Alterations in serotonin receptor-induced contractility of bovine lateral saphenous vein in cattle grazing endophyte-infected tall fescue

As part of a 2-yr study documenting the physiologic impact of grazing endophyte-infected tall fescue on growing cattle, 2 experiments were conducted to characterize and evaluate effects of grazing 2 levels of toxic endophyte-infected tall fescue pastures on vascular contractility and serotonin receptors. Experiment 1 examined vasoconstrictive activities of 5-hydroxytryptamine (5HT), α-methylserotonin (ME5HT; a 5HT(2) receptor agonist), d-lysergic acid (LSA), and ergovaline (ERV) on lateral saphenous veins collected from steers immediately removed from a high-endophyte-infected tall fescue pasture (HE) or a low-endophyte-infected mixed-grass (LE) pasture. Using the same pastures, Exp. 2 evaluated effects of grazing 2 levels of toxic endophyte-infected tall fescue on vasoconstrictive activities of (±)-1-(2,5-dimethoxy-4-iodophenyl)-2-aminopropane hydrochloride (DOI), BW 723C86 (BW7), CGS-12066A (CGS), and 5-carboxamidotryptamine hemiethanolate maleate (5CT), agonists for 5HT(2A),( 2B), 5HT(1B), and 5HT(7) receptors, respectively. One-half of the steers in Exp. 2 were slaughtered immediately after removal from pasture, and the other one-half were fed finishing diets for >91 d before slaughter. For Exp. 1, maximal contractile intensities were greater (P < 0.05) for steers grazing LE pastures than HE pastures for 5HT (73.3 vs. 48.9 ± 2.1%), ME5HT (52.7 vs. 24.9 ± 1.5%), and ERV (65.7 vs. 49.1 ± 2.6%). Onset of contractile response did not differ for 5HT (P = 0.26) and ERV (P = 0.93), but onset of ME5HT contraction was not initiated (P < 0.05) in HE steers until 10(-4) compared with 10(-5) M in LE-grazing steers. For Exp. 2, maximal contractile intensities achieved with DOI were 35% less (P < 0.05), whereas those achieved with 5CT were 37% greater (P < 0.05), in steers grazing HE pastures. Contractile response to CGS did not differ between pasture groups, and there was an absence of contractile response to BW7 in both groups. There were no differences between endophyte content in contractile responses after animals were finished for >91 d. Experiment 1 demonstrated that grazing of HE pastures for 89 to 105 d induces functional alterations in blood vessels, as evidenced by reduced contractile capacity and altered serotonergic receptor activity. Experiment 2 demonstrated that grazing HE pastures alters vascular responses, which may be mediated through altered serotonin receptor activities, and these alterations may be ameliorated by the removal of ergot alkaloid exposure as demonstrated by the absence of differences in finished steers.

Bovine neuronal vesicular glutamate transporter activity is inhibited by ergovaline and other ergopeptines

l-Glutamate (Glu) is a major excitatory neurotransmitter responsible for neurotransmission in the vertebrate central nervous system. Vesicular Glu transporters VGLUT1 and VGLUT2 concentrate (50mM) Glu [Michaelis constant (measuring affinity), or K(m),=1 to 4mM] into synaptic vesicles (SV) for subsequent release into the synaptic cleft of glutamatergic neurons. Vesicular Glu transporter activity is dependent on vacuolar H(+)-ATPase function. Previous research has shown that ergopeptines contained in endophyte-infected tall fescue interact with dopaminergic and serotoninergic receptors, thereby affecting physiology regulated by these neuron types. To test the hypothesis that ergopeptine alkaloids inhibit VGLUT activity of bovine cerebral SV, SV were isolated from cerebral tissue of Angus-cross steers that were naive to ergot alkaloids. Immunoblot analysis validated the enrichment of VGLUT1, VGLUT2, synaptophysin 1, and vacuolar H(+)-ATPase in purified SV. Glutamate uptake assays demonstrated the dependence of SV VGLUT-like activity on the presence of ATP, H(+)-gradients, and H(+)-ATPase function. The effect of ergopeptines on VGLUT activity was evaluated by ANOVA. Inhibitory competition (IC(50)) experiments revealed that VGLUT-mediated Glu uptake (n=9) was inhibited by ergopeptine alkaloids: bromocriptine (2.83±0.59μM)<ergotamine (20.5±2.77μM)<ergocornine (114±23.1μM)<ergovaline (137±6.55μM). Subsequent ergovaline kinetic inhibition analysis (n=9; Glu=0.05, 0.10, 0.50, 1, 2, 4, 5mM) demonstrated no change in apparent K(m). However, the maximum reaction rate (V(max)) of Glu uptake was decreased when evaluated in the presence of 50, 100, and 200μM ergovaline, suggesting that ergovaline inhibited SV VGLUT activity through a noncompetitive mechanism. The findings of this study suggest cattle with fescue toxicosis may have a decreased glutamatergic neurotransmission capacity due to consumption of ergopeptine alkaloids.

