SOME VIEWS OF EXTENSION WORK IN PUBLIC AFFAIRS

Teaching/Communication/Extension/Profession,

Afrotheria genome; overestimation of genome size and distinct chromosome GC content revealed by flow karyotyping

AbstractAfrotheria genome size is reported to be over 50% larger than that of human, but we show that this is a gross overestimate. Although genome sequencing in Afrotheria is not complete, extensive homology with human has been revealed by chromosome painting. We provide new data on chromosome size and GC content in four Afrotherian species using flow karyotyping. Genome sizes are 4.13Gb in aardvark, 4.01Gb in African elephant, 3.69Gb in golden mole and 3.31Gb in manatee, whereas published results show a mean of 5.18Gb for Afrotheria. Genome GC content shows a negative correlation with size, indicating that this is due to differences in the amount of AT-rich sequences. Low genome GC content and small variance in chromosome GC content are characteristic of aardvark and elephant and may be associated with the high degree of conserved synteny, suggesting that these are features of the Afrotherian ancestral genome

The UDF05 follow-up of the Hubble Ultra Deep Field. I. The faint-end slope of the Lyman Break Galaxy Population at z ~ 5

We present the UDF05 HST program, which consists of three disjoint fields—NICP12, NICP34, plus the HUDF—with deep ACS (F606W, F775W, and F850LP) and NICMOS (F110W and F160W) imaging. Here we use the ACS data for the NICP12 and HUDF fields to implement a (V − i) − (i − z) selection criterion that allows us to identify a sample of 101 (133) z ~ 5 Lyman break galaxies (LBGs) down to z850 = 28.5 (29.25) mag in NICP12 (HUDF). We construct the rest-frame 1400 Å LBG luminosity function (LF) over the range M1400 = [ − 21.4, − 17.1] , i.e. down to ~0.04L* at z ~ 5, and use Subaru Deep Field results (Yoshida et al. 2006) to constrain our LF at the bright end (M1400 ≥ − 22.2). We show that (1) different assumptions regarding the LBG SED distribution, dust properties, and intergalactic absorption result in a 25% variation in the number density of LBGs at z ~ 5; (2) under consistent assumptions for dust properties and intergalactic absorption, the HUDF is ~30% underdense in z ~ 5 LBGs relative to the NICP12 field, a variation which is well explained by cosmic variance; and (3) the faint-end slope of the LF does not depend on the input parameters, and has a value of α ~ − 1.6, similar to the faint-end slope of the LF of z ~ 3 and z ~ 6 LBGs. Our study therefore supports no variation in the faint end of the LBG LF over the whole redshift range z ~ 3 to z ~ 6. Based on a comparison with semianalytical models, we speculate that the z ~ 5 LBGs might have a top-heavy IMF

Use of materials in nest construction by Pied Flycatchers Ficedula hypoleuca reflects localised habitat and geographical location.

Capsule Pied Flycatchers use different materials to construct their nests according to localised habitat and geographical location. Aims This study tested the hypotheses that birds would use the leaves they normally encountered within their breeding territories and that nest composition varied between geographical locations. Methods In Lancashire, Pied Flycatcher nests were collected from nestboxes built in locations dominated by different tree species and were deconstructed to determine which materials were used. Results Materials found in nests generally reflected the localised habitat around the nest rather than showing evidence of active collection from distant sources of material. Nests from Lancashire were significantly different in composition when compared with published data for nests from north Wales and central Spain. The use of moss was dominated by the use of one species in all but two nests. Conclusion Pied Flycatchers exhibit plasticity in nest construction behaviour because they were opportunistic in their choice of most nesting materials although they may be selective in their choice of moss

Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity

Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia and is now grown in tropical regions worldwide. Here we provide a high-quality genome assembly for cassava with improved contiguity, linkage, and completeness; almost 97% of genes are anchored to chromosomes. We find that paleotetraploidy in cassava is shared with the related rubber tree Hevea, providing a resource for comparative studies. We also sequence a global collection of 58 Manihot accessions, including cultivated and wild cassava accessions and related species such as Ceará or India rubber (M. glaziovii), and genotype 268 African cassava varieties. We find widespread interspecific admixture, and detect the genetic signature of past cassava breeding programs. As a clonally propagated crop, cassava is especially vulnerable to pathogens and abiotic stresses. This genomic resource will inform future genome-enabled breeding efforts to improve this staple crop

DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity

DNA replication timing and three-dimensional (3D) genome organization are associated with distinct epigenome patterns across large domains. However, whether alterations in the epigenome, in particular cancer-related DNA hypomethylation, affects higher-order levels of genome architecture is still unclear. Here, using Repli-Seq, single-cell Repli-Seq, and Hi-C, we show that genome-wide methylation loss is associated with both concordant loss of replication timing precision and deregulation of 3D genome organization. Notably, we find distinct disruption in 3D genome compartmentalization, striking gains in cell-to-cell replication timing heterogeneity and loss of allelic replication timing in cancer hypomethylation models, potentially through the gene deregulation of DNA replication and genome organization pathways. Finally, we identify ectopic H3K4me3-H3K9me3 domains from across large hypomethylated domains, where late replication is maintained, which we purport serves to protect against catastrophic genome reorganization and aberrant gene transcription. Our results highlight a potential role for the methylome in the maintenance of 3D genome regulation

Crises and collective socio-economic phenomena: simple models and challenges

Financial and economic history is strewn with bubbles and crashes, booms and busts, crises and upheavals of all sorts. Understanding the origin of these events is arguably one of the most important problems in economic theory. In this paper, we review recent efforts to include heterogeneities and interactions in models of decision. We argue that the Random Field Ising model (RFIM) indeed provides a unifying framework to account for many collective socio-economic phenomena that lead to sudden ruptures and crises. We discuss different models that can capture potentially destabilising self-referential feedback loops, induced either by herding, i.e. reference to peers, or trending, i.e. reference to the past, and account for some of the phenomenology missing in the standard models. We discuss some empirically testable predictions of these models, for example robust signatures of RFIM-like herding effects, or the logarithmic decay of spatial correlations of voting patterns. One of the most striking result, inspired by statistical physics methods, is that Adam Smith's invisible hand can badly fail at solving simple coordination problems. We also insist on the issue of time-scales, that can be extremely long in some cases, and prevent socially optimal equilibria to be reached. As a theoretical challenge, the study of so-called "detailed-balance" violating decision rules is needed to decide whether conclusions based on current models (that all assume detailed-balance) are indeed robust and generic.Comment: Review paper accepted for a special issue of J Stat Phys; several minor improvements along reviewers' comment

3D MHD Coronal Oscillations About a Magnetic Null Point: Application of WKB Theory

This paper is a demonstration of how the WKB approximation can be used to help solve the linearised 3D MHD equations. Using Charpit's Method and a Runge-Kutta numerical scheme, we have demonstrated this technique for a potential 3D magnetic null point, ${\bf{B}}=(x,\epsilon y -(\epsilon +1)z)$. Under our cold plasma assumption, we have considered two types of wave propagation: fast magnetoacoustic and Alfv\'en waves. We find that the fast magnetoacoustic wave experiences refraction towards the magnetic null point, and that the effect of this refraction depends upon the Alfv\'en speed profile. The wave, and thus the wave energy, accumulates at the null point. We have found that current build up is exponential and the exponent is dependent upon $\epsilon$. Thus, for the fast wave there is preferential heating at the null point. For the Alfv\'en wave, we find that the wave propagates along the fieldlines. For an Alfv\'en wave generated along the fan-plane, the wave accumulates along the spine. For an Alfv\'en wave generated across the spine, the value of $\epsilon$ determines where the wave accumulation will occur: fan-plane ($\epsilon=1$), along the $x-$axis ($0<\epsilon <1$) or along the $y-$axis ($\epsilon>1$). We have shown analytically that currents build up exponentially, leading to preferential heating in these areas. The work described here highlights the importance of understanding the magnetic topology of the coronal magnetic field for the location of wave heating.Comment: 26 pages, 12 figure