Therapeutic efficacy and safety of chaperonin 10 in patients with rheumatoid arthritis: A double-blind randomised trial

Background Chaperonin 10 (heat shock protein 10, XToll(TM)) has anti-inflammatory properties related to the inhibition of Toll-like receptor signalling pathways. Our aim was to establish whether chaperonin 10 is safe and effective in the treatment of rheumatoid arthritis. Methods in this randomised, double-blind, multicentre study, 23 patients with moderate to severe active rheumatoid arthritis receiving disease-modifying antirheumatic drugs were randomly allocated to three treatment groups receiving intravenous chaperonin 10 twice weekly for 12 weeks at doses of 5 mg (n=8), 7.5 mg (8), or 10 mg (7). The primary outcomes were change in disease activity score (DAS28) and improvement of core disease measures (American College of Rheumatology response score) from baseline to week 12. All analyses were done by intention to treat. This study is registered with the Australian Clinical Trials Registry, number ACTRNO12606000041550. Findings Primary endpoint measures improved from day 14 in all groups and continued to improve to day 84. By end of study, a 20% improvement of core disease measures was seen in six (86%, 95% Cl 43-100), a 50% improvement in four (57%, 14-86), and a 70% improvement in two (29%, 0-57) patients given the highest dose of chaperonin 10. Clinical remission (as defined by a DAS28

Seawater carbonate chemistry and echinoderm Asterias rubens biological processes during experiments, 2011

We compared effects of exposure to predicted near-future (2100) ocean acidification (OA; pH 7.7) and normal seawater (Control; pH 8.1) on immune and stress responses in the adult sea star Asterias rubens. Analyses were made after one week and after six months of continuous exposure. Following one week exposure to acidified water, the pH of coelomic fluid was significantly reduced. Levels of the chaperon Hsp70 were elevated while key cellular players in immunity, coelomocytes, were reduced by approximately 50%. Following long-term exposure (six months) levels of Hsp70 returned to control values, whereas immunity was further impaired, evidenced by the reduced phagocytic capacity of coelomocytes and inhibited activation of p38 MAP-kinase. Such impacts of reduced seawater pH may have serious consequences for resistance to pathogens in a future acidified ocean.

Heat and water stress induce unique transcriptional signatures of heat-shock proteins and transcription factors in grapevine

Grapevine is an extremely important crop worldwide.In southern Europe, post-flowering phases of the growth cycle can occur under high temperatures, excessive light, and drought conditions at soil and/or atmospheric level. In this study, we subjected greenhouse grown grapevine, variety Aragonez, to two individual abiotic stresses, water deficit stress(WDS), and heat stress (HS). The adaptation of plants to stress is a complex response triggered by cascades of molecular net works involved in stress perception, signal transduction, and the expression of specific stress-related genes and metabolites. Approaches such as array-based transcript profiling allow assessing the expression of thousands of genes in control and stress tissues. Using microarrays, we analyzed the leaf transcriptomic profile of the grapevine plants. Photosynthesis measurements verified that the plants were significantly affected by the stresses applied. Leaf gene expression was obtained using a high-throughput transcriptomic grapevine array, the 23K custom-made Affymetrix Vitis GeneChip. We identified 1,594 genes as differentially expressed between control and treatments and grouped them into ten major functional categories using MapMan software. The transcriptome of Aragonez was more significantly affected by HS when compared with WDS. The number of genes coding for heat-shock proteins and transcription factors expressed solely in response to HS suggesting their expression as unique signatures of HS. However, across-talk between the response pathways to both stresses was observed at the level of AP2/ERF transcription factors.

Heat shock response in bacteria with large genomes: lessons from rhizobia

Rhizobia are important soil bacteria due to their ability to establish nitrogen-fixing symbioses with legume plants. In this dual lifestyle, as free-living bacteria or as plant symbiont, rhizobia are often exposed to different environmental stresses. The present chapter overviews the current knowledge on the heat shock response of rhizobia, highlighting how these large genome bacteria respond to heat from a transcriptional point of view. Response to heat shock in rhizobia involves genome wide changes in the transcriptome that may affect more than 30% of the genome and involve all replicons. In addition to the expected upregulation of genes already known to be involved in stress response (dnaK, groEL, ibpA, clpB), the reports on the heat shock response in rhizobia also showed particular aspects of stress response in these resourceful bacteria. The transcriptional response to heat in rhizobia includes the overexpression of a large number of genes involved in transcription and carbohydrate transport and metabolism. Additional studies are needed in order to better understand the transcriptional regulation of stress response in bacteria with large genomes.

Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers

Background The sequencing, de novo assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species with unprecedented ease. Reliable and accurate de novo assembly and annotation of transcriptomes, however, is a critically important step for transcriptome assemblies generated from short read sequences. Typical benchmarks for assembly and annotation reliability have been performed with model species. To address the reliability and accuracy of de novo transcriptome assembly in non-model species, we generated an RNAseq dataset for an intertidal gastropod mollusc species, Nerita melanotragus, and compared the assembly produced by four different de novo transcriptome assemblers; Velvet, Oases, Geneious and Trinity, for a number of quality metrics and redundancy. Results Transcriptome sequencing on the Ion Torrent PGM™ produced 1,883,624 raw reads with a mean length of 133 base pairs (bp). Both the Trinity and Oases de novo assemblers produced the best assemblies based on all quality metrics including fewer contigs, increased N50 and average contig length and contigs of greater length. Overall the BLAST and annotation success of our assemblies was not high with only 15-19% of contigs assigned a putative function. Conclusions We believe that any improvement in annotation success of gastropod species will require more gastropod genome sequences, but in particular an increase in mollusc protein sequences in public databases. Overall, this paper demonstrates that reliable and accurate de novo transcriptome assemblies can be generated from short read sequencers with the right assembly algorithms. Keywords: Nerita melanotragus; De novo assembly; Transcriptome; Heat shock protein; Ion torrent

Pathogenesis of Fallopian tube damage caused by Chlamydia trachomatis infections

Chlamydia trachomatis is the leading cause of bacterial sexually transmitted disease worldwide resulting in 4–5 million new cases of Chlamydia annually and an estimated 100 million cases per annum. Infections of the lower female genital tract (FGT) frequently are asymptomatic so they often remain undiagnosed or untreated. If infections are either not resolved, or are left untreated, chlamydia can ascend to the upper FGT and infect the fallopian tubes (FTs) causing salpingitis that may lead to functional damage of the FTs and tubal factor infertility (TFI). Clinical observations and experimental data have indicated a role for antibodies against C. trachomatis proteins such as the 60 kDa heat-shock protein 60 (cHSP60) in the immunopathogenesis of TFI. When released from infected cells cHSP60 can induce pro-inflammatory immune responses that may functionally impair the FTs leading to fibrosis and luminal occlusion. Chlamydial pathogenesis of irreversible and permanent tubal damage is a consequence of innate and adaptive host immune responses to ongoing or repeated infections. The extracellular matrix (ECM) that is regulated by metalloproteinases (MMPs) may also be modified by chlamydial infections of the FGT. This review will highlight protective and pathogenic immune responses to ongoing and repeated chlamydial infections of the FGT. It will also present two recent hypotheses to explain mechanisms that may contribute to FT damage during a C. trachomatis infection. If Chlamydia immunopathology can be controlled it might yield a method of inducing fibrosis and thus provide a means of non-surgical permanent contraception for women.

A candidate gene association study for growth performance in an improved Giant Freshwater Prawn (Macrobrachium rosenbergii) culture line

A candidate gene approach using type I single nucleotide polymorphism (SNP) markers can provide an effective method for detecting genes and gene regions that underlie phenotypic variation in adaptively significant traits. In the absence of available genomic data resources, transcriptomes were recently generated in Macrobrachium rosenbergii to identify candidate genes and markers potentially associated with growth. The characterisation of 47 candidate loci by ABI re-sequencing of four cultured and eight wild samples revealed 342 putative SNPs. Among these, 28 SNPs were selected in 23 growth-related candidate genes to genotype in 200 animals selected for improved growth performance in an experimental GFP culture line in Vietnam. The associations between SNP markers and individual growth performance were then examined. For additive and dominant effects, a total of three exonic SNPs in glycogen phosphorylase (additive), heat shock protein 90 (additive and dominant) and peroxidasin (additive), and a total of six intronic SNPs in ankyrin repeats-like protein (additive and dominant), rolling pebbles (dominant), transforming growth factor-β induced precursor (dominant), and UTP-glucose-1-phosphate uridylyltransferase 2 (dominant) genes showed significant associations with the estimated breeding values in the experimental animals (P =0.001−0.031). Individually, they explained 2.6−4.8 % of the genetic variance (R2=0.026−0.048). This is the first large set of SNP markers reported for M. rosenbergii and will be useful for confirmation of associations in other samples or culture lines as well as having applications in marker-assisted selection in future breeding programs.

