Subcellular RNA distribution and its change during human embryonic stem cell differentiation.

The spatial localization of RNA within cells is closely related to its function and also involved in cell fate determination. However, the atlas of RNA distribution within cells and dynamic changes during the developmental process are largely unknown. In this study, five subcellular components, including cytoplasmic extract, membrane extract, soluble nuclear extract, chromatin-bound nuclear extract, and cytoskeletal extract, were isolated and the rules of subcellular RNA distribution in human embryonic stem cells (hESCs) and its change during hESC differentiation are summarized for the first time. The overall distribution patterns of coding and non-coding RNAs are revealed. Interestingly, some developmental genes are found to be transcribed but confined to the chromatin in undifferentiated hESC. Unexpectedly, alternative splicing and polyadenylation endow spatial heterogeneity among different isoforms of the same gene. Finally, the dynamic pattern of RNA distribution during hESC differentiation is characterized, which provides new clues for a comprehensive understanding hESC pluripotency and differentiation.

De novo genes with an lncRNA origin encode unique human brain developmental functionality.

Human de novo genes can originate from neutral long non-coding RNA (lncRNA) loci and are evolutionarily significant in general, yet how and why this all-or-nothing transition to functionality happens remains unclear. Here, in 74 human/hominoid-specific de novo genes, we identified distinctive U1 elements and RNA splice-related sequences accounting for RNA nuclear export, differentiating mRNAs from lncRNAs, and driving the origin of de novo genes from lncRNA loci. The polymorphic sites facilitating the lncRNA-mRNA conversion through regulating nuclear export are selectively constrained, maintaining a boundary that differentiates mRNAs from lncRNAs. The functional new genes actively passing through it thus showed a mode of pre-adaptive origin, in that they acquire functions along with the achievement of their coding potential. As a proof of concept, we verified the regulations of splicing and U1 recognition on the nuclear export efficiency of one of these genes, the ENSG00000205704, in human neural progenitor cells. Notably, knock-out or over-expression of this gene in human embryonic stem cells accelerates or delays the neuronal maturation of cortical organoids, respectively. The transgenic mice with ectopically expressed ENSG00000205704 showed enlarged brains with cortical expansion. We thus demonstrate the key roles of nuclear export in de novo gene origin. These newly originated genes should reflect the novel uniqueness of human brain development.

Genome-wide analysis of pseudogenes reveals HBBP1's human-specific essentiality in erythropoiesis and implication in ß-thalassemia.

The human genome harbors 14,000 duplicated or retroposed pseudogenes. Given their functionality as regulatory RNAs and low conservation, we hypothesized that pseudogenes could shape human-specific phenotypes. To test this, we performed co-expression analyses and found that pseudogene exhibited tissue-specific expression, especially in the bone marrow. By incorporating genetic data, we identified a bone-marrow-specific duplicated pseudogene, HBBP1 (η-globin), which has been implicated in ß-thalassemia. Extensive functional assays demonstrated that HBBP1 is essential for erythropoiesis by binding the RNA-binding protein (RBP), HNRNPA1, to upregulate TAL1, a key regulator of erythropoiesis. The HBBP1/TAL1 interaction contributes to a milder symptom in ß-thalassemia patients. Comparative studies further indicated that the HBBP1/TAL1 interaction is human-specific. Genome-wide analyses showed that duplicated pseudogenes are often bound by RBPs and less commonly bound by microRNAs compared with retropseudogenes. Taken together, we not only demonstrate that pseudogenes can drive human evolution but also provide insights on their functional landscapes.

Effects of azithromycin on feeding behavior and nutrition accumulation of Daphnia magna under the different exposure pathways.

