The Crystal Structure of the Defense Conferring Rice Protein OsJAC1 Reveals a Carbohydrate Binding Site on the Dirigent-like Domain.

Pesticides are routinely used to prevent severe losses in agriculture. This practice is under debate because of its potential negative environmental impact and selection of resistances in pathogens. Therefore, the development of disease resistant plants is mandatory. It was shown that the rice (Oryza sativa) protein OsJAC1 enhances resistance against different bacterial and fungal plant pathogens in rice, barley, and wheat. Recently we reported possible carbohydrate interaction partners for both domains of OsJAC1 (a jacalin-related lectin (JRL) and a dirigent (DIR) domain), however, a mechanistic understanding of its function is still lacking. Here, we report crystal structures for both individual domains and the complex of galactobiose with the DIR domain, which revealed a new carbohydrate binding motif for DIR proteins. Docking studies of the two domains led to a model of the full-length protein. Our findings offer insights into structure and binding properties of OsJAC1 and its possible function in pathogen resistance.

X-ray detection of a nova in the fireball phase.

Novae are caused by runaway thermonuclear burning in the hydrogen-rich envelopes of accreting white dwarfs, which leads to a rapid expansion of the envelope and the ejection of most of its mass1,2. Theory has predicted the existence of a 'fireball' phase following directly on from the runaway fusion, which should be observable as a short, bright and soft X-ray flash before the nova becomes visible in the optical3-5. Here we report observations of a bright and soft X-ray flash associated with the classical Galactic nova YZ Reticuli 11 h before its 9 mag optical brightening. No X-ray source was detected 4 h before and after the event, constraining the duration of the flash to shorter than 8 h. In agreement with theoretical predictions4,6-8, the source's spectral shape is consistent with a black-body of 3.27+0.11-0.33 × 105 K (28.2+0.9-2.8 eV), or a white dwarf atmosphere, radiating at the Eddington luminosity, with a photosphere that is only slightly larger than a typical white dwarf.

Development of a histopathological index for skeletal muscle analysis in Rattus norvegicus (Rodentia: Muridae).

Skeletal muscle histopathological changes induced or caused by pathologies in animal models, can impair functionality, being the main focus of therapeutic studies. This study aimed to propose a histopathological index to assess, in a quantitative manner, skeletal muscle changes induced by experimental protocols for Rodentia's models. For the development, evaluation of fit and parsimony, replicability, and sensitivity index, Wistar rats from experiments with the same experimental design, but with different variation factors, were used to achieve different levels of damage. The anterior tibial muscle of these animals was collected, processed histologically, and stained with hematoxylin and eosin. The adjustment and parsimony of the index were availed through Confirmatory Factor Analysis, reproducibility for evaluation of three people trained through the Intra-Class Correlation, and the discrimination capacity through a one-way ANOVA Test. We pointed out the adjustment for the proposed index while the ICC showed high reproducibility (n = 56; k = 3; ICC = 0.9790) and differences in the extent of damage between groups, following the hierarchical association promoted by experimental model stresses. The results show that the proposed index has a good fit and parsimony (χ2 = 426.34; p < 0.0001), in addition to being easily replicable by other researchers who know the morphology of muscle tissue and its morphological changes. It is worth mentioning that the development of tools that facilitate histopathological analysis, and that can quantitatively express the findings, are of great importance for the studies of regenerative science, reinforcing the relevance of this study.

Pathogen Resistance Depending on Jacalin-Dirigent Chimeric Proteins Is Common among Poaceae but Absent in the Dicot Arabidopsis as Evidenced by Analysis of Homologous Single-Domain Proteins.

MonocotJRLs are Poaceae-specific two-domain proteins that consist of a jacalin-related lectin (JRL) and a dirigent (DIR) domain which participate in multiple developmental processes, including disease resistance. For OsJAC1, a monocotJRL from rice, it has been confirmed that constitutive expression in transgenic rice or barley plants facilitates broad-spectrum disease resistance. In this process, both domains of OsJAC1 act cooperatively, as evidenced from experiments with artificially separated JRL- or DIR-domain-containing proteins. Interestingly, these chimeric proteins did not evolve in dicotyledonous plants. Instead, proteins with a single JRL domain, multiple JRL domains or JRL domains fused to domains other than DIR domains are present. In this study, we wanted to test if the cooperative function of JRL and DIR proteins leading to pathogen resistance was conserved in the dicotyledonous plant Arabidopsis thaliana. In Arabidopsis, we identified 50 JRL and 24 DIR proteins, respectively, from which seven single-domain JRL and two single-domain DIR candidates were selected. A single-cell transient gene expression assay in barley revealed that specific combinations of the Arabidopsis JRL and DIR candidates reduced the penetration success of barley powdery mildew. Strikingly, one of these pairs, AtJAX1 and AtDIR19, is encoded by genes located next to each other on chromosome one. However, when using natural variation and analyzing Arabidopsis ecotypes that express full-length or truncated versions of AtJAX1, the presence/absence of the full-length AtJAX1 protein could not be correlated with resistance to the powdery mildew fungus Golovinomyces orontii. Furthermore, an analysis of the additional JRL and DIR candidates in a bi-fluorescence complementation assay in Nicotiana benthamiana revealed no direct interaction of these JRL/DIR pairs. Since transgenic Arabidopsis plants expressing OsJAC1-GFP also did not show increased resistance to G. orontii, it was concluded that the resistance mediated by the synergistic activities of DIR and JRL proteins is specific for members of the Poaceae, at least regarding the resistance against powdery mildew. Arabidopsis lacks the essential components of the DIR-JRL-dependent resistance pathway.

