ALBERT

Description: The capacity of apomixis to generate maternal clones through seed reproduction has made it a useful characteristic for the fixation of heterosis in plant breeding. It has been observed that apomixis displays pronounced intra- and interspecific diversification, but the genetic mechanisms underlying this diversification remains elusive, obstructing the exploitation of this phenomenon in practical breeding programs. By capitalizing on molecular information in mapping populations, we describe and assess a statistical design that deploys linkage analysis to estimate and test the pattern and extent of apomictic differences at various levels from genotypes to species. The design is based on two reciprocal crosses between two individuals each chosen from a hermaphrodite or monoecious species. A multinomial distribution likelihood is constructed by combining marker information from two crosses. The EM algorithm is implemented to estimate the rate of apomixis and test its difference between two plant populations or species as the parents. The design is validated by computer simulation. A real data analysis of two reciprocal crosses between hickory ( Carya cathayensis ) and pecan ( C. illinoensis ) demonstrates the utilization and usefulness of the design in practice. The design provides a tool to address fundamental and applied questions related to the evolution and breeding of apomixis.

Description: Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows. These workflows, coupled with the ease of use of the environment, provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks and, within the context of the same environment, to visualize and further interrogate their results. This bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research.

Description: Aims Nitrogen (N) fertilization and lime addition may affect soil microbial and nematode communities and ecosystem functions through changing environmental conditions, such as soil pH and soil organic carbon. The objectives of this experiment were to examine the impact of N input and liming on soil microbial and nematode communities and to identify the key environmental determinant of community composition in a century-old fertilization and crop rotation experiment. Methods The field experiment consisting of a 3-year crop rotation regime was established in 1911 in southeastern USA. Four treatments, (i) no-input control, (ii) NPK with winter legume, (iii) PK with legume and lime and (iv) NPK with legume and lime, were included in this study. Soil samples collected at the 0–5cm depth were used to determine the bacterial growth rate by the 3 H-thymidine incorporation technique. Incorporation of 13 C into neutral lipids, glycolipids and phospholipid fatty acids (PLFAs) was measured after incubation of soil with 13 C-labeled acetate for 24h. Free-living nematodes in fresh soil were extracted using a density sucrose centrifugal flotation method and identified to trophic group level. Important Findings Liming resulted in a 10-fold increase in bacterial growth rates compared with the no-input control, whereas N fertilization had no significant effect. Multivariate analysis of PLFA profiles showed that soil microbial community composition was different among the four treatments; the difference was primarily driven by soil pH. PLFAs indicative of Gram-negative bacteria covaried with soil pH, but not those of fungi and actinobacteria. Liming enhanced 13 C incorporation into neutral lipids, glycolipids and phospholipids by 2–15 times. In addition, 13 C incorporation into 16:0, 16:19, 18:19, 18:17 and 18:26 were greater than other PLFAs, suggesting that Gram-negative bacteria and fungi were more active and sensitive to simple C input. Bacterivorous nematodes were the dominant trophic group in the soil, but no significant differences in nematode communities were found among the treatments. Our results suggest that soil pH had a greater impact than N fertilization on soil microbial community composition and activity in a crop rotation system including legumes.

Description: The BL Lacertae object 1ES 1440+122 was observed in the energy range from 85 GeV to 30 TeV by the VERITAS array of imaging atmospheric Cherenkov telescopes. The observations, taken between 2008 May and 2010 June and totalling 53 h, resulted in the discovery of -ray emission from the blazar, which has a redshift z = 0.163. 1ES 1440+122 is detected at a statistical significance of 5.5 standard deviations above the background with an integral flux of (2.8 ± 0.7 stat ± 0.8 sys ) x 10 –12  cm –2  s –1 (1.2 per cent of the Crab Nebula's flux) above 200 GeV. The measured spectrum is described well by a power law from 0.2 to 1.3 TeV with a photon index of 3.1 ± 0.4 stat ± 0.2 sys . Quasi-simultaneous multiwavelength data from the Fermi Large Area Telescope (0.3–300 GeV) and the Swift X-ray Telescope (0.2–10 keV) are additionally used to model the properties of the emission region. A synchrotron self-Compton model produces a good representation of the multiwavelength data. Adding an external-Compton or a hadronic component also adequately describes the data.

