Some Characteristics of Pseudomonas 0–3 which Utilizes Polyvinyl Alcohol

Pseudomonas 0–3 strain which was isolated from soil can grow on polyvinyl alcohol (PVA) as a sole carbon source. When 0.5 per cent of PVA (500, 1500 or 2000) was employed as the carbon source in the culture medium, PVA was almost completely lost from the culture fluid after a week and the concentration of total organic carbon measured by a TOC analyzer decreased from the initial value of about 2700 ppm to 250~300 ppm after 7~10 days culture. This bacterium was found to produce and secrete an inducible enzyme which degrade PVA. The way by which this enzyme degrades PVA was examined and the results were obtained which suggested that PVA was broken down oxidatively in a way of endowise splitting. However, the mechanism of PVA degradation has not been clarified yet. The optimum pH and temperature for enzyme activity were examined and they were 7.5~8.5 and 35~45°C, respectively. Morphological and biological characteristics of this bacterium were examined and it was similar to a strain of Pseudomonas boreopolis.     

Body temperatures during three long-distance polar swims in water of 0–3 °C

1.

We report body temperature responses in a single individual to 3 swims of 1000 m or longer in ice-cold water (0–3 °C) during which he swam the normal crawl stroke with his face in the water whilst wearing only a swimming costume, swimming cap and goggles.     

Perk Ablation Ameliorates Myelination in S63del-Charcot–Marie–Tooth 1B Neuropathy

In peripheral nerves, P0 glycoprotein accounts for more than 20% of myelin protein content. P0 is synthesized by Schwann cells, processed in the endoplasmic reticulum (ER) and enters the secretory pathway. However, the mutant P0 with S63 deleted (P0S63del) accumulates in the ER lumen and induces a demyelinating neuropathy in Charcot–Marie–Tooth disease type 1B (CMT1B)–S63del mice. Accumulation of P0S63del in the ER triggers a persistent unfolded protein response. Protein kinase RNA-like endoplasmic reticulum kinase (PERK) is an ER stress sensor that phosphorylates eukaryotic initiation factor 2 alpha (eIF2alpha) in order to attenuate protein synthesis. We have shown that increasing phosphophorylated-eIF2alpha (P-eIF2alpha) is a potent therapeutic strategy, improving myelination and motor function in S63del mice. Here, we explore the converse experiment: Perk haploinsufficiency reduces P-eIF2alpha in S63del nerves as expected, but surprisingly, ameliorates, rather than worsens S63del neuropathy. Motor performance and myelin abnormalities improved in S63del//Perk+/− compared with S63del mice. These data suggest that mechanisms other than protein translation might be involved in CMT1B/S63del neuropathy. In addition, Perk deficiency in other cells may contribute to demyelination in a non–Schwann-cell autonomous manner.     

Excitation dynamics in strongly bounded associates of B800–850 and B800–830 complexes from photosynthetic purple bacterium Thiorhodospira sibirica

Strongly bounded associates of B800–850 (LH2) and B800–830 (LH3) complexes from photosynthetic purple bacterium Thiorhodospira sibirica were investigated. It was shown that associates contain 8–10 complexes (LH2:LH3 ≈ 1:1). Absorption spectra of the monomer LH2 and the monomer LH3 complexes were calculated. Excitation of B800 absorption band of associates results in: (i) intracomplex excitation energy transfer from B800 to B830 or B850 with time constant of about 500 fs; (ii) intercomplex excitation energy transfer from B820 band of LH3 complex to B850 band of LH2 complex with time constant of about 2.5 ps; (iii) excitation deactivation in B850 band of LH2 complex with time constant of about 800 ps. Signal polarization at long-wavelength side of associates absorption spectrum near 900 nm was negative (?0.1). The interaction of LH3 and LH2 complexes in associates is, to some extent, analogous to the interaction of LH2 and LH1 complexes in chromatophores. Time constant of excitation energy transfer between LH3 and LH2 complexes in associates may be regarded as a minimal time constant for energy transfer between the peripheral and core antenna complexes.     

