Enrichment of adeno-associated virus serotype 5 full capsids by anion exchange chromatography with dual salt elution gradients

Adeno-associated virus-based gene therapies have demonstrated substantial therapeutic benefit for the treatment of genetic disorders. In manufacturing processes, viral capsids are produced with and without the encapsidated gene of interest. Capsids devoid of the gene of interest, or “empty” capsids, represent a product-related impurity. As a result, a robust and scalable method to enrich full capsids is crucial to provide patients with as much potentially active product as possible. Anion exchange chromatography has emerged as a highly utilized method for full capsid enrichment across many serotypes due to its ease of use, robustness, and scalability. However, achieving sufficient resolution between the full and empty capsids is not trivial. In this work, anion exchange chromatography was used to achieve empty and full capsid resolution for adeno-associated virus serotype 5. A salt gradient screen of multiple salts with varied valency and Hofmeister series properties was performed to determine optimal peak resolution and aggregate reduction. Dual salt effects were evaluated on the same product and process attributes to identify any synergies with the use of mixed ion gradients. The modified process provided as high as ≥75% AAV5 full capsids (≥3-fold enrichment based on the percent full in the feed stream) with near baseline separation of empty capsids and achieved an overall vector genome step yield of >65%.     

High-efficiency and multilocus targeted integration in CHO cells using CRISPR-mediated donor nicking and DNA repair inhibitors

Efforts to leverage clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) for targeted genomic modifications in mammalian cells are limited by low efficiencies and heterogeneous outcomes. To aid method optimization, we developed an all-in-one reporter system, including a novel superfolder orange fluorescent protein (sfOrange), to simultaneously quantify gene disruption, site-specific integration (SSI), and random integration (RI). SSI strategies that utilize different donor plasmid formats and Cas9 nuclease variants were evaluated for targeting accuracy and efficiency in Chinese hamster ovary cells. Double-cut and double-nick donor formats significantly improved targeting accuracy by 2.3–8.3-fold and 19–22-fold, respectively, compared to standard circular donors. Notably, Cas9-mediated donor linearization was associated with increased RI events, whereas donor nicking minimized RI without sacrificing SSI efficiency and avoided low-fidelity outcomes. A screen of 10 molecules that modulate the major mammalian DNA repair pathways identified two inhibitors that further enhance targeting accuracy and efficiency to achieve SSI in 25% of transfected cells without selection. The optimized methods integrated transgene expression cassettes with 96% efficiency at a single locus and with 53%–55% efficiency at two loci simultaneously in selected clones. The CRISPR-based tools and methods developed here could inform the use of CRISPR/Cas9 in mammalian cell lines, accelerate mammalian cell line engineering, and support advanced recombinant protein production applications.     

Primary structure effects on peptide group hydrogen exchange

The rate of exchange of peptide group NH hydrogens with the hydrogens of aqueous solvent is sensitive to neighboring side chains. To evaluate the effects of protein side chains, all 20 naturally occurring amino acids were studied using dipeptide models. Both inductive and steric blocking effects are apparent. The additivity of nearest-neighbor blocking and inductive effects was tested in oligo-and polypeptides and, suprisingly, confirmed. Reference rates for alanine-containing peptides were determined and effects of temperature considered. These results provide the information necessary to evaluate measured protein NH to ND exchange rates by comparing them with rates to be expected for the same amino acid sequence is unstructured aligo- and polypeptides. The application of this approach to protein studies is discussed. © 1993 Wiley-Liss, Inc.     

Molecular magnetic materials from polyoxometalates

The significance of polyoxometalates in the field of molecular magnetism is discussed. We show that this kind of inorganic complexes provides remarkable examples for the study of the exchange interactions in clusters. On the other hand, we examine the possibility of using these metal oxide anions as magnetic components of molecular materials containing organic tetrathiafulvalenes as electron donor molecules.     