Biochemical and Initial Structural Characterization of the Monocot Chimeric Jacalin OsJAC1.

The monocot chimeric jacalin OsJAC1 from Oryza sativa consists of a dirigent and a jacalin-related lectin domain. The corresponding gene is expressed in response to different abiotic and biotic stimuli. However, there is a lack of knowledge about the basic function of the individual domains and their contribution to the physiological role of the entire protein. In this study, we have established a heterologous expression in Escherichia coli with high yields for the full-length protein OsJAC1 as well as its individual domains. Our findings showed that the secondary structure of both domains is dominated by ß-strand elements. Under reducing conditions, the native protein displayed clearly visible transition points of thermal unfolding at 59 and 85 °C, which could be attributed to the lectin and the dirigent domain, respectively. Our study identified a single carbohydrate-binding site for each domain with different specificities towards mannose and glucose (jacalin domain), and galactose moieties (dirigent domain), respectively. The recognition of different carbohydrates might explain the ability of OsJAC1 to respond to different abiotic and biotic factors. This is the first report of specific carbohydrate-binding activity of a DIR domain, shedding new light on its function in the context of this monocot chimeric jacalin.

Structural characterisation of pretreated solids from flow-through liquid hot water treatment of sugarcane bagasse in a fixed-bed reactor.

Untreated sugarcane bagasse and sugarcane bagasse pretreated with flow-through liquid hot water (LHW) treatment (170-207°C and 204-250 ml/min) in a fixed-bed reactor have been structurally characterised. Field emission gun scanning electron microscopy (FEG-SEM) and transmission electron microscopy (TEM) were used to investigate changes in the residues, in particular due to the fate of lignin. FEG-SEM results show that the LHW treatment modified the surface morphology of the pretreated bagasse with lignin droplets being observed on the fibre surface. TEM showed an increase in the plant cell wall porosity and lignin migration across the plant cell wall. Increases in pretreatment temperature were observed to increase the average size and density of lignin droplets on the fibre surface. The results provide evidence that for LHW flow-through treatment, just as for batch treatment, lignin repolymerisation and deposition on the surface of pretreated sugarcane bagasse is an important consideration.

An exotic cause of exudative enteropathy.

PATIENT: Male, 50 FINAL DIAGNOSIS: Exudative enteropathy Symptoms: Abdominal pain • diarrhea • fever • hyponatremia • lymphadenopathy • weight loss MEDICATION: - Clinical Procedure: - Specialty: - OBJECTIVE: Unusual clinical course. BACKGROUND: Protein-losing enteropathy is a rare cause of hypoproteinemia. Erosive and non-erosive gastrointestinal diseases as well as vascular disorders that result in increased central venous pressure or mesenteric lymphatic obstruction may result in protein loss via the gastrointestinal tract. CASE REPORT: We present the case of a 50-year-old man with protein-losing enteropathy, who had profuse diarrhea, abdominal pain, lymphadenopathy, fever, and a weight loss of 10 kg in the preceding 2 months. Extensive work-up revealed infection with Giardia lamblia. We review clinical signs and symptoms, laboratory findings, and imaging studies, and discuss potential pitfalls in establishing the diagnosis. CONCLUSIONS: To the best of our knowledge, this represents one of the few published cases of intestinal giardiasis as a cause of protein-losing enteropathy in an immunocompetent adult. The diagnosis of lambliasis should be based on a combination of stool cultures and serum serology, and in cases of high clinical suspicion, an endoscopy and biopsy of the upper GI tract is recommended.

Comparison of pretreatment methods for rye straw in the second generation biorefinery: effect on cellulose, hemicellulose and lignin recovery.

