Linking ice and gas in the Serpens low-mass star-forming region

Context. The interaction between dust, ice, and gas during the formation of stars produces complex organic molecules. While observations indicate that several species are formed on ice-covered dust grains and are released into the gas phase, the exact chemical interplay between solid and gas phases and their relative importance remain unclear. Aims. Our goal is to study the interplay between dust, ice, and gas in regions of low-mass star formation through ice- and gas-mapping and by directly measuring gas-to-ice ratios. This provides constraints on the routes that lead to the chemical complexity that is observed in solid and gas phases. Methods. We present observations of gas-phase methanol (CH3OH) and carbon monoxide (13CO and C18O) at 1.3 mm towards ten low-mass young protostars in the Serpens SVS 4 cluster from the SubMillimeter Array (SMA) and the Atacama Pathfinder EXperiment (APEX) telescope. We used archival data from the Very Large Telescope (VLT) to derive abundances of ice H2O, CO, and CH3OH towards the same region. Finally, we constructed gas-ice maps of SVS 4 and directly measured CO and CH3OH gas-to-ice ratios. Results. The SVS 4 cluster is characterised by a global temperature of 15 ± 5 K. At this temperature, the chemical behaviours of CH3OH and CO are anti-correlated: larger variations are observed for CH3OH gas than for CH3OH ice, whereas the opposite is seen for CO. The gas-to-ice ratios (Ngas/Nice) range from 1–6 for CO and 1.4 × 10−4–3.7 × 10−3 for CH3OH. The CO gas-maps trace an extended gaseous component that is not sensitive to the effect of freeze-out. Because of temperature variations and dust heating around 20 K, the frozen CO is efficiently desorbed. The CH3OH gas-maps, in contrast, probe regions where methanol is predominantly formed and present in ices and is released into the gas phase through non-thermal desorption mechanisms. Conclusions. Combining gas- and ice-mapping techniques, we measure gas-to-ice ratios of CO and CH3OH in the SVS 4 cluster. The CH3OH gas-to-ice ratio agrees with values that were previously reported for embedded Class 0/I low-mass protostars. We find that there is no straightforward correlation between CO and CH3OH gas with their ice counterparts in the cluster. This is likely related to the complex morphology of SVS 4: the Class 0 protostar SMM 4 and its envelope lie in the vicinity, and the outflow associated with SMM 4 intersects the cluster. This study serves as a pathfinder for future observations with ALMA and the James Webb Space Telescope (JWST) that will provide high-sensitivity gas-ice maps of molecules more complex than methanol. Such comparative maps will be essential to constrain the chemical routes that regulate the chemical complexity in star-forming regions.

RH mapping by sequencing: chromosome-scale assembly of the duck genome

Like many other species, the duck genome has been sequenced thanks to the technological breakthrough provided by the emergence of Next Generation Sequencing (NGS). The resulting de novo assemblies are however made of thousands of scattered scaffolds. To achieve chromosome-scale contiguity, long-range intermediate genome maps remain indispensable. Radiation Hybrid (RH) maps have been used to assist the generation of chromosome-scale genome assemblies by taking advantage of the high density SNP chips that provide a large number of markers that can be efficiently genotyped on the panel.In the absence of such a resource in duck, we sequenced 100 hybrid clones of a duck RH panel enabling direct genotyping of the assembly scaffolds on the panel. The rationale is to use scaffolds as markers and to genotype the scaffolds by sequencing the clones: the presence/absence of a scaffold in a particular sequenced hybrid is attested by the presence/absence of reads mapping specifically to this scaffold. The detection of scaffolds exhibiting a chromosomal breakage resulting from the irradiation process revealed itself to be a critical issue of this genotyping by sequencing process. This process resulted in the construction of RH vectors for 2,027 scaffolds, representing a total of about 1 Gb of sequences (95% of the current Duck genome assembly). The subsequent linkage analysis enabled the construction of RH maps and therefore to organize, i.e. order and orient, the scaffolds into pseudomolecules associated to the corresponding duck chromosomes. We describe here the whole mapping process, from sequence-based genotyping to the construction of comparative maps, as well as few examples of intra-chromosomal rearrangements that have been identified by the comparison with the chicken, turkey and zebra finch genomes and subsequently confirmed by FISH.We describe a method to order and orient sequence scaffolds into super-scaffolds spanning entire chromosomes. The method, which requires a pre-existing RH panel and sequence scaffolds from an NGS assembly, relies on a shallow sequencing of the RH clones. This approach was applied to the duck genome and produced chromosome-scale scaffolds for 29 out of the 41 duck chromosomes.