The genetic diversity of ampeloviruses in Australian pineapples and their association with mealybug wilt disease

Pineapple mealybug wilt-associated virus 1 (PMWaV-1), 2 (PMWaV-2) and -3 (PMWaV-3) have been detected in Australian commercial pineapple crops, along with a previously undescribed ampelovirus, for which the name Pineapple mealybug wilt-associated virus 5 (PMWaV-5) is proposed. Partial sequences extending from open reading frame 1b through to the heat shock protein homologue were obtained for PMWaV-1, -3 and -5. Phylogenetic analyses of selected regions of these sequences indicated that PMWaV-5 is a distinct species and most closely related to PMWaV-1. The amino acid sequence variation observed in the RNA-dependent RNA polymerase region of PMWaV-1 isolates was 95.8–98.4% and of PMWaV-3 isolates was 92.2–99.5%. In surveys of mealybug wilt disease (MWD) affected crops, none of the four viruses was clearly associated with the disease at all survey sites. A statistically significant association (P < 0.001) between the presence of PMWaV-2 and symptoms was observed at one survey site (site 3), but the virus was at a low incidence at the remaining three survey sites. By contrast, although PMWaV-1 and -3 were equally distributed between symptomless and MWD-affected plants at site 3, there was a statistically significant (P < 0.001) association between each of these two viruses and MWD at sites 1 and 4. At site 2, there was a statistically significant (P < 0.001) association only between PMWaV-3 and MWD. PMWaV-1 was the most commonly found of the four viruses and conversely PMWaV-5 was only occasionally found. Australian isolates of PMWaV-1, -2 and -3 were transmitted by the mealybug species Dysmicoccus brevipes.

ERAP2 functional knockout in humans does not alter surface heavy chains or HLA-B27, inflammatory cytokines or endoplasmic reticulum stress markers

Introduction Single nucleotide polymorphisms in ERAP2 are strongly associated with ankylosing spondylitis (AS). One AS-associated single nucleotide polymorphism, rs2248374, causes a truncated ERAP2 protein that is degraded by nonsense-mediated decay. Approximately 25% of the populations of European ancestry are therefore natural ERAP2 knockouts. We investigated the effect of this associated variant on HLA class I allele presentation, surface heavy chains, endoplasmic reticulum (ER) stress markers and cytokine gene transcription in AS. Methods Patients with AS and healthy controls with either AA or GG homozygous status for rs2248374 were studied. Antibodies to CD14, CD19-ECD, HLA-A-B-C, Valpha7.2, CD161, anti-HC10 and anti-HLA-B27 were used to analyse peripheral blood mononuclear cells. Expression levels of ER stress markers (GRP78 and CHOP) and proinflammatory genes (tumour necrosis factor (TNF), IL6, IL17 and IL22) were assessed by qPCR. Results There was no significant difference in HLAclass I allele presentation or major histocompatibility class I heavy chains or ER stress markers GRP78 and CHOP or proinflammatory gene expression between genotypes for rs2248374 either between cases, between cases and controls, and between controls. Discussion Large differences were not seen in HLAB27 expression or cytokine levels between subjects with and without ERAP2 in AS cases and controls. This suggests that ERAP2 is more likely to influence AS risk through other mechanisms.

Characterization of Precursor PfHsp60 in Plasmodium falciparum Cytosol during Its Asexual Development in Human Erythrocytes

Mitochondrial heat shock protein 60 (Hsp60) is a nuclear encoded gene product that gets post-translationally translocated into the mitochondria. Using multiple approaches such as immunofluorescence experiments, isoelectric point analysis with two-dimensional gel electrophoresis, and mass spectrometric identification of the signal peptide, we show that Hsp60 from Plasmodium falciparum (PfHsp60) accumulates in the parasite cytoplasm during the ring, trophozoite, and schizont stages of parasite development before being imported into the parasite mitochondria. Using co-immunoprecipitation experiments with antibodies specific to cytoplasmic PfHsp90, PfHsp70-1, and PfHsp60, we show association of precursor PfHsp60 with cytoplasmic chaperone machinery. Metabolic labeling involving pulse and chase indicates translocation of the precursor pool into the parasite mitochondrion during chase. Analysis of results obtained with Geldanamycin treatment confirmed precursor PfHsp60 to be one of the clients for PfHsp90. Cytosolic chaperones bind precursor PfHsp60 prior to its import into the mitochondrion of the parasite. Our data suggests an inefficient co-ordination in the synthesis and translocation of mitochondrial PfHsp60 during asexual growth of malaria parasite in human erythrocytes.