Brain-derived neurotrophic factor-activated astrocytes produce mechanical allodynia in neuropathic pain

Neuropathic pain management is challenging for physicians and a vexing problem for basic researchers. Recent studies reveal that activated spinal astrocytes may play a vital role in nerve injury-induced neuropathic pain, although the mechanisms are not fully understood. We have found increased glial fibrillary acidic protein (GFAP) expression, a hallmark of reactive gliosis, and elevated brain-derived neurotrophic factor (BDNF) expression in the dorsal horn in a rat model of allodynia induced by spinal nerve ligation (SNL). The high GFAP expression and mechanical allodynia that SNL induces were prevented by the intrathecal injection of the BDNF-sequestering fusion protein TrkB/Fc. Additionally, mechanical allodynia and GFAP overexpression was induced by the spinal administration of exogenous BDNF to naive rats, and exogenous BDNF given together with fluorocitrate, an astrocytic metabolism inhibitor, inhibited allodynia and GFAP upregulation. Exogenous BDNF also activated the astrocytes directly when tested in vitro. Furthermore, intrathecal administration of BDNF-stimulated astrocytes also induced mechanical allodynia in naive rats. All of these results indicate that astrocytes activated by BDNF might contribute to mechanical allodynia development in neuropathic pain in rats.

Genetic responses to nanostructured calcium-phosphate-coated implants

Nanostructured calcium phosphate (CaP) has been histologically and biomechanically proven to enhance osseointegration of implants; however, conventional techniques were not sufficiently sensitive to capture its biological effects fully. Here, we compared the conventional removal torque (RTQ) evaluation and gene expression in tissues around nanostructured CaP-coated implants, using real-time RT-PCR, with those of uncoated implants, in a rabbit model. At 2 wks, RTQ values were significantly higher, alkaline phosphatase (ALP) expression was significantly higher, and runt-related transcription factor 2 and tumor necrosis factor-α expressions were significantly lower in the coated than in the uncoated implants. This indicates that inflammatory responses were suppressed and osteoprogenitor activity increased around the CaP-coated surface. At 4 wks, although RTQ values did not significantly differ between the 2 groups, ALP and osteocalcin (OCN) were significantly up-regulated in the coated group, indicating progressive mineralization of the bone around the implant. Moreover, an osteoclast marker, adenosine triphosphatase, which indicates acidification of the resorption lacunae, was significantly higher for the coated implants, suggesting gradual resorption of the CaP coating. This study reveals detailed genetic responses to nanostructured CaP-coated implants and provides evidence that the effect of nanotopography is significant during the osseointegration cascade.

The feasibility of light microscopic measurements of intercellular spaces in squamous epithelium in the lower-esophagus of GERD patients