Antibiotics had been paid more and more attention to their toxicity to non-target aquatic organisms in the aquatic environment. As azithromycin (AZI) was an important antibiotic pollutant in water, its toxicity to aquatic organisms had been investigated. In this study, the potential aquatic ecological risk of AZI was identified by assessing the toxicity on the feeding behavior and physiological function of Daphnia magna (D. magna) under the different exposure pathways (aqueous phase exposure vs. food phase exposure). For the food Chlorella pyrenoidosa (C. pyrenoidosa), AZI could inhibit the growth and nutrition accumulation with concentration- and time-response relationship. For D. magna, the feeding behavior was inhibited by AZI under the aqueous phase exposure pathway. However, the feeding behavior was inhibited firstly and then reversed into promotion in the low and medium concentration groups and was continually promoted in the high concentration group under the food phase exposure pathway. The accumulation of polysaccharides and total protein were decreased in D. magna n the high concentration group under the aqueous phase exposure pathway, while the accumulation of polysaccharides and crude fat were decreased in the high concentration group under the food phase exposure pathway. The activity of amylase (AMS) and trypsin in D. magna were decreased after exposure to AZI under the aqueous phase exposure pathway. On the other hand, the activity of AMS in the medium and high concentration groups was decreased under the food phase exposure pathway, but the activity of trypsin was decreased in the medium concentration group and increased in the high concentration group. The levels of ROS in D. magna were also measured and increased in both exposure pathways except in the low concentration group under the food phase exposure pathway, indicating the oxidative stress injury of D. magna. Our results showed that AZI could affect the digestive enzyme activities and oxidative stress-antioxidative system, ultimately leading to the change of D. magna's feeding behavior and nutrition accumulation. These results also provided a comprehensive perspective to evaluate the toxic effects of non-lethal dose antibiotics to non-target aquatic organisms via different exposure pathways.

[Histological structure of the trabecular meshwork in the eyeball: challenging the traditional concept and preliminary findings in rabbits, rats and mice].

OBJECTIVE: To verify that the trabecular meshwork (TM) in the wall of the eyeball consists of smooth muscle fibers instead of collagen fibers or endothelial cells. METHODS: Eighteen fresh eyeballs from 3 rabbits, 3 SD rats and 3 mice were sectioned along the sagittal plane and sliced after paraffin embedding for HE staining, VG staining, Masson staining, α-SMA immunohistochemistry or CD31 immunohistochemistry. These slices were observed under microscope and the structure of the TM was compared with those of scleral collagen fibers, ciliary muscles and endothelial cells. RESULTS: HE staining of the eyeball slices from the 3 animal species resulted in purplish red staining of the TM, which was highly consistent with ciliary muscle fibers. The cell?like structures on the surface of the TM were not clearly outlined, with flat nuclei showing a dark purple staining; these structures did not show obvious boundaries from the TM. Ciliary muscle fibers, which were smooth muscle cells in nature, were aligned in bundles in various directions. The longitudinally sectioned cells were flat and contained purplish cytoplasm and highly flattened nuclei. Scleral collagen fibers were stained dark red with a few fibroblasts sandwiched among them. The long axis of the fibroblasts was in parallel with that of the collagen fibers. The outline of the fibroblast was not clear and the nucleus was flat in dark blue. The vascular endothelial cells presented with different morphologies and contained light purplish cytoplasm and dark nuclei, protruding into the vascular cavity. VG staining of the TM revealed a pale red filamentous structure, and the collagen fibers were stained bright red. Masson staining of the TM showed a reticular structure consisting mainly of dark red fibers intermingled with thin green fibers. Scleral collagen fibers presented with a cord?like green wavy structure. The endothelial cells were green and flat, while the ciliary smooth muscle fibers were purple. In immunohistochemistry for α?SMA, the TM and the ciliary smooth muscle fibers showed a strong positivity in the cytoplasm, while the scleral collagen fibers and vascular endothelial cells showed negative staining; immunohistochemistry for CD31 showed no obvious positive staining in the TM, collagen fibers or ciliary smooth muscle cells from all the animals in spite of slight differences among them. CONCLUSION: The TM consists mainly of smooth muscle fibers with a thin layer of peripheral endomysium without endothelial cells.

Toxicity studies of tetracycline on Microcystis aeruginosa and Selenastrum capricornutum.

The assays of first exposure and second exposure effects with tetracycline (TC) on the freshwater cyanobacterium Microcystis aeruginosa and chlorophyceae Selenastrum capricornutum were investigated by determining a battery of parameters including algal biomass, chlorophyll fluorescence index Fv/Fm, superoxide dismutase (SOD) and malonaldehyde (MDA) in this study. In general, TC could significantly inhibit the growth and physiological progress including primary photochemistry and antioxidant system. However, upon the second exposure, the inhibitory effects of TC were decreased compared to the first exposure. And it suggests that Fv/Fm, SOD and MDA were more sensitive than algal biomass. In addition, M. aeruginosa showed stronger survivability than S. capriconutum.