An alternative clamp loading pathway via the T4 clamp loader gp44/62-DNA complex

In bacteriophage T4, a clamp loading pathway that utilizes the T4 clamp loader (gp44/62) and ATP hydrolysis initially to form a complex with the clamp (gp45) has been demonstrated, followed by interaction with DNA and closing of the clamp. However, the recent observation that gp45 exists as an opened form in solution raises the possibility of other pathways for clamp loading. In this study, an alternative clamp loading sequence is evaluated in which gp44/62 first recognizes the DNA substrate and then sequesters the clamp from solution and loads it onto DNA. This pathway differs in terms of the initial formation of a gp44/62-DNA complex that is capable of loading gp45. In this work, we demonstrate ATP-dependent DNA binding by gp44/62. Among various DNA structures that were tested, gp44/62 binds specifically to primer-template DNA but not to single-stranded DNA or blunt-end duplex DNA. By tracing the dynamic clamp closing with pre-steady-state FRET measurements, we show that the clamp loader-DNA complex is functional in clamp loading. Furthermore, pre-steady-state ATP hydrolysis experiments suggest that 1 equiv of ATP is hydrolyzed when gp44/62 binds to DNA, and additional ATP hydrolysis is associated with the completion of the clamp loading process. We also investigated the detailed kinetics of binding of MANT-nucleotide to gp44/62 through stopped-flow FRET and demonstrated a conformational change as the result of ATP, but not ADP binding. The collective kinetic data allowed us to propose and evaluate a sequence of steps describing this alternative pathway for clamp loading and holoenzyme formation.     

The insecticidal activity and action mode of an imidacloprid analogue, 1‐(3‐pyridylmethyl)‐2‐nitroimino‐imidazolidine

Neonicotinoids, such as imidacloprid, are key insecticides extensively used for control of Nilaparvata lugens. However, imidacloprid resistance has been reported in many Asian countries in recent years. To understand the roles of the chlorine atom of pyridyl group on insecticidal activity and resistance, the atom was removed to generate an imidacloprid analogue DC‐Imi (DesChlorine Imidacloprid). DC‐Imi showed significantly higher toxicity than imidacloprid in the susceptible strain of N. lugens, but had medium level cross‐resistance in an imidacloprid‐resistant strain. In Xenopus oocyte expressed nicotinic acetylcholine receptors (nAChRs) Nlα1/rβ2, the inward currents evoked by DC‐Imi were detected and could be blocked by typical nAChRs antagonist dihydro‐β‐erythroidine (DHβE), which demonstrated that DC‐Imi acted as an agonist on insect nAChRs. The efficacy of DC‐Imi on Nlα1/rβ2 was 1.8‐fold higher than that of imidacloprid. In addition, the influence of an imidacloprid resistance associated mutation (Y151S) on agonist potencies was evaluated. Compared with the wild‐type receptor, the mutation reduced maximal inward current of DC‐Imi to 55.6% and increased half maximal effective concentration (EC₅₀) to 3.53‐fold. Compared with imidacloprid (increasing EC₅₀ to 2.38‐fold of wild‐type receptor), Y151S mutation decreased DC‐Imi potency more significantly. The results indicated that the selective and possibly high toxicities could be achieved through the modification of 6‐chloro‐3‐pyridyl group in imidacloprid and other neonicotinoids.     

Trans-Golgi Network-Located AP1 Gamma Adaptins Mediate Dileucine Motif-Directed Vacuolar Targeting in Arabidopsis

Membrane proteins on the tonoplast are indispensible for vacuolar functions in plants. However, how these proteins are transported to the vacuole and how they become separated from plasma membrane proteins remain largely unknown. In this study, we used Arabidopsis thaliana vacuolar ion transporter1 (VIT1) as a reporter to study the mechanisms of tonoplast targeting. We showed that VIT1 reached the tonoplast through a pathway involving the endoplasmic reticulum (ER), Golgi, trans-Golgi network (TGN), prevacuolar compartment, and tonoplast. VIT1 contains a putative N-terminal dihydrophobic type ER export signal, and its N terminus has a conserved dileucine motif (EKQTLL), which is responsible for tonoplast targeting. In vitro peptide binding assays with synthetic VIT1 N terminus identified adaptor protein complex-1 (AP1) subunits that interacted with the dileucine motif. A deficiency of AP1 gamma adaptins in Arabidopsis cells caused relocation of tonoplast proteins containing the dileucine motif, such as VIT1 and inositol transporter1, to the plasma membrane. The dileucine motif also effectively rerouted the plasma membrane protein SCAMP1 to the tonoplast. Together with subcellular localization studies showing that AP1 gamma adaptins localize to the TGN, we propose that the AP1 complex on the TGN mediates tonoplast targeting of membrane proteins with the dileucine motif.     

