A new chromosome-assigned Mongolian gerbil genome allows characterization of complete centromeres and a fully heterochromatic chromosome

This is the final version. Available on open access from Oxford University Press via the DOI in this recordData Availability: All sequencing data and the genome are available under SRA BioProject PRJNA397533. Specific accession numbers can be found in supplementary material S1, Supplementary Material online. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JAODIK000000000. The version described in this paper is version JAODIK010000000. The genetic map, a vcf of the genetic markers and their genotypes in the mapping panel, the gff of the gene annotations, the gff of the repetitive element annotations, and “Supplemental_Material 3_codebase.zip”, can be found in the Dryad repository here: Brekke, Thomas D. (2022), Data for “The origin of a new chromosome in gerbils”, Dryad, Dataset, https://doi.org/10.5061/dryad.1vhhmgqws.Chromosome-scale genome assemblies based on ultralong-read sequencing technologies are able to illuminate previously intractable aspects of genome biology such as fine-scale centromere structure and large-scale variation in genome features such as heterochromatin, GC content, recombination rate, and gene content. We present here a new chromosome-scale genome of the Mongolian gerbil (Meriones unguiculatus), which includes the complete sequence of all centromeres. Gerbils are thus the one of the first vertebrates to have their centromeres completely sequenced. Gerbil centromeres are composed of four different repeats of length 6, 37, 127, or 1,747 bp, which occur in simple alternating arrays and span 1-6 Mb. Gerbil genomes have both an extensive set of GC-rich genes and chromosomes strikingly enriched for constitutive heterochromatin. We sought to determine if there was a link between these two phenomena and found that the two heterochromatic chromosomes of the Mongolian gerbil have distinct underpinnings: Chromosome 5 has a large block of intraarm heterochromatin as the result of a massive expansion of centromeric repeats, while chromosome 13 is comprised of extremely large (>150 kb) repeated sequences. In addition to characterizing centromeres, our results demonstrate the importance of including karyotypic features such as chromosome number and the locations of centromeres in the interpretation of genome sequence data and highlight novel patterns involved in the evolution of chromosomes.Leverhulme TrustNatural Environment Research Council (NERC)Ministerio de Economía y Competitivida

Symptoms associated with victimization in patients with schizophrenia and related disorders

Background: Patients with psychoses have an increased risk of becoming victims of violence. Previous studies have suggested that higher symptom levels are associated with a raised risk of becoming a victim of physical violence. There has been, however, no evidence on the type of symptoms that are linked with an increased risk of recent victimization. Methods: Data was taken from two studies on involuntarily admitted patients, one national study in England and an international one in six other European countries. In the week following admission, trained interviewers asked patients whether they had been victims of physical violence in the year prior to admission, and assessed symptoms on the Brief Psychiatric Rating Scale (BPRS). Only patients with a diagnosis of schizophrenia or related disorders (ICD-10 F20–29) were included in the analysis which was conducted separately for the two samples. Symptom levels assessed on the BPRS subscales were tested as predictors of victimization. Univariable and multivariable logistic regression models were fitted to estimate adjusted odds ratios. Results: Data from 383 patients in the English sample and 543 patients in the European sample was analysed. Rates of victimization were 37.8% and 28.0% respectively. In multivariable models, the BPRS manic subscale was significantly associated with victimization in both samples. Conclusions: Higher levels of manic symptoms indicate a raised risk of being a victim of violence in involuntary patients with schizophrenia and related disorders. This might be explained by higher activity levels, impaired judgement or poorer self-control in patients with manic symptoms. Such symptoms should be specifically considered in risk assessments

Multi-Instrument Observations of a Geomagnetic Storm and its Effects on the Arctic Ionosphere: A Case Study of the 19 February 2014 Storm:Observations of a Geomagnetic Storm

We present a multiinstrumented approach for the analysis of the Arctic ionosphere during the 19 February 2014 highly complex, multiphase geomagnetic storm, which had the largest impact on the disturbance storm-time index that year. The geomagnetic storm was the result of two powerful Earth-directed coronal mass ejections (CMEs). It produced a strong long lasting negative storm phase over Greenland with a dominant energy input in the polar cap. We employed global navigation satellite system (GNSS) networks, geomagnetic observatories, and a specific ionosonde station in Greenland. We complemented the approach with spaceborne measurements in order to map the state and variability of the Arctic ionosphere. In situ observations from the Canadian CASSIOPE (CAScade, Smallsat and IOnospheric Polar Explorer) satellite's ion mass spectrometer were used to derive ion flow data from the polar cap topside ionosphere during the event. Our research specifically found that (1) thermospheric O/N2 measurements demonstrated significantly lower values over the Greenland sector than prior to the storm time. (2) An increased ion flow in the topside ionosphere was observed during the negative storm phase. (3) Negative storm phase was a direct consequence of energy input into the polar cap. (4) Polar patch formation was significantly decreased during the negative storm phase. This paper addresses the physical processes that can be responsible for this ionospheric storm development in the northern high latitudes. We conclude that ionospheric heating due to the CME's energy input caused changes in the polar atmosphere resulting in Ne upwelling, which was the major factor in high-latitude ionosphere dynamics for this storm. This research was originally published in Radio Science. © 2017 Wile

Fluctuating optimum and temporally variable selection on breeding date in birds and mammals

