Bases are called using Illumina pipeline Casava 1.8.Reads are mapped to the drosophila genome using Tophat2. Refseq annotations of known exon junctions are provided with -G option.Number of reads on each gene were counted using custom script, and differentially expressed genes were called using edgeR.Genome_build: Dm3Supplementary_files_format_and_content: tab-delimited text file listing the number of reads on each gene

Bases are called using Illumina pipeline Casava 1.8.Reads are mapped to the drosophila genome using Tophat2. Refseq annotations of known exon junctions are provided with -G option.Number of reads on each gene were counted using custom script, and differentially expressed genes were called using edgeR.Genome_build: Dm3Supplementary_files_format_and_content: tab-delimited text file listing the number of reads on each gene

Aging of immune organs, termed as immunosenescence, is suspected to promote systemic inflammation and age-associated disease. The cause of immunosenescence and how it promotes disease, however, has remained unclear. We report that the Drosophila fat body, a major immune organ, undergoes immunosenescence andmounts strong systemic inflammation that leads to deregulation of immune deficiency (IMD) signaling in the midgut of old animals. Inflamed old fat bodies secrete circulating peptidoglycan recognition proteins that repress IMD activity in the midgut, thereby promoting gut hyperplasia. Further, fat body immunosenecence is caused by age-associated lamin-B reduction specifically in fat body cells, which then contributes to heterochromatin loss and derepression of genes involved in immune responses. As lamin-associated heterochromatin domains are enriched for genes involved in immune response in both Drosophila and mammalian cells, our findings may provide insights into the cause and consequence of immunosenescence during mammalian aging.

Cellular architectural proteins often participate in organ development and maintenance. Although functional decay of some of these proteins during aging is known, the cell-type-specific developmental role and the cause and consequence of their subsequent decay remain to be established especially in mammals. By studying lamins, the nuclear structural proteins, we demonstrate that lamin-B1 functions specifically in the thymic epithelial cells (TECs) for proper thymus organogenesis. An up-regulation of proinflammatory cytokines in the intra-thymic myeloid immune cells during aging accompanies a gradual reduction of lamin-B1 in adult TECs. We show that these cytokines can cause senescence and lamin-B1 reduction of the young adult TECs. Lamin-B1 supports the expression of TEC genes that can help maintain the adult TEC subtypes we identified by single-cell RNA-sequencing, thymic architecture, and function. Thus, structural proteins involved in organ building and maintenance can undergo inflammation-driven decay which can in turn contribute to age-associated organ degeneration.

We present the largest-ever sample of 79 Ly? emitters (LAEs) at z?7.0 selected in the COSMOS and CDFS fields of the LAGER project (the Lyman Alpha Galaxies in the Epoch of Reionization). Our newly amassed ultradeep narrowband exposure and deeper/wider broadband images have more than doubled the number of LAEs in COSMOS, and we have selected 30 LAEs in the second field CDFS. We detect two large-scale LAE-overdense regions in the COSMOS that are likely protoclusters at the highest redshift to date. We perform injection and recovery simulations to derive the sample incompleteness. We show that significant incompleteness comes from blending with foreground sources, which, however, has not been corrected in LAE luminosity functions (LFs) in the literature. The bright-end bump in the Ly? LF in COSMOS is confirmed with six (two newly selected) luminous LAEs (L-Ly? > 10(43.3) erg s(?1)). Interestingly, the bump is absent in CDFS, in which only one luminous LAE is detected. Meanwhile, the faint-end LFs from the two fields agree well with each other. The six luminous LAEs in COSMOS coincide with two LAE-overdense regions, while such regions are not seen in CDFS. The bright-end LF bump could be attributed to ionized bubbles in a patchy reionization. It appears associated with cosmic overdensities and thus supports an inside-out reionization topology at z?7.0, i.e., the high-density peaks were ionized earlier compared to the voids. An average neutral hydrogen fraction of x(H i)?0.2?0.4 is derived at z?7.0 based on the cosmic evolution of the Ly? LF.

