Resveratrol and para-coumarate serve as ring precursors for coenzyme Q biosynthesis

Coenzyme Q (Q or ubiquinone) is a redox-active polyisoprenylated benzoquinone lipid essential for electron and proton transport in the mitochondrial respiratory chain. The aromatic ring 4-hydroxybenzoic acid (4HB) is commonly depicted as the sole aromatic ring precursor in Q biosynthesis despite the recent finding that para-aminobenzoic acid (pABA) also serves as a ring precursor in Saccharomyces cerevisiae Q biosynthesis. In this study, we employed aromatic ¹³C₆-ring-labeled compounds including ¹³C₆-4HB, ¹³C₆-pABA, ¹³C₆-resveratrol, and ¹³C₆-coumarate to investigate the role of these small molecules as aromatic ring precursors in Q biosynthesis in Escherichia coli, S. cerevisiae, and human and mouse cells. In contrast to S. cerevisiae, neither E. coli nor the mammalian cells tested were able to form ¹³C₆-Q when cultured in the presence of ¹³C₆-pABA. However, E. coli cells treated with ¹³C₆-pABA generated ¹³C₆-ring-labeled forms of 3-octaprenyl-4-aminobenzoic acid, 2-octaprenyl-aniline, and 3-octaprenyl-2-aminophenol, suggesting UbiA, UbiD, UbiX, and UbiI are capable of using pABA or pABA-derived intermediates as substrates. E. coli, S. cerevisiae, and human and mouse cells cultured in the presence of ¹³C₆-resveratrol or ¹³C₆-coumarate were able to synthesize ¹³C₆-Q. Future evaluation of the physiological and pharmacological responses to dietary polyphenols should consider their metabolism to Q.     

Increased phosphate transport of Arabidopsis thaliana Pht1;1 by site‐directed mutagenesis of tyrosine 312 may be attributed to the disruption of homomeric interactions

Members of the Pht1 family of plant phosphate (Pi) transporters play vital roles in Pi acquisition from soil and in planta Pi translocation to maintain optimal growth and development. The study of the specificities and biochemical properties of Pht1 transporters will contribute to improving the current understanding of plant phosphorus homeostasis and use‐efficiency. In this study, we show through split in vivo interaction methods and in vitro analysis of microsomal root tissues that Arabidopsis thaliana Pht1;1 and Pht1;4 form homomeric and heteromeric complexes. Transient and heterologous expression of the Pht1;1 variants, Pht1;1^Y312D, Pht1;1^Y312A and Pht1;1^Y312F, was used to analyse the role of a putative Pi binding residue (Tyr 312) in Pht1;1 transporter oligomerization and function. The homomeric interaction among Pht1;1 proteins was disrupted by mutation of Tyr 312 to Asp, but not to Ala or Phe. In addition, the Pht1;1^Y312D variant conferred enhanced Pi transport when expressed in yeast cells. In contrast, mutation of Tyr 312 to Ala or Phe did not affect Pht1;1 transport kinetics. Our study demonstrates that modifications to the Pht1;1 higher‐order structure affects Pi transport, suggesting that oligomerization may serve as a regulatory mechanism for modulating Pi uptake.     

Effect of Optogenetic Stimulus on the Proliferation and Cell Cycle Progression of Neural Stem Cells

Modulation of stem cell proliferation is a crucial aspect of neural developmental biology and regenerative medicine. To investigate the effect of optical stimulation on neural stem cell proliferation, cells transduced with channelrhodopsin-2 (ChR2) were used to analyze changes in cell proliferation and cell cycle distribution after light stimulation. Blue light significantly inhibited cell proliferation and affected the cell cycle, which increased the percentage of cells in G₁ phase and reduced the percentage in S phase. It is likely that the influence of blue light on cell proliferation and the cell cycle was mediated by membrane depolarization, which induced accumulation of p21 and p27 proteins. Our data provide additional specific evidence that membrane depolarization may inhibit neural stem cell proliferation.     

