De novo transcriptome assembly reveals sex-specific selection acting on evolving neo-sex chromosomes in Drosophila miranda.

BackgroundThe Drosophila miranda neo-sex chromosome system is a useful resource for studying recently evolved sex chromosomes. However, the neo-Y genomic assembly is fragmented due to the accumulation of repetitive sequence. Furthermore, the separate assembly of the neo-X and neo-Y chromosomes into genomic scaffolds has proven to be difficult, due to their low level of sequence divergence, which in coding regions is about 1.5%. Here, we de novo assemble the transcriptome of D. miranda using RNA-seq data from several male and female tissues, and develop a bioinformatic pipeline to separately reconstruct neo-X and neo-Y transcripts.ResultsWe obtain 2,141 transcripts from the neo-X and 1,863 from the neo-Y. Neo-Y transcripts are generally shorter than their homologous neo-X transcripts (N50 of 2,048-bp vs. 2,775-bp) and expressed at lower levels. We find that 24% of expressed neo-Y transcripts harbor nonsense mutation within their open reading frames, yet most non-functional neo-Y genes are expressed throughout all of their length. We find evidence of gene loss of male-specific genes on the neo-X chromosome, and transcriptional silencing of testis-specific genes from the neo-X.ConclusionsNonsense mediated decay (NMD) has been implicated to degrade transcripts containing pre-mature termination codons (PTC) in Drosophila, but rampant description of neo-Y genes with pre-mature stop codons suggests that it does not play a major role in down-regulating transcripts from the neo-Y. Loss or transcriptional down-regulation of genes from the neo-X with male-biased function provides evidence for beginning demasculinization of the neo-X. Thus, evolving sex chromosomes can rapidly shift their gene content or patterns of gene expression in response to their sex-biased transmission, supporting the idea that sex-specific or sexually antagonistic selection plays a major role in the evolution of heteromorphic sex chromosomes

Three-body spin-orbit forces from chiral two-pion exchange

Using chiral perturbation theory, we calculate the density-dependent spin-orbit coupling generated by the two-pion exchange three-nucleon interaction involving virtual $\Delta$-isobar excitation. From the corresponding three-loop Hartree and Fock diagrams we obtain an isoscalar spin-orbit strength $F_{\rm so}(k_f)$ which amounts at nuclear matter saturation density to about half of the empirical value of $90$MeVfm$^5$. The associated isovector spin-orbit strength $G_{\rm so}(k_f)$ comes out about a factor of 20 smaller. Interestingly, this three-body spin-orbit coupling is not a relativistic effect but independent of the nucleon mass $M$. Furthermore, we calculate the three-body spin-orbit coupling generated by two-pion exchange on the basis of the most general chiral $\pi\pi NN$-contact interaction. We find similar (numerical) results for the isoscalar and isovector spin-orbit strengths $F_{\rm so}(k_f)$ and $G_{\rm so}(k_f)$ with a strong dominance of the p-wave part of the $\pi\pi NN$-contact interaction and the Hartree contribution.Comment: 8 pages, 4figure, published in : Physical Review C68, 054001 (2003

Understanding residents’ capacities to support evacuated populations : A study of earthquake and tsunami evacuation for Napier Hill, Napier, Aotearoa New Zealand.

Due to a large regional subduction zone (the Hikurangi subduction zone) and localised faults, Napier City located on the East Coast of Aotearoa/New Zealand is vulnerable to earthquake and tsunami events. On feeling a long or strong earthquake people will need to evacuate immediately inland or to higher ground to avoid being impacted by a tsunami, of which the first waves could start to arrive within 20 minutes (based on the Hikurangi earthquake and tsunami scenario presented in Power et al., 2018). Napier Hill is one such area of higher land, and it is estimated that up to 12,000 people could evacuate there in the 20 minutes following a long or strong earthquake. To understand the capacity of Napier Hill residents to support evacuees, three focus groups were held with a diverse sample of residents from Napier Hill on 21 and 22 July 2019. A follow up email was sent to all participants a week after the focus groups, containing a link to a short six question survey, which was completed by 68 people, most of whom were additional to the focus group attendees. Data from the focus groups and the survey was analysed qualitatively using thematic analysis. The findings highlight that in general people were happy to host evacuees and offer support if they were in a position to do so. However, key issues in being able to offer support included the likely lack of resources available after a disaster, ranging from basic needs though to agency support. The research findings will directly inform Napier City Council and Hawke’s Bay Civil Defence Emergency Management Group’s planning for future readiness and response by providing valuable insights for evacuation planningfalseWellingtonHawke's Bay Civil Defence Emergency Management Grou