The Human Leukocyte Antigen–presented Ligandome of B Lymphocytes

Peptides presented by human leukocyte antigen (HLA) molecules on the cell surface play a crucial role in adaptive immunology, mediating the communication between T cells and antigen presenting cells. Knowledge of these peptides is of pivotal importance in fundamental studies of T cell action and in cellular immunotherapy and transplantation. In this paper we present the in-depth identification and relative quantification of 14,500 peptide ligands constituting the HLA ligandome of B cells. This large number of identified ligands provides general insight into the presented peptide repertoire and antigen presentation. Our uniquely large set of HLA ligands allowed us to characterize in detail the peptides constituting the ligandome in terms of relative abundance, peptide length distribution, physicochemical properties, binding affinity to the HLA molecule, and presence of post-translational modifications. The presented B-lymphocyte ligandome is shown to be a rich source of information by the presence of minor histocompatibility antigens, virus-derived epitopes, and post-translationally modified HLA ligands, and it can be a good starting point for solving a wealth of specific immunological questions. These HLA ligands can form the basis for reversed immunology approaches to identify T cell epitopes based not on in silico predictions but on the bona fide eluted HLA ligandome.Peptides presented by human leukocyte antigen (HLA)¹ molecules on the cell surface play a crucial role in immunology and mediate the communication between T cells and antigen presenting cells. Knowledge of these peptides is of pivotal importance in fundamental studies of T cell action, the design of T-cell-mediated therapies such as tumor immunotherapy (1), and the treatment of hematological malignancies through a combination of hematopoietic stem cell transplantation and donor lymphocyte infusion (2). In addition, T cells can play an important role in organ rejection following transplantation.The presented HLA class I ligands are the products of the intracellular processing machinery, with its continuous cycle of protein synthesis and degradation (3). Much is known about the proteins involved in antigen processing, but high fidelity ligand/epitope predictions are at present not possible. The discovery of additional involved enzymes (3, 4) and the exciting discovery of peptide splicing (5) have shown that antigen processing is even more complex than was previously thought. Moreover, gene expression studies have shown many nonstandard, unexpected protein products, including the production of antigens derived from aberrant protein fragments as a result of expression in alternative reading frames (6). Several studies report the identification of HLA ligands (7–10). Many results have been collected and discussed in a recent review on the large-scale analysis of HLA class I ligands (11). Collectively, these reports illustrate the need for in-depth elucidation of the HLA ligandome.Elucidation of T cell epitopes has traditionally been achieved with the use of a forward immunological approach, as pioneered by Hunt and coworkers (12, 13). In this approach, the cognate peptide of T cells with the appropriate activity profile is elucidated via repeated rounds of chromatographic separation in combination with T cell recognition assays. Because T cells are not always available from the start, reverse immunological approaches (14–17) have been developed to predict T cell epitopes through a combination of bioinformatics and in vitro proteasome digests. Predicted epitopes are synthesized and tested for their capability to activate T cells. The main disadvantage of this approach is that less than 0.1% of the peptides that survive intracellular processing are presented on HLA class I molecules (3).Therefore, we developed a large-scale peptidomics approach that is a reverse immunology approach based not on algorithms but on the bona fide eluted ligandome, which means that the identified peptides are known to have survived processing and are bona fide HLA ligands. Once the ligandome has been identified as comprehensively as possible, T cells can subsequently be selected on the basis of the immunological question at hand, as will be illustrated in a separate paper.² The development of MHC exchange tetramers for finding relevant T cell epitopes is instrumental to this approach (18, 19).To improve ligandome coverage, we applied and compared three off-line first dimension separation techniques, followed by on-line nano-HPLC-tandem MS.The tandem mass spectra were interrogated by being matched against the International Protein Index (IPI) human database (20). In a second step, post-translation modifications (phosphorylation, cysteinylation) were allowed in the database search. In a third step, the tandem mass spectra were matched against a newly in-house developed database for the optimal identification of polymorphic ligands to find potential minor histocompatibility antigens (21). This led to the identification of ∼14,000 HLA class I ligands, the majority of which also were relatively quantitated. Next, we analyzed the peptides constituting our ligandome in as much detail as possible to confirm the correct identification of the vast majority of the ligands. We achieved this through a combination of several physicochemical and biological checks and comparison with existing ligand and epitope databases.Finally, as an additional quality check, we illustrated the functional relevance of the ligandome through the identification of both previously known and new minor histocompatibility antigens, virus-derived epitopes, and post-translationally modified HLA ligands (phosphorylated ligands and cysteinylated ligands) (22–24). This is the largest ligandome reported to date, and it allows general insight into the presented peptide repertoire. This study supports the building of the “immunopeptidome” as has recently been suggested (25). A proteomics approach can be used as a starting point for contributions to immunology by providing a peptidome landscape in many immunological studies, both fundamental and applied.     

