Integrating ATAC-seq and RNA-seq to identify differentially expressed genes with chromatin-accessible changes during photosynthetic establishment in Populus leaves.

Leaves are the primary photosynthetic organs, providing essential substances for tree growth. It is important to obtain an anatomical understanding and regulatory network analysis of leaf development. Here, we studied leaf development in Populus Nanlin895 along a development gradient from the newly emerged leaf from the shoot apex to the sixth leaf (L1 to L6) using anatomical observations and RNA-seq analysis. It indicated that mesophyll cells possess obvious vascular, palisade, and spongy tissue with distinct intercellular spaces after L3. Additionally, vacuoles fuse while epidermal cells expand to form pavement cells. RNA-seq analysis indicated that genes highly expressed in L1 and L2 were related to cell division and differentiation, while those highly expressed in L3 were enriched in photosynthesis. Therefore, we selected L1 and L3 to integrate ATAC-seq and RNA-seq and identified 735 differentially expressed genes (DEGs) with changes in chromatin accessibility regions within their promoters, of which 87 were transcription factors (TFs), such as ABI3VP1, AP-EREBP, MYB, NAC, and GRF. Motif enrichment analysis revealed potential regulatory functions for the DEGs through upstream TFs including TCP, bZIP, HD-ZIP, Dof, BBR-BPC, and MYB. Overall, our research provides a potential molecular foundation for regulatory network exploration in leaf development during photosynthesis establishment.

Daphnia magna uptake and excretion of luminescence-labelled polystyrene nanoparticle as visualized by high sensitivity real-time optical imaging.

The environmental and ecological consequences of nanoplastics (NPs) draw increasing research interests and social concerns. However, the in situ and real-time detection of NPs from living organisms and transferring media remains as a major technical obstacle for scientific investigation. Herein we report a novel time-gated imaging (TGI) strategy capable of real-time visualizing the intake of NPs by an individual living organism, which is based on the polystyrene NPs labelled with lanthanide up-conversion luminescence. The limit of detection (LOD) of the TGI apparatus was 600 pg (SNR = 3) in a field of view of 2.4 × 3.8 mm. Taking Daphnia magna as the aquatic model, we investigated the dynamics of uptake and accumulation of NPs (500 µg/L) for 24 h, and the subsequent excretion process (in clean medium) for 48 h, and quantitively analyzed the distribution and the overall mass of NPs deposited in D. magna. The uptake of NPs via filter-feeding occurred in a few minutes, whereas a longer accumulation was found, in a timescale of several hours. And similar behaviors (bi-phase elimination) were also seen in the excretion, indicating the migration of NPs into the circulatory system. The average mass of NPs accumulated in an individual D. magna was ∼12 ng after 24 h exposure, indicating that D. magna as a filter feeder tends to retain NPs. The observed NPs accumulation in D. magna exemplifies the potential risk of aquatic ecosystem on exposure to NP contamination.

PdeHCA2 affects biomass in Populus by regulating plant architecture, the transition from primary to secondary growth, and photosynthesis.

MAIN CONCLUSION: PdeHCA2 regulates the transition from primary to secondary growth, plant architecture, and affects photosynthesis by targeting PdeBRC1 and controlling the anatomy of the mesophyll, and intercellular space, respectively. Branching, secondary growth, and photosynthesis are vital developmental processes of woody plants that determine plant architecture and timber yield. However, the mechanisms underlying these processes are unknown. Here, we report that the Populus transcription factor High Cambium Activity 2 (PdeHCA2) plays a role in the transition from primary to secondary growth, vascular development, and branching. In Populus, PdeHCA2 is expressed in undifferentiated provascular cells during primary growth, in phloem cells during secondary growth, and in leaf veins, which is different from the expression pattern of its homolog in Arabidopsis. Overexpression of PdeHCA2 has pleiotropic effects on shoot and leaf development; overexpression lines showed delayed growth of shoots and leaves, reduced photosynthesis, and abnormal shoot branching. In addition, auxin-, cytokinin-, and photosynthesis-related genes were differentially regulated in these lines. Electrophoretic mobility shift assays and transcriptome analysis indicated that PdeHCA2 directly up-regulates the expression of BRANCHED1 and the MADS-box gene PdeAGL9, which regulate plant architecture, by binding to cis-elements in the promoters of these genes. Taken together, our findings suggest that HCA2 regulates several processes in woody plants including vascular development, photosynthesis, and branching by affecting the proliferation and differentiation of parenchyma cells.