Binding of the molecular chaperone αB-crystallin to Aβ amyloid fibrils inhibits fibril elongation.

The molecular chaperone αB-crystallin is a small heat-shock protein that is upregulated in response to a multitude of stress stimuli, and is found colocalized with Aβ amyloid fibrils in the extracellular plaques that are characteristic of Alzheimer's disease. We investigated whether this archetypical small heat-shock protein has the ability to interact with Aβ fibrils in vitro. We find that αB-crystallin binds to wild-type Aβ(42) fibrils with micromolar affinity, and also binds to fibrils formed from the E22G Arctic mutation of Aβ(42). Immunoelectron microscopy confirms that binding occurs along the entire length and ends of the fibrils. Investigations into the effect of αB-crystallin on the seeded growth of Aβ fibrils, both in solution and on the surface of a quartz crystal microbalance biosensor, reveal that the binding of αB-crystallin to seed fibrils strongly inhibits their elongation. Because the lag phase in sigmoidal fibril assembly kinetics is dominated by elongation and fragmentation rates, the chaperone mechanism identified here represents a highly effective means to inhibit fibril proliferation. Together with previous observations of αB-crystallin interaction with α-synuclein and insulin fibrils, the results suggest that this mechanism is a generic means of providing molecular chaperone protection against amyloid fibril formation.

果实对酵母拮抗菌和外源水杨酸诱导的抗病性应答机理

用生物和非生物因子来进行采后病害的防治，是一个非常有效的方法。诱导抗性作为控制果蔬采后病害的生物技术，已成为该领域的一个研究热点。然而诱导抗性的机制非常复杂，涉及到寄主、病原菌、激发子之间的相互作用关系。本研究主要利用酵母拮抗菌Pichia membranefaciens和SA处理果实，观察其抗性诱导表达和对采后青霉病菌（Penicillium expansum）的抑制作用，并从蛋白质组学水平上对诱导抗性的机理进行了分析。研究结果表明： 1、酵母拮抗菌P. membranefaciens (5 × 107 cells·ml-1)和SA(0.5 mM)处理采后甜樱桃果实，能够明显地降低病害的发病率和病斑直径。酵母菌和SA处理影响到了果实抗氧化酶的活性，同时还改变了POD同工酶谱和甜樱桃果实的总蛋白含量，并诱导了新的蛋白质条带产生。用光学显微镜和扫描电子显微镜技术观察发现，在in vitro条件下P. membranefaciens能够紧密地结合与病原菌的菌丝，而在in vivo条件下这种结合较为松散。 2、借鉴其它模式植物的方法，我们建立了一整套适用于多汁类植物材料的蛋白质组学研究方法。对于芒果，桃，甜樱桃、苹果以及冬枣等果实，都取得了重复性非常好的2-D图谱。我们应用该技术进一步研究了P. membranefaciens (1 × 108 cells·ml-1)以及SA (0.5 mM)处理对桃果实蛋白质组的诱导影响。结果显示，两种激发子处理都能够诱导桃果实产生抗性，从而减轻青霉病引起的腐烂。在诱导处理1 d以后，酵母拮抗菌和SA分别诱导22和16个蛋白的差异表达。质谱鉴定的蛋白属于6大类：代谢，防御反应，转录，能量途径以及细胞结构。有6个蛋白受到两种激发子的共同调控。其中，4种蛋白(包括glutathione peroxidase, polyphenol oxidase precursor, catalase和methionine sulfoxide reductase) 属于抗氧化蛋白，涉及到活性氧代谢。另2个蛋白（Major allergen Pru av 1和peroxidase）是病程相关蛋白，直接参与植物的防御反应。同时一些磷酸化酶和转录因子也受到两种激发子的调节从而参与果实的抗病反应。酶学测定和Northern杂交的结果表明，拮抗菌与SA处理均能影响过氧化氢酶活性及其基因的表达。 3、采前用较高浓度SA (2 mM) 短时间（10s）处理不同成熟期的甜樱桃果实，能够明显降低果实青霉病的病斑直径，并能减轻较低成熟度果实的发病率。在没有接菌的情况下，SA诱导了33个差异表达的蛋白，其中用质谱鉴定出了26个。而在接种病原菌的情况下，SA诱导了19个差异表达的蛋白，并鉴定出了其中的12个。这些蛋白分别涉及到代谢、防御反应、转录、能量途径、信号转导等过程。在没有接种病原菌的情况下，SA处理诱导了Putative DnaJ heat shock protein, PR1-like protein, Peroxidase, Major allergen Pru av 1 (Pru a 1)和Catalase等与抗病有关的蛋白。而在接种病原菌的情况下，诱导了PR1-like protein, Peroxidase和Catalase蛋白的差异表达。通过酶活性测定以及对细胞学定位的研究，我们发现在没有接种病原菌的情况下，POD的活性受到SA的诱导。但是在接种病原菌以后，诱导效果不明显。

