A saturated genetic linkage map of autotetraploid alfalfa (Medicago sativa L.) developed using genotyping-by-sequencing is highly syntenous with the Medicago truncatula genome.

A genetic linkage map is a valuable tool for quantitative trait locus mapping, map-based gene cloning, comparative mapping, and whole-genome assembly. Alfalfa, one of the most important forage crops in the world, is autotetraploid, allogamous, and highly heterozygous, characteristics that have impeded the construction of a high-density linkage map using traditional genetic marker systems. Using genotyping-by-sequencing (GBS), we constructed low-cost, reasonably high-density linkage maps for both maternal and paternal parental genomes of an autotetraploid alfalfa F1 population. The resulting maps contain 3591 single-nucleotide polymorphism markers on 64 linkage groups across both parents, with an average density of one marker per 1.5 and 1.0 cM for the maternal and paternal haplotype maps, respectively. Chromosome assignments were made based on homology of markers to the M. truncatula genome. Four linkage groups representing the four haplotypes of each alfalfa chromosome were assigned to each of the eight Medicago chromosomes in both the maternal and paternal parents. The alfalfa linkage groups were highly syntenous with M. truncatula, and clearly identified the known translocation between Chromosomes 4 and 8. In addition, a small inversion on Chromosome 1 was identified between M. truncatula and M. sativa. GBS enabled us to develop a saturated linkage map for alfalfa that greatly improved genome coverage relative to previous maps and that will facilitate investigation of genome structure. GBS could be used in breeding populations to accelerate molecular breeding in alfalfa

Efficient image copy detection using multi-scale fingerprints

Inspired by multi-resolution histogram, we propose a multi-scale SIFT descriptor to improve the discriminability. A series of SIFT descriptions with different scale are first acquired by varying the actual size of each spatial bin. Then principle component analysis (PCA) is employed to reduce them to low dimensional vectors, which are further combined into one 128-dimension multi-scale SIFT description. Next, an entropy maximization based binarization is employed to encode the descriptions into binary codes called fingerprints for indexing the local features. Furthermore, an efficient search architecture consisting of lookup tables and inverted image ID list is designed to improve the query speed. Since the fingerprint building is of low-complexity, this method is very efficient and scalable to very large databases. In addition, the multi-scale fingerprints are very discriminative such that the copies can be effectively distinguished from similar objects, which leads to an improved performance in the detection of copies. The experimental evaluation shows that our approach outperforms the state of the art methods.Inspired by multi-resolution histogram, we propose a multi-scale SIFT descriptor to improve the discriminability. A series of SIFT descriptions with different scale are first acquired by varying the actual size of each spatial bin. Then principle component analysis (PCA) is employed to reduce them to low dimensional vectors, which are further combined into one 128-dimension multi-scale SIFT description. Next, an entropy maximization based binarization is employed to encode the descriptions into binary codes called fingerprints for indexing the local features. Furthermore, an efficient search architecture consisting of lookup tables and inverted image ID list is designed to improve the query speed. Since the fingerprint building is of low-complexity, this method is very efficient and scalable to very large databases. In addition, the multi-scale fingerprints are very discriminative such that the copies can be effectively distinguished from similar objects, which leads to an improved performance in the detection of copies. The experimental evaluation shows that our approach outperforms the state of the art methods

Long-Term Nutrient Variations in the Bohai Sea Over the Past 40 Years

As China's only continental sea, the Bohai Sea is a relatively closed environment and is vulnerable to natural changes and human activities. In this paper, the long-term variations in nutrients in the Bohai Sea and the potential influencing factors were analyzed based on historical summer and winter data from 1978 to 2016. The results showed that the concentrations of dissolved inorganic nitrogen (DIN) in the Bohai Sea continuously increased from 1990 and rapidly increased after 2002, the phosphate (PO 4 -P) concentration exhibited a decreasing trend, and the silicate (SiO 3 -Si) concentration decreased from 1978 to 1987 and increased from 1987 to 2008. The nutrient concentrations were lower in summer than in winter, and the bottom concentrations were higher than the surface concentrations in summer, whereas the vertical differences were insignificant in winter. The dominant factor determining the long-term variations in DIN were atmospheric deposition and nonpoint sources due to various human activities; the primary factors affecting PO 4 -P were riverine inputs and nonpoint sources related to natural changes and human activities; the primary factors afftecting SiO 3 -Si were riverine inputs. The N/P ratio followed the DIN variation, the Si/P ratio followed the SiO 3 -Si variation, and the Si/N ratio decreased. The nutrient ratios were lower at the bottom than at the surface and were lower in winter than in summer. The nutrient limitation changed from nitrogen limitation to phosphorus and silicon limitations. The long-term nutrient variations in the Bohai Sea have potential ecological impacts on the local red tide features

