Signatures Of Regions Research Articles

The topology and geometry of neural representations

A central question for neuroscience is how to characterize brain representations of perceptual and cognitive content. An ideal characterization should distinguish different functional regions with robustness to noise and idiosyncrasies of individual brains that do not correspond to computational differences. Previous studies have characterized brain representations by their representational geometry, which is defined by the representational dissimilarity matrix (RDM), a summary statistic that abstracts from the roles of individual neurons (or responses channels) and characterizes the discriminability of stimuli. Here, we explore a further step of abstraction: from the geometry to the topology of brain representations. We propose topological representational similarity analysis, an extension of representational similarity analysis that uses a family of geotopological summary statistics that generalizes the RDM to characterize the topology while de-emphasizing the geometry. We evaluate this family of statistics in terms of the sensitivity and specificity for model selection using both simulations and functional MRI (fMRI) data. In the simulations, the ground truth is a data-generating layer representation in a neural network model and the models are the same and other layers in different model instances (trained from different random seeds). In fMRI, the ground truth is a visual area and the models are the same and other areas measured in different subjects. Results show that topology-sensitive characterizations of population codes are robust to noise and interindividual variability and maintain excellent sensitivity to the unique representational signatures of different neural network layers and brain regions.

No evidence of active galactic nucleus features in the nuclei of Arp 220 from JWST/NIRSpec IFS

Context. Arp 220 is the nearest ultra-luminous infrared galaxy. It shows evidence of 100 pc scale molecular outflows that are likely connected with galaxy-scale outflows traced by ionised and neutral gas. The two highly obscured nuclei of Arp 220 are sites of intense star formation, with extreme (far-infrared based) star formation rate surface densities, ΣSFR ≳ 103 M⊙ yr−1 kpc−2. Despite extensive investigations that searched for active galactic nucleus (AGN) activity in the Arp 220 nuclei, direct evidence remains elusive. Aims. We present JWST/NIRSpec integral field spectroscopy (IFS) observations covering the 0.9 − 5.1 μm wavelength range of the innermost (5″ × 4″, i.e. 1.8 × 1.5 kpc) regions of Arp 220. The primary goal is to investigate the potential presence of AGN signatures in the nuclear regions by analysing the spectra extracted from circular apertures with a radius of 55 pc (0.15″) around each of the two nuclei. Methods. The analysis aims to identify highly ionised gas emission lines (with ionisation potential > 54 eV) and other spectral features indicative of AGN activity. Atomic and molecular gas kinematics were also taken into account to study the outflow signatures at < 60 pc scales. Results. We identify ∼70 atomic and ∼50 molecular emission lines in the nuclear spectra of Arp 220. We used recombination line ratios to measure optical extinctions in the range AV ∼ 11 − 14 mag. High-ionisation lines are not detected, except for the [Mg IV] line at 4.49 μm, which we interpret as due to shocks rather than to AGN ionisation. We identify broadening and multiple kinematic components in the H I and H2 lines caused by outflows and shocks, with velocities up to ∼550 km s−1. Significantly higher velocities (up to ∼900 km s−1) are detected in the off-nuclear regions, but they do not conclusively represent direct evidence for AGN activity. Broad-line region components are not detected in any permitted emission line within the NIRSpec wavelength range. Conclusions. Even with the unprecedented sensitivity of JWST/NIRSpec IFS, achieving an unambiguous identification or exclusion of the presence of an AGN in the Arp 220 system remains challenging because of its extreme dust obscuration.

Recent replenishment of aliphatic organics on Ceres from a large subsurface reservoir.

Ceres hosts notable aliphatic-organic concentrations, ranging from approximately 5 to >30 weight % in specific surface areas. The origins and persistence of these organics are under debate due to the intense aliphatic organic signature and radiation levels in Ceres' orbit, which would typically lead to their destruction, hindering detection. To investigate this, we conducted laboratory experiments to replicate how the signature of the organic-rich regions would degrade due to radiation. Our findings indicate a fast degradation rate, implying the exposure of buried organics within the past few million years. This degradation rate, coupled with observed quantities, implies that the aliphatics must be present in substantial quantities within the shallow subsurface. Our estimates suggest an initial aliphatic abundance 2 to 30 times greater than currently observed, surpassing significantly the levels found in carbonaceous chondrites, indicating either a significant concentration or remarkable purity.

