Briefly Bound to Activate: Transient Binding of a Second Catalytic Magnesium Activates the Structure and Dynamics of CDK2 Kinase for Catalysis

SummaryWe have determined high-resolution crystal structures of a CDK2/Cyclin A transition state complex bound to ADP, substrate peptide, and MgF3−. Compared to previous structures of active CDK2, the catalytic subunit of the kinase adopts a more closed conformation around the active site and now allows observation of a second Mg2+ ion in the active site. Coupled with a strong [Mg2+] effect on in vitro kinase activity, the structures suggest that the transient binding of the second Mg2+ ion is necessary to achieve maximum rate enhancement of the chemical reaction, and Mg2+ concentration could represent an important regulator of CDK2 activity in vivo. Molecular dynamics simulations illustrate how the simultaneous binding of substrate peptide, ATP, and two Mg2+ ions is able to induce a more rigid and closed organization of the active site that functions to orient the phosphates, stabilize the buildup of negative charge, and shield the subsequently activated γ-phosphate from solvent

Potential Reductions in Greenhouse Gas and Fine Particulate Matter Emissions Using Corn Stover for Ethanol Production in China

Corn stover is an abundant raw material that can be used to produce ethanol and reduce air pollution. This paper studied the potential reductions in greenhouse gas (GHG) and fine particulate matter (PM2.5) emissions across China if corn stover was used for ethanol production. Field surveys in nine provincial regions were conducted. Life-cycle assessment (LCA) was used to assess the GHG and PM2.5 emissions from a corn stover based ethanol system. The LCA system boundaries included several process stages from corn planting to ethanol fuel used in vehicles. Corn stover geographical distributions and emission reduction factors were combined. Results showed that the total surplus quantity of corn stover in China was 86.2 million metric tons (Mt) in 2015. It was sufficient to reach the ethanol production target set by the Chinese government. In the scenario that 38.5 Mt or 44.6% of corn stover surplus were used for ethanol production, the total potential emission reductions were 36.5 Mt CO2-eq GHG and 450.9 kt PM2.5. Among the 31 provincial regions in China, the reduction potentials varied from 0.001 to 8.9 Mt CO2-eq for GHG and from 0.013 to 109.7 kt for PM2.5. This study provided useful information to policy makers, researchers and industry managers who work on environmental control and corn stover management

De novo intestine-specific transcriptome of the brown planthopper Nilaparvata lugens revealed potential functions in digestion, detoxification and immune response

AbstractThe brown planthopper (Nilaparvata lugens, BPH) is the most serious rice plant pests in Asia. In this study, we performed transcriptome-wide analysis on BPH intestine. We obtained more than 26 million sequencing reads that were then assembled into 53,553 unigenes with a mean size of 388bp. Based on similarity search with the nucleotide sequences available at NCBI, BPH intestine-specific transcriptome analysis identified 21,405 sequences. Assembled sequences were annotated with gene description, gene ontology and clusters of orthologous group terms. The digestion-, defense- and xenobiotic metabolism-related genes were abundantly detected in the transcripts from BPH intestine. Many novel genes including 33 digestion-related genes, 25 immune responsive genes and 27 detoxification-related genes are first reported here. We investigated the gene expression patterns at the transcript levels in different tissues by quantitative real-time PCR analysis, which revealed that some genes had intestine-specific expression, implicating their potential significance for BPH management

Mechanisms and applications of radiation-induced oxidative stress in regulating cancer immunotherapy