Structure–function analysis of cytochromes P450 2B

In the last 4 years, breakthroughs were made in the field of P450 2B (CYP2B) structure–function through determination of one ligand-free and two inhibitor-bound X-ray crystal structures of CYP2B4, which revealed many of the structural features required for binding ligands of different size and shape. Large conformational changes of several plastic regions of CYP2B4 can dramatically reshape the active site of the enzyme to fit the size and shape of the bound ligand without perturbing the overall P450 fold. Solution biophysical studies using isothermal titration calorimetry (ITC) have revealed the large difference in the thermodynamic parameters of CYP2B4 in binding inhibitors of different ring chemistry and side chains. Other studies have revealed that the effects of site-specific mutations on steady-state kinetic parameters and mechanism-based inactivation are often substrate dependent. These findings agree with the structural data that the enzymes adopt different conformations to bind various ligands. Thus, the substrate specificity of an individual enzyme is determined not only by active site residues but also non-active site residues that modulate conformational changes that are important for substrate access and rearrangement of the active site to accommodate the bound substrate.     

Aβ1–42 reduces P-glycoprotein in the blood–brain barrier through RAGE–NF-κB signaling

The reduced clearance of amyloid-β peptide (Aβ) from the brain partly accounts for the neurotoxic accumulation of Aβ in Alzheimer''s disease (AD). Recently, it has been suggested that P-glycoprotein (P-gp), which is an efflux transporter expressed on the luminal membrane of the brain capillary endothelium, is capable of transporting Aβ out of the brain. Although evidence has shown that restoring P-gp reduces brain Aβ in a mouse model of AD, the molecular mechanisms underlying the decrease in P-gp expression in AD is largely unknown. We found that Aβ_1–42 reduced P-gp expression in the murine brain endothelial cell line bEnd.3, which was consistent with our in vivo data that P-gp expression was significantly reduced, especially near amyloid plaques in the brains of five familial AD mutations (5XFAD) mice that are used as an animal model for AD. A neutralizing antibody against the receptor for advanced glycation end products (RAGE) and an inhibitor of nuclear factor-kappa B (NF-κB) signaling prevented the decrease in Aβ_1–42-induced P-gp expression, suggesting that Aβ reduced P-gp expression through NF-κB signaling by interacting with RAGE. In addition, we observed that the P-gp reduction by Aβ was rescued in bEnd.3 cells receiving inductive signals or factors from astrocytes making contacts with endothelial cells (ECs). These results support that alterations of astrocyte–EC contacts were closely associated with P-gp expression. This suggestion was further supported by the observation of a loss of astrocyte polarity in the brains of 5XFAD mice. Taken together, we found that P-gp downregulation by Aβ was mediated through RAGE–NF-κB signaling pathway in ECs and that the contact between astrocytes and ECs was an important factor in the regulation of P-gp expression.Alzheimer''s disease (AD) is a neurodegenerative disorder that is characterized by a progressive loss of cognitive function leading to dementia. The major pathological hallmark of AD is the deposition of neurotoxic amyloid-β peptide (Aβ) within the brain.¹ The amyloid hypothesis proposes that the accumulation of Aβ is caused by an imbalance between Aβ production and clearance.² Although genetic alterations increase the production of Aβ in rare familial AD, reduced Aβ clearance from the brain likely accounts for sporadic AD, which is much more common.³ The mechanisms that are involved in clearing Aβ from the brain include enzymatic degradation, perivascular drainage, and the most significant, active transport across the blood–brain barrier (BBB).⁴The BBB regulates molecular exchanges at the interface between the blood and the brain.⁵ It plays a critical role in maintaining the brain microenvironment.⁶ The BBB, which is formed by cerebral endothelial cells (ECs) and which, interacts with astrocytes, neurons, pericytes, and the extracellular matrix, is organized into a neurovascular unit.^{7, 8} Although the relationship between BBB breakdown and AD pathology is unclear,⁹ it has been proposed that the BBB loses its Aβ clearing capability, thus increasing amyloid deposition in the outer capillary membrane and resulting in the distortion of the neurovascular unit with neuronal loss.¹⁰Recently, it has been suggested that P-glycoprotein (P-gp), which is an ATP-driven efflux transporter that is highly expressed in the luminal membrane of the brain capillary endothelium, is also involved in the clearance of Aβ from the brain.¹¹ P-gp, which is able to transport various kinds of substrates, has been shown to play an important role in clearing toxic substances in the brain and protecting it from harmful molecules in the circulation.¹² Along with other BBB properties, P-gp expression is induced when ECs are in contact with astrocytes in vitro and in vivo.^{13, 14} ECs respond to inductive signals or factors from astrocytes that encircle the capillary endothelium.¹³Several lines of evidence have shown that P-gp plays an important role in Aβ clearance. It has been shown in vitro that P-gp mediates the transport of Aβ and that blocking P-gp function reduces the clearance of Aβ.^{15, 16} In addition, cerebral Aβ deposition in elderly non-demented individuals has been demonstrated to be inversely correlated with brain capillary P-gp expression.¹⁷ Furthermore, in P-gp knockout mice, Aβ deposition is increased by the reduced efflux of Aβ,¹⁸ while it has been shown that restoring P-gp at the BBB reduces brain Aβ in a mouse model of AD.¹⁹ However, the molecular mechanisms underlying the decrease in P-gp expression that is observed in AD have not been identified. We found that Aβ decreased P-gp expression by increasing nuclear factor-kappa B (NF-κB) through an interaction with the receptor for advanced glycation end products (RAGE). Moreover, we observed that the P-gp reduction by Aβ was rescued by inductive signals or factors from astrocytes that made contact with ECs in bEnd.3 cells. These results suggested that alterations in astrocyte–EC contact in AD likely decrease P-gp expression by Aβ. Together, we identified a mechanism by which the Aβ–RAGE interaction mediated the downregulation of P-gp in the BBB by increasing NF-κB signaling in AD and that astrocyte–EC contact played a critical role in maintaining P-gp expression.     