Lipid-Enhanced Photoprotection of LHCII in Membrane Nanodisc by Reducing Chlorophyll Triplet Production.

Carotenoid (Car) quenching chlorophyll triplet state (3Chl a*), an unwanted photosensitizer yielding harmful reactive oxygen species, is crucial for the survival of oxygenic photosynthetic organisms. For the major light-harvesting complex of photosystem II (LHCII) in isolated form, 3Chl a* is deactivated via sub-nanosecond Chl-to-Car triplet excitation energy transfer by lutein in the central domain of LHCII; however, the mechanistic difference from LHCII in vivo remains to be explored. To investigate the intrinsic Car-photoprotection properties of LHCII in a bio-mimicking circumstance, we reconstituted trimeric spinach LHCII into the discoidal membrane of nanosize made from l-α-phosphatidylcholine and examined the triplet excited dynamics. Time-resolved optical absorption combined with circular dichroism spectroscopies revealed that, with reference to LHCII in buffer, LHCII in the membrane nanodisc shows appreciable conformational variation in the neoxanthin and the Lut621 domains and in the Chl a-terminal cluster owing to the lipid-protein interactions, which, in turn, alters the triplet population of Lut620 and Lut621 and their partition. Importantly, the unquenched 3Chl a* population in the complex was reduced by 60%, indicating that LHCII in the membrane adopts a conformation that is optimized for the alleviation of photoinhibition.

MicroRNA­125a­mediated regulation of the mevalonate signaling pathway contributes to high glucose­induced proliferation and migration of vascular smooth muscle cells.

Hyperglycemia contributes to the excessive proliferation and migration of vascular smooth muscle cells (VSMC), which are closely associated with atherosclerosis. MicroRNAs (miRNAs/miRs) constitute a novel class of gene regulators, which have important roles in various pathological conditions. The aim of the present study was to identify miRNAs involved in the high glucose (HG)­induced VSMC phenotype switch, and to investigate the underlying mechanism. miRNA sequencing and reverse transcription­quantitative PCR results indicated that inhibition of miR­125a expression increased the migration and proliferation of VSMCs following HG exposure, whereas the overexpression of miR­125a abrogated this effect. Furthermore, dual­luciferase reporter assay results identified that 3­hydroxy­3-methyglutaryl­coA reductase (HMGCR), one of the key enzymes in the mevalonate signaling pathway, is a target of miR­125a. Moreover, HMGCR knockdown, similarly to miR­125a overexpression, suppressed HG­induced VSMC proliferation and migration. These results were consistent with those from the miRNA target prediction programs. Using a rat model of streptozotocin­induced diabetes mellitus, it was demonstrated that miR­125a expression was gradually downregulated, and that the expressions of key enzymes in the mevalonate signaling pathway in the aortic media were dysregulated after several weeks. In addition, it was found that HG­induced excessive activation of the mevalonate signaling pathway in VSMCs was suppressed following transfection with a miR­125a mimic. Therefore, the present results suggest that decreased miR­125a expression contributed to HG­induced VSMC proliferation and migration via the upregulation of HMGCR expression. Thus, miR­125a­mediated regulation of the mevalonate signaling pathway may be associated with atherosclerosis.

Uptake and Translocation of Styrene Maleic Anhydride Nanoparticles in Murraya exotica Plants As Revealed by Noninvasive, Real-Time Optical Bioimaging.

This work reports the in vivo uptake and translocation of PNPs in the one-year grown terrestrial plant, Murraya exotica ( M. exotica), as investigated by two-photon excitation and time-resolved (TPE-TR) optical imaging with a large field of view (FOV, 32 × 32 mm2) in a noninvasive and real-time manner. The PNPs (⟨ Rh⟩ = 12 ± 4.5 nm) synthesized from poly(styrene- co-maleic anhydride) (SMA) were Eu-luminescence labeled (λL ≈ 617 nm). On exposing the roots of living M. exotica plants to the colloidal suspension of SMA PNPs at different concentrations, the spatiotemporal evolution of SMA PNPs along plant stems (60 mm in length) were monitored by TPE-TR imaging, which rendered rich information on the uptake and translocation of PNPs without any interference from the autofluorescence of the plant tissues. The TPE-TR imaging combined with the high-resolution anatomy revealed an intercell-wall route in the lignified epidermis of M. exotica plants for SMA PNP uptake and translocation, as well as the similar accumulation kinetics at different positions along the plant stems. We modeled the accumulation kinetics with Gaussian distribution to account for the trapping probability of a SMA PNP by the lignified cell walls, allowing the statistical parameters, the average trapping time ( tm) and its variance (σ), to be derived for the quantification of the PNP accumulation in individual plants. The TPE-TR imaging and the analysis protocols established herein will be helpful in exploring the mechanism of plant-PNP interaction under physiological condition.

