Fast generation of mock galaxy catalogues with COLA

We investigate the feasibility of using COmoving Lagrangian Acceleration (COLA) technique to efficiently generate galaxy mock catalogues that can accurately reproduce the statistical properties of observed galaxies. Our proposed scheme combines the subhalo abundance matching (SHAM) procedure with COLA simulations, utilizing only three free parameters: the scatter magnitude ($\sigma_{\rm scat}$) in SHAM, the initial redshift ($z_{\rm init}$) of the COLA simulation, and the time stride ($da$) used by COLA. In this proof-of-concept study, we focus on a subset of BOSS CMASS NGC galaxies within the redshift range $z\in [0.45, 0.55]$. We perform $\mathtt{GADGET}$ simulation and low-resolution COLA simulations with various combinations of $(z_{\rm init}, da)$, each using $1024^{3}$ particles in an $800~h^{-1}{\rm Mpc}$ box. By minimizing the difference between COLA mock and CMASS NGC galaxies for the monopole of the two-point correlation function (2PCF), we obtain the optimal $\sigma_{\rm scat}$. We have found that by setting $z_{\rm init}=29$ and $da=1/30$, we achieve a good agreement between COLA mock and CMASS NGC galaxies within the range of 4 to $20~h^{-1}{\rm Mpc}$, with a computational cost two orders of magnitude lower than that of the N-body code. Moreover, a detailed verification is performed by comparing various statistical properties, such as anisotropic 2PCF, three-point clustering, and power spectrum multipoles, which shows similar performance between GADGET mock and COLA mock catalogues with the CMASS NGC galaxies. Furthermore, we assess the robustness of the COLA mock catalogues across different cosmological models, demonstrating consistent results in the resulting 2PCFs. Our findings suggest that COLA simulations are a promising tool for efficiently generating mock catalogues for emulators and machine learning analyses in exploring the large-scale structure of the Universe.Comment: 24 pages, 14 figures, 4 table

Lineage-specific accelerated sequences underlying primate evolution

Understanding the mechanisms underlying phenotypic innovation is a key goal of comparative genomic studies. Here, we investigated the evolutionary landscape of lineage-specific accelerated regions (LinARs) across 49 primate species. Genomic comparison with dense taxa sampling of primate species significantly improved LinAR detection accuracy and revealed many novel human LinARs associated with brain development or disease. Our study also yielded detailed maps of LinARs in other primate lineages that may have influenced lineage-specific phenotypic innovation and adaptation. Functional experimentation identified gibbon LinARs, which could have participated in the developmental regulation of their unique limb structures, whereas some LinARs in the Colobinae were associated with metabolite detoxification which may have been adaptive in relation to their leaf-eating diet. Overall, our study broadens knowledge of the functional roles of LinARs in primate evolution

Reference genome of wild goat (<i>capra aegagrus</i>) and sequencing of goat breeds provide insight into genic basis of goat domestication

BACKGROUND: Domestic goats (Capra hircus) have been selected to play an essential role in agricultural production systems, since being domesticated from their wild progenitor, bezoar (Capra aegagrus). A detailed understanding of the genetic consequences imparted by the domestication process remains a key goal of evolutionary genomics. RESULTS: We constructed the reference genome of bezoar and sequenced representative breeds of domestic goats to search for genomic changes that likely have accompanied goat domestication and breed formation. Thirteen copy number variation genes associated with coat color were identified in domestic goats, among which ASIP gene duplication contributes to the generation of light coat-color phenotype in domestic goats. Analysis of rapidly evolving genes identified genic changes underlying behavior-related traits, immune response and production-related traits. CONCLUSION: Based on the comparison studies of copy number variation genes and rapidly evolving genes between wild and domestic goat, our findings and methodology shed light on the genetic mechanism of animal domestication and will facilitate future goat breeding. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1606-1) contains supplementary material, which is available to authorized users

The complete chloroplast genome sequence of Eriobotrya fragrans

Eriobotrya fragrans Champion ex Bentham is a potential medicinal plant of the genus Eriobotrya Lindl in the family Rosaceae. To better determine its phylogenetic location with respect to the other Rosaceae species, the complete chloroplast genome of E. fragrans was sequenced. The whole E. fragrans chloroplast genome is 159,286 bp in length, consisting of a pair of inverted repeat (IR) regions of 26,343 bp, one large single-copy (LSC) region of 87,301 bp, and one small single-copy (SSC) region of 19,299 bp. The overall GC content of the whole chloroplast genome is 36.7%. Further, phylogenetic analysis using maximum likelihood with TVM + F+R2 model strongly supports the relationship: sisterhood of E. fragrans and E. japonica, followed by three species of Pyrus L