The study aims to determine whether light microscopy can be used to accurately measure the diameters of intercellular spaces between squamous epithelial cells in the lower esophagus, and whether changes in this outcome measure can be used as a diagnostic marker for gastroesophageal reflux disease (GERD). The study has two parts. Part 1 involves 42 asymptomatic controls and 119 patients with typical symptoms of GERD, including 58 with erosive esophagitis (EE), and 61 patients with nonerosive gastroesophageal reflux disease (NERD). All biopsies were taken from the lower esophagus. All samples were observed using an immersion objective, after which diameters were measured by computer-assisted morphometry. Part 2 involves 61 individuals who were randomly selected from part 1, including 19 controls, 13 with NERD and 29 with EE. Diameter measurements using both light microscopy and transmission electron microscopy (TEM) were performed for samples of 61 individuals. Samples from a total of 61 individuals (31 male, 30 female, mean age 44.3 ± 16.0 years) were observed using both light microscopy and TEM. Both methods showed significant differences between control and disease groups; the outcomes from the two methods had a certain correlation (r = 0.605, P = 0.000). Morphometric analysis of all 161 individuals (83 males, 78 females, mean age 41.4 ± 15.7) showed mean diameters from light microscopy to be 0.58 ± 0.16 µm for controls, 1.07 ± 0.30 µm for NERD, and 1.29 ± 0.20 µm for EE; differences between control and disease groups were significant (P<0.05). The optimal cut-off value from receiver operator characteristic analysis was 0.85 µm. Diagnoses were validated using the combination of symptoms of GERD, endoscopy, and 24 h ambulatory pH monitoring as the gold standard. At the optimal cutoff, sensitivity was 93.3% and specificity was 100%. The diameters of the intercellular spaces in squamous epithelium of lower esophagus from controls and in patients with GERD can be quantitatively measured using light microscopy. Dilated diameters can serve as a sensitive, specific, and objective indicator for diagnosis of GERD.

Diagnostic algorithm to differentiate lymphoma from inflammation in feline small intestinal biopsy samples

Differentiating between inflammatory bowel disease (IBD) and small intestinal lymphoma in cats is often difficult, especially when only endoscopic biopsy specimens are available for evaluation. However, a correct diagnosis is imperative for proper treatment and prognosis. A retrospective study was performed using surgical and endoscopic intestinal biopsy specimens from 63 cats with a history of chronic diarrhea or vomiting or weight loss. A diagnosis of lymphoma or inflammation was based on microscopic examination of hematoxylin and eosin (HE)-stained sections alone, HE-stained sections plus results of immunohistochemical labeling (IHC) for CD3e and CD79a, and HE staining, immunophenotyping, and polymerase chain reaction (PCR) results for B and/or T cell clonality. In addition, various histomorphologic parameters were evaluated for significant differences between lymphoma and IBD using Fisher's exact test. The sensitivity and specificity of each parameter in the diagnosis of lymphoma were also determined. Results of Bayesian statistical analysis demonstrated that combining histologic evaluation of small intestinal biopsy specimens with immunophenotyping and analysis of clonality of lymphoid infiltrates results in more accurate differentiation of neoplastic versus inflammatory lymphocytes. Important histologic features that differentiated intestinal lymphoma from IBD included lymphoid infiltration of the intestinal wall beyond the mucosa, epitheliotropism (especially intraepithelial nests and plaques), heterogeneity, and nuclear size of lymphocytes. Based on the results of this study, a stepwise diagnostic algorithm that first uses histologic assessment, followed by immunophenotyping and then PCR to determine clonality of the lymphocytes, was developed to more accurately differentiate between intestinal lymphoma and IBD.

Clinical outcomes of ovulation induction with metformin, clomiphene citrate and human menopausal gonadotrophin in polycystic ovary syndrome

This pilot study evaluated the effects of coadministration of metformin with clomiphene citrate (CC) and human menopausal gonadotrophin (HMG) in women with CC-resistant polycystic ovary syndrome (PCOS). Sixty women with PCOS were randomly assigned to receive 3 months' treatment with metformin or placebo together with CC and HMG. Transvaginal ultrasound was used to monitor follicular development and ovulation was induced by human chorionic gonadotrophin (HCG). The number of dominant follicles, the oestradiol level on the day HCG was given and the amount of HMG required were significantly lower in the metformin group than in the placebo group, whereas the mono-ovulatory rate and pregnancy rate in the third cycle were significantly higher. The cumulative pregnancy rate in the metformin group (43.3%) was higher than in the placebo group (20.0%), but this difference did not reach statistical significance. In conclusion, coadministration of metformin with CC and HMG reduced the amount of HMG required and increased the mono-ovulatory rate and pregnancy rate.