The increasing interest in lignocellulose-based biorefineries boosts the further development of the needed pretreatment methods for preprocessing biomass. There are a large number of different processes that are being investigated; however research is made mostly based on different types of biomass with the same pretreatment or several modifications of the same process for a given type of biomass. In this work a comparison of promising chemical pretreatments using the same biomass was performed. Organosolv (OS), Steam (SE) and Liquid-Hot-Water (LHW) processes were used for the pretreatment of rye straw and the treated solids further enzymatically hydrolyzed. Best results for carbohydrate and lignin yield were found for the OS pretreatment followed close by the LHW and SE with similar results. All of the processes showed satisfactory performance for the pretreatment of lignocellulosic biomass for application in the second generation biorefinery.

Target evaluation of the non-coding csRNAs reveals a link of the two-component regulatory system CiaRH to competence control in Streptococcus pneumoniae R6.

The two-component regulatory system CiaRH of Streptococcus pneumoniae controls 25 genes, five of which specify homologous small non-coding csRNAs (cia-dependent small RNAs). The csRNAs were predicted to act regulatory as base-pairing sRNAs, but their targets have not been identified. By csRNA gene inactivations we established that the major phenotypes associated with a hyperactive CiaRH system, enhanced ß-lactam resistance and prevention of genetic competence, are dependent on the csRNAs. Computational target predictions and evaluations by translational fusions identified six genes to be under csRNA control: spr0081, spr0371, spr0159, spr0551, spr1097 and spr2043(comC). Measuring the effect of single csRNAs on three targets indicated that they acted additively. One of the targets, comC(spr2043), encoding the precursor of the competence stimulating pheromone CSP, constitutes a link of CiaRH to competence control. Partially disrupting predicted csRNA-comC complementarity led to strongly diminished repression by the csRNAs and to transformability in a strain with a hyperactive CiaRH. Thus, a hyperactive CiaRH system prevents competence development by csRNA-dependent post-transcriptional repression of CSP production. The csRNAs are also involved in competence regulation in the wild-type strain R6, but their activity is only apparent in the absence of the protease gene htrA, another CiaRH regulon member.

Pressure assisted stabilization of biocatalysts at elevated temperatures: characterization by dynamic light scattering.

The effect of pressure, at elevated temperatures, is reported on the activity and stability of a thermophilic endo-ß-glucanase from the filamentous fungus Talaromyces emersonii. The production of reduced sugars after treatment at different temperatures and pressures is used as a measure of the activity and stability of the enzyme. The activity of the enzyme is maintained to higher temperatures with increasing pressure. For example, the relative activity of endo-ß-glucanase decreases to 30% after 4 h at 75°C and 1 bar, whereas it is preserved at 100% after 6 h at 75°C and 230 bar. High-pressure dynamic light scattering is used to characterize the hydrodynamic radius of the enzyme as a function of pressure, temperature, and time. At higher temperature the hydrodynamic radius increases with time, whereas increasing pressure suppresses this effect. Changes in the hydrodynamic radius are correlated with the activity measurements obtained at elevated pressures, since the changes in the hydrodynamic radius indicate structural changes of the enzyme, which cause the deactivation.

One-week once-daily triple therapy with esomeprazole, moxifloxacin, and rifabutin for eradication of persistent Helicobacter pylori resistant to both metronidazole and clarithromycin.

AIM: To investigate a 1-week once-daily triple therapy with esomeprazole, moxifloxacin, and rifabutin for rescue therapy of Helicobacter pylori infection. METHODS: Consecutive patients (n = 103) with at least one previous treatment failure and H. pylori infection resistant to both metronidazole and clarithromycin were treated with esomeprazole 40 mg, moxifloxacin 400 mg, and rifabutin 300 mg, given once daily for 7 days. Eradication was confirmed by histology and culture. CYP2C19 status was determined by polymerase chain reaction-restriction fragment length polymorphism. RESULTS: Intention-to-treat and per-protocol eradication rates were 77.7% (68.4-85.3) and 83.3% (74.4-90.2). Five patients discontinued prematurely (4.8%). Eradication was achieved in 93.1% of poor/intermediate metabolizers and in 78.8% of homozygous extensive metabolizers (p = .14). Eradication rates in patients with one, two, three, and four or more previous failures were 78.3%, 89.6%, 68.6%, and 88.9%, respectively (p = .21). The regimen was effective in seven of nine patients who previously failed quadruple therapy. Post-treatment resistance to moxifloxacin and rifabutin was detected in two (12.5%) and five (31%) patients after treatment failure. CONCLUSION: Once-daily triple therapy with esomeprazole, moxifloxacin, and rifabutin is a promising, safe, and convenient regimen for rescue therapy of H. pylori infection that may serve as a valuable alternative to quadruple therapy, particularly for patients with intolerance to amoxicillin.