Main conclusion This study demonstrates that brassinosteroid is essential for seedling and shoot growth in moso bamboo. The shoot of moso bamboo is known to grow extremely fast. The roles of phytohormones in such fast growth of bamboo shoot remain unclear. Here we reported that endogenous brassinosteroid (BR) is a major factor promoting bamboo shoot internode elongation. Reducing endogenous brassinosteroid level by its biosynthesis inhibitor propiconazole stunted shoot growth in seedling stage, whereas exogenous BR application promoted scale leaf elongation and the inclination of lamina joint of leaves and scale leaves. Genome-wide transcriptome analysis identified hundreds of genes whose expression levels are altered by BR and propiconazole in shoots and roots of bamboo seedling. The data show that BR regulates cell wall-related genes, hydrogen peroxide catabolic genes, and auxin-related genes. Our study demonstrates an essential role of BR in fast growth bamboo shoots and identifies a large number of BR-responsive genes in bamboo seedlings.

We presented an adaptation of the TSA-seq antibody based method to map chromatin at the nuclear lamina from lower numbers of cells, which we term chromatin-based TSA-seq or cTSA-seq. We provide evidence that the method maps closed heterochromatin at or near the nuclear lamina that is in the B-compartment and show that it is useful down to 50,000 cells. We applied this emthod to the early G1 cell population to verify its utility and show that telomeric ends are indeed nl-proximal during this stage. We further provide evidence that the early G1 lADs profile is reminiscent of the profiles observed for oncogene-induced senescence.

Protoclusters, the progenitors of the most massive structures in the Universe, have been identified at redshifts of up to 6.6 (refs. (1-6)). Besides exploring early structure formation, searching for protoclusters at even higher redshifts is particularly useful to probe the reionization. Here we report the discovery of the protocluster LAGER-z7OD1 at a redshift of 6.93, when the Universe was only 770 million years old and could be experiencing rapid evolution of the neutral hydrogen fraction in the intergalactic medium(7,8). The protocluster is identified by an overdensity of 6 times the average galaxy density, and with 21 narrowband selected Lyman-alpha galaxies, among which 16 have been spectroscopically confirmed. At redshifts similar to or above this record, smaller protogroups with fewer members have been reported(9,10). LAGER-z7OD1 shows an elongated shape and consists of two subprotoclusters, which would have merged into one massive cluster with a present-day mass of 3.7 x 10(15) solar masses. The total volume of the ionized bubbles generated by its member galaxies is found to be comparable to the volume of the protocluster itself, indicating that we are witnessing the merging of the individual bubbles and that the intergalactic medium within the protocluster is almost fully ionized. LAGER-z7OD1 thus provides a unique natural laboratory to investigate the reionization process.

We report phonon densities of states (DOS) of iron measured by nuclear resonant inelastic x-ray scattering to 153 gigapascals and calculated from ab initio theory. Qualitatively, they are in agreement, but the theory predicts density at higher energies. From the DOS, we derive elastic and thermodynamic parameters of iron, including shear modulus, compressional and shear velocities, heat capacity, entropy, kinetic energy, zero-point energy, and Debye temperature. In comparison to the compressional and shear velocities from the preliminary reference Earth model (PREM) seismic model, our results suggest that Earth's inner core has a mean atomic number equal to or higher than pure iron, which is consistent with an iron-nickel alloy.

We report phonon densities of states (DOS) of iron measured by nuclear resonant inelastic x-ray scattering to 153 gigapascals and calculated from ab initio theory. Qualitatively, they are in agreement, but the theory predicts density at higher energies. From the DOS, we derive elastic and thermodynamic parameters of iron, including shear modulus, compressional and shear velocities, heat capacity, entropy, kinetic energy, zero-point energy, and Debye temperature. In comparison to the compressional and shear velocities from the preliminary reference Earth model (PREM) seismic model, our results suggest that Earth's inner core has a mean atomic number equal to or higher than pure iron, which is consistent with an iron-nickel alloy.