Excess fluoride interferes with chloride-channel-dependent endocytosis in ameloblasts

Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause cystic fibrosis (CF). Both CF and dental fluorosis result in protein retention in mature enamel. We hypothesized that excess fluoride might cause protein retention by interfering with CFTR function, resulting in abnormal expression of proteases and pathological endocytosis. Millimolar concentrations of fluoride reduced uptake of Emdogain, an enamel matrix derivative, in ameloblast-like PABSo-E cells, while stimulating an acidic intracellular environment at the same time. When CFTR function was inhibited by either an siRNA or a chloride channel inhibitor, CFTRinh-172, fluoride's effect on Emdogain uptake was partially blocked. Treatment of cells with CFTR siRNA down-regulated expression of proteases MMP20 and KLK4 and increased intracellular pH. We conclude that excess fluoride inhibits endocytic activity of ameloblasts through the CFTR chloride channel or other chloride channels. The intracellular pH might be the key mechanism by which abnormal proteolytic activity and defective endocytosis cause the residual protein observed in enamel of patients with CF and dental fluorosis.

The rag locus of Porphyromonas gingivalis might arise from Bacteroides via horizontal gene transfer

Porphyromonas gingivalis is regarded as one of the risk factors of periodontitis. P. gingivalis exhibits a wide variety of genotypes. Many insertion sequences (ISs), located in their chromosomes, made P. gingivalis differentiate into virulent and avirulent strains. In this research, we investigated the prevalence of P. gingivalis in the gingival crevicular fluid (GCF) among periodontitis patients from Zhenjiang, China, detected the P. gingivalis rag locus distributions by multiplex polymerase chain reaction (PCR), and analyzed the origin of the P. gingivalis rag locus based on evolution. There were three rag locus variants co-existing in Zhenjiang. The results showed that the rag locus may be associated with severe periodontitis. This work also firstly ascertained that the rag locus might arise, in theory, from Bacteroides sp. via horizontal gene transfer.

Predation by Coccinella septempunctata and Harmonia axyridis (Coleoptera: Coccinellidae) on Aphis glycines (Homoptera: Aphididae)

Coccinella septempunctata L. and Harmonia axyridis Pallas are key natural enemies of soybean aphid, Aphis glycines Matsumura, in North America. Third instars, adult females, and adult males of both C. septempunctata and H. axyridis exhibited a type II functional response for predation toward adult soybean aphids at 26 +/- 1 degrees C. In C. septempunctata, the functional response curve of adult males differed from those of third instars and adult females, but there was no difference between third instars and adult females. In H. axyridis, the functional response curves of larvae, adult females, and adult males all differed significantly. Third instars and adult females consumed significantly more soybean aphids than did adult males at prey densities of 150 and 180 aphids per arena for C. septempunctata and at prey densities of 60, 90, 120, 150, and 180 aphids per arena for H. axyridis. The theoretical maximum daily predation rate of adult aphids by C. septempunctata was predicted to be 204 per third instar, 277 per adult female, and 166 per adult male, and 244, 156, and 73, respectively, for H. axyridis. Third instars and adult females of both species consumed significantly more aphids than did adult males on soybean plants with the recommended action threshold of 250 soybean aphids per plant. Both C. septempunctata and H. axyridis have high predation capacities and are important in suppressing soybean aphid populations.

Gemcitabine in combination with intraperitoneal cisplatin in advanced hepatobiliary cancers

e15666

Background: Standard chemotherapy for advanced hepatobiliary cancers remains undefined. This study was to observe the therapeutic effect of gemcitabine combined with intraperitoneal cisplatin for the treatment of advanced hepatobiliary cancers and analyze their toxicities. Methods: Patients with measurable hepatobiliary cancers were unrandomized into gemcitabine (GEM) + cisplatin (DDP) (GEM group) and epirubicin (EPI) + DDP (EPI group). GEM was used intravenously by infusion for 30 min with the dose to 1,000 mg/m2 on day 1 and 8; cisplatin was infused intraperitoneal with a dose of 25mg/m2 on day1, 3 and 5. Twenty-one days counted as one cycle. After 2 cycles, treatment efficacy and adverse events were evaluated according to WHO criteria. Results: A total of 76 patients were enrolled from May 2004 to May 2006, with 30 patients for EPI group and 46 patients for GEM group, and all the patients were eligible for effectiveness analysis. Among GEM group patients, there was no complete response. The partial response rate was 32.61% and clinical benefit response (CR+ PR +SD) was 67.39%. All those data mentioned above were significantly higher than that of EPI group. The main adverse re-ction was hematologic toxicity, while nonhematologic toxicity was mild. Conclusions: This study demonstrated that combination gemcitabine with intraperitoneal infusion of cisplatin was an effective and safety treatment for the patients with advanced hepatobiliary cancers.