The developmental dynamics of the Populus stem transcriptome.

The Populus shoot undergoes primary growth (longitudinal growth) followed by secondary growth (radial growth), which produces biomass that is an important source of energy worldwide. We adopted joint PacBio Iso-Seq and RNA-seq analysis to identify differentially expressed transcripts along a developmental gradient from the shoot apex to the fifth internode of Populus Nanlin895. We obtained 87 150 full-length transcripts, including 2081 new isoforms and 62 058 new alternatively spliced isoforms, most of which were produced by intron retention, that were used to update the Populus annotation. Among these novel isoforms, there are 1187 long non-coding RNAs and 356 fusion genes. Using this annotation, we found 15 838 differentially expressed transcripts along the shoot developmental gradient, of which 1216 were transcription factors (TFs). Only a few of these genes were reported previously. The differential expression of these TFs suggests that they may play important roles in primary and secondary growth. AP2, ARF, YABBY and GRF TFs are highly expressed in the apex, whereas NAC, bZIP, PLATZ and HSF TFs are likely to be important for secondary growth. Overall, our findings provide evidence that long-read sequencing can complement short-read sequencing for cataloguing and quantifying eukaryotic transcripts and increase our understanding of the vital and dynamic process of shoot development.

Clinical and molecular genetic analysis of a Chinese family with congenital X-linked adrenal hypoplasia caused by novel mutation 1268delA in the DAX-1 gene.

Congenital X-linked adrenal hypoplasia (AHC) is a rare disease characterized by primary adrenal insufficiency before adolescence and by hypogonadotropic hypogonadism (HHG) during adolescence. In this paper, we present a Chinese family with AHC. Two brothers, misdiagnosed with adrenal insufficiency of unknown etiology at the age of 9, were correctly diagnosed with AHC when delayed puberty, HHG, and testicular defects were observed. We investigated the clinical features and identified the dosage-sensitive sex reversal AHC critical region of the X chromosome gene 1 (DAX-1) mutation in this kindred. Direct sequencing of the DAX-1 gene revealed that the two siblings have a novel mutation (1268delA) of which their mother is a heterozygous carrier. This mutation causes a frameshift and a premature stop codon at position 436, encoding a truncated protein. It is important to increase knowledge of the mutational spectrum in genes related to this disease, linking phenotype to genotype.

[Effects of overexpression of decorin on matrix metalloproteinases 2 and 9 in rat mesangial and tubular cells].

OBJECTIVE: To investigate the effects of overexpression of decorin (DCN), one of the small leucine-rich proteoglycans, on the expression of extracellular matrix molecules in glomerular mesangial and tubular cells. METHODS: Recombinant adenovirus vector containing DCN gene (Ad/DCN) was constructed, and recombinant adenovirus containing LacZ gene (Ad/LacZ) was used as control vector. Rat renal glomerular mesangial cells of the line RMC and tubular cells of the line HK-2 were cultured and divided into following groups: high glucose + Ad/DCN transfection (experimental), high glucose + Ad/LacZ transfection (vector control), high glucose + neutralizing antibody against transforming growth factor (TGF)-beta 1 (positive control), high glucose non-transfection (PBS control), and low glucose culture (normal control) groups. Western blotting was used to detect the protein expression of decorin, TGF-beta 1, collagen type IV, MMP-2, and MMP-9. RESULTS: The DCN protein expression was low only in the low glucose group, and was up-regulated in other groups, especially in the Ad/DCN group, so as the expression of TGF-beta 1 and collagen type IV, while the ratio of TGF-beta 1 to decorin is increased in both RMC and HK-2 cells. The expression levels of MMP-2 and MMP-9 decreased in the high-glucose-cultured RMC cells and increased in the high-glucose-cultured HK-2 cells, however, adenovirus-mediated transfection of decorin gene reversed all of these changes, and had almost the same effects on reducing the protein expression of TGF-beta 1 collagen type IV, MMP-2, and MMP-9 as anti-TGF-beta 1 antibody. CONCLUSION: The agents increasing the decorin expression in mesangial and tubular cells may help prevent the development and progression of diabetic nephropathy. Overexpression of decorin may be a useful tool for developing new therapeutic application for the treatment of diabetic nephropathy.