International audienceTemporal variation in natural selection is predicted to strongly impact the evolution and demography of natural populations, with consequences for the rate of adaptation, evolution of plasticity, and extinction risk. Most of the theory underlying these predictions assumes a moving optimum phenotype, with predictions expressed in terms of the temporal variance and autocorrelation of this optimum. However, empirical studies seldom estimate patterns of fluctuations of an optimum phenotype, precluding further progress in connecting theory with observations. To bridge this gap, we assess the evidence for temporal variation in selection on breeding date by modeling a fitness function with a fluctuating optimum, across 39 populations of 21 wild animals, one of the largest compilations of long-term datasets with individual measurements of trait and fitness components. We find compelling evidence for fluctuations in the fitness function, causing temporal variation in the magnitude, but not the direction of selection. However, fluctuations of the optimum phenotype need not directly translate into variation in selection gradients, because their impact can be buffered by partial tracking of the optimum by the mean phenotype. Analyzing individuals that reproduce in consecutive years, we find that plastic changes track movements of the optimum phenotype across years, especially in bird species, reducing temporal variation in directional selection. This suggests that phenological plasticity has evolved to cope with fluctuations in the optimum, despite their currently modest contribution to variation in selection

Genetic variance in fitness indicates rapid contemporary adaptive evolution in wild animals

Funding: Hoge Veluwe great tits: the NIOO-KNAW, ERC, and numerous funding agencies; Wytham great tits: Biotechnology and Biological Sciences Research Council, ERC, and the UK Natural Environment Research Council (NERC).The rate of adaptive evolution, the contribution of selection to genetic changes that increase mean fitness, is determined by the additive genetic variance in individual relative fitness. To date, there are few robust estimates of this parameter for natural populations, and it is therefore unclear whether adaptive evolution can play a meaningful role in short-term population dynamics. We developed and applied quantitative genetic methods to long-term datasets from 19 wild bird and mammal populations and found that, while estimates vary between populations, additive genetic variance in relative fitness is often substantial and, on average, twice that of previous estimates. We show that these rates of contemporary adaptive evolution can affect population dynamics and hence that natural selection has the potential to partly mitigate effects of current environmental change.PostprintPeer reviewe

Molecular imaging of rheumatoid arthritis by radiolabelled monoclonal antibodies: new imaging strategies to guide molecular therapies

The closing of the last century opened a wide variety of approaches for inflammation imaging and treatment of patients with rheumatoid arthritis (RA). The introduction of biological therapies for the management of RA started a revolution in the therapeutic armamentarium with the development of several novel monoclonal antibodies (mAbs), which can be murine, chimeric, humanised and fully human antibodies. Monoclonal antibodies specifically bind to their target, which could be adhesion molecules, activation markers, antigens or receptors, to interfere with specific inflammation pathways at the molecular level, leading to immune-modulation of the underlying pathogenic process. These new generation of mAbs can also be radiolabelled by using direct or indirect method, with a variety of nuclides, depending upon the specific diagnostic application. For studying rheumatoid arthritis patients, several monoclonal antibodies and their fragments, including anti-TNF-α, anti-CD20, anti-CD3, anti-CD4 and anti-E-selectin antibody, have been radiolabelled mainly with 99mTc or 111In. Scintigraphy with these radiolabelled antibodies may offer an exciting possibility for the study of RA patients and holds two types of information: (1) it allows better staging of the disease and diagnosis of the state of activity by early detection of inflamed joints that might be difficult to assess; (2) it might provide a possibility to perform ‘evidence-based biological therapy’ of arthritis with a view to assessing whether an antibody will localise in an inflamed joint before using the same unlabelled antibody therapeutically. This might prove particularly important for the selection of patients to be treated since biological therapies can be associated with severe side-effects and are considerably expensive. This article reviews the use of radiolabelled mAbs in the study of RA with particular emphasis on the use of different radiolabelled monoclonal antibodies for therapy decision-making and follow-up

Valence QCD: Connecting QCD to the Quark Model

A valence QCD theory is developed to study the valence quark properties of hadrons. To keep only the valence degrees of freedom, the pair creation through the Z graphs is deleted in the connected insertions; whereas, the sea quarks are eliminated in the disconnected insertions. This is achieved with a new ``valence QCD'' lagrangian where the action in the time direction is modified so that the particle and antiparticle decouple. The theory has the vector and axial $U(2N_F)$ symmetry in the particle-antiparticle space. Through lattice simulation, it appears that this is dynamically broken down to $U_q(N_F) \times U_{\bar{q}}(N_F)$. Furthermore, the lattice simulation reveals spin degeneracy in the hadron masses and SU(6) relations in the ratios of $F_A/D_A, F_S/D_S$, and $\mu^n/\mu^p$. This leads to an approximate $U_q(2N_F) \times U_{\bar{q}}(2N_F)$ symmetry which is the basis for the valence quark model. We find that the masses of N, $\Delta, \rho, \pi, a_1$, and $a_0$ all drop precipitously compared to their counterparts in the quenched QCD calculation. This is interpreted as due to the disapperance of the `constituent' quark mass which is dynamically generated through tadpole diagrams. Form the near degeneracy between N and $\Delta$ for the quark masses we have studied (ranging from one to four times the strange mass), we conclude that the origin of the hyper-fine splitting in the baryon is largely attibuted to the Goldstone boson exchanges between the quarks. These are the consequences of lacking chiral symmetry in valence QCD. We discuss its implication on the models of hadrons.Comment: 68 pages, LaTex, 36 postscript figures including 1 color figur