No significant financial relationships to disclose.

Effect of squid ink melanin-Fe on iron deficiency anemia remission

The present study was designed to evaluate the effect of a new iron tonic (squid ink melanin-Fe [SM-Fe]) on remission of iron deficiency anemia (IDA) using a rat model of IDA. The rat IDA model was established with low-iron diet feeding and caudal vein blooding. Then different dosages of SM-Fe were given to the rats once a day by intragastric administration, with FeSO4 and FeCl3 as positive control. The content of Hemoglobin (Hb), red blood cell (RBC), hematocrit (HCT), and mean corpuscular volume (MCV) were analyzed in addition to the contents of serum iron (SI) and intracellular free erythrocyte protoporphyrin (FEP). The content of malondialdehyde (MDA) and the activity of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) in serum was also measured. The results showed that anemia caused by iron deficiency was established as a consequence of the low-iron diets. SM-Fe showed an effective restoration action by returning Hb, RBC, HCT, MCV, SI, and FEP in IDA animals to normal values. An antioxidant effect was also observed that reduced MDA level, enhanced the activities of SOD and GSH-Px in serum, and protected erythrocytes from the injury of reactive oxygen species as a consequence of SM-Fe intake. In comparison with FeSO4 and FeCl3, higher bioavailability of iron and fewer side effects were also observed. In conclusion, SM-Fe remitted iron deficiency anemia symptoms significantly, suggesting that SM-Fe might contribute to improving hemopoietic function in IDA rats and might be exploited as a safe, efficient new iron tonic.

Epithelial stem/progenitor cells in lung postnatal growth, maintenance, and repair

The adult lung consists of a trachea leading into a system of branched airways ending in millions of alveolar sacs. It contains many different epithelial cell types arranged in precise patterns along the proximodistal axis. Each region of the lung has the capacity to repair through the proliferation of different epithelial cell types. However, the precise identity of the cells mediating repair is not fully resolved. To address this problem, we are using genetic lineage-labeling techniques in the mouse. The tools we have made will also be useful for understanding how progenitor cell behavior is regulated under normal and pathological conditions.

Effect of subcutaneously administered diclazuril on the output of Eimeria species oocysts by experimentally infected rabbits

The effect of subcutaneously injected diclazuril on the output of Eimeria species oocysts was studied in experimentally infected rabbits. Diclazuril was administered either prophylactically at 0.5, 1 or 2 mg/kg bodyweight two days before each rabbit was inoculated with 20,000 oocysts of a mixed-species field isolate of Eimeria or therapeutically at 1, 2 or 4 mg/kg bodyweight five days after they were inoculated. The prophylactic treatments significantly reduced (P<0.05) the output of oocysts in faeces and the numbers in the rabbits' livers at all doses. The therapeutic treatment at 4 mg/kg also caused a significant reduction (P<0.05) in oocyst shedding, but the lower doses resulted in only a moderate reduction. The shedding of the pathogenic species Eimeria stiedae, Eimeria magna, Eimeria irresidua, Eimeria flavescens, Eimeria piriformis and Eimeria intestinalis was significantly reduced (P<0.05) in all the treated groups. The burden of oocysts in the livers of the therapeutic groups (4000 to 9000) were significantly lower (P<0.05) than in the inoculated but untreated control group (23,000), but higher than in the prophylactic groups (around 1000).