Shotgun metagenomic sequencing reveals skin microbial variability from different facial sites

Biogeography (body site) is known to be one of the main factors influencing the composition of the skin microbial community. However, site-associated microbial variability at a fine-scale level was not well-characterized since there was a lack of high-resolution recognition of facial microbiota across kingdoms by shotgun metagenomic sequencing. To investigate the explicit microbial variance in the human face, 822 shotgun metagenomic sequencing data from Han Chinese recently published by our group, in combination with 97 North American samples from NIH Human Microbiome Project (HMP), were reassessed. Metagenomic profiling of bacteria, fungi, and bacteriophages, as well as enriched function modules from three facial sites (forehead, cheek, and the back of the nose), was analyzed. The results revealed that skin microbial features were more alike in the forehead and cheek while varied from the back of the nose in terms of taxonomy and functionality. Analysis based on biogeographic theories suggested that neutral drift with niche selection from the host could possibly give rise to the variations. Of note, the abundance of porphyrin-producing species, i.e., Cutibacterium acnes, Cutibacterium avidum, Cutibacterium granulosum, and Cutibacterium namnetense, was all the highest in the back of the nose compared with the forehead/cheek, which was consistent with the highest porphyrin level on the nose in our population. Sequentially, the site-associated microbiome variance was confirmed in American populations; however, it was not entirely consistent. Furthermore, our data revealed correlation patterns between Propionibacterium acnes bacteriophages with genus Cutibacterium at different facial sites in both populations; however, C. acnes exhibited a distinct correlation with P. acnes bacteriophages in Americans/Chinese. Taken together, in this study, we explored the fine-scale facial site-associated changes in the skin microbiome and provided insight into the ecological processes underlying facial microbial variations

Structure and Interstitial Deuterium site of ß-phase ZrNi Deuteride

ß-ZrNiD1-x (for x≈0.1, near the ß-γ phase boundary) was found to possess a triclinic P1(overline) structure as determined by high-resolution neutron power diffraction. This is very different from the widely accepted orthohombic and distorted orthorhombic Cmcm structures previously proposed. In contrast to the single type of D site associated with these latter structures, the true ß-ZrNiD1-x structure contains two crystallographically distinct interstitial D sites: Zr4Ni2 octahedral sites and Zr4 tetrahedral sites, alternately ordered along the a direction. From first-principles calculations, the total energy of the P1(overline) structure was found to be ≈0.24 eV per unit cell lower than Cmcm-symmetry ZrNiD and could be rationalized in terms of different D local-bonding configurations and metal-deuterium interactions. Resultant phonon calculations based on this structure were also consistnet with the measured neutron vibrational spectrum

A Mott insulator continuously connected to iron pnictide superconductors

Iron-based superconductivity develops near an antiferromagnetic order and out of a bad metal normal state, which has been interpreted as originating from a proximate Mott transition. Whether an actual Mott insulator can be realized in the phase diagram of the iron pnictides remains an open question. Here we use transport, transmission electron microscopy, X-ray absorption spectroscopy, and neutron scattering to demonstrate that NaFe$_{1-x}$Cu$_x$As near $x\approx 0.5$ exhibits real space Fe and Cu ordering, and are antiferromagnetic insulators with the insulating behavior persisting above the N\'eel temperature, indicative of a Mott insulator. Upon decreasing $x$ from $0.5$, the antiferromagnetic ordered moment continuously decreases, yielding to superconductivity around $x=0.05$. Our discovery of a Mott insulating state in NaFe$_{1-x}$Cu$_x$As thus makes it the only known Fe-based material in which superconductivity can be smoothly connected to the Mott insulating state, highlighting the important role of electron correlations in the high-$T_{\rm c}$ superconductivity.Comment: in press, Nat. Commun., 4 figures, supplementary information available upon reques

The impact of giant jellyfish Nemopilema nomurai blooms on plankton communities in a temperate marginal sea