Field cress genome mapping: Integrating linkage and comparative maps with cytogenetic analysis for rDNA carrying chromosomes

Field cress (Lepidium campestre L.), despite its potential as a sustainable alternative oilseed plant, has been underutilized, and no prior attempts to characterize the genome at the genetic or molecular cytogenetic level have been conducted. Genetic maps are the foundation for anchoring and orienting annotated genome assemblies and positional cloning of candidate genes. Our principal goal was to construct a genetic map using integrated approaches of genetic, comparative and cytogenetic map analyses. In total, 503 F2 interspecific hybrid individuals were genotyped using 7,624 single nucleotide polymorphism markers. Comparative analysis demonstrated that ~57% of the sequenced loci in L. campestre were congruent with Arabidopsis thaliana (L.) genome and suggested a novel karyotype, which predates the ancestral crucifer karyotype. Aceto-orcein chromosome staining and fluorescence in situ hybridization (FISH) analyses confirmed that L. campestre, L. heterophyllum Benth. and their hybrids had a chromosome number of 2n = 2x = 16. Flow cytometric analysis revealed that both species possess 2C roughly 0.4 picogram DNA. Integrating linkage and comparative maps with cytogenetic map analyses assigned two linkage groups to their particular chromosomes. Future work could incorporate FISH utilizing A. thaliana mapped BAC clones to allow the chromosomes of field cress to be identified reliably.

Molecular mapping of YrTZ2, a stripe rust resistance gene in wild emmer accession TZ-2 and its comparative analyses with Aegilops tauschii

ABSTRACTWheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating disease that can cause severe yield losses. Identification and utilization of stripe rust resistance genes are essential for effective breeding against the disease. Wild emmer accession TZ-2, originally collected from Mount Hermon, Israel, confers near-immunity resistance against several prevailing Pst races in China. A set of 200 F6:7 recombinant inbred lines (RILs) derived from a cross between susceptible durum wheat cultivar Langdon and TZ-2 was used for stripe rust evaluation. Genetic analysis indicated that the stripe rust resistance of TZ-2 to Pst race CYR34 was controlled by a single dominant gene, temporarily designated YrTZ2. Through bulked segregant analysis (BSA) and SSR mapping, YrTZ2 was located on chromosome arm 1BS and flanked by SSR markers Xwmc230 and Xgwm413 with genetic distance of 0.8 cM (distal) and 0.3 cM (proximal), respectively. By applying wheat 90K iSelect SNP genotyping assay, 11 polymorphic loci (consist of 250 SNP markers) closely linked with YrTZ2 were identified. YrTZ2 was further delimited into a 0.8 cM genetic interval between SNP marker IWB19368 and SSR marker Xgwm413, and co-segregated with SNP marker IWB28744 (attached with 28 SNP markers). Comparative genomics analyses revealed high level of collinearity between the YrTZ2 genomic region and the orthologous region of Aegilops tauschii 1DS. The genomic region between loci IWB19368 and IWB31649 harboring YrTZ2 is orthologous to a 24.5 Mb genomic region between AT1D0112 and AT1D0150, spanning 15 contigs on chromosome 1DS. The genetic and comparative maps of YrTZ2 provide framework for map-based cloning and marker-assisted selection (MAS) of YrTZ2.