[Construction and identification of recombinant adenovirus expressing rat proteoglycan II].

OBJECTIVE: To construct recombinant adenovirus expressing rat proteoglycan II (Ad-DCN) and to study its biological features. METHODS: Rat DCN gene was inserted into an E1 and E3-substituted adenovirus shuttle plasmid. And this shuttle plasmid including DCN was recombined with AdEasy-1 in BJ5183-AD-1 electroporation competent cells to form recombinant adenovirus-DCN plasmid, which was further transfected into Ad293 cells to passage adenovirus. The control recombinant adenovirus, Ad-LacZ, was also constructed in the same way. After plaque forming trail and adjusted with PBS, Ad-DCN and Ad-LacZ were obtained with titer 1x10(9) pfu x ml(-1). PCR, Western blot and MTT analysis were used to detect the expression of DCN or the bioactivity of expressed DCN. RESULT: DCN was detected in Ad-DCN infected CHO cells by PCR and Western blot, but not in Ad-LacZ infected CHO cells. MTT analysis results showed that the supernatant from the culture of Ad-DCN infected CHO cells could abrogate the inhibitive effect of TGFbeta1 on proliferation of CCL-64 cells. The proliferation rate of TGFbeta1 + Ad-DCN treated cells was significantly higher than that of TGFbeta1 + Ad-lacz or TGFbeta1 treated cells [(0.5252 +/-0.04 compared with 0.2826 +/-0.02 or 0.2918 +/-0.02) OD, P <0.05] and lower than that of control cells [(0.9332 +/-0.08) OD, P <0.05]. CONCLUSION: The constructed recombinant adenovirus can express biologically active decorin.

[Studies on Smads at transcription level in liver fibrosis of mice with Schistosomiasis japonica].

OBJECTIVE: To study Smads involved in TGF-beta signal transduction at the transcription level during the development of liver fibrosis in BALB/c mice infected by Schistosoma japonicum. METHODS: BALB/c mice infected with cercariae of S. japonicum were used as liver fibrosis models. Liver specimens were harvested at 8, 12, 16 and 24 weeks after infection and normal control were sacrificed at the 24th week. A part of the liver specimens were preserved for pathologic examination and the other part was frozen for the detection of mRNA level of Smad 2, Smad 3, Smad 4 and Smad 7. RESULTS: The level of Smad 3 mRNA was significantly higher than that of control at the later stage, while the mRNA level of Smad 2 decreased at 12 and at 24 weeks, respectively. No significant difference in the mRNA level of Smad 4 and Smad 7 was observed between the infection group and the control. CONCLUSION: Smad 3 may induce the development of liver fibrosis in mice infected by S. japonicum while Smad 2 may induce the development of liver fibrosis at early stage and inhibit it at later stage.

Effects of pioglitazone on expressions of matrix metalloproteinases 2 and 9 in kidneys of diabetic rats.