Radiotherapy (RT) is an effective treatment option for cancer patients, which induces the production of reactive oxygen species (ROS) and causes oxidative stress (OS), leading to the death of tumor cells. OS not only causes apoptosis, autophagy and ferroptosis, but also affects tumor immune response. The combination of RT and immunotherapy has revolutionized the management of various cancers. In this process, OS caused by ROS plays a critical role. Specifically, RT-induced ROS can promote the release of tumor-associated antigens (TAAs), regulate the infiltration and differentiation of immune cells, manipulate the expression of immune checkpoints, and change the tumor immune microenvironment (TME). In this review, we briefly summarize several ways in which IR induces tumor cell death and discuss the interrelationship between RT-induced OS and antitumor immunity, with a focus on the interaction of ferroptosis with immunogenic death. We also summarize the potential mechanisms by which ROS regulates immune checkpoint expression, immune cells activity, and differentiation. In addition, we conclude the therapeutic opportunity improving radiotherapy in combination with immunotherapy by regulating OS, which may be beneficial for clinical treatment

Bis[N-benzyl-2-(quinolin-8-yl­oxy)acetamide]dichloridocopper(II) acetonitrile solvate monohydrate

In the title complex, [CuCl2(C18H16N2O2)2]·CH3CN·H2O, the six-coordinated Cu atom is in a distorted octa­hedral geometry with the donor centers of two O atoms and two N atom from two bidentate ligands, and two chloride ions. In the crystal, pairs of inter­molecular N—H⋯ Cl hydrogen bonds form centrosymmetric dimers and inter­molecular O—H⋯ O hydrogen bonds between the ligand and the uncoordinated water mol­ecules link the dimers into chains parallel to the c axis

Evaluation of cloned cells, animal model, and ATRA sensitivity of human testicular yolk sac tumor

The testicular yolk sac tumor (TYST) is the most common neoplasm originated from germ cells differentiated abnormally, a major part of pediatric malignant testicular tumors. The present study aimed at developing and validating the in vitro and vivo models of TYST and evaluating the sensitivity of TYST to treatments, by cloning human TYST cells and investigating the histology, ultra-structure, growth kinetics and expression of specific proteins of cloned cells. We found biological characteristics of cloned TYST cells were similar to the yolk sac tumor and differentiated from the columnar to glandular-like or goblet cells-like cells. Chromosomes for tumor identification in each passage met nature of the primary tumor. TYST cells were more sensitive to all-trans-retinoic acid which had significantly inhibitory effects on cell proliferation. Cisplatin induced apoptosis of TYST cells through the activation of p53 expression and down-regulation of Bcl- expression. Thus, we believe that cloned TYST cells and the animal model developed here are useful to understand the molecular mechanism of TYST cells and develop potential therapies for human TYST

Determination of heavy metals in chinese prickly ash from different production areas using inductively coupled plasma-mass spectrometry

Purpose: To determine the heavy metal content of Chinese prickly ash (CPA) produced in various areas of China.Methods: CPA samples collected from different production areas in China were subjected to microwave digestion, and the contents of copper (Cu), nickel (Ni), chromium (Cr), lead (Pb), cadmium (Cd), arsenic (As), mercury (Hg), tin (Sn), and antimony (Sb) were determined by inductively coupled plasma-mass spectrometry (ICP-MS).Results: Heavy metal levels in the CPA samples followed the order: Cu (3.29-24.17 mg/kg) > Cr (0.04-7.33 mg/kg) > Ni (0.88-6.86 mg/kg) > Pb (0.00-3.84 mg/kg) > As (0.0011-1.08 mg/kg) > Cd (0.029-0.211 mg/kg) > Sb (0.03-0.21 mg/kg) > Sn (0.00-0.15 mg/kg) > Hg (0.000-0.032 mg/kg). Metal-to-metal correlation studies showed that there were significant correlations between Cu-Cr (p = -4.02), Cu-Ni (p = 0.561), Cu-As (p = 0.554) and Ni-As (p = 0.428) at the 0.01 level. Also, some metal-to-metal correlations were observed in Pb-Cr (p = 0.351), Pb-Cu (p = -0.310), Sb-Cd (p = 0.322), Sb-Hg (p = 0.311) and Cd-Sn (p = 0.309) at the 0.05 level. The highest concentrations of Pb and As in CPA exceeded the maximum permissible limits in China. Based on current safety standards, the concentrations of heavy metals in these CPA samples mean they are safe for human consumption.Conclusions: The status of heavy metal concentrations of CPA should be further investigated in Sichuan, Shaanxi, Shanxi and Jiangsu. In addition, ICP-MS is a reliable and rapid technique for the determination of the heavy metals in CPA.Keywords: Chinese prickly ash, Heavy metals, Inductively-coupled plasma-mass spectrometry, Food safet