Description: We investigate the properties of haloes, galaxies and black holes to z  = 0 in the high-resolution hydrodynamical simulation MassiveBlack-II (MBII) which evolves a cold dark matter cosmology in a comoving volume V box  = (100 Mpc h –1 ) 3 . MBII is the highest resolution simulation of this size which includes a self-consistent model for star formation, black hole accretion and associated feedback. We provide a simulation browser web application which enables interactive search and tagging of the MBII data set and publicly release our galaxy catalogues. We find that baryons affect strongly the halo mass function (MF), with 20–33 per cent change in the halo abundance below the knee of the MF ( M halo  〈 10 13.2 M h –1 at z  = 0) when compared to dark-matter-only simulations. We provide a fitting function for the halo MF out to redshift z  = 11 and discuss its limitations. We study the halo occupation distribution and clustering of galaxies, in particular the evolution and scale dependence of stochasticity and bias finding reasonable agreement with observational data. The shape of the cosmic spectral energy distribution of galaxies in MBII is consistent with observations, but lower in amplitude. The Galaxy stellar mass function (GSMF) function is broadly consistent with observations at z  ≥ 2. At z  〈 2, the population of passive low-mass ( M *  〈 10 9 M ) galaxies in MBII makes the GSMF too steep compared to observations whereas at the high-mass end ( M *  〉 10 11 M ) galaxies hosting bright AGNs make significant contributions to the GSMF. The quasar bolometric luminosity function is also largely consistent with observations. We note however that more efficient AGN feedback is necessary for the largest, rarest objects/clusters at low redshifts.

Description: Aims Drought affected by atmosphere–ocean cycle is a dominant factor influencing tree radial growth of sandy Mongolian pine ( Pinus sylvestris var. mongolica ) and regional vegetation dynamics in Hulunbuir, China. However, historical droughts and its correlations with tree radial growth and atmosphere–ocean cycle in this area have been little tested. Methods We developed tree-ring chronologies of Mongolian pine from Hulunbuir, Inner Mongolia, China and analyzed the correlations between tree-ring width index, the normalized difference vegetation index and Palmer drought severity index (PDSI), then developed a linear model to reconstruct the drought variability from 1829 to 2009. Long-term trends and its linkages with atmosphere–ocean cycle were performed by the power spectral, wavelet and teleconnection analysis. Important Findings The local moisture variations affected largely the regional vegetation dynamics and tree-ring growth of Mongolia pine in the forest–grassland transition. Using tree-ring width chronology of Mongolian pine, the reconstruction explains 49.2% of PDSI variance during their common data period (1951–2005). The reconstruction gives a broad-scale regional representation of PDSI in the Hulunbuir area, with drought occurrences in the 1850s, 1900s, 1920s, mid-1930s and at the turn of the 21st century. Comparisons with other tree-ring drought reconstructions and historical records reveal some common drought periods and drying trends in recent decades at the northern margin zones of the East Asian summer monsoon (EASM). The drying trends in these zones occurred earlier than weakening of the EASM. A REDFIT spectral analysis shows significant peaks at 7.2, 3.9, 2.7–2.8, 2.4 and 2.2 years with a 0.05 significance level, and 36.9, 18.1 and 5.0 years with 0.1 significance level. Wavelet analysis also shows similar cycles. Drought variations in the study area significantly correlated with sea surface temperatures in the western tropical Pacific Ocean and middle and northern Indian Ocean, and the Pacific Decadal Oscillation and North Atlantic Oscillation. This suggests a possible linkage with the El Niño-Southern Oscillation, the EASM and the Westerlies.

