In planta imaging of pyridine nucleotides using second-generation fluorescent protein biosensors

Redox changes of pyridine nucleotides in cellular compartments are highly dynamic and their equilibria are under the influence of various reducing and oxidizing reactions. To obtain spatiotemporal data on pyridine nucleotides in living plant cells, typical biochemical approaches require cell destruction. To date, genetically encoded fluorescent biosensors are considered to be the best option to bridge the existing technology gap, as they provide a fast, accurate, and real-time readout. However, the existing pyridine nucleotides genetically encoded fluorescent biosensors are either sensitive to pH change or slow in dissociation rate. Herein, we employed the biosensors which generate readouts that are pH stable for in planta measurement of NADH/NAD+ ratio and NADPH level. We generated transgenic Arabidopsis lines that express these biosensors in plastid stroma and cytosol of whole plants and pollen tubes under the control of CaMV 35S and LAT52 promoters, respectively. These transgenic biosensor lines allow us to monitor real-time dynamic changes in NADH/NAD+ ratio and NADPH level in the plastids and cytosol of various plant tissues, including pollen tubes, root hairs, and mesophyll cells, using a variety of fluorescent instruments. We anticipate that these valuable transgenic lines may allow improvements in plant redox biology studies.

A converged ubiquitin-proteasome pathway for the degradation of TOC and TOM tail-anchored receptors

In plants, thousands of nucleus-encoded proteins translated in the cytosol are sorted to chloroplasts and mitochondria by binding to specific receptors of the TOC (translocon on the outer chloroplast membrane) and the TOM (translocon on the outer mitochondrial membrane) complexes for import into those organelles. The degradation pathways for these receptors are unclear. Here, we discovered a converged ubiquitin-proteasome pathway for the degradation of Arabidopsis thaliana TOC and TOM tail-anchored receptors. The receptors are ubiquitinated by E3 ligase(s) and pulled from the outer membranes by the AAA+ adenosine triphosphatase CDC48, after which a previously uncharacterized cytosolic protein, transmembrane domain (TMD)-binding protein for tail-anchored outer membrane proteins (TTOP), binds to the exposed TMDs at the C termini of the receptors and CDC48, and delivers these complexes to the 26S proteasome.

Bioenergetics of pollen tube growth in Arabidopsis thaliana revealed by ratiometric genetically encoded biosensors

Pollen tube is the fastest-growing plant cell. Its polarized growth process consumes a tremendous amount of energy, which involves coordinated energy fluxes between plastids, the cytosol, and mitochondria. However, how the pollen tube obtains energy and what the biological roles of pollen plastids are in this process remain obscure. To investigate this energy-demanding process, we developed second-generation ratiometric biosensors for pyridine nucleotides which are pH insensitive between pH 7.0 to pH 8.5. By monitoring dynamic changes in ATP and NADPH concentrations and the NADH/NAD⁺ ratio at the subcellular level in Arabidopsis (Arabidopsis thaliana) pollen tubes, we delineate the energy metabolism that underpins pollen tube growth and illustrate how pollen plastids obtain ATP, NADPH, NADH, and acetyl-CoA for fatty acid biosynthesis. We also show that fermentation and pyruvate dehydrogenase bypass are not essential for pollen tube growth in Arabidopsis, in contrast to other plant species like tobacco and lily.

Differential RNA Editing and Intron Splicing in Soybean Mitochondria during Nodulation

Nitrogen fixation in soybean consumes a tremendous amount of energy, leading to substantial differences in energy metabolism and mitochondrial activities between nodules and uninoculated roots. While C-to-U RNA editing and intron splicing of mitochondrial transcripts are common in plant species, their roles in relation to nodule functions are still elusive. In this study, we performed RNA-seq to compare transcript profiles and RNA editing of mitochondrial genes in soybean nodules and roots. A total of 631 RNA editing sites were identified on mitochondrial transcripts, with 12% or 74 sites differentially edited among the transcripts isolated from nodules, stripped roots, and uninoculated roots. Eight out of these 74 differentially edited sites are located on the matR transcript, of which the degrees of RNA editing were the highest in the nodule sample. The degree of mitochondrial intron splicing was also examined. The splicing efficiencies of several introns in nodules and stripped roots were higher than in uninoculated roots. These include nad1 introns 2/3/4, nad4 intron 3, nad5 introns 2/3, cox2 intron 1, and ccmFc intron 1. A greater splicing efficiency of nad4 intron 1, a higher NAD4 protein abundance, and a reduction in supercomplex I + III2 were also observed in nodules, although the causal relationship between these observations requires further investigation.