Signatures of selection analyses reveal genomic differences among three heavy pig breeds that constitute the genetic backbone of a dry-cured ham production system

The Italian pig farming industry is unique in its focus on raising heavy pigs primarily for the production of high-quality dry-cured hams. These products require pigs to be slaughtered at a live weight of around 170 kg at 9 months of age. The primary breeds used in this system are Italian Duroc, Italian Landrace, and Italian Large White which are crossed to produce lines that meet standard requirements. Over the past four decades, selection and breeding programmes for these breeds have been subjected to distinct selective pressures to highlight the characteristics of each breed. In this study, we investigated the genome of these breeds by analysing high-density single nucleotide polymorphism data from over 9 000 pigs to scan for signatures of selection using four different methods, two within breeds and two across breeds. This allowed to identify the genomic regions that differentiate these breeds as well as any relevant genes and biological terms. On a global scale, we found that the Italian Duroc breed exhibited a higher genetic differentiation from the Italian Landrace and Italian Large White breeds, with a pairwise FST value of 0.20 compared with the 0.13 between Italian Landrace and Italian Large White. This may reflect either their different origins or the different breeding goals, which are more similar for the Italian Landrace and Italian Large White breeds. Despite these genetic differences at a global level, few signatures of selection regions reached complete fixation, possibly due to challenges in detecting selection linked to quantitative polygenic traits. The differences among the three breeds are confirmed by the low level of overlap in the regions detected. Genetic enrichment analyses of the three breeds revealed pathways and genes related to various productive traits associated with growth and fat deposition. This may indicate a common selection direction aimed at enhancing specific production traits, though different biological mechanisms are likely targeted by the same directional selection in these three breeds. Therefore, these genes may play a critical role in determining the distinctive characteristics of Italian Duroc, Italian Landrace, and Italian Large White, and potentially influence the traits in crossbred pigs derived from them. Overall, the insights gained from this study will contribute to understanding how directional selection has shaped the genome of these heavy pig breeds and to better address selection strategies aimed at enhancing the meat processing industry linked with dry-cured ham production chains.

Immune gene regulation is associated with age and environmental adversity in a nonhuman primate.

Phenotypic aging is ubiquitous across mammalian species, suggesting shared underlying mechanisms of aging. Aging is linked to molecular changes to DNA methylation and gene expression, and environmental factors, such as severe external challenges or adversities, can moderate these age-related changes. Yet, it remains unclear whether environmental adversities affect gene regulation via the same molecular pathways as chronological, or 'primary', aging. Investigating molecular aging in naturalistic animal populations can fill this gap by providing insight into shared molecular mechanisms of aging and the effects of a greater diversity of environmental adversities - particularly those that can be challenging to study in humans or laboratory organisms. Here, we characterised molecular aging - specifically, CpG methylation - in a sample of free-ranging rhesus macaques living off the coast of Puerto Rico (n samples = 571, n individuals = 499), which endured a major hurricane during our study. Age was associated with methylation at 78,661 sites (31% of all sites tested). Age-associated hypermethylation occurred more frequently in areas of active gene regulation, while hypomethylation was enriched in regions that show less activity in immune cells, suggesting these regions may become de-repressed in older individuals. Age-associated hypomethylation also co-occurred with increased chromatin accessibility while hypermethylation showed the opposite trend, hinting at a coordinated, multi-level loss of epigenetic stability during aging. We detected 32,048 CpG sites significantly associated with exposure to a hurricane, and these sites overlapped age-associated sites, most strongly in regulatory regions and most weakly in quiescent regions. Together, our results suggest that environmental adversity may contribute to aging-related molecular phenotypes in regions of active gene transcription, but that primary aging has specific signatures in non-regulatory regions.

Multi-omics analyses and machine learning prediction of oviductal responses in the presence of gametes and embryos.