Detecting Identity by Descent and Homozygosity Mapping in Whole-Exome Sequencing Data

The detection of genetic segments of Identical by Descent (IBD) in Genome-Wide Association Studies has proven successful in pinpointing genetic relatedness between reportedly unrelated individuals and leveraging such regions to shortlist candidate genes. These techniques depend on high-density genotyping arrays and their effectiveness in diverse sequence data is largely unknown. Due to decreasing costs and increasing effectiveness of high throughput techniques for whole-exome sequencing, an influx of exome sequencing data has become available. Studies using exomes and IBD-detection methods within known pedigrees have shown that IBD can be useful in finding hidden genetic candidates where known relatives are available. We set out to examine the viability of using IBD-detection in whole exome sequencing data in population-wide studies. In doing so, we extend GERMLINE, a method to detect IBD from exome sequencing data by finding small slices of matching alleles between pairs of individuals and extending them into full IBD segments. This algorithm allows for efficient population-wide detection in dense data. We apply this algorithm to a cohort of Crohn''s Disease cases where whole-exome and GWAS array data is available. We confirm that GWAS-based detected segments are highly accurate and predictive of underlying shared variation. Where segments inferred from GWAS are expected to be of high accuracy, we compare exome-based detection accuracy of multiple detection strategies. We find detection accuracy to be prohibitively low in all assessments, both in terms of segment sensitivity and specificity. Even after isolating relatively long segments beyond 10cM, exome-based detection continued to offer poor specificity/sensitivity tradeoffs. We hypothesize that the variable coverage and platform biases of exome capture account for this decreased accuracy and look toward whole genome sequencing data as a higher quality source for detecting population-wide IBD.     

Lactacystin诱导帕金森病大鼠黑质胶质细胞的变化

目的观察蛋白酶体抑制剂Lactacystin诱导大鼠黑质胶质细胞的变化、炎性介质NF-κB的表达。方法采用立体定向术将蛋白酶体抑制剂Lactacystin 10μg注射至大鼠黑质部位,免疫组织化学法观察黑质区多巴胺(DA)能神经元、小胶质细胞、星形胶质细胞的变化,炎性介质核转录因子κB(NF-κB)的表达。结果注射Lactacystin 3周,阿朴吗啡腹腔注射后出现典型旋转行为;8周后实验组大鼠损毁侧黑质酪氨酸羟化酶(TH)阳性细胞数明显减少,黑质小胶质细胞及星形胶质细胞的数量均增加,NF-κB表达增强。结论蛋白酶体抑制剂Lactacystin能激活大鼠黑质小胶质细胞及星形胶质细胞,诱导炎性介质表达。     

Generation and analysis of 10 000 ESTs from the half‐smooth tongue sole Cynoglossus semilaevis and identification of microsatellite and SNP markers

Three normalized cDNA libraries were constructed, two of which were constructed from reproductive tissues ovary and testis, and the other one from pooled immune tissues including head kidney, intestine, liver and spleen. A total of 10 542 clones were sequenced generating 10 128 expressed sequence tags (ESTs). Cluster analysis indicated a total of 5808 unique sequences including 1712 contigs and 4096 singletons. A total of 4249 (73%) of the unique ESTs had significant hits to the non‐redundant protein database, 2253 of which were annotated using Gene Ontology (GO) terms. A total of 311 microsatellites (with 246 having sufficient flanking sequences for primer design) and 6294 putative SNPs were identified. These genome resources provide the material basis for future microarray development, marker validation and genetic linkage and QTL analysis.     

