Chromosomal instability in Afrotheria: fragile sites, evolutionary breakpoints and phylogenetic inference from genome sequence assemblies

Background: Extant placental mammals are divided into four major clades (Laurasiatheria, Supraprimates, Xenarthra and Afrotheria). Given that Afrotheria is generally thought to root the eutherian tree in phylogenetic analysis of large nuclear gene data sets, the study of the organization of the genomes of afrotherian species provides new insights into the dynamics of mammalian chromosomal evolution. Here we test if there are chromosomal bands with a high tendency to break and reorganize in Afrotheria, and by analyzing the expression of aphidicolin-induced common fragile sites in three afrotherian species, whether these are coincidental with recognized evolutionary breakpoints. Results: We described 29 fragile sites in the aardvark (OAF) genome, 27 in the golden mole (CAS), and 35 in the elephant-shrew (EED) genome. We show that fragile sites are conserved among afrotherian species and these are correlated with evolutionary breakpoints when compared to the human (HSA) genome. Inddition, by computationally scanning the newly released opossum (Monodelphis domestica) and chicken sequence assemblies for use as outgroups to Placentalia, we validate the HSA 3/21/5 chromosomal synteny as a rare genomic change that defines the monophyly of this ancient African clade of mammals. On the other hand, support for HSA 1/19p, which is also thought to underpin Afrotheria, is currently ambiguous. Conclusion: We provide evidence that (i) the evolutionary breakpoints that characterise human syntenies detected in the basal Afrotheria correspond at the chromosomal band level with fragile sites, (ii) that HSA 3p/21 was in the amniote ancestor (i.e., common to turtles, lepidosaurs, crocodilians, birds and mammals) and was subsequently disrupted in the lineage leading to marsupials. Its expansion to include HSA 5 in Afrotheria is unique and (iii) that its fragmentation to HSA 3p/21 + HSA 5/21 in elephant and manatee was due to a fission within HSA 21 that is probably shared by all Paenungulata

A comparison study on criteria to select the most adequate weighting matrix

The practice of spatial econometrics revolves around a weighting matrix, which is often supplied by the user on previous knowledge. This is the so-called W issue. Probably, the aprioristic approach is not the best solution although, presently, there are few alternatives for the user. Our contribution focuses on the problem of selecting aWmatrix from among a finite set of matrices, all of them considered appropriate for the case. We develop a new and simple method based on the entropy corresponding to the distribution of probability estimated for the data. Other alternatives, which are common in current applied work, are also reviewed. The paper includes a large study of Monte Carlo to calibrate the effectiveness of our approach compared to others. A well-known case study is also included

The importance of non‐diffusional factors in determining photosynthesis of two contrasting quinoa ecotypes (Chenopodium quinoa willd.) subjected to salinity conditions

The broad distribution of quinoa in saline and non‐saline environments is reflected in variations in the photosynthesis‐associated mechanisms of different ecotypes. The aim of this study was to characterize the photosynthetic response to high salinity (0.4 M NaCl) of two contrasting Chilean genotypes, Amarilla (salt‐tolerant, salares ecotype) and Hueque (salt‐sensitive, coastal ecotype). Our results show that saline stress induced a significant decrease in the K+/Na+ ratio in roots and an increase in glycine betaine in leaves, particularly in the sensitive genotype (Hueque). Measurement of the photosynthesis‐related parameters showed that maximum CO2 assimilation (Amax) in control plants was comparable between genotypes (ca. 9–10 μmol CO2 m−2 s−1). However, salt treatment produced different responses, with Amax values decreasing by 65.1% in the sensitive ecotype and 37.7% in the tolerant one. Although both genotypes maintained mesophyll conductance when stomatal restrictions were removed, the biochemical components of Amarilla were impaired to a lesser extent under salt stress conditions: for example, the maximum rate of ribulose‐1,5‐ bisphosphate carboxylase/oxygenase (RubisCO; Vcmax) was not as affected in Amarilla, revealing that this enzyme has a higher affinity for its substrate in this genotype and, thus, a better carboxylation efficiency. The present results show that the higher salinity tolerance of Amarilla was also due to its ability to control non‐diffusional components, indicating its superior photosynthetic capacity compared to Hueque, particularly under salt stress conditions

Is mammalian chromosomal evolution driven by regions of genome fragility?