The oviduct is the site of fertilization and preimplantation embryo development in mammals. Evidence suggests that gametes alter oviductal gene expression. To delineate the adaptive interactions between the oviduct and gamete/embryo, we performed a multi-omics characterization of oviductal tissues utilizing bulk RNA-sequencing (RNA-seq), single-cell RNA-sequencing (scRNA-seq), and proteomics collected from distal and proximal at various stages after mating in mice. We observed robust region-specific transcriptional signatures. Specifically, the presence of sperm induces genes involved in pro-inflammatory responses in the proximal region at 0.5 days post-coitus (dpc). Genes involved in inflammatory responses were produced specifically by secretory epithelial cells in the oviduct. At 1.5 and 2.5 dpc, genes involved in pyruvate and glycolysis were enriched in the proximal region, potentially providing metabolic support for developing embryos. Abundant proteins in the oviductal fluid were differentially observed between naturally fertilized and superovulated samples. RNA-seq data were used to identify transcription factors predicted to influence protein abundance in the proteomic data via a novel machine learning model based on transformers of integrating transcriptomics and proteomics data. The transformers identified influential transcription factors and correlated predictive protein expressions in alignment with the in vivo-derived data. In conclusion, our multi-omics characterization and subsequent in vivo confirmation of proteins/RNAs indicate that the oviduct is adaptive and responsive to the presence of sperm and embryos in a spatiotemporal manner.

The nucleosynthetic fingerprint of the outermost protoplanetary disk and early Solar System dynamics.

Knowledge of the nucleosynthetic isotope composition of the outermost protoplanetary disk is critical to understand the formation and early dynamical evolution of the Solar System. We report the discovery of outer disk material preserved in a pristine meteorite based on its chemical composition, organic-rich petrology, and 15N-rich, deuterium-rich, and 16O-poor isotope signatures. We infer that this outer disk material originated in the comet-forming region. The nucleosynthetic Fe, Mg, Si, and Cr compositions of this material reveal that, contrary to current belief, the isotope signature of the comet-forming region is ubiquitous among outer Solar System bodies, possibly reflecting an important planetary building block in the outer Solar System. This nucleosynthetic component represents fresh material added to the outer disk by late accretion streamers connected to the ambient molecular cloud. Our results show that most Solar System carbonaceous asteroids accreted material from the comet-forming region, a signature lacking in the terrestrial planet region.

Towards a neuroimaging biomarker for predicting cognitive behavioural therapy outcomes in treatment-naive depression: Preliminary findings

Clear prognostic indicators of cognitive behavioural therapy (CBT) are lacking for depression. This study aims to identify a biomarker that predicts CBT outcomes in depression. We developed a machine learning algorithm to predict post-CBT Hamilton Depression Rating Scale (HAMD) using pre-CBT regional homogeneity (ReHo). We examined transcriptomic signatures of regions with CBT-related ReHo changes. Twenty-five patients completed CBT and had increased ReHo in the dorsolateral prefrontal cortex (DLPFC) following CBT. Pre-CBT ReHo in left DLPFC was shown to be a predictor of post-HAMD scores. We identified left DLPFC ReHo as a neuroimaging biomarker for therapeutic effects of CBT in depression.

Automated imaging and identification of proteoforms directly from ovarian cancer tissue

The molecular identification of tissue proteoforms by top-down mass spectrometry (TDMS) is significantly limited by throughput and dynamic range. We introduce AutoPiMS, a single-ion MS based multiplexed workflow for top-down tandem MS (MS2) directly from tissue microenvironments in a semi-automated manner. AutoPiMS directly off human ovarian cancer sections allowed for MS2 identification of 73 proteoforms up to 54 kDa at a rate of <1 min per proteoform. AutoPiMS is directly interfaced with multifaceted proteoform imaging MS data modalities for the identification of proteoform signatures in tumor and stromal regions in ovarian cancer biopsies. From a total of ~1000 proteoforms detected by region-of-interest label-free quantitation, we discover 303 differential proteoforms in stroma versus tumor from the same patient. 14 of the top proteoform signatures are corroborated by MSI at 20 micron resolution including the differential localization of methylated forms of CRIP1, indicating the importance of proteoform-enabled spatial biology in ovarian cancer.