Abstract(#br)This study focused on the bloom-developing process of the giant jellyfish, Nemopilema nomurai , on phytoplankton and microzooplankton communities. Two repeated field observations on the jellyfish bloom were conducted in June 2012 and 2014 in the southern Yellow Sea where blooms of N . nomurai were frequently observed. We demonstrated that the bloom was made up of two stages, namely the developing stage and the mature stage. Total chlorophyll a increased and the concentrations of inorganic nutrients decreased during the developing stage, while both concentrations maintained stable and at low levels during the mature stage. Our analysis revealed that phosphate excreted by growing N . nomurai promoted the growth of phytoplankton at the developing stage. At the mature stage, size compositions of microzooplankton were altered and tended to be smaller via a top-down process, while phytoplankton compositions, affected mainly through a bottom-up process, shifted to be less diatoms and cryptophytes but more dinoflagellates

Patterns of human social contact and contact with animals in Shanghai, China

East Asia is as a principal hotspot for emerging zoonotic infections. Understanding the likely pathways for their emergence and spread requires knowledge on human-human and human-animal contacts, but such studies are rare. We used self-completed and interviewer-completed contact diaries to quantify patterns of these contacts for 965 individuals in 2017/2018 in a high-income densely-populated area of China, Shanghai City. Interviewer-completed diaries recorded more social contacts (19.3 vs. 18.0) and longer social contact duration (35.0 vs. 29.1 hours) than self-reporting. Strong age-assortativity was observed in all age groups especially among young participants (aged 7–20) and middle aged participants (25–55 years). 17.7% of participants reported touching animals (15.3% (pets), 0.0% (poultry) and 0.1% (livestock)). Human-human contact was very frequent but contact with animals (especially poultry) was rare although associated with frequent human-human contact. Hence, this densely populated area is more likely to act as an accelerator for human-human spread but less likely to be at the source of a zoonosis outbreak. We also propose that telephone interview at the end of reporting day is a potential improvement of the design of future contact surveys

Novel insights on the encapsulation mechanism of PLGA terminal groups on ropivacaine

Currently, the influences of free terminal groups (hydroxyl, carboxyl and ester) of PLGA on encapsulating active pharmaceutical ingredient are relatively ambiguous even though PLGA types were defined as critical quality attributes in vast majority of design of experiment process. In this study, emulsion method combined with premix membrane emulsification technique has been used to encapsulate ropivacaine (RVC), a small molecule local anesthetic in clinical. Based on the narrow particle size distribution, the influences and mechanisms of the terminal groups on properties of ropivacaine loaded microspheres have been investigated in detail. It was found that microspheres prepared by PLGA with hydroxyl or ester groups exhibited lower encapsulation efficiency but faster in vitro release rate than that of carboxyl groups. In the meanwhile, on microcosmic level analysis by quartz crystal microbalance with dissipation, atomic force microscope and confocal laser scanning microscopy, we attributed this distinction to the specific interaction between ropivacaine and different terminal groups. Subsequently, the reaction activation centers were verified by density functional simulation calculation and frontier molecular orbital theory at molecular level. Additionally, pharmacokinetics and pharmacodynamic research of infiltration anesthesia model were performed to compare sustained release ability, duration and intensity of the anesthetic effect in vivo. Finally, potential safety and toxicity were evaluated by the biochemical analysis. This study not only provides a novel mechanism of drug encapsulation process but also potential flexible selections in terms of various anesthesia indications in clinical

Genome-Wide Identification and Functional Characterization of the Heat Shock Factor Family in Eggplant (Solanum melongena L.) under Abiotic Stress Conditions

Plant heat shock factors (Hsfs) play crucial roles in various environmental stress responses. Eggplant (Solanum melongena L.) is an agronomically important and thermophilic vegetable grown worldwide. Although the functions of Hsfs under environmental stress conditions have been characterized in the model plant Arabidopsis thaliana and tomato, their roles in responding to various stresses remain unclear in eggplant. Therefore, we characterized the eggplant SmeHsf family and surveyed expression profiles mediated by the SmeHsfs under various stress conditions. Here, using reported Hsfs from other species as queries to search SmeHsfs in the eggplant genome and confirming the typical conserved domains, we identified 20 SmeHsf genes. The SmeHsfs were further classified into 14 subgroups on the basis of their structure. Additionally, quantitative real-time PCR revealed that SmeHsfs responded to four stresses—cold, heat, salinity and drought—which indicated that SmeHsfs play crucial roles in improving tolerance to various abiotic stresses. The expression pattern of SmeHsfA6b exhibited the most immediate response to the various environmental stresses, except drought. The genome-wide identification and abiotic stress-responsive expression pattern analysis provide clues for further analysis of the roles and regulatory mechanism of SmeHsfs under environmental stresses