TISIDB: an integrated repository portal for tumor-immune system interactions

SUMMARY

The interaction between tumor and immune system plays a crucial role in both cancer development and treatment response. To facilitate comprehensive investigation of tumor-immune interactions, we have designed a user-friendly web portal TISIDB, which integrated multiple types of data resources in oncoimmunology. First, we manually curated 4176 records from 2530 publications, which reported 988 genes related to anti-tumor immunity. Second, genes associated with the resistance or sensitivity of tumor cells to T cell-mediated killing and immunotherapy were identified by analyzing high-throughput screening and genomic profiling data. Third, associations between any gene and immune features, such as lymphocytes, immunomodulators and chemokines, were pre-calculated for 30 TCGA cancer types. In TISIDB, biologists can cross-check a gene of interest about its role in tumor-immune interactions through literature mining and high-throughput data analysis, and generate testable hypotheses and high quality figures for publication.

AVAILABILITY AND IMPLEMENTATION

http://cis.hku.hk/TISIDB.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

[The influence of lumbar sympathetic ganglion radiofrequency thermocoagulation on the activation of microglia in rats with diabetic neuropathic pain]

OBJECTIVE

To observe the influence of lumbar sympathetic ganglion radiofrequency thermocoagulation on the activation of spinal microglia in rats with diabetic neuropathic pain (DNP).

METHODS

Thirty-six painful diabetic Sprague-Dawley rats induced by 60 mg/kg streptozotocin (STZ) intraperitoneal injection were randomly divided into diabetic neuropathic pain group (group DNP, n=12), Sham operation group (group Sham, n=12) and radiofrequency thermocoagulation group (group R, n=12). Meanwhile another 12 age-matched rats were allocated as normal control group (group N), rats in group N received intraperitoneal injection of equal volume of normal saline. Twenty-eight days after STZ injection, rats in group R received L3 lumbar sympathetic ganglia radiofrequency thermocoagulation on the left side under X-ray guideline after anesthesia with damage time 60 s and damage temperature 60 ℃. Rats in group Sham received puncture positioning, but not thermocoagulation therapy. The mechanical paw withdrawal threshold (PWT) were performed before STZ injection, 7, 14, 21, 28 days after STZ injection and 1, 3, 5, 7, 14 days after radiofrequency thermocoagulation, respectively. Blood glucose were performed before STZ injection, 3, 28 days after STZ injection and 1, 14days after radiofrequency thermocoagulation. After the final behavioral testing, L3-L5 spinal cord tissues were removed to exam the expression of microglia marker OX42 by Western blotting and immunofluorescence technique, and the changes in the expression of inflammation factor IL-1β, IL-6, TNF-α were detected by ELISA technique.

RESULTS

Compared with group N, after 14, 21, 28 days of STZ injection and 1, 3, 5, 7, 14 days of radiofrequency thermocoagulation, the PWT of group DNP and group Sham decreased significantly (P<0.05); Before radiofrequency thermocoagulation, the PWT of rats in group DNP was (3.84±0.83) g, the PWT of rats in group R was (4.45±0.88) g, there was no statistically significant difference between group DNP and group R (t=1.514, P>0.05), but after radiofrequency thermocoagulation, compared with DNP group, the PWT of rats in group R increased significantly (P<0.05), and lasted to 14 d after radiofrequency thermocoagulation. The ratio of spinal microglia marker OX42 and GAPDH, the expression of inflammation factor IL-1β, IL-6, and TNF-α in group N were 0.074±0.023, (35.93±6.16) pg/ml, (92.11±13.23) pg/ml, and (169.50±22.64) pg/ml, respectively. The ratio of spinal microglia marker OX42 and GAPDH, the expression of inflammation factor IL-1β, IL-6, and TNF-α in group DNP were 1.023±0.185, (73.82±9.25) pg/ml, (155.33±21.82) pg/ml, and (298.30±33.21) pg/ml, respectively. The ratio of spinal microglia marker OX42 and GAPDH, the expression of inflammation factor IL-1β, IL-6, and TNF-α in group Sham were 0.951±0.103, (73.00±7.54) pg/ml, (151.02±24.26) pg/ml, and (294.01±36.37) pg/ml, respectively. The ratio of spinal microglia marker OX42 and GAPDH, the expression of inflammation factor IL-1β, IL-6, and TNF-α in group R were 0.563±0.019, (51.81±7.36) pg/ml, (123.24±16.13) pg/ml, and (229.23±29.16) pg/ml, respectively. Compared with group N, the expression of spinal microglia marker OX42 and inflammation factor IL-1β, IL-6, and TNF-α in group DNP, group Sham and group R increased significantly (F=7.501, 348.698, 568.021, 145.110, all P<0.05). Compared with DNP group, the expression of spinal microglia marker OX42 and inflammation factor IL-1β, IL-6, and TNF-α of group R reduced significantly (all P<0.05).