The Signature of the Northern Galactic Center Region in Low-velocity UV Absorption

The Galactic Center (GC) is surrounded by plasma lobes that extend up to ∼14 kpc above and below the plane. Until now, UV absorption studies of these lobes have only focused on high-velocity components (∣v LSR∣ > 100 km s−1) because low- and intermediate-velocity (LIV) components (∣v LSR∣ < 100 km s−1) are blended with foreground interstellar medium. To overcome this difficulty, we present a differential experiment to compare the LIV absorption between different structures within the GC region, including the Fermi Bubbles (FBs; seen in gamma rays), the eROSITA Bubbles (eBs; seen in X-rays), and the Loop I North Polar Spur (LNPS) association, an X-ray and radio feature within the northern eB. We use far-UV spectra from Hubble Space Telescope to measure LIV Si iv absorption in 61 active galactic nuclei sight lines, of which 21 pass through the FBs, 53 pass through the eBs, and 18 pass through the LNPS. We also compare our measurements to those in the literature from sight lines covering the disk–halo interface and circumgalactic medium (CGM). We find that the FBs and eBs have enhancements in measured columns of 0.22–0.29 dex in log. We also remove the contribution of a modeled disk and CGM component from the measured Si iv columns and find that the northern eB still retains a Si iv enhancement of 0.62 dex in log. A similar enhancement is not seen in the southern eB. Since a notable difference between the northern and southern eBs is the presence of the LNPS association in the nothern bubble, the northern eB enhancement may be caused by the LNPS.

Trade-off in genome turnover events leading to adaptive evolution of Microcystis aeruginosa species complex

BackgroundNumerous studies in the past have expanded our understanding of the genetic differences of global distributed cyanobacteria that originated around billions of years ago, however, unraveling how gene gain and loss drive the genetic evolution of cyanobacterial species, and the trade-off of these evolutionary forces are still the central but poorly understood issues.ResultsTo delineate the contribution of gene flow in mediating the hereditary differentiation and shaping the microbial evolution, a global genome-wide study of bloom-forming cyanobacterium, Microcystis aeruginosa species complex, provided robust evidence for genetic diversity, reflected by enormous variation in gene repertoire among various strains. Mathematical extrapolation showed an ‘open’ microbial pan-genome of M. aeruginosa species, since novel genes were predicted to be introduced after new genomes were sequenced. Identification of numerous horizontal gene transfer’s signatures in genome regions of interest suggested that genome expansion via transformation and phage-mediated transduction across bacterial lineage as an evolutionary route may contribute to the differentiation of Microcystis functions (e.g., carbohydrate metabolism, amino acid metabolism, and energy metabolism). Meanwhile, the selective loss of some dispensable genes at the cost of metabolic versatility is as a mean of adaptive evolution that has the potential to increase the biological fitness.ConclusionsNow that the recruitment of novel genes was accompanied by a parallel loss of some other ones, a trade-off in gene content may drive the divergent differentiation of M. aeruginosa genomes. Our study provides a genetic framework for the evolution of M. aeruginosa species and illustrates their possible evolutionary patterns.

Peritumoral Radiomics for Identification of Telomerase Reverse Transcriptase Promoter Mutation in Patients With Glioblastoma Based on Preoperative MRI.

Purpose: To evaluate the value of intra- and peritumoral deep learning (DL) features based on multi-parametric magnetic resonance imaging (MRI) for identifying telomerase reverse transcriptase (TERT) promoter mutation in glioblastoma (GBM). Methods: In this study, we included 229 patients with GBM who underwent preoperative MRI in two hospitals between November 2016 and September 2022. We used four 2D Convolutional Neural Networks (GoogLeNet, DenseNet121, VGG16, and MobileNetV3-Large) to extract intra- and peritumoral DL features. The Mann-Whitney U test, Pearson correlation analysis, least absolute shrinkage and selection operator, and logistic regression analysis were used for feature selection and construction of DL radiomics (DLR) signatures in different regions. These multi-parametric and multi-region signatures were combined to identify TERT promoter mutation. The area under the receiver operating characteristic curve (AUC) was used to evaluate the effects of the signatures. Results: The signatures based on the DL features from the peritumoral regions with expansion distances of 2mm, 8mm, and 10mm using the GoogLeNet architecture correlated with the optimal AUC values (test set: .823, .753, and .768) in the T2-weighted, T1-weighted contrast-enhanced, and T1-weighted images. Using the stacking fusion method, DLR with multi-parameter and multi-region fusion achieved the best discrimination with AUC values of .948 and .902 in the training and test sets, respectively. Conclusions: The radiomics model based on the fusion of multi-parameter MRI intra- and peritumoral DLR signatures may help to identify TERT promoter mutation in patients with GBM.

