ALBERT

Description: Bacterial sRNAs are a class of small regulatory RNAs of about 40–500 nt in length; they play multiple biological roles through binding to their target mRNAs or proteins. Therefore, elucidating sRNA targets is very important. However, only targets of a few sRNAs have been described. To facilitate sRNA functional studies such as developing sRNA target prediction models, we updated the sRNATarBase database, which was initially developed in 2010. The new version (recently moved to http://ccb1.bmi.ac.cn/srnatarbase/ ) contains 771 sRNA-target entries manually collected from 213 papers, and 23 290 and 11 750 predicted targets from sRNATarget and sTarPicker, respectively. Among the 771 entries, 475 and 17 were involved in validated sRNA–mRNA and sRNA–protein interactions, respectively, while 279 had no reported interactions. We also presented detailed information for 316 binding regions of sRNA-target mRNA interactions and related mutation experiments, as well as new features, including NCBI sequence viewer, sRNA regulatory network, target prediction-based GO and pathway annotations, and error report system. The new version provides a comprehensive annotation of validated sRNA-target interactions, and will be a useful resource for bacterial sRNA studies.

Description: The optical and optical/near-infrared pseudo-bolometric light curves of 85 stripped-envelope supernovae (SNe) are constructed using a consistent method and a standard cosmology. The light curves are analysed to derive temporal characteristics and peak luminosity L p , enabling the construction of a luminosity function. Subsequently, the mass of 56 Ni synthesized in the explosion, along with the ratio of ejecta mass to ejecta kinetic energy, are found. Analysis shows that host-galaxy extinction is an important factor in accurately determining luminosity values as it is significantly greater than Galactic extinction in most cases. It is found that broad-lined SNe Ic (SNe Ic-BL) and gamma-ray burst SNe are the most luminous subtypes with a combined median L p , in erg s –1 , of log( L p ) = 43.00 compared to 42.51 for SNe Ic, 42.50 for SNe Ib, and 42.36 for SNe IIb. It is also found that SNe Ic-BL synthesize approximately twice the amount of 56 Ni compared with SNe Ic, Ib, and IIb, with median M Ni = 0.34, 0.16, 0.14, and 0.11 M , respectively. SNe Ic-BL, and to a lesser extent SNe Ic, typically rise from L p /2 to L p more quickly than SNe Ib/IIb; consequently, their light curves are not as broad.

Description: For the saddle point problem arising from the finite element discretization of the hybrid formulation of the time-harmonic eddy current problem, we propose an alternating positive-semidefinite splitting (APSS) preconditioner which is based on two positive-semidefinite splittings of the saddle point matrix. It is proved that the corresponding APSS iteration method is unconditionally convergent. We show that the new preconditioner is much easier to implement than the block alternating splitting implicit preconditioner proposed in Bai (2012, Numer. Linear Algebra Appl. , 19 , 914–936) when they are used to accelerate the convergence rate of Krylov subspace methods such as GMRES. Numerical examples are given to show the effectiveness of our proposed preconditioner.

Description: Snub-nosed monkeys (genus Rhinopithecus ) are a group of endangered colobines endemic to South Asia. Here, we re-sequenced the whole genomes of 38 snub-nosed monkeys representing four species within this genus. By conducting population genomic analyses, we observed a similar load of deleterious variation in snub-nosed monkeys living in both smaller and larger populations and found that genomic diversity was lower than that reported in other primates. Reconstruction of Rhinopithecus evolutionary history suggested that episodes of climatic variation over the past 2 million years, associated with glacial advances and retreats and population isolation, have shaped snub-nosed monkey demography and evolution. We further identified several hypoxia-related genes under selection in R. bieti (black snub-nosed monkey), a species that exploits habitats higher than any other nonhuman primate. These results provide the first detailed and comprehensive genomic insights into genetic diversity, demography, genetic burden, and adaptation in this radiation of endangered primates.