基于叶绿体基因组数据的芸香科属间系统发育初步分析（专题约稿）

该研究在人工控制水分条件下,设置3个干旱胁迫处理,选用3个主栽油菜品种‘陇油10号’、‘陇油2号’、‘青杂5号’幼苗进行盆栽试验,测定干旱胁迫条件下叶片相对含水量、叶绿素含量、光合气体交换参数及叶绿素荧光参数等指标,考察各指标在干旱胁迫过程中的变化特征,并通过主成分分析(PCA)和隶属函数法评价品种的抗旱性及其主要响应因子,以揭示西北地区油菜幼苗响应干旱胁迫的光合调控机制。结果表明：(1)各品种油菜幼苗的叶片相对含水量(RWC)均随干旱胁迫程度的递增而逐渐降低,最大水分亏缺(WSD)却逐渐上升。(2)各品种油菜幼苗叶片的叶绿素a含量、叶绿素总含量随着干旱胁迫程度的递增而先增加后递减,且同一种幼苗在不同处理间差异显著。(3)各品种油菜幼苗叶片的净光合速率(P_n)、水分利用效率(WUE)、单株生物量、气孔导度(G_s)、胞间CO₂浓度(C_i)均在受到干旱胁迫时迅速降低,且同一品种幼苗在不同处理间差异显著,而其叶片蒸腾速率(T_r)在干旱胁迫下无显著变化。(4)各品种油菜幼苗叶片光化学猝灭系数(qP)和非光化学猝灭系数(NPQ)随着干旱胁迫程度的递增先增加后递减,最大光化学效率(F_v/F_m)和电子传递速率(ETR)在受到干旱胁迫时迅速降低,且同一品种幼苗在不同处理间差异显著。(5)主成分分析结果表明,在油菜幼苗受到干旱胁迫时RWC、C_i、G_s、P_n、WUE、叶绿素总含量、叶绿素a含量和NPQ起主要调控作用;隶属函数法综合评价表明,3个品种油菜幼苗耐旱能力由高到低依次为‘陇油10号’＞‘陇油2号’＞‘青杂5号’。     

The effect of charcoal production on carbon cycling in African biomes

Using biomass for charcoal production in sub-Saharan Africa (SSA) may change carbon stock dynamics and lead to irreversible changes in the carbon balance, yet we have little understanding of whether these dynamics vary by biome in this region. Currently, charcoal production contributes up to 7% of yearly deforestation in tropical regions, with carbon emissions corresponding to 71.2 million tonnes of CO₂ and 1.3 million tonnes of CH₄. With a projected increased demand for charcoal in the coming decades, even low harvest rates may throw the carbon budget off-balance due to legacy effects. Here, we parameterized the dynamic global vegetation model LPJ-GUESS for six SSA biomes and examined the effect of charcoal production on net ecosystem exchange (NEE), carbon stock sizes and recovery time for tropical rain forest, montane forest, moist savanna, dry savanna, temperate grassland and semi-desert. Under historical charcoal regimes, tropical rain forests and montane forests transitioned from net carbon sinks to net sources, that is, mean cumulative NEE from −3.56 ± 2.59 kg C/m² to 2.46 ± 3.43 kg C/m² and −2.73 ± 2.80 kg C/m² to 1.87 ± 4.94 kg C/m² respectively. Varying charcoal production intensities resulted in tropical rain forests showing at least two times higher carbon losses than the other biomes. Biome recovery time varied by carbon stock, with tropical and montane forests taking about 10 times longer than the fast recovery observed for semi-desert and temperate grasslands. Our findings show that high biomass biomes are disproportionately affected by biomass harvesting for charcoal, and even low harvesting rates strongly affect vegetation and litter carbon and their contribution to the carbon budget. Therefore, the prolonged biome recoveries imply that current charcoal production practices in SSA are not sustainable, especially in tropical rain forests and montane forests, where we observe longer recovery for vegetation and litter carbon stocks.     