Transcriptome profiling and digital gene expression by deep-sequencing in normal/regenerative tissues of planarian Dugesia japonica

AbstractPlanarians exhibit an extraordinary ability to regenerate lost body parts which is attributed to an abundance of pluripotent somatic stem cells called neoblasts. In this article, we report a transcriptome sequence of a Planaria subspecies Dugesia japonica derived by high-throughput sequencing. In addition, we researched transcriptome changes during different periods of regeneration by using a tag-based digital gene expression (DGE) system. Consequently, 11,913,548 transcriptome sequencing reads were obtained. Finally, these reads were eventually assembled into 37,218 unique unigenes. These assembled unigenes were annotated with various methods. Transcriptome changes during planarian regeneration were investigated by using a tag-based DGE system. We obtained a sequencing depth of more than 3.5million tags per sample and identified a large number of differentially expressed genes at various stages of regeneration. The results provide a fairly comprehensive molecular biology background to the research on planarian development, particularly with regard to its regeneration progress

Genome-wide transcriptional analysis of temperature shift in L. interrogans serovar lai strain 56601

BACKGROUND: Leptospira interrogans is an important mammalian pathogen. Transmission from an environmental source requires adaptation to a range of new environmental conditions in the organs and tissues of the infected host. Several studies have shown that a shift in culture temperature from 28°C to 37°C, similar to that encountered during infection of a host from an environmental source, is associated with differential synthesis of several proteins of the outer membrane, periplasm and cytoplasm. The whole genome of the Leptospira interrogans serogroup Icterohaemorrhagiae serovar lai type strain #56601 was sequenced in 2003 and microarrays were constructed to compare differential transcription of the whole genome at 37°C and 28°C. RESULTS: DNA microarray analyses were used to investigate the influence of temperature on global gene expression in L. interrogans grown to mid-exponential phase at 28°C and 37°C. Expression of 106 genes differed significantly at the two temperatures. The differentially expressed genes belonged to nine functional categories: Cell wall/membrane biogenesis genes, hemolysin genes, heat shock proteins genes, intracellular trafficking and secretion genes, two-component system and transcriptional regulator genes, information storage and processing genes, chemotaxis and flagellar genes, metabolism genes and genes with no known homologue. Real-time reverse transcription-PCR assays confirmed the microarray data. CONCLUSION: Microarray analyses demonstrated that L. interrogans responds globally to temperature alteration. The data delineate the spectrum of temperature-regulated gene expression in an important human pathogen and provide many new insights into its pathogenesis

Radial Growth of Qilian Juniper on the Northeast Tibetan Plateau and Potential Climate Associations

There is controversy regarding the limiting climatic factor for tree radial growth at the alpine treeline on the northeastern Tibetan Plateau. In this study, we collected 594 increment cores from 331 trees, grouped within four altitude belts spanning the range 3550 to 4020 m.a.s.l. on a single hillside. We have developed four equivalent ring-width chronologies and shown that there are no significant differences in their growth-climate responses during 1956 to 2011 or in their longer-term growth patterns during the period AD 1110–2011. The main climate influence on radial growth is shown to be precipitation variability. Missing ring analysis shows that tree radial growth at the uppermost treeline location is more sensitive to climate variation than that at other elevations, and poor tree radial growth is particularly linked to the occurrence of serious drought events. Hence water limitation, rather than temperature stress, plays the pivotal role in controlling the radial growth of Sabina przewalskii Kom. at the treeline in this region. This finding contradicts any generalisation that tree-ring chronologies from high-elevation treeline environments are mostly indicators of temperature changes