A general overview of the multifactorial adaptation to cold: biochemical mechanisms and strategies.

Cold environments are more frequent than people think. They include deep oceans, cold lakes, snow, permafrost, sea ice, glaciers, cold soils, cold deserts, caves, areas at elevations greater than 3000m, and also artificial refrigeration systems. These environments are inhabited by a diversity of eukaryotic and prokaryotic organisms that must adapt to the hard conditions imposed by cold. This adaptation is multifactorial and includes (i) sensing the cold, mainly through the modification of the liquid-crystalline membrane state, leading to the activation of a two-component system that transduce the signal; (ii) adapting the composition of membranes for proper functions mainly due to the production of double bonds in lipids, changes in hopanoid composition, and the inclusion of pigments; (iii) producing cold-adapted proteins, some of which show modifications in the composition of amino acids involved in stabilizing interactions and structural adaptations, e.g., enzymes with high catalytic efficiency; and (iv) producing ice-binding proteins and anti-freeze proteins, extracellular polysaccharides and compatible solutes that protect cells from intracellular and extracellular ice. However, organisms also respond by reprogramming their metabolism and specifically inducing cold-shock and cold-adaptation genes through strategies such as DNA supercoiling, distinctive signatures in promoter regions and/or the action of CSPs on mRNAs, among others. In this review, we describe the main findings about how organisms adapt to cold, with a focus in prokaryotes and linking the information with findings in eukaryotes.

Spatial proteomics landscape and immune signature analysis of renal sample of lupus nephritis based on laser-captured microsection

ObjectiveWe aimed to reveal a spatial proteomic and immune signature of kidney function regions in lupus nephritis (LN).Material and methodsThe laser capture microdissection (LCM) was used to isolate the glomerulus, tubules, and interstitial of the kidney from paraffin samples. The data-independent acquisition (DIA) method was used to collect proteomics data. The bioinformatic analysis was performed.ResultsA total of 49,658 peptides and 4056 proteins were quantitated. Our results first showed that a high proportion of activated NK cells, naive B cells, and neutrophils in the glomerulus, activated NK cells in interstitial, and resting NK cells were accumulated in tubules in LN. The immune-related function analysis of differential expression proteins in different regions indicated that the glomerulus and interstitial were major sites of immune disturbance and regulation connected with immune response activation. Furthermore, we identified 7, 8, and 9 hub genes in LN’s glomerulus, renal interstitial, and tubules. These hub genes were significantly correlated with the infiltration of immune cell subsets. We screened out ALB, CTSB, LCN2, A2M, CDC42, VIM, LTF, and CD14, which show higher performance as candidate biomarkers after correlation analysis with clinical indexes. The function within three regions of the kidney was analyzed. The differential expression proteins (DEGs) between interstitial and glomerulus were significantly enriched in the immune-related biological processes, and myeloid leukocyte-mediated immunity and cellular response to hormone stimulus. The DEGs between tubules and glomerulus were significantly enriched in cell activation and leukocyte-mediated immunity. While the DEGs between tubules and interstitial were enriched in response to lipid, antigen processing, and presentation of peptide antigen response to oxygen-containing compound, the results indicated a different function within kidney regions.ConclusionsCollectively, we revealed spatial proteomics and immune signature of LN kidney regions by combined using LCM and DIA.

Rheology of granular rafts.

Rheology of macroscopic particle-laden interfaces, called "granular rafts," has been experimentally studied in the simple shear configuration. The shear-stress relation obtained from a classical rheometer exhibits the same behavior as a Bingham fluid, and the viscosity diverges with the surface fraction according to evolutions similar to 2D suspensions. The velocity field of the particles that constitute the granular raft has been measured in the stationary state. These measurements reveal nonlocal rheology similar to dry granular materials. Close to the walls of the rheometer cell, one can observe regions of large local shear rate while in the middle of the cell a quasistatic zone exists. This flowing region, characteristic of granular matter, is described in the framework of an extended kinetic theory showing the evolution of the velocity profile with the imposed shear stress. Measuring the probability density functions of the instantaneous local shear rate, we provide evidence of a balance between positive and negative instantaneous local shear rate. This behavior is the signature of a quasistatic region inside the granular raft.