Backbone Flexibility of CDR3 and Immune Recognition of Antigens

Conformational entropy is an important component of protein–protein interactions; however, there is no reliable method for computing this parameter. We have developed a statistical measure of residual backbone entropy in folded proteins by using the ?–ψ distributions of the 20 amino acids in common secondary structures. The backbone entropy patterns of amino acids within helix, sheet or coil form clusters that recapitulate the branching and hydrogen bonding properties of the side chains in the secondary structure type. The same types of residues in coil and sheet have identical backbone entropies, while helix residues have much smaller conformational entropies. We estimated the backbone entropy change for immunoglobulin complementarity-determining regions (CDRs) from the crystal structures of 34 low-affinity T-cell receptors and 40 high-affinity Fabs as a result of the formation of protein complexes. Surprisingly, we discovered that the computed backbone entropy loss of only the CDR3, but not all CDRs, correlated significantly with the kinetic and affinity constants of the 74 selected complexes. Consequently, we propose a simple algorithm to introduce proline mutations that restrict the conformational flexibility of CDRs and enhance the kinetics and affinity of immunoglobulin interactions. Combining the proline mutations with rationally designed mutants from a previous study led to 2400-fold increase in the affinity of the A6 T-cell receptor for Tax-HLAA2. However, this mutational scheme failed to induce significant binding changes in the already-high-affinity C225–Fab/huEGFR interface. Our results will serve as a roadmap to formulate more effective target functions to design immune complexes with improved biological functions.     

肝癌肿瘤浸润淋巴细胞（TIL）体外扩增及特性研究

探讨从原发性肝癌（hepatocellular carcinoma,HCC）患者的术后肿瘤组织中分离肿瘤浸润性淋巴细胞（tumor-infiltrating lymphocyte,TIL）,并进行体外大量扩增的方法。在该研究工作中,组织标本来源于术后的肿瘤癌旁组织,经过组织破碎、酶消化后,采用不连续密度梯度离心分离其中淋巴细胞。分离的淋巴细胞先采用大剂量重组人白介素2（IL-2）（2 000 U/mL）进行引发,然后采用同种异体的外周血单核细胞作为饲养细胞进行扩增。针对9例原发性肝癌术后标本,所分离的TIL均能成功进行培养扩增,扩增后细胞数为（1~5.5）×10^9。扩增倍数为111~572。扩增后的TIL,表型检测发现CD3＋细胞的比例为（90.3±9.4）%,CD3＋CD4＋细胞的比例为（24.9±14.1）%,CD3＋CD8＋细胞的比例为（56.4±20.2）%,CD3＋CD56＋细胞的比例为（14.8±12.6）%。杀伤检测结果显示,肝癌TIL对非自体肿瘤细胞系HepG2和Bel-7402有较强的杀伤作用。因此,采用该改良的方法,原发性肝癌的TIL在体外可以成功进行培养扩增,并具有较强抗肿瘤活性,可以作为肝癌术后巩固性免疫治疗的一种手段。     

Meta-analysis of vitamin D receptor gene polymorphisms and benign prostatic hyperplasia risk

The association between vitamin D receptor (VDR) gene polymorphisms and risk of benign prostatic hyperplasia (BPH) has been investigated in numerous publications, but published results remain inconclusive. Hence, we conducted this meta-analysis to derive a more precise conclusion. Four polymorphisms (Taq-I, Bsm-I, Apa-I, and Fok-I) of the VDR gene with risk of BPH from six case–control studies and one cohort study involving 2,248 individuals were identified from PubMed and China National Knowledge Internet databases up to November 20, 2013 (updated on March 5, 2014). After data extraction, the meta-analysis was performed using Comprehensive Meta-Analysis software. All four VDR polymorphisms were not associated with the risk of BPH [Taq-I: OR 0.61, 95 % CI (0.38–1.24) for tt vs. TT; Bsm-I: OR 1.27, 95 % CI (0.96–1.69) for bb vs. BB; Apa-I: OR 1.26, 95 % CI (0.64–2.46) for aa vs. AA; Fok-I: OR 0.95, 95 % CI (0.60–1.50) for ff vs. FF]. Subgroup analysis according to ethnicity for Taq-I polymorphism also showed that the polymorphism was not associated with risk of BPH for either Caucasians [OR 0.74, 95 % CI (0.31–1.78) for tt vs. TT] or Asians [OR 0.35, 95 % CI (0.11–1.11) for tt vs. TT]. However, results of this meta-analysis should be treated with caution because this meta-analysis has several limitations. We propose to conduct a high-quality study with large sample size to further identify the association between VDR gene polymorphisms and BPH susceptibility.     