Advances in Hippo pathway in malignant skin tumors

The classic targeted therapy for skin malignant tumors has issues such as efficacy attenuation, drug resistance, and recurrence. Finding new treatment targets is of great significance for patients with skin malignant tumors. The Hippo signaling pathway plays an important role in tumor proliferation, invasion, drug resistance and immunity. Targeted drugs through the Hippo signaling pathway have shown good application prospects in the combination therapy of skin malignant tumors, and are considered as an effective way to solve the problems of efficacy attenuation and drug resistance in targeted therapy in the future. This article reviews the physiological processes and potential mechanisms of Hippo pathway in skin malignant tumors, and discusses its role and significance in targeted combination therapy

A comprehensive clinical diagnostic score system for prediction of coronary artery spasm in patients with acute chest pain

Background: Currently, there is no validated multivariate model to predict probability of coronary artery spasm (CAS) in patients with acute chest pain. Methods: A total of 976 consecutive patients with acute chest pain were enrolled. Patients were divided into two groups based on the presence of significant CAS. To adjust potential confounders, a multivariable analysis was performed and a clinical diagnostic score system for CAS was utilized for score derivation. Results: Multivariable analysis model selected 6 predictors for CAS. The integer score was assigned to each predictors: angina at rest alone (10 points), positive of hyperventilation test (8 points), allergies (3 points), asthma, ST-segment elevation and myocardial bridge (2 points each). We showed that the clinical diagnostic score system had accuracy in predicting CAS, as measured by the area under the curve (AUC), which was 0.952–0.966. The cut-off baseline value for the clinical diagnostic score system was set to 11–12 points with specificity of 91.0–93.3% and sensitivity of 90.7–92.9%, respectively. Conclusion: A clinical diagnostic score system was derived and validated as an accurate tool for estimating the pretest probability of CAS in patients with acute chest pain. Keywords: Acute chest pain, Coronary artery spasm, Clinical diagnostic score syste

Complete plastome of a subtropical tree Eriobotrya malipoensis (Rosaceae) in Yunnan

Eriobotrya malipoensis Kuan is an important wild woody evergreen tree within the genus Eriobotrya Lindl belonging the family Rosaceae. To better determine its phylogenetic location with respect to the other Eriobotrya species, the complete plastome of E. malipoensis was sequenced. The whole plastome is 159,313 bp in length, consisting of a pair of inverted repeat (IR) regions of 26,344 bp, one large single-copy (LSC) region of 87,270 bp, and one small single-copy (SSC) region of 19,355 bp. The overall G + C content of the whole plastome is 36.7%. Further, maximum likelihood phylogenetic analyse (TVM + F+R2 model) was conducted using 14 complete plastome of the Rosaceae. Our phylogeny supports the relationships: sisterhood of the E. malipoensis and E. fragrans Champ, flowed E. japonica Lindl

Screening of Indica-Japonica Specific Molecular Markers and Establishment of Discrimination System

【Objective】Accurate differentiation of indica-japonica nature in rice is of great importance in the aspects of advantage utilization and evolutionary studies of indica-japonica subspecies hybrids. Molecular markers designed based on nucleotide sequence differences between indica rice and japonica rice have been widely used to discriminate indica-japonica in rice. However, it remains unclear whether these published molecular markers for indica-japonica discrimination still show indica-japonica specificity in experimental materials with diverse genetic backgrounds; moreover, the current indica-japonica discrimination is mostly based on the comparison between the line to be tested and two control varieties, which cannot reflect the indica-japonica similarity between the line to be tested and the indica (japonica) subspecies population. Therefore, it is necessary to screen a set of molecular markers that can show indica-japonica specificity in all diverse genetic materials and to establish an indica-japonica group discrimination system to objectively discriminate indica-japonica in rice.【Method】In the Rice Diversity Germplasm Platform 2 (RDP2), which represents the genetic diversity of rice in the world, 92 rice varieties (lines) we selected that retained population genetic diversity based on the genotypes of 70000 SNP molecular markers, and screened 51 pairs of previously reported molecular markers for indica-japonica discrimination; and selected 5 indica rice and 5 japonica rice to form indica and japonica discrimination groups based on the clustering results of indica-japonica-specific molecular markers, and used indica discrimination values to quantify rice indica-japonica.【Result】Twenty-four pairs of indica-japonicaspecific molecular markers were screened out of 51 pairs (both indica/japonica rice clusters showed specific band types with a frequency of higher than 69.5%), which were evenly distributed on 12 chromosomes of rice. Based on the banding results of the indica-japonica-specific molecular markers, a clustering analysis of indica-japonica nature was performed. Ninety-two varieties (lines) could be divided into 2 clusters of indica and japonica rice; and the clustering results were in perfect consitant with the known indica-japonica nature of these varieties (lines). Based on the clustering results, a cluster discrimination system was constructed and indica discrimination values were calculated for 10 randomly selected varieties (lines). Among them, there were 1 indica-leaning line, 1 japonica-leaning line, 4 indica lines and 4 japonica lines, and the quantitative discrimination of their indica-japonica nature was accurately achieved.【Conclusion】In this study, we screened a set of molecular markers for indica-japonica identification in materials with rich genetic background, and established an indica-japonica discrimination system based on indica-japonica clusters, which can be used to discriminate indica-japonica of rice efficiently and accurately