CONCLUSION

The lumbar sympathetic ganglion radiofrequency thermocoagulation can alleviate diabetic neuropathic pain. The mechanism may relate with the inhibition of spinal microglia activation and the lower expression of inflammation factor.

Suppressing stathmin-l can inhibit chkl protein expression and reduce the invasion and tumorigenicity of cervical cancer cells

The purpose of this study was to evaluate the effects of stathmin-l on chkl protein expression in cervical cancer cells and the influ- ences on the cells' invasion and tumorigenicity. Suppressed stathmin-l expression in Hela cells and C33A cells by lentiviral vector were utilized. Real time PCR and Western blot were used to examine the expression of chkl. Cell proliferation and invasion were stud- ied using MTT assays and transwell migration assays.The differences of tumorigenicity in vivo were explored using xenograft experi- ments. In addition, stathmin-l expressions in 24 cervical cancer patients were studied without regional lymph nodes metastasis and 16 metastatic patients by immunohistochemistry assays and real time PCR. This study found downregulating stathmin-l reduced chkl ex- pressions and the proliferation and invasion in cervical cancer cells and reduced the tumorigenicity of tumor cells.

Male-specific association of the APC rs383830 T allele with the risk of coronary heart disease

APC is a tumor suppressor gene that is involved in the processes of cell migration and adhesion, transcriptional activation, and apoptosis. The goal of this study was to evaluate the contribution of the APC rs383830 polymorphism to coronary heart disease (CHD) in Han Chinese. A total of 783 patients with CHD and 737 controls were tested in the current association study. Although our study did not identify an association between the APC rs383830 polymorphism and CHD, a breakdown analysis by gender indicated there was a significant contribution of the rs383830 T allele to the risk of CHD in males (P = 0.046, odds ratio = 1.267, 95% confidence interval = 1.004-1.598). In conclusion, our study suggested a male-specific association of the APC rs383830 polymorphism with CHD.

Three-dimensional fast magnetic reconnection driven by relativistic ultraintense femtosecond lasers

Three-dimensional fast magnetic reconnection driven by two ultraintense femtosecond laser pulses is investigated by relativistic particle-in-cell simulation, where the two paralleled incident laser beams are shot into a near-critical plasma layer to form a magnetic reconnection configuration in self-generated magnetic fields. A reconnection X point and out-of-plane quadrupole field structures associated with magnetic reconnection are formed. The reconnection rate is found to be faster than that found in previous two-dimensional Hall magnetohydrodynamic simulations and electrostatic turbulence contribution to the reconnection electric field plays an essential role. Both in-plane and out-of-plane electron and ion accelerations up to a few MeV due to the magnetic reconnection process are also obtained.

Colloidal cutin-like substances cross-linked to siderophore decomposition products mobilizing plutonium from contaminated soils

Relatively recently, inorganic colloids have been invoked to reconcile the apparent contradictions between expectations based on classical dissolved-phase Pu transport and field observations of "enhanced" Pu mobility (Kersting et al. Nature 1999, 397, 56-59). A new paradigm for Pu transport is mobilization and transport via biologically produced ligands. This study for the first time reports a new finding of Pu being transported, at sub-pM concentrations, by a cutin-like natural substance containing siderophore-like moieties and virtually all mobile Pu. Most likely, Pu is complexed by chelating groups derived from siderophores that are covalently bound to a backbone of cutin-derived soil degradation products, thus revealing the history of initial exposure to Pu. Features such as amphiphilicity and small size make this macromolecule an ideal collector for actinides and other metals and a vector for their dispersal. Cross-linking to the hydrophobic domains (e.g., by polysaccharides) gives this macromolecule high mobility and a means of enhancing Pu transport. This finding provides a new mechanism for Pu transport through environmental systems that would not have been predicted by Pu transport models.

Energetic electrons emitted from ethanol droplets irradiated by femtosecond laser pulses

We investigate the angular distribution and the energy spectrum of hot electrons emitted from ethanol droplets irradiated by linearly polarized 150-fs laser pulses at an intensity of 10(16) W/cm(2). Two hot electron jets symmetrically with respect to the laser propagation direction are observed within the polarization plane. This is due to the spherical geometry of droplets in the intense laser field. The maximum energy of the hot electrons is found to be more than 600 keV. Particle-in-cell simulations suggest that the resonance absorption is the main mechanism for hot electron generation.