TEMP: a computational method for analyzing transposable element polymorphism in populations

Insertions and excisions of transposable elements (TEs) affect both the stability and variability of the genome. Studying the dynamics of transposition at the population level can provide crucial insights into the processes and mechanisms of genome evolution. Pooling genomic materials from multiple individuals followed by high-throughput sequencing is an efficient way of characterizing genomic polymorphisms in a population. Here we describe a novel method named TEMP, specifically designed to detect TE movements present with a wide range of frequencies in a population. By combining the information provided by pair-end reads and split reads, TEMP is able to identify both the presence and absence of TE insertions in genomic DNA sequences derived from heterogeneous samples; accurately estimate the frequencies of transposition events in the population and pinpoint junctions of high frequency transposition events at nucleotide resolution. Simulation data indicate that TEMP outperforms other algorithms such as PoPoolationTE, RetroSeq, VariationHunter and GASVPro. TEMP also performs well on whole-genome human data derived from the 1000 Genomes Project. We applied TEMP to characterize the TE frequencies in a wild Drosophila melanogaster population and study the inheritance patterns of TEs during hybrid dysgenesis. We also identified sequence signatures of TE insertion and possible molecular effects of TE movements, such as altered gene expression and piRNA production. TEMP is freely available at github: https://github.com/JialiUMassWengLab/TEMP.git.     

Defence Signalling Pathways Involved in Plant Resistance and Phosphite-Mediated Control of Phytophthora Cinnamomi

Phytophthora cinnamomi is one of the most devastating plant pathogens worldwide. Current control of P. cinnamomi in natural ecosystems primarily relies on chemical phosphite (Phi). To investigate host- and Phi-mediated resistance, A. thaliana ecotypes and mutants defective in salicylic acid (SA), jasmonic acid (JA), ethylene (ET) and abscisic acid (ABA) signalling pathways were screened for susceptibility to P. cinnamomi. In contrast to Col-0, the aba2-4 mutant, deficient in the synthesis of ABA, was susceptible suggesting a role for ABA in resistance to P. cinnamomi. Phi treatment increased resistance in aba2-4, but not to the level of Col-0, suggesting that Phi may act through both ABA-dependent and ABA-independent pathways. Phi treatment or P. cinnamomi inoculation of Col-0 down-regulated AtMYC2, a positive regulator of ABA signalling, which negatively regulates JA/ET-related pathogenesis-related genes, such as PDF1.2, whilst positively regulating JA-mediated herbivore responses such as VSP and PI. Consistent with this, P. cinnamomi or Phi treatment caused up-regulation of PDF1.2 and THI2.1 and down-regulation of VSP2 and the ABA-responsive gene RD22. Despite the up-regulation of JA/ET-dependent defence genes, the JA-defective mutant, jar1-1 and ET-defective mutants, ein2-1 and etr1-3, showed wild-type levels of resistance to P. cinnamomi, suggesting that these JA/ET defences are not required for resistance to P. cinnamomi. These results suggest that the resistance response of Col-0 act, at least in part, through a mechanism dependent on ABA synthesis, which appears independent of the interaction between ABA and elements of the JA/ET pathway, whilst Phi-mediated resistance, although inducing a response resembling the resistance response of Col-0, is independent of ABA signalling.