Structure of desheptapeptide (B24–B30) insulin in a new crystal form

The structure of desheptapeptide (B24–B30) insulin (DHPI) in a new crystal form (form B) has been determined and refined to 0.2 nm resolution. The crystals were obtained under the same crystallization condition as previously reported crystal form (form A). The overall structures of the two crystal forms are similar but obvious differences can be observed in crystal packing and local conformation. The crystal structures of the two forms show that the two independent molecules in an asymmetric unit from a DHPI dimer, and the dimer formation buries more than 18.20 and 16.95 nm² of solvent accessible surfaces for form A and form B DHPI, respectively, the largest among insulin and insulin analogs ever reported. Close examination at crystal packing shows that the dimer-forming surface of DHPI, namely Surface II, is normally present in the association of insulin and insulin analogs in their crystal structures. The results demonstrate that Surface II is crucially important for the formation of two crystal forms under the same crystallization condition.     

Synthesis and disulfide bond connectivity–activity studies of a kalata B1-inspired cyclopeptide against dengue NS2B–NS3 protease

Kalata B1 is a plant protein with remarkable thermal, chemical and enzymatic stability. Its potential applications could be centered on the possibility of using its cyclic structure and cystine knot motif as a scaffold for the design of stable pharmaceuticals. To discover potent dengue NS2B–NS3 protease inhibitors, we have prepared various kalata B1 analogues by varying the amino acid sequence. Mass spectrometric and biochemical investigations of these analogues revealed a cyclopeptide whose two fully oxidized forms are substrate-competitive inhibitors of the dengue viral NS2B–NS3 protease. Both oxidized forms showed potent inhibition with K_i of 1.39 ± 0.35 and 3.03 ± 0.75 μM, respectively.     

Blood Lead Levels in Children Aged 0–6 Years Old in Hunan Province,China from 2009–2013

Objectives

The aim of this study is to describe blood lead levels (BLLs) and the prevalence of elevated blood lead levels (EBLLs) in children aged 0–6 years old and to analyze the BLL trend in children from 2009 to 2013 in China.

Methods

A total of 124,376 children aged 0–6 years old were recruited for this study from January 1^st 2009 to December 31^st 2013. Their blood lead levels were analyzed using atomic absorption spectrometry.

Results

The median BLL was 64.3 μg/L (IQR: 49.6–81.0), and the range was 4.3–799.0 μg/L. Blood lead levels were significantly higher in boys (66.0 μg/L) than in girls (61.9 μg/L) (P<0.001). The overall prevalence of BLLs≥100 μg/L was 10.54% in children aged 0–6 years in Hunan Province. Between 2009 and 2013, the prevalence of EBLLs (≥100 μg/L) decreased from 18.31% to 4.26% in children aged 0–6 years and increased with age. The prevalence of EBLLs has dramatically decreased in two stages (2009–2010 and 2012–2013), with a slight fluctuation in 2010 and 2011.