Halorubrum kocurii sp. nov., an archaeon isolated from a saline lake

A Gram-negative, non-motile, neutrophilic, rod-shaped, extremely halophilic archaeon, designated strain BG-1(T), was isolated from a salt lake, Lake Bagaejinnor, in Inner Mongolia, China. Strain BG-1(T) was able to grow at 25-55 degrees C, required at least 2.5 M NaCl for growth (with an optimum at 3.4 M NaCl) and grew at pH 6.0-9.0 (with an optimum at pH 7.5). Hypotonic treatment with less than 2.0 M NaCl caused cell lysis. Phylogenetic analysis of the almost-complete 16S rRNA gene sequence positioned the isolate within the genus Halorubrum in the family Halobacteriaceae. Strain BG-1(T) was most closely related to Halorubrum aidingense 31-hong(T) (98.8% sequence similarity), Halorubrum saccharovorum NCIMB 2081(T) (98.6%), Halorubrum lacusprofundi ACAM 34(T) (98.6%) and Halorubrum lipolyticum 9-3(T) (98.4%). However, values for DNA-DNA hybridization between strain BG-1(T) and the most closely related members of the genus Halorubrum were below 40%. Analysis of the polar lipids of strain BG-1(T) revealed the presence of mannosyl-2-sulfate-(1-4)-glycosyl-archaeol, the main glycolipid found in neutrophilic species of the genus Halorubrum. The G+C content of the genomic DNA was 69.4 mol% (T(m)). Comparison of the phenotypic characteristics of the strain with those of Halorubrum species supported the conclusion that BG-1(T) represents a novel species within this genus, for which the name Halorubrum kocurii sp. nov. is proposed. The type strain is BG-1(T) (=CECT 7322(T) =CGMCC 1.7018(T) =JCM 14978(T)).

Phenotypic variation within European carriers of the Y-chromosomal gr/gr deletion is independent of Y-chromosomal background

BACKGROUND

Previous studies have compared sperm phenotypes between men with partial deletions within the AZFc region of the Y chromosome and non-carriers, with variable results. In this study, a separate question was investigated, the basis of the variation in sperm phenotype within gr/gr deletion carriers, which ranges from normozoospermia to azoospermia. Differences in the genes removed by independent gr/gr deletions, the occurrence of subsequent duplications or the presence of linked modifying variants elsewhere on the chromosome have been suggested as possible causal factors. This study set out to test these possibilities in a large sample of gr/gr deletion carriers with known phenotypes spanning the complete range.

RESULTS

In total, 169 men diagnosed with gr/gr deletions from six centres in Europe and one in Australia were studied. The DAZ and CDY1 copies retained, the presence or absence of duplications and the Y-chromosomal haplogroup were characterised. Although the study had good power to detect factors that accounted for >or=5.5% of the variation in sperm concentration, no such factor was found. A negative effect of gr/gr deletions followed by b2/b4 duplication was found within the normospermic group, which remains to be further explored in a larger study population. Finally, significant geographical differences in the frequency of different subtypes of gr/gr deletions were found, which may have relevance for the interpretation of case control studies dealing with admixed populations.

CONCLUSIONS

The phenotypic variation of gr/gr carriers in men of European origin is largely independent of the Y-chromosomal background.

Cellular membranes and lipid-binding domains as attractive targets for drug development

Interdisciplinary research focused on biological membranes has revealed them as signaling and trafficking platforms for processes fundamental to life. Biomembranes harbor receptors, ion channels, lipid domains, lipid signals, and scaffolding complexes, which function to maintain cellular growth, metabolism, and homeostasis. Moreover, abnormalities in lipid metabolism attributed to genetic changes among other causes are often associated with diseases such as cancer, arthritis and diabetes. Thus, there is a need to comprehensively understand molecular events occurring within and on membranes as a means of grasping disease etiology and identifying viable targets for drug development. A rapidly expanding field in the last decade has centered on understanding membrane recruitment of peripheral proteins. This class of proteins reversibly interacts with specific lipids in a spatial and temporal fashion in crucial biological processes. Typically, recruitment of peripheral proteins to the different cellular sites is mediated by one or more modular lipid-binding domains through specific lipid recognition. Structural, computational, and experimental studies of these lipid-binding domains have demonstrated how they specifically recognize their cognate lipids and achieve subcellular localization. However, the mechanisms by which these modular domains and their host proteins are recruited to and interact with various cell membranes often vary drastically due to differences in lipid affinity, specificity, penetration as well as protein-protein and intramolecular interactions. As there is still a paucity of predictive data for peripheral protein function, these enzymes are often rigorously studied to characterize their lipid-dependent properties. This review summarizes recent progress in our understanding of how peripheral proteins are recruited to biomembranes and highlights avenues to exploit in drug development targeted at cellular membranes and/or lipid-binding proteins.