BACKGROUND: A fundamental question in comparative genomics concerns the identification of mechanisms that underpin chromosomal change. In an attempt to shed light on the dynamics of mammalian genome evolution, we analyzed the distribution of syntenic blocks, evolutionary breakpoint regions, and evolutionary breakpoints taken from public databases available for seven eutherian species (mouse, rat, cattle, dog, pig, cat, and horse) and the chicken, and examined these for correspondence with human fragile sites and tandem repeats. RESULTS: Our results confirm previous investigations that showed the presence of chromosomal regions in the human genome that have been repeatedly used as illustrated by a high breakpoint accumulation in certain chromosomes and chromosomal bands. We show, however, that there is a striking correspondence between fragile site location, the positions of evolutionary breakpoints, and the distribution of tandem repeats throughout the human genome, which similarly reflect a non-uniform pattern of occurrence. CONCLUSION: These observations provide further evidence that certain chromosomal regions in the human genome have been repeatedly used in the evolutionary process. As a consequence, the genome is a composite of fragile regions prone to reorganization that have been conserved in different lineages, and genomic tracts that do not exhibit the same levels of evolutionary plasticity

Modelling the behaviour of microbulk Micromegas in Xenon/trimethylamine gas

We model the response of a state of the art micro-hole single-stage charge amplication device (`microbulk' Micromegas) in a gaseous atmosphere consisting of Xenon/trimethylamine at various concentrations and pressures. The amplifying structure, made with photo-lithographic techniques similar to those followed in the fabrication of gas electron multipliers (GEMs), consisted of a 100 um-side equilateral-triangle pattern with 50 um-diameter holes placed at its vertexes. Once the primary electrons are guided into the holes by virtue of an optimized field configuration, avalanches develop along the 50 um-height channels etched out of the original doubly copper-clad polyimide foil. In order to properly account for the strong field gradients at the holes' entrance as well as for the fluctuations of the avalanche process (that ultimately determine the achievable energy resolution), we abandoned the hydrodynamic framework, resorting to a purely microscopic description of the electron trajectories as obtained from elementary cross-sections. We show that achieving a satisfactory description needs additional assumptions about atom-molecule (Penning) transfer reactions and charge recombination to be made

Negative serology of Fasciola hepatica infection in patients with liver cancer in Peru: A preliminary report

Introduction: The etiology of several hepatocellular carcinoma (HCC) cases remains largely unknown. Although Fasciola hepatica has been associated with liver fibrosis in Latin America, it has not yet been associated with HCC. This study aimed to determine the existence of specific IgG antibodies against F. hepatica in the serum samples of HCC patients. Methods: In total, 13 serum samples from 13 HCC patients were screened using Fas2-ELISA. Results: Fas2-ELISA demonstrated negative results in all HCC patients included in this study. Conclusions: The pre-existence of F. hepatica infection in HCC patients needs to be further investigated in epidemiological and experimental studies

Gaseous time projection chambers for rare event detection: Results from the T-REX project. II. Dark matter