An integrative analysis of lipidomics and transcriptomics in various mouse brain regions in response to real-ambient PM2.5 exposure

Exposure to Fine particulate matter (PM2.5) has been associated with various neurological disorders. However, the underlying mechanisms of PM2.5-induced adverse effects on the brain are still not fully defined. Multi-omics analyses could offer novel insights into the mechanisms of PM2.5-induced brain dysfunction. In this study, a real-ambient PM2.5 exposure system was applied to male C57BL/6 mice for 16 weeks, and lipidomics and transcriptomics analysis were performed in four brain regions. The findings revealed that PM2.5 exposure led to 548, 283, 304, and 174 differentially expressed genes (DEGs), as well as 184, 89, 228, and 49 distinctive lipids in the hippocampus, striatum, cerebellum, and olfactory bulb, respectively. Additionally, in most brain regions, PM2.5-induced DEGs were mainly involved in neuroactive ligand-receptor interaction, cytokine-cytokine receptor interaction, and calcium signaling pathway, while PM2.5-altered lipidomic profile were primarily enriched in retrograde endocannabinoid signaling and biosynthesis of unsaturated fatty acids. Importantly, mRNA-lipid correlation networks revealed that PM2.5-altered lipids and DEGs were obviously enriched in pathways involving in bile acid biosynthesis, De novo fatty acid biosynthesis, and saturated fatty acids beta-oxidation in brain regions. Furthermore, multi-omics analyses revealed that the hippocampus was the most sensitive part to PM2.5 exposure. Specifically, dysregulation of Pla2g1b, Pla2g, Alox12, Alox15, and Gpx4 induced by PM2.5 were closely correlated to the disruption of alpha-linolenic acid, arachidonic acid and linoleic acid metabolism in the hippocampus. In summary, our findings highlight differential lipidomic and transcriptional signatures of various brain regions by real-ambient PM2.5 exposure, which will advance our understanding of potential mechanisms of PM2.5-induecd neurotoxicity.

Genomic inbreeding estimation, runs of homozygosity, and heterozygosity-enriched regions uncover signals of selection in the Quarter Horse racing line.

With the advent of genomics, significant progress has been made in the genetic improvement of livestock species, particularly through increased accuracy in predicting breeding values for selecting superior animals and the possibility of performing a high-resolution genetic scan throughout the genome of an individual. The main objectives of this study were to estimate the individual genomic inbreeding coefficient based on runs of homozygosity (FROH ), to identify and characterize runs of homozygosity and heterozygosity (ROH and ROHet, respectively; length and distribution) throughout the genome, and to map selection signatures in relevant chromosomal regions in the Quarter Horse racing line. A total of 336 animals registered with the Brazilian Association of Quarter Horse Breeders (ABQM) were genotyped. One hundred and twelve animals were genotyped using the Equine SNP50 BeadChip (Illumina, USA), with 54,602 single nucleotide polymorphisms (SNPs; 54K). The remaining 224 samples were genotyped using the Equine SNP70 BeadChip (Illumina, USA) with 65,157 SNPs (65K). To ensure data quality, we excluded animals with a call rate below 0.9. We also excluded SNPs located on non-autosomal chromosomes, as well as those with a call rate below 0.9 or a p-value below 1 × 10-5 for Hardy-Weinberg equilibrium. The results indicate moderate to high genomic inbreeding, with 46,594 ROH and 16,101 ROHet detected. In total, 30 and 14 candidate genes overlap with ROH and ROHet regions, respectively. The ROH islands showed genes linked to crucial biological processes, such as cell differentiation (CTBP1, WNT5B, and TMEM120B), regulation of glucose metabolic process (MAEA and NKX1-1), heme transport (PGRMC2), and negative regulation of calcium ion import (VDAC1). In ROHet, the islands showed genes related to respiratory capacity (OR7D19, OR7D4G, OR7D4E, and OR7D4J) and muscle repair (EGFR and BCL9). These findings could aid in selecting animals with greater regenerative capacity and developing treatments for muscle disorders in the QH breed. This study serves as a foundation for future research on equine breeds. It can contribute to developing reproductive strategies in animal breeding programs to improve and preserve the Quarter Horse breed.

