteur de Montevideo; UruguayFil: Hernández, Martín. Facultad de Ciencias; UruguayFil: Calleros, Lucía. Facultad de Ciencias; UruguayFil: Carretto, Luis. Facultad de Ciencias; UruguayFil: Velilla, Alejandra Vanesa. Universidad Nacional de Mar del Plata; ArgentinaFil: Morsella, Claudia. Universidad Nacional de Mar del Plata; ArgentinaFil: Méndez, Alejandra. Universidad Nacional de Mar del Plata; ArgentinaFil: Gioffré, Andrea Karina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentin

Indigenous ancestry and admixture in the uruguayan population

The Amerindian group known as the Charrúas inhabited Uruguay at the timing of European colonial contact. Even though they were extinguished as an ethnic group as a result of a genocide, Charrúan heritage is part of the Uruguayan identity both culturally and genetically. While mitochondrial DNA studies have shown evidence of Amerindian ancestry in living Uruguayans, here we undertake whole-genome sequencing of 10 Uruguayan individuals with self-declared Charruan heritage. We detect chromosomal segments of Amerindian ancestry supporting the presence of indigenous genetic ancestry in living descendants. Specific haplotypes were found to be enriched in “Charrúas” and rare in the rest of the Amerindian groups studied. Some of these we interpret as the result of positive selection, as we identified selection signatures and they were located mostly within genes related to the infectivity of specific viruses. Historical records describe contacts of the Charrúas with other Amerindians, such as Guaraní, and patterns of genomic similarity observed here concur with genomic similarity between these groups. Less expected, we found a high genomic similarity of the Charrúas to Diaguita from Argentinian and Chile, which could be explained by geographically proximity. Finally, by fitting admixture models of Amerindian and European ancestry for the Uruguayan population, we were able to estimate the timing of the first pulse of admixture between European and Uruguayan indigenous peoples in approximately 1658 and the second migration pulse in 1683. Both dates roughly concurring with the Franciscan missions in 1662 and the foundation of the city of Colonia in 1680 by the Spanish.ANII: FSDA_1_2017_1_14364