As part of the T-REX project, a number of R&D and prototyping activities have been carried out during the last years to explore the applicability of Micromegas-read gaseous TPCs in rare event searches like double beta decay (DBD), axion research and low-mass WIMP searches. While in the companion paper we focus on DBD, in this paper we focus on the results regarding the search for dark matter candidates, both axions and WIMPs. Small ultra-low background Micromegas detectors are used to image the x-ray signal expected in axion helioscopes like CAST at CERN. Background levels as low as $0.8\times 10^{-6}$ c keV$^{-1}$cm$^{-2}$s$^{-1}$ have already been achieved in CAST while values down to $\sim10^{-7}$ c keV$^{-1}$cm$^{-2}$s$^{-1}$ have been obtained in a test bench placed underground in the Laboratorio Subterr\'aneo de Canfranc. Prospects to consolidate and further reduce these values down to $\sim10^{-8}$ c keV$^{-1}$cm$^{-2}$s$^{-1}$will be described. Such detectors, placed at the focal point of x-ray telescopes in the future IAXO experiment, would allow for 10$^5$ better signal-to-noise ratio than CAST, and search for solar axions with $g_{a\gamma}$ down to few 10$^{12}$ GeV$^{-1}$, well into unexplored axion parameter space. In addition, a scaled-up version of these TPCs, properly shielded and placed underground, can be competitive in the search for low-mass WIMPs. The TREX-DM prototype, with $\sim$0.300 kg of Ar at 10 bar, or alternatively $\sim$0.160 kg of Ne at 10 bar, and energy threshold well below 1 keV, has been built to test this concept. We will describe the main technical solutions developed, as well as the results from the commissioning phase on surface. The anticipated sensitivity of this technique might reach $\sim10^{-44}$ cm$^2$ for low mass ($<10$ GeV) WIMPs, well beyond current experimental limits in this mass range.Comment: Published in JCAP. New version with erratum incorporated (new figure 14

D1S80 Single-Locus Discrimination Among African Populations

The highly polymorphic D1S80 locus has no known genetic function. However, this variable number of tandem repeats (VNTR) locus has been highly valuable in forensic identification. In this study we report the allele and genotype frequencies of five African populations (Benin, Cameroon, Egypt, Kenya, and Rwanda), which can be used as databases to help characterize populations and identify individuals. The allele frequencies were used to infer genetic associations through phylogenetic, principal component, and G test statistical analyses. Compliance with Hardy-Weinberg equilibrium expectations was determined as were FST estimates, theta p values, and power of discrimination assessment for each population. Our analyses of 28 additional populations demonstrate that the D1S80 locus alone can be used to discriminate geographic and ethnic groups. We have generated databases useful for human identification and phylogenetic studies

Star-forming galaxies versus low- and high-excitation radio AGN in the VLA-COSMOS 3GHz Large Project

We study the composition of the faint radio population selected from the VLA-COSMOS 3GHz Large Project, a radio continuum survey performed at 10 cm wavelength. The survey covers the full 2 square degree COSMOS field with mean $rms\sim2.3$ $\mu$Jy/beam, cataloging 10,899 source components above $5\times rms$. By combining these radio data with UltraVISTA, optical, near-infrared, and Spitzer/IRAC mid-infrared data, as well as X-ray data from the Chandra Legacy, and Chandra COSMOS surveys, we gain insight into the emission mechanisms within our radio sources out to redshifts of $z\sim5$. From these emission characteristics we classify our souces as star forming galaxies or AGN. Using their multi-wavelength properties we further separate the AGN into sub-samples dominated by radiatively efficient and inefficient AGN, often referred to as high- and low-excitation emission line AGN. We compare our method with other results based on fitting of the sources' spectral energy distributions using both galaxy and AGN spectral models, and those based on the infrared-radio correlation. We study the fractional contributions of these sub-populations down to radio flux levels of $\sim$10 $\mu$Jy. We find that at 3 GHz flux densities above $\sim$400 $\mu$Jy quiescent, red galaxies, consistent with the low-excitation radio AGN class constitute the dominant fraction. Below densities of $\sim$200 $\mu$Jy star-forming galaxies begin to constitute the largest fraction, followed by the low-excitation, and X-ray- and IR-identified high-excitation radio AGN.Comment: 7 pages, 3 figures, The many facets of extragalactic radio surveys: towards new scientific challenges, Bologna 20-23 October 201