植物分子伴侣热休克蛋白90（Hsp90）的分子作用机理及抗逆基因工程研究

热激蛋白90是广泛存在于各类细菌和真核生物中的一类高度保守的分子伴侣，它对维持细胞生命是绝对必需的。对Hsp90的相关认知主要来源于对动物和酵母细胞的研究，植物Hsp90的研究甚少。由于植物的特殊性，因此对植物Hsp90的研究是对Hsp90未知功能的有力补充。拟南芥中有7个Hsp90蛋白，其中AtHsp90-1、AtHsp90-2、AtHsp90-3和AtHsp90-4定位在细胞质中，AtHsp90-5、AtHsp90-6和AtHsp90-7分别定位在叶绿体、线粒体和内质网中。本文对拟南芥中的AtHsp90-1、AtHsp90-2、AtHsp90-5、AtHsp90-6和AtHsp90-7五个基因进行了克隆，并分别利用酵母互补、双杂交和拟南芥过表达体系几个层面进行了功能分析。 我们利用酵母穿梭载体p416GPD构建了五个AtHsp90基因的酵母表达载体，将其转入Hsp90基因点突变和条件型缺失的酵母菌株iG170D和R0005中。酵母功能互补实验表明细胞质定位的AtHsp90-1和AtHsp90-2可以在各种胁迫条件下互补酵母Hsp90的功能，而定位于细胞器中的AtHsp90-5、 AtHsp90-6和AtHsp90- 7则在任何条件下都不能互补酵母Hsp90的功能。我们还对转基因酵母进行了液体培养的动态观测和细胞膜完整性检测，其结果和固体培养的结果一致。这说明细胞质Hsp90的功能具有一定的保守性，细胞器Hsp90的功能有其特殊性。 热激蛋白90在执行其生物功能时，需要和大量的辅助因子相互作用，因此我们利用酵母双杂交体系检测了AtHsp90-1、AtHsp90-2、AtHsp90-5、AtHsp90-6和AtHsp90-7五个Hsp90蛋白和Hsp70、p23、Cyp40、NOS等几个辅助因子之间的相互作用情况。双杂交结果显示AtHsp90-1和AtHsp90-2几乎不和所选的这几个辅助因子相互作用，AtHsp90-5可以和所有的辅助因子相互作用、AtHsp90-6可以和除Hsp70以外的辅助因子相互作用，AtHsp90-7也可以和所有的辅助因子相互作用但和Hsp70及Hsp70t-2和互作较其他辅助因子弱一些。可以看出胞质Hsp90和细胞器Hsp90在和辅助因子相互作用时有一定的差异。 为了进一步了解拟南芥个Hsp90基因在抗非生物逆境中的作用，我们又将AtHsp90-2、AtHsp90-5、AtHsp90-7基因插入植物表达载体pBI121，用农杆菌介导的浸蕾法将这三个基因转入拟南芥并在其中过量表达，并研究了这些基因的过表达植株的种子和幼苗对多种模拟非生物逆境的响应。结果显示，转基因种子和幼苗对ABA、盐(NaCl)、干旱(甘露醇)、高温、氧化、高钙等非生物逆境都表现出了敏感，转细胞器Hsp90的种子和幼苗比转细胞质Hsp90的更为敏感。但在高浓度钙离子胁迫下，幼苗表现情况与盐、旱和氧化等非生物逆境处理下的情况正好相反，转细胞器Hsp90的幼苗比转细胞质Hsp90的长得健壮。这些结果表明Hsp90参与了植物抵抗非生物逆境的反应，其作用可能是通过ABA和Ca2+途径实现的，然而体内Hsp90的动态平衡可能才是植物抵抗非生物逆境的关键。