Description: Solar-cycle-related variation of differential rotation is investigated through analysing the rotation rates of magnetic fields, distributed along latitudes and varying with time at the time interval of 1976 August to 2008 April. More pronounced differentiation of rotation rates is found to appear at the ascending part of a Schwabe cycle than at the descending part on an average. The coefficient B in the standard form of differential rotation, which represents the latitudinal gradient of rotation, may be divided into three parts within a Schwabe cycle. Part 1 spans from the start to the fourth year of a Schwabe cycle, within which the absolute B is approximately a constant or slightly fluctuates. Part 2 spans from the fourth to the seventh year, within which the absolute B decreases. Part 3 spans from the seventh year to the end, within which the absolute B increases. Strong magnetic fields repress differentiation of rotation rates, so that rotation rates show less pronounced differentiation, but weak magnetic fields seem to just reflect differentiation of rotation rates. The solar-cycle-related variation of solar differential rotation is inferred to be the result of both the latitudinal migration of the surface torsional pattern and the repression of the strong magnetic activity to differentiation of rotation rates. The north–south asymmetry in solar rotation is investigated as well, and the Northern hemisphere should rotate faster than the southern in cycles 21–23.

Description: Azinomycin B is a hybrid polyketide/nonribosomal peptide natural product and possesses antitumor activity by interacting covalently with duplex DNA and inducing interstrand crosslinks. In the biosynthetic study of azinomycin B, a gene ( orf1 ) adjacent to the azinomycin B gene cluster was found to be essential for the survival of the producer, Streptomyces sahachiroi ATCC33158. Sequence analyses revealed that Orf1 belongs to the HTH_42 superfamily of conserved bacterial proteins which are widely distributed in pathogenic and antibiotic-producing bacteria with unknown functions. The protein exhibits a protective effect against azinomycin B when heterologously expressed in azinomycin-sensitive strains. EMSA assays showed its sequence nonspecific binding to DNA and structure-specific binding to azinomycin B-adducted sites, and ChIP assays revealed extensive association of Orf1 with chromatin in vivo . Interestingly, Orf1 not only protects target sites by protein–DNA interaction but is also capable of repairing azinomycin B-mediated DNA cross-linking. It possesses the DNA glycosylase-like activity and specifically repairs DNA damage induced by azinomycin B through removal of both adducted nitrogenous bases in the cross-link. This bifunctional protein massively binds to genomic DNA to reduce drug attack risk as a novel DNA binding protein and triggers the base excision repair system as a novel DNA glycosylase.

Description: Circular RNA (circRNA) is a group of RNA family generated by RNA circularization, which was discovered ubiquitously across different species and tissues. However, there is no global view of tissue specificity for circRNAs to date. Here we performed the comprehensive analysis to characterize the features of human and mouse tissue-specific (TS) circRNAs. We identified in total 302 853 TS circRNAs in the human and mouse genome, and showed that the brain has the highest abundance of TS circRNAs. We further confirmed the existence of circRNAs by reverse transcription polymerase chain reaction (RT-PCR). We also characterized the genomic location and conservation of these TS circRNAs and showed that the majority of TS circRNAs are generated from exonic regions. To further understand the potential functions of TS circRNAs, we identified microRNAs and RNA binding protein, which might bind to TS circRNAs. This process suggested their involvement in development and organ differentiation. Finally, we constructed an integrated database TSCD (Tissue-Specific CircRNA Database: http://gb.whu.edu.cn/TSCD ) to deposit the features of TS circRNAs. This study is the first comprehensive view of TS circRNAs in human and mouse, which shed light on circRNA functions in organ development and disorders.

Description: The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb.org ), the US data center for the global PDB archive, makes PDB data freely available to all users, from structural biologists to computational biologists and beyond. New tools and resources have been added to the RCSB PDB web portal in support of a ‘Structural View of Biology.’ Recent developments have improved the User experience, including the high-speed NGL Viewer that provides 3D molecular visualization in any web browser, improved support for data file download and enhanced organization of website pages for query, reporting and individual structure exploration. Structure validation information is now visible for all archival entries. PDB data have been integrated with external biological resources, including chromosomal position within the human genome; protein modifications; and metabolic pathways. PDB-101 educational materials have been reorganized into a searchable website and expanded to include new features such as the Geis Digital Archive.