Description: We assemble 3524 quasars from the Sloan Digital Sky Survey (SDSS) with repeated observations to search for variations of the narrow $\rm C\,\small {IV}\,\lambda \lambda 1548,1551$ and $\rm Mg\,\small {II}\,\lambda \lambda 2796,2803$ absorption doublets in spectral regions shortward of 7000 Å in the observed frame, which corresponds to time-scales of about 150–2643 d in the quasar rest frame. In these quasar spectra, we detect 3580 C iv absorption systems with z abs  = 1.5188–3.5212 and 1809 Mg ii absorption systems with z abs  = 0.3948–1.7167. In term of the absorber velocity (β) distribution in the quasar rest frame, we find a substantial number of C iv absorbers with β 〈 0.06, which might be connected to absorption of quasar outflows. The outflow absorption peaks at $\upsilon \approx 2000\,\rm km\,s^{-1}$ and drops rapidly below this peak value. Among 3580 C iv absorption systems, 52 systems (~1.5 per cent) show obvious variations in equivalent widths in the absorber rest frame ( W r ): 16 enhanced, 16 emerged, 12 weakened and 8 disappeared systems, respectively. We find that changes in W r 1548 are related neither to the time-scales of the two SDSS observations nor to absorber velocities in the quasar rest frame. Variable absorption in low-ionization species is important to constrain the physical conditions of the absorbing gas. There are two variable Mg ii absorption systems measured from SDSS spectra detected by Hacker et al. However, in our Mg ii absorption sample, we find that neither shows variable absorption with confident levels of 〉4 for 2796 lines and 〉3 for 2803 lines.

Description: Small RNA-directed DNA methylation (RdDM) is an important epigenetic pathway in Arabidopsis that controls the expression of multiple genes and several developmental processes. RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and DICER-LIKE 3 (DCL3) are necessary factors in 24-nt small interfering RNA (siRNA) biogenesis, which is part of the RdDM pathway. Here, we found that Increase in BONSAI Methylation 1 (IBM1), a conserved JmjC family histone demethylase, is directly associated with RDR2 and DCL3 chromatin. The mutation of IBM1 induced the hypermethylation of H3K9 and DNA non-CG sites within RDR2 and DCL3 , which repressed their expression. A genome-wide analysis suggested that the reduction in RDR2 and DCL3 expression affected siRNA biogenesis in a locus-specific manner and disrupted RdDM-directed gene repression. Together, our results suggest that IBM1 regulates gene expression through two distinct pathways: direct association to protect genes from silencing by preventing the coupling of histone and DNA methylation, and indirect silencing of gene expression through RdDM-directed repression.

Description: The fore-arc mantle above a subducting slab is a unique site where complex partial melting, melt/fluid–rock interaction, and deformation of mantle rocks occur. To constrain these geological and geodynamic processes we analyzed the deformation microstructures, crystal preferred orientations (CPOs or fabrics), and water content in natural harzburgites that occur as exhumed massifs in the North Qilian suture zone, NW China. These harzburgites are very fresh, and have mineral assemblages of olivine (~81–87 vol. %), orthopyroxene (~11–17 vol. %), clinopyroxene (~1–2 vol. %), and spinel (~1 vol. %). Detailed analyses of mineral textures, CPO patterns, and rotation axis distributions suggest that the plastic deformation of olivine and pyroxene was accommodated by activating a series of slip systems of dislocation. The olivine (A-/D-type fabric) shows dominant (010)[100] and/or (001)[100] slip systems, as well as other minor [100]-glide, {0 kl }[100], and [001]-glide slip systems. The orthopyroxene shows dominant (100)[001] and subordinate (010)[001] slip systems, with minor (100)[010] and (100)[0 vw ] slip systems. The water content is extremely low in the orthopyroxene (38–44 ppm by weight), equilibrated olivine (4–7 ppm), and bulk-rock samples (9–14 ppm). Previously published refractory mineral and whole-rock compositions, as well as estimated low-pressure (~1–2 GPa), high-temperature (~1100–1300°C), low-stress (~1–4 MPa) and water-poor conditions of deformation, suggest that these harzburgites represent a remnant of fossil fore-arc lithospheric mantle that was probably both formed (experienced partial melting and high-temperature melt/fluid–rock reaction) and deformed in a young and warm fore-arc mantle setting (i.e. juvenile subduction zone). Based on these results, a refined schematic model of olivine fabric distributions in subduction zones is proposed. In this model, the A-/D-type olivine fabrics are inferred to be prevalent in fore-arc lithospheric mantle. The opposing polarizing directions of A-/D-type olivine fabrics with other underlying anisotropic sources in the mantle wedge (e.g. B-type olivine fabrics and oriented serpentinite layers) may weaken the trench-parallel fast S-wave anisotropy contributed by the deformed fore-arc mantle, and thus provide an alternative explanation for the short or nearly null delay times of local shear-wave splitting (sourced from intra-slab earthquakes) that have been detected in some fore-arc regions. In addition, topotactic antigorite fabrics after the A-/D-type olivine fabric might play a minor role in contributing to the low P- and S-wave velocities, high V p / V s ratios, and large seismic anisotropies that are typically observed in fore-arc mantle.