Nuclear activity in z &amp;lt; 0.3 QSO 2’s mainly triggered by galaxy mergers

ABSTRACT We investigate the role of the close environment on the nuclear activity of a sample of 436 nearby (z &amp;lt; 0.3) QSO 2’s – selected from SDSS-III spectra, via comparison of their environment and interaction parameters with those of a control sample of 1308 galaxies. We have used the corresponding SDSS images to obtain the number of neighbour galaxies N, tidal strength parameter Q and asymmetry parameters. We find a small excess of N in the QSOs compared to its three controls, and no difference in Q. The main difference is an excess of asymmetry in the QSOs hosts, which is almost twice that of the control galaxies. This difference is not due to the hosts’ morphology, since there is no difference in their Galaxy Zoo classifications. HST images of two highly asymmetric QSO 2 hosts of our sample show that both sources have a close companion (at projected separations ∼ 5 kpc), which we thus conclude is the cause of the observed asymmetry in the lower resolution SDSS images. The mean projected radius of the controls is 〈r〉 = 8.53 ± 0.06 kpc, while that of the QSO hosts is 〈r〉 = 9.39 ± 0.12 kpc, supporting the presence of interaction signatures in the outer regions of the QSO hosts. Our results favour a scenario in which nuclear activity in QSO 2’s is triggered by close galaxy interactions – when the distance between the host and companion is of the order of the galaxy radius, implying that they are already in the process of merger.

Runs of homozygosity and signatures of selection for number of oocytes and embryos in the Gir Indicine cattle.

Runs of homozygosity (ROH) and signatures of selection are the results of selection processes in livestock species that have been shown to affect several traits in cattle. The aim of the current work was to verify the profile of ROH and inbreeding depression in the number of total (TO) and viable oocytes (VO) and the number of embryos (EMBR) in Gir Indicine cattle. In addition, we aim to identify signatures of selection, genes, and enriched regions between Gir subpopulations sorted by breeding value for these traits. The genotype file contained 2093 animals and 420,718 SNP markers. Breeding values used to sort Gir animals were previously obtained. ROH and signature of selection analyses were performed using PLINK software, followed by ROH-based (FROH) and pedigree-based inbreeding (Fped) and a search for genes and their functions. An average of 50 ± 8.59 ROHs were found per animal. ROHs were separated into classes according to size, ranging from 1 to 2Mb (ROH1-2Mb: 58.17%), representing ancient inbreeding, ROH2-4Mb (22.74%), ROH4-8Mb (11.34%), ROH8-16Mb (5.51%), and ROH>16Mb (2.24%). Combining our results, we conclude that the increase in general FROH and Fped significantly decreases TO and VO; however, in different chromosomes traits can increase or decrease with FROH. In the analysis for signatures of selection, we identified 15 genes from 47 significant genomic regions, indicating differences in populations with high and low breeding value for the three traits.

Whole Genome Sequencing Provides Information on the Genomic Architecture and Diversity of Cultivated Gilthead Seabream (Sparus aurata) Broodstock Nuclei.

The gilthead seabream (Sparus aurata) is a species of relevance for the Mediterranean aquaculture industry. Despite the advancement of genetic tools for the species, breeding programs still do not often include genomics. In this study, we designed a genomic strategy to identify signatures of selection and genomic regions of high differentiation among populations of farmed fish stocks. A comparative DNA pooling sequencing approach was applied to identify signatures of selection in gilthead seabream from the same hatchery and from different nuclei that had not been subjected to genetic selection. Identified genomic regions were further investigated to detect SNPs with predicted high impact. The analyses underlined major genomic differences in the proportion of fixed alleles among the investigated nuclei. Some of these differences highlighted genomic regions, including genes involved in general metabolism and development already detected in QTL for growth, size, skeletal deformity, and adaptation to variation of oxygen levels in other teleosts. The obtained results pointed out the need to control the genetic effect of breeding programs in this species to avoid the reduction of genetic variability within populations and the increase in inbreeding level that, in turn, might lead to an increased frequency of alleles with deleterious effects.