Induced pseudoscalar form factor of the nucleon at two-loop order in chiral perturbation theory

We calculate the imaginary part of the induced pseudoscalar form factor of the nucleon $G_P(t)$ in the framework of two-loop heavy baryon chiral perturbation theory. The effect of the calculated three-pion continuum on the pseudoscalar constant $g_P = (m_\mu/2M) G_P(t=-0.877m_\mu^2)$ measurable in ordinary muon capture $\mu^-p\to \nu_\mu n$ turns out to be negligibly small. Possible contributions from counterterms at two-loop order are numerically smaller than the uncertainty of the dominant pion-pole term proportional to the pion-nucleon coupling constant $g_{\pi N}= 13.2\pm 0.2$. We conclude that a sufficiently accurate representation of the induced pseudoscalar form factor of the nucleon at low momentum transfers $t$ is given by the sum of the pion-pole term and the Adler-Dothan-Wolfenstein term: $G_P(t) = 4g_{\pi N} M f_\pi/ (m_\pi^2 -t)- 2g_A M^2 /3$, with $= (0.44 \pm 0.02)$ fm$^2$ the axial mean square radius of the nucleon.Comment: 6 pages, 2 figures, accepted for publication in Physical Review

Mean eigenvalues for simple, simply connected, compact Lie groups

We determine for each of the simple, simply connected, compact and complex Lie groups SU(n), Spin$(4n+2)$ and $E_6$ that particular region inside the unit disk in the complex plane which is filled by their mean eigenvalues. We give analytical parameterizations for the boundary curves of these so-called trace figures. The area enclosed by a trace figure turns out to be a rational multiple of $\pi$ in each case. We calculate also the length of the boundary curve and determine the radius of the largest circle that is contained in a trace figure. The discrete center of the corresponding compact complex Lie group shows up prominently in the form of cusp points of the trace figure placed symmetrically on the unit circle. For the exceptional Lie groups $G_2$, $F_4$ and $E_8$ with trivial center we determine the (negative) lower bound on their mean eigenvalues lying within the real interval $[-1,1]$. We find the rational boundary values -2/7, -3/13 and -1/31 for $G_2$, $F_4$ and $E_8$, respectively.Comment: 12 pages, 8 figure

An Algebraic-Coding Equivalence to the Maximum Distance Separable Conjecture

We formulate an Algebraic-Coding Equivalence to the Maximum Distance Separable Conjecture. Specifically, we present novel proofs of the following equivalent statements. Let $(q,k)$ be a fixed pair of integers satisfying $q$ is a prime power and $2\leq k \leq q$. We denote by $\mathcal{P}_q$ the vector space of functions from a finite field $\mathbb{F}_q$ to itself, which can be represented as the space $\mathcal{P}_q := \mathbb{F}_q[x]/(x^q-x)$ of polynomial functions. We denote by $\mathcal{O}_n \subset \mathcal{P}_q$ the set of polynomials that are either the zero polynomial, or have at most $n$ distinct roots in $\mathbb{F}_q$. Given two subspaces $Y,Z$ of $\mathcal{P}_q$, we denote by $\langle Y,Z \rangle$ their span. We prove that the following are equivalent. [A] Suppose that either: 1. $q$ is odd 2. $q$ is even and $k \not\in \{3, q-1\}$. Then there do not exist distinct subspaces $Y$ and $Z$ of $\mathcal{P}_q$ such that: 3. $dim(\langle Y, Z \rangle) = k$ 4. $dim(Y) = dim(Z) = k-1$. 5. $\langle Y, Z \rangle \subset \mathcal{O}_{k-1}$ 6. $Y, Z \subset \mathcal{O}_{k-2}$ 7. $Y\cap Z \subset \mathcal{O}_{k-3}$. [B] Suppose $q$ is odd, or, if $q$ is even, $k \not\in \{3, q-1\}$. There is no integer $s$ with $q \geq s > k$ such that the Reed-Solomon code $\mathcal{R}$ over $\mathbb{F}_q$ of dimension $s$ can have $s-k+2$ columns $\mathcal{B} = \{b_1,\ldots,b_{s-k+2}\}$ added to it, such that: 8. Any $s \times s$ submatrix of $\mathcal{R} \cup \mathcal{B}$ containing the first $s-k$ columns of $\mathcal{B}$ is independent. 9. $\mathcal{B} \cup \{[0,0,\ldots,0,1]\}$ is independent. [C] The MDS conjecture is true for the given $(q,k)$.Comment: This is version: 5.6.18. arXiv admin note: substantial text overlap with arXiv:1611.0235