Helicobacter pylori in gastric corpus of patients 20 years after partial gastric resection.

AIM: To determine the long-term prevalence of Helicobacter pylori (H pylori) gastritis in patients after partial gastric resection due to peptic ulcer, and to compare the severity of H pylori-positive gastritis in the corpus mucosa between partial gastrectomy patients and matched controls. METHODS: Endoscopic biopsies were obtained from 57 patients after partial gastric resection for histological examination using hematoxylin/eosin and Warthin-Starry staining. Gastritis was graded according to the updated Sydney system. Severity of corpus gastritis was compared between H pylori-positive partial gastrectomy patients and H pylori-positive duodenal ulcer patients matched for age and gender. RESULTS: In partial gastrectomy patients, surgery was performed 20 years (median) prior to evaluation. In 25 patients (43.8%) H pylori was detected histologically in the gastric remnant. Gastric atrophy was more common in H pylori-positive compared to H pylori-negative partial gastrectomy patients (P<0.05). The severity of corpus gastritis was significantly lower in H pylori-positive partial gastrectomy patients compared to duodenal ulcer patients (P<0.01). There were no significant differences in the activity of gastritis, atrophy and intestinal metaplasia between the two groups. CONCLUSION: The long-term prevalence of H pylori gastritis in the gastric corpus of patients who underwent partial gastric resection due to peptic ulcer disease is comparable to the general population. The expression of H pylori gastritis in the gastric remnant does not resemble the gastric cancer phenotype.

Reliable detection of macrolide-resistant Helicobacter pylori via fluorescence in situ hybridization in formalin-fixed tissue.

Macrolide-resistant Helicobacter (H.) pylori represent an increasing therapeutic problem. Macrolide resistance is usually determined phenotypically in vitro with methods such as E-test or agar dilution test. A prerequisite for those tests, however, is bacterial culture that is not routinely set up in the course of gastroscopy. In contrast, formalin-fixed, paraffin-embedded biopsies are regularly available from patients who have undergone gastroscopy. In such biopsies macrolide-resistant H. pylori can be detected by the genotype-based technique of fluorescence in situ hybridization (FISH). Experience gained by this new method, however, is still extremely limited, especially in formalin-fixed tissue. Therefore, we retrospectively investigated formalin-fixed, paraffin-embedded biopsy specimens by FISH in 104 patients suffering from therapy-resistant H. pylori gastritis. To test the accuracy of FISH, we initially examined specimens from 53 patients for whom results of the E-test were available. Next we analyzed biopsies from another 51 patients that had been selected since phenotypical resistance testing had failed despite documented culturing attempts. In all 104 patients, H. pylori was detected by FISH and could thus be investigated for macrolide resistance. Overall, macrolide-resistant bacteria were found in 71 patients (68.3%). In 49 of 53 patients (92.4%), FISH and E-test returned identical results (no significant discordance according to McNemar's chi(2)-test). Taken together, our study demonstrates that FISH is a highly sensitive and reliable method for detecting macrolide-resistant H. pylori in formalin-fixed, paraffin-embedded biopsy specimens, which represents the routine method of processing tissue obtained upon gastroscopy.

Functional analysis of the cag pathogenicity island in Helicobacter pylori isolates from patients with gastritis, peptic ulcer, and gastric cancer.

Helicobacter pylori is the causative agent of a variety of gastric diseases, but the clinical relevance of bacterial virulence factors is still controversial. Virulent strains carrying the cag pathogenicity island (cagPAI) are thought to be key players in disease development. Here, we have compared cagPAI-dependent in vitro responses in H. pylori isolates obtained from 75 patients with gastritis, peptic ulcer, and gastric cancer (n = 25 in each group). AGS gastric epithelial cells were infected with each strain and assayed for (i) CagA expression, (ii) translocation and tyrosine phosphorylation of CagA, (iii) c-Src inactivation, (iv) cortactin dephosphorylation, (v) induction of actin cytoskeletal rearrangements associated with cell elongation, (vi) induction of cellular motility, and (vii) secretion of interleukin-8. Interestingly, we found high but similar prevalences of all of these cagPAI-dependent host cell responses (ranging from 56 to 80%) among the various groups of patients. This study revealed CagA proteins with unique features, CagA subspecies of various sizes, and new functional properties for the phenotypic outcomes. We further showed that induction of AGS cell motility and elongation are two independent processes. Our data corroborate epidemiological studies, which indicate a significant association of cagPAI presence and functionality with histopathological findings in gastritis, peptic ulcer, and gastric cancer patients, thus emphasizing the importance of the cagPAI for the pathogenicity of H. pylori. Nevertheless, we found no significant association of the specific H. pylori-induced responses with any particular patient group. This may indicate that the determination of disease development is highly complex and involves multiple bacterial and/or host factors.