Description: The C 4 plants, whose first product of photosynthetic CO 2 fixation is a four-carbon acid, have evolved independently many times. Crassulacean acid metabolism (CAM) is a biological mechanism known to exhibit some C 4 characteristics such as the C 3 cycle during daylight and demonstrates the C 4 cycle at night. There are also various C 3 -CAM intermediates, whose CAM pathway can be induced by environmental changes. However, neither fungus-induced CAM nor Theaceae CAM have been reported previously. Here, we show that CAM could be generated by fungus infection in Camellia oleifera Abel. young leaves, even at a location of a single leaf where the upper part had been transformed into a succulent one, while the lower part remained unchanged. The early photosynthetic products of dark-grown C. oleifera succulent leaves were malate, whereas C. oleifera normal leaves and light-grown succulent leaves incorporated most of 14 C into the primary photosynthetic product 3-phosphoglycerate. Camellia oleifera succulent leaves have a lower absolute 13 C value, much lower photorespiration rates and lower transpiration rates during the day than those of C. oleifera normal leaves. Like a typical CAM plant, stomata of C. oleifera succulent leaves closed during the daylight, but opened at night, and therefore had a detectable CO 2 compensation point in darkness. Net photosynthetic rates ( P n ) fluctuated diurnally and similarly with stomatal aperture. No light intensity saturation could be defined for C. oleifera succulent leaves. C 4 key enzymes in C. oleifera succulent leaves were increased at both the transcriptional/translational levels as well as at the enzyme activity level.

Description: Although there are many studies to show a key role of transposable elements (TEs) in adaptive evolution of higher organisms, little is known about the molecular mechanisms. In this study, we found that a partial TE ( Taguchi ) inserted in the cis -regulatory region of the silkworm ecdysone oxidase (EO) gene, which encodes a crucial enzyme to reduce the titer of molting hormone (20-hydroxyecdysone, 20E). The TE insertion occurred during domestication of silkworm and the frequency of the TE insertion in the domesticated silkworm ( Bombyx mori ) is high, 54.24%. The linkage disequilibrium in the TE inserted strains of the domesticated silkworm was elevated. Molecular population genetics analyses suggest that this TE insertion is adaptive for the domesticated silkworm. Luminescent reporter assay shows that the TE inserted in the cis -regulatory region of the EO gene functions as a 20E-induced enhancer of the gene expression. Further, phenotypic bioassay indicates that the silkworm with the TE insertion exhibited more stable developmental phenotype than the silkworm without the TE insertion when suffering from food shortage. Thus, the inserted TE in the cis -regulatory region of the EO gene increased developmental uniformity of silkworm individuals through regulating 20E metabolism, partially explaining transformation of a domestication developmental trait in the domesticated silkworm. Our results emphasize the exceptional role of gene expression regulation in developmental transition of domesticated animals.

Description: In Neurospora crassa , the methionine synthase gene met-8 plays a key role in methionine synthesis. In this study, we found that MET-8 protein levels were compromised in several mutants defective in proper heterochromatin formation. Bioinformatics analysis revealed a 50-kb AT-rich region adjacent to the met-8 promoter. ChIP assays confirmed that trimethylated H3K9 was enriched in this region, indicating that heterochromatin may form upstream of met-8 . In an H3K9R mutant strain, the output of met-8 was dramatically reduced, similar to what we observed in mutant strains that had defective heterochromatin formation. Furthermore, the production of ectopically expressed met-8 at the his-3 locus in the absence of a normal heterochromatin environment was inefficient, whereas ectopic expression of met -8 downstream of two other heterochromatin domains was efficient. In addition, our data show that the expression of mig-6 was also controlled by an upstream 4.2-kb AT-rich region similar to that of the met-8 gene, and we demonstrate that the AT-rich regions adjacent to met-8 or mig-6 are required for their peak expression. Our study indicates that met-8 and mig-6 may represent a novel type of gene, whose expression relies on the proper formation of a nearby heterochromatin region.