A High-Resolution Comparative Chromosome Map of Cricetus cricetus and Peromyscus eremicus Reveals the Involvement of Constitutive Heterochromatin in Breakpoint Regions

Compared to humans and other mammals, rodent genomes, specifically Muroidea species, underwent intense chromosome reshuffling in which many complex structural rearrangements occurred. This fact makes them preferential animal models for studying the process of karyotype evolution. Here, we present the first combined chromosome comparative maps between 2 Cricetidae species, Cricetus cricetus and Peromyscus eremicus, and the index species Mus musculus and Rattus norvegicus. Comparative chromosome painting was done using mouse and rat paint probes together with in silico analysis from the Ensembl genome browser database. Hereby, evolutionary events (inter- and intrachromosomal rearrangements) that occurred in C. cricetus and P. eremicus since the putative ancestral Muroidea genome could be inferred, and evolutionary breakpoint regions could be detected. A colocalization of constitutive heterochromatin and evolutionary breakpoint regions in each genome was observed. Our results suggest the involvement of constitutive heterochromatin in karyotype restructuring of these species, despite the different levels of conservation of the C. cricetus (derivative) and P. eremicus (conserved) genomes.

CONVERSION OF FORMER INDUSTRIAL PORTS INTO TOURIST ATTRACTIONS. HAS INTEGRATION BEEN ACHIEVED?

The transformation of redundant port facilities has become a priority in many cities willing to attract a larger number of tourists. From Baltimore‟s successful initiative to Barcelona‟s dissemination of the model in Europe, one city after another have implemented the same examples with few variations. The objective of the research is to analyze the renovation of former industrial ports in two medium-size cities: Plymouth and Malaga, focusing on whether the projects have matched the initial objectives to turn the facilities into tourist attractions as well as to integrate them in the city life. The methodological process is based on a comparative analysis of five different issues, namely external accessibility, internal mobility, activities, heritage protection and general integration in the urban context. The research process has ended up in the production of comparative maps. Major differences between both examples can be found in the integration of heritage, both cultural and natural, the consolidation of a mix of uses and the existence of physical barriers between the port and the rest of the city.

The Sea Lamprey Meiotic Map Resolves Ancient Vertebrate Genome Duplications

Gene and genome duplications serve as an important reservoir of material for the evolution of new biological functions. It is generally accepted that many genes present in vertebrate genomes owe their origin to two whole genome duplications that occurred deep in the ancestry of the vertebrate lineage. However, details regarding the timing and outcome of these duplications are not well resolved. We present high-density meiotic and comparative genomic maps for the sea lamprey, a representative of an ancient lineage that diverged from all other vertebrates approximately 550 million years ago. Linkage analyses yielded a total of 95 linkage groups, similar to the estimated number of germline chromosomes (1N ~ 99), spanning a total of 5,570.25 cM. Comparative mapping data yield strong support for one ancient whole genome duplication but do not strongly support a hypothetical second event. Rather, these comparative maps reveal several evolutionary independent segmental duplications occurring over the last 600+ million years of chordate evolution. This refined history of vertebrate genome duplication should permit more precise investigations into the evolution of vertebrate gene functions.

A Novel Detection Method of Paper Defects Based on Visual Attention Mechanism

In this paper, an improved paper defects detection method based on visual attention mechanism computation model is presented. First, multi-scale feature maps are extracted by linear filtering. Second, the comparative maps are obtained by carrying out center-surround difference operator. Third, the saliency map is obtained by combining conspicuity maps, which is gained by combining the multi-scale comparative maps. Last, the seed point of watershed segmentation is determined by competition among salient points in the saliency map and the defect regions are segmented from the background. Experimental results show the efficiency of the approach for paper defects detection.

A Novel Detection Method of Paper Defects Based on Visual Attention Mechanism

In this paper, an improved paper defects detection method based on visual attention mechanism computation model is presented. First, multi-scale feature maps are extracted by linear filtering. Second, the comparative maps are obtained by carrying out center-surround difference operator. Third, the saliency map is obtained by combining conspicuity maps, which is gained by combining the multi-scale comparative maps. Last, the seed point of watershed segmentation is determined by competition among salient points in the saliency map and the defect regions are segmented from the background. Experimental results show the efficiency of the approach for paper defects detection.