Identification of candidate antigens for serologic detection of Helicobacter pylori-infected patients with gastric carcinoma.

Helicobacter pylori colonizes the stomach of almost half the world population and is a causative agent of gastric carcinomas and duodenal ulcers. Only a small fraction of infected people will develop these severe illnesses and a predictive test to identify people at high risk would greatly benefit disease management. Our study aimed to identify conserved bacterial antigens that may be useful for the development of such a diagnostic test. High-resolution immunoproteomics by 2-dimensional electrophoresis of H. pylori 26695 proteins was carried out with sera from infected patients with either duodenal ulcer (n=30) or gastric carcinoma (n=30), 2 clinically divergent conditions. According to their antigen recognition patterns clear groups of patients were identified. Although this classification did not correspond to the clinical status, it may be correlated to other bacterial or host factors that influence the outcome of infection. In general antigen recognition patterns were found to be highly variable, however by utilizing powerful image analysis and statistical tests the recognition of 14 antigenic protein species was found to differ significantly (p<0.01) between both diseases. Particular protein species of GroEL, HyuA, GroES and AtpA appear to be useful surrogate markers for gastric carcinoma detection and consequently should be considered for further prospective studies to assess their predictive value. For one protein species of AtpA, evidence was found that different post-translational modifications may confer different immunogenicities.

A prospective, randomized study of quadruple therapy and high-dose dual therapy for treatment of Helicobacter pylori resistant to both metronidazole and clarithromycin.

BACKGROUND AND AIM: Failure of primary anti-H. pylori therapy results in a high rate of antimicrobial resistance. Here, we investigated the efficacy of high-dose dual therapy and quadruple therapy as salvage treatments for eradication of H. pylori resistant to both metronidazole and clarithromycin. PATIENTS AND METHODS: Patients with at least one treatment failure and infected with H. pylori resistant to both metronidazole and clarithromycin, were randomized to receive either omeprazole 4 x 40 mg and amoxicillin 4 x 750 mg; or omeprazole 2 x 20 mg, bismuthcitrate 4 x 107 mg, metronidazole 4 x 500 mg and tetracycline 4 x 500 mg. Both regimens were given for 14 days. In cases of persistent infection, a cross-over therapy was performed. RESULTS: Eighty-four patients were randomized. Cure of H. pylori infection was achieved in 31 patients after dual therapy and in 35 patients after quadruple therapy (per protocol: 83.8% (95% CI, 67.9-93.8) and 92.1% (95% CI, 78.6-98.3), respectively (p=0.71); intention to treat: 75.6% (95% CI: 59.7-87.6) and 81.4% (95% CI: 66.6-91.6), respectively (p=0.60)). Cross-over therapy was performed in six of nine patients, four of whom were cured of the infection. CONCLUSION: Both high-dose dual therapy and quadruple therapy are effective in curing H. pylori infection resistant to both metronidazole and clarithromycin in patients who experienced previous treatment failures.

Prevalence of Helicobacter pylori vacA, cagA and iceA genotypes in Nigerian patients with duodenal ulcer disease.

Distinct virulence factors of Helicobacter pylori have been associated with clinical outcome of the infection; however, considerable variations have been reported from different geographic regions. Data on genotypes of African H. pylori isolates are sparse. The aim of this study was to determine the prevalence of specific genotypes of H. pylori in Nigerian patients with duodenal ulcer and non-ulcer dyspepsia. H. pylori was cultured from endoscopic biopsies obtained from 41 Nigerian patients (19 with duodenal ulcer, 22 with non-ulcer dyspepsia). The vacA alleles, cagA and iceA genotypes were determined by PCR. The vacA s1,m1 and s1,m2 genotypes were found in 26.3% and 22.7%, and in 73.7% and 72.7% of H. pylori isolates from patients with duodenal ulcer and non-ulcer dyspepsia, respectively. The iceA1 genotype was present in 94.7% and 86.4% of isolates from duodenal ulcer and non-ulcer dyspepsia patients, respectively. cagA+ infection was found predominantly (> 90%) in Nigerian H. pylori isolates irrespective of the clinical diagnosis. In conclusion, vacA s1,m2, iceA1 and cagA+ are common genotypes of H. pylori isolated from Nigerian patients. As in several other developing countries there seems to be no association between these genotypes and duodenal ulcer disease.