Conclusions

Both BLLs and the prevalence of EBLLs in children aged 0–6 years old declined substantially from 2009 to 2013 in Hunan Province; however, both remain at unacceptably high levels compared to developed countries. Comprehensive strategies are required to further reduce blood lead levels in children.     

Heat Shock–Induced Fluctuations in Clock and Light Signaling Enhance Phytochrome B–Mediated Arabidopsis Deetiolation

Moderately warm constant ambient temperatures tend to oppose light signals in the control of plant architecture. By contrast, here we show that brief heat shocks enhance the inhibition of hypocotyl growth induced by light perceived by phytochrome B in deetiolating Arabidopsis thaliana seedlings. In darkness, daily heat shocks transiently increased the expression of PSEUDO-RESPONSE REGULATOR7 (PRR7) and PRR9 and markedly enhanced the amplitude of the rhythms of LATE ELONGATED HYPOCOTYL (LHY) and CIRCADIAN CLOCK ASSOCIATED1 (CCA1) expression. In turn, these rhythms gated the hypocotyl response to red light, in part by changing the expression of PHYTOCHROME INTERACTING FACTOR4 (PIF4) and PIF5. After light exposure, heat shocks also reduced the nuclear abundance of CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) and increased the abundance of its target ELONGATED HYPOCOTYL5 (HY5). The synergism between light and heat shocks was deficient in the prr7 prr9, lhy cca1, pif4 pif5, cop1, and hy5 mutants. The evening element (binding site of LHY and CCA1) and G-box promoter motifs (binding site of PIFs and HY5) were overrepresented among genes with expression controlled by both heat shock and red light. The heat shocks experienced by buried seedlings approaching the surface of the soil prepare the seedlings for the impending exposure to light by rhythmically lowering LHY, CCA1, PIF4, and PIF5 expression and by enhancing HY5 stability.     

Ceramicines B–D,new antiplasmodial limonoids from Chisocheton ceramicus

Three new limonoids, ceramicines B–D (1–3), have been isolated from the bark of Chisocheton ceramicus. Structures and stereochemistry of 1–3 were fully elucidated and characterized by 2D NMR analysis. Ceramicines exhibited a moderate antiplasmodial activity.     

曹天钦学术基金会评选出本刊 2 0 0 0年优秀论文

曹天钦学术基金会最近对本刊 2 0 0 0年发表的优秀论文进行了评选。根据基金会评选细则 (见本刊 1998年第 6期 6 17页 ) ,由《生物化学与生物物理学报》编辑部根据论文的质量 (至少有一位审稿专家评为甲级 ) ,从 2 0 0 0年已发表的 137篇论文中推荐 9篇参加优秀学术论文的评选 ,然后由基金会聘请专家对所推荐论文进行了评选 ,结果公布如下 :优秀论文奖 :杨运桂 ,徐京宁 ,胡泰山 ,钱友存 ,杨胜利 ,龚　毅。信号肽疏水性的提高促进青毒素Ｇ酰化酶分泌。生物化学与生物物理学报 ,2 0 0 0 ,32 (2 ) :16 3— 16 8(专家点评 :这是一篇有关人工信号…     

Isoquercetin protects cortical neurons from oxygen–glucose deprivation–reperfusion induced injury via suppression of TLR4–NF-кB signal pathway

In the present study, oxygen–glucose deprivation followed by reperfusion (OGD/R), an in vitro model of ischemia, was used to evaluate the neuroprotective effect of isoquercetin in primary culture of rat cortical neuronal cells. It was found that isoquercetin administered prior to the insult could prevent OGD/R-induced intracellular calcium concentrations ([Ca²⁺]_i) increase, lactate dehydrogenase (LDH) release and cell viability decrease. For the first time, isoquercetin is described as a neuroprotective agent that potentially explains the alleviation and prevention from OGD/R-induced injury in neurons. Mechanistic studies showed that the neuroprotective effect of isoquercetin was carried out by anti-inflammatory signaling pathway of inhibiting protein expression of toll-like receptor 4 (TLR4) and nuclear factor-kappa B (NF-κB), and mRNA expression of TNF-α and IL-6, accompanied by the anti-apoptotic signaling pathway of deactivation of extracellular-regulated kinase (ERK), Jun kinase (JNK) and p38, and inhibition of activity of caspase-3. Therefore, these studies highlighted the confirmation of isoquercetin, a flavonoid compound, as an anti-inflammation and anti-apoptosis factor which might be used as a therapeutic strategy for the ischemia/reperfusion (I/R) brain injury and related diseases.