BACKGROUND: The changes in matrix metalloproteinase-2 (MMP-2) and matrix metalloproteinase-9 (MMP-9) expressions were examined in the kidneys of diabetic rats to investigate the degradative pathway of collagen type IV (C-IV) and the protective effects of pioglitazone on an experimental model of diabetic nephropathy. METHODS: In 54 SD rats used in our study, 18 served as normal controls. Diabetes mellitus was induced in 36 age- and weight-matched rats by intraperitoneal injection of streptozotocin (70 mg/kg); 18 of the diabetic rats were allocated at random to receive pioglitazone [20 mg.kg(-1).d(-1)] in their drinking water and 18 served as diabetic controls. Rats were killed after 2, 4, or 8 weeks of treatment. Kidneys were examined pathomorphologically and the expressions of MMP-2, MMP-9, and C-IV were analyzed by immunohistochemistry, and the results were quantified by image analysis techniques. RESULTS: Diabetes mellitus was associated with a decrease in the expression of MMP-2 in the glomeruli (P < 0.05, vs control). By contrast, MMP-2 expression in the interstitium increased, but not significantly (P > 0.05, vs control). The expression of MMP-9 did not show any change when comparing the three groups (P > 0.05, vs control). STZ-diabetic rats were also associated with an increase in the expression of C-IV in the glomeruli and the interstitium (P < 0.05, vs control). All diabetes-associated changes in MMP-2 expression were attenuated by pioglitazone treatment in association with reduced C-IV accumulation. CONCLUSIONS: These results indicate that a decrease in MMP-2 expression in the glomeruli of diabetic rats may lead to impairment of C-IV degradation and contribute to the matrix accumulation in diabetic nephropathy. Pioglitazone treatment, which can attenuate the decrease of glomerular MMP-2 and the increase of C-IV degradation, has curative effects on diabetic nephropathy.

[Expression of matrix metalloproteinase-2 and-9 in kidney of diabetic rats].

OBJECTIVE: To investigate the expression of matrix metalloproteinase-2 (MMP-2), matrix metalloproteinase-9(MMP-9), transforming growth factor beta(1)(TGF-beta(1)) and IV-collagen (C-IV) in kidneys of diabetic rats. METHODS: Rat diabetic model was induced by streptozotocin (70 mg/kg), and kidneys were examined pathologically and the expressions of MMP- 2, MMP-9, TGF-beta(1) and C-IV were studied by immunohistochemistry. The results were analyzed by imaging quantitative analysis technique. RESULT: Immunoreactive MMP-2 and MMP-9 were mainly expressed in the mesangial cells, endothelial cells, parietal layer of Bowman's capsule and tubular cells. The expression of MMP-2 was significantly weaker in the glomeluri of diabetic rats than that of the control animals (P<0.05), while the expression of TGF-beta(1) and C-IV in the glomeluri of diabetic rats was significantly stronger than that of the controls (P%lt;0.05). The expression of MMP-9 didn't show significant different in glomeluri of the two groups (P>0.05). CONCLUSION: Expression of MMP-2 in glomeluri is decreased in diabetic rats, which may be related to the increased TGF-beta(1) and in turns promote the accumulation of C-IV.

Influence factors of serum fibrosis markers in liver fibrosis.

AIM: To analyze the factors which influence the serum levels of hyaluronic acid (HA), type III pro-collagen (PCIII), laminin (LN) and type IV collagen (C-IV) in liver fibrosis. METHODS: The serum specimens from 141 chronic hepatitis patients were assayed for fibrosis indexes including HA, PCIII, LN and C-IV with radioimmunoassay (RIA) and liver function indexes by an automatic biochemistry analyzer. The patients were then divided into consistent group and inconsistent group. The patients'clinical manifestations were recorded, routine blood pictures were done by a blood counter and analyzer (AC-900). Liver biopsy specimens were examined path-morphologically. The inner diameters of portal vein, splenic vein and thickness of spleen were all measured by ultrasonography. RESULTS: Sixteen patients (14.16%) had serum fibrosis indexes inconsistent with histological stage of their hepatic fibrosis. Their serum fibrosis indexes did not correlate with the stage of hepatic fibrosis (P>0.05), but were positively correlated with the grade of inflammation (chi2=12.07, P<0.05). At the same time, serum albumin (ALB) and the ratio of albumin and globulin (A/G) were significantly increased (t=3.06, P<0.01), (t=3.70, P<0.01). Serum levels of glutamic-pyruvic transaminase (ALT), glutamic-oxaloacetic transaminase (AST), gamma-glutamyl transferase (GGT) and globulin (GLB) were all significantly decreased (t=2.45, P<0.05), (t=2.33, P<0.05), (t=2.08, P<0.05), (t=3.03, P<0.01). Weary degree also decreased more obviously (chi2=7.52, P<0.05), but other clinical manifestations, routine blood indexes, serum levels of alkaline phosphatase (AKP), total bilirubin (TBIL), total protein (TP), width of main portal vein, width of splenic vein and thickness of spleen had no significant change (P>0.05). CONCLUSION: Serum fibrosis indexes can be influenced by the grade of inflammation, some liver function indexes and clinical manifestations. Comprehensive analysis is necessary for its proper interpretation.