Significant hydrogen exchange protection in GroEL-bound DHFR is maintained during iterative rounds of substrate cycling.

An unresolved key issue in the mechanism of protein folding assisted by the molecular chaperone GroEL is the nature of the substrate protein bound to the chaperonin at different stages of its reaction cycle. Here we describe the conformational properties of human dihydrofolate reductase (DHFR) bound to GroEL at different stages of its ATP-driven folding reaction, determined by hydrogen exchange labeling and electrospray ionization mass spectrometry. Considerable protection involving about 20 hydrogens is observed in DHFR bound to GroEL in the absence of ATP. Analysis of the line width of peaks in the mass spectra, together with fluorescence quenching and ANS binding studies, suggest that the bound DHFR is partially folded, but contains stable structure in a small region of the polypeptide chain. DHFR rebound to GroEL 3 min after initiating its folding by the addition of MgATP was also examined by hydrogen exchange, fluorescence quenching, and ANS binding. The results indicate that the extent of protection of the substrate protein rebound to GroEL is indistinguishable from that of the initial bound state. Despite this, small differences in the quenching coefficient and ANS binding properties are observed in the rebound state. On the basis of these results, we suggest that GroEL-assisted folding of DHFR occurs by minor structural adjustments to the partially folded substrate protein during iterative cycling, rather than by complete unfolding of this protein substrate on the chaperonin surface.     

Characterization of a buried neutral histidine residue in Bacillus circulans xylanase: NMR assignments, pH titration, and hydrogen exchange.

Bacillus circulans xylanase contains two histidines, one of which (His 156) is solvent exposed, whereas the other (His 149) is buried within its hydrophobic core. His 149 is involved in a network of hydrogen bonds with an internal water and Ser 130, as well as a potential weak aromatic-aromatic interaction with Tyr 105. These three residues, and their network of interactions with the bound water, are conserved in four homologous xylanases. To probe the structural role played by His 149, NMR spectroscopy was used to characterize the histidines in BCX. Complete assignments of the 1H, 13C, and 15N resonances and tautomeric forms of the imidazole rings were obtained from two-dimensional heteronuclear correlation experiments. An unusual spectroscopic feature of BCX is a peak near 12 ppm arising from the nitrogen bonded 1H epsilon 2 of His 149. Due to its solvent inaccessibility and hydrogen bonding to an internal water molecule, the exchange rate of this proton (4.0 x 10(-5) s-1 at pH*7.04 and 30 degrees C) is retarded by > 10(6)-fold relative to an exposed histidine. The pKa of His 156 is unperturbed at approximately 6.5, as measured from the pH dependence of the 15N- and 1H-NMR spectra of BCX. In contrast, His 149 has a pKa < 2.3, existing in the neutral N epsilon 2H tautomeric state under all conditions examined. BCX unfolds at low pH and 30 degrees C, and thus His 149 is never protonated significantly in the context of the native enzyme. The structural importance of this buried histidine is confirmed by the destablizing effect of substituting a phenylalanine or glutamine at position 149 in BCX.     

Ligand recognition in μ opioid receptor: experimentally based modeling of μ opioid receptor binding sites and their testing by ligand docking

For three-dimensional understanding of the mechanisms that control potency and selectivity of the ligand binding at the atomic level, we have analysed opioid receptor-ligand interaction based on the receptor's 3D model. As a first step, we have constructed molecular models for the multiple opioid receptor subtypes using bacteriorhodopsin as a template. The S-activated dihydromorphine derivatives should serve as powerful tools in mapping the three-dimensional structure of the μ opioid receptor, including the nature of the agonist-mediated conformational change that permits G protein-coupling to ‘second messenger’ effector molecules, and in identifying specific ligand-binding contacts with the μ opioid receptor. The analyses of the interactions of some opioid ligands with the predicted ligand binding sites are consistent with the results of the affinity labeling experiments.