Solid‐State Lithium/Selenium–Sulfur Chemistry Enabled via a Robust Solid‐Electrolyte Interphase

Lithium/selenium‐sulfur batteries have recently received considerable attention due to their relatively high specific capacities and high electronic conductivity. Different from the traditional encapsulation strategy for suppressing the shuttle effect, an alternative approach to directly bypass polysulfide/polyselenide formation via rational solid‐electrolyte interphase (SEI) design is demonstrated. It is found that the robust SEI layer that in situ forms during charge/discharge via interplay between rational cathode design and optimal electrolytes could enable solid‐state (de)lithiation chemistry for selenium‐sulfur cathodes. Hence, Se‐doped S_22.2Se/Ketjenblack cathodes can attain a high reversible capacity with minimal shuttle effects during long‐term and high rate cycling. Moreover, the underlying solid‐state (de)lithiation mechanism, as evidenced by in situ ⁷Li NMR and in operando synchrotron X‐ray probes, further extends the optimal sulfur confinement pore size to large mesopores and even macropores that have been long considered as inferior sulfur or selenium host materials, which play a crucial role in developing high volumetric energy density batteries. It is expected that the findings in this study will ignite more efforts to tailor the compositional/structure characteristics of the SEI layers and the related ionic transport across the interface by electrode structure, electrolyte solvent, and electrolyte additive screening.     

Comparative Fluxome and Metabolome Analysis of Formate as an Auxiliary Substrate for Penicillin Production in Glucose‐Limited Cultivation of Penicillium chrysogenum

During glucose‐limited growth, a substantial input of adenosine triphosphate (ATP) is required for the production of β‐lactams by the filamentous fungus Penicillium chrysogenum. Formate dehydrogenase has been confirmed in P. chrysogenum for formate oxidation allowing an extra supply of ATP, and coassimilation of glucose and formate has the potential to increase penicillin production and biomass yield. In this study, the steady‐state metabolite levels and fluxes in response to cofeeding of formate as an auxiliary substrate in glucose‐limited chemostat cultures at the dilution rates (D) of both 0.03 h^?1 and 0.05 h^?1 are determined to evaluate the quantitative impact on the physiology of a high‐yielding P. chrysogenum strain. It is observed that an equimolar addition of formate is conducive to an increase in both biomass yield and penicillin production at D = 0.03 h^?1, while this is not the case at D = 0.05 h^?1. In addition, a higher cytosolic redox status (NADH/NAD⁺), a higher intracellular glucose level, and lower penicillin productivity are only observed upon formate addition at D = 0.05 h^?1, which are virtually absent at D = 0.03 h^?1. In conclusion, the results demonstrate that the effect of formate as an auxiliary substrate on penicillin productivity in the glucose‐limited chemostat cultivations of P. chrysogenum is not only dependent on the formate/glucose ratio as published before but also on the specific growth rate. The results also imply that the overall process productivity and quality regarding the use of formate should be further explored in an actual industrial‐scale scenario.     

Cold‐inducible protein RBM3 mediates hypothermic neuroprotection against neurotoxin rotenone via inhibition on MAPK signalling

Mild hypothermia and its key product, cold‐inducible protein RBM3, possess robust neuroprotective effects against various neurotoxins. However, we previously showed that mild hypothermia fails to attenuate the neurotoxicity from MPP⁺, one of typical neurotoxins related to the increasing risk of Parkinson disease (PD). To better understand the role of mild hypothermia and RBM3 in PD progression, another known PD‐related neurotoxin, rotenone (ROT) was utilized in this study. Using immunoblotting, cell viability assays and TUNEL staining, we revealed that mild hypothermia (32°C) significantly reduced the apoptosis induced by ROT in human neuroblastoma SH‐SY5Y cells, when compared to normothermia (37°C). Meanwhile, the overexpression of RBM3 in SH‐SY5Y cells mimicked the neuroprotective effects of mild hypothermia on ROT‐induced cytotoxicity. Upon ROT stimulation, MAPK signalling like p38, JNK and ERK, and AMPK and GSK‐3β signalling were activated. When RBM3 was overexpressed, only the activation of p38, JNK and ERK signalling was inhibited, leaving AMPK and GSK‐3β signalling unaffected. Similarly, mild hypothermia also inhibited the activation of MAPKs induced by ROT. Lastly, it was demonstrated that the MAPK (especially p38 and ERK) inhibition by their individual inhibitors significantly decreased the neurotoxicity of ROT in SH‐SY5Y cells. In conclusion, these data demonstrate that RBM3 mediates mild hypothermia‐related neuroprotection against ROT by inhibiting the MAPK signalling of p38, JNK and ERK.