The HLA-DRB1 shared epitope is not associated with antibodies against cyclic citrullinated peptide in Chinese patients with rheumatoid arthritis

OBJECTIVE

Rheumatoid arthritis (RA) is a destructive autoimmune polyarthritis that has been associated with a group of human leucocyte antigen (HLA)-DRB1 alleles that share a common amino-acid sequence at residues 70-74 called the shared epitope (SE). Recently, anti-cyclic citrullinated peptide (CCP) antibodies have also been reported to be associated with HLA-DR4 and have gained wide acceptance as early diagnostic markers for RA in Caucasian patients. The current study was performed to investigate whether the association between the SE (HLA-DRB1 0401/04/05/10) and anti-CCP antibodies is also present in Chinese Han patients with RA.

METHODS

One hundred and four RA patients and 122 healthy controls were recruited. HLA-DR4 was detected by the sequence-specific primer polymerase chain reaction (SSP-PCR) phototyping method. Anti-CCP antibodies and immunoglobulin M rheumatoid factor (IgM-RF) were measured by enzyme-linked immunosorbent assay (ELISA) and laser nephelometry, respectively.

RESULTS

Of the Chinese patients with RA, 76.5% exhibited anti-CCP antibodies compared with none of the controls (76.5% vs. 0%, p<0.001). The prevalence of the SE was significantly higher in patients with RA compared with controls [p = 0.010, odds ratio (OR) = 2.42, 95% confidence interval (CI) = 1.16-5.07]. Among the HLA-DR4 alleles, the presence of HLA-DRB1 0401 was significantly higher in RA patients than in controls (p = 0.0118, OR = 9.68, 95% CI = 1.13-448.8). In our study we found that the SE was not associated with production of anti-CCP antibodies (p = 0.2899, OR = 1.920, 95% CI = 0.52-8.89).

CONCLUSIONS

The prevalence of the SE is significantly lower in Chinese RA patients, as compared with previous reports of a study using a Caucasian cohort, indicating that distinct genetic risk factors might be associated with anti-CCP antibody production. These data emphasized the complexity of the genetic effects of the major histocompatibility complex on the RA phenotype.

Evaluation of virtual screening performance of support vector machines trained by sparsely distributed active compounds

Virtual screening performance of support vector machines (SVM) depends on the diversity of training active and inactive compounds. While diverse inactive compounds can be routinely generated, the number and diversity of known actives are typically low. We evaluated the performance of SVM trained by sparsely distributed actives in six MDDR biological target classes composed of a high number of known actives (983-1645) of high, intermediate, and low structural diversity (muscarinic M1 receptor agonists, NMDA receptor antagonists, thrombin inhibitors, HIV protease inhibitors, cephalosporins, and renin inhibitors). SVM trained by regularly sparse data sets of 100 actives show improved yields at substantially reduced false-hit rates compared to those of published studies and those of Tanimoto-based similarity searching method based on the same data sets and molecular descriptors. SVM trained by very sparse data sets of 40 actives (2.4%-4.1% of the known actives) predicted 17.5-39.5%, 23.0-48.1%, and 70.2-92.4% of the remaining 943-1605 actives in the high, intermediate, and low diversity classes, respectively, 13.8-68.7% of which are outside the training compound families. SVM predicted 99.97% and 97.1% of the 9.997 M PUBCHEM and 167K remaining MDDR compounds as inactive and 2.6%-8.3% of the 19,495-38,483 MDDR compounds similar to the known actives as active. These suggest that SVM has substantial capability in identifying novel active compounds from sparse active data sets at low false-hit rates.

A support vector machines approach for virtual screening of active compounds of single and multiple mechanisms from large libraries at an improved hit-rate and enrichment factor

Support vector machines (SVM) and other machine-learning (ML) methods have been explored as ligand-based virtual screening (VS) tools for facilitating lead discovery. While exhibiting good hit selection performance, in screening large compound libraries, these methods tend to produce lower hit-rate than those of the best performing VS tools, partly because their training-sets contain limited spectrum of inactive compounds. We tested whether the performance of SVM can be improved by using training-sets of diverse inactive compounds. In retrospective database screening of active compounds of single mechanism (HIV protease inhibitors, DHFR inhibitors, dopamine antagonists) and multiple mechanisms (CNS active agents) from large libraries of 2.986 million compounds, the yields, hit-rates, and enrichment factors of our SVM models are 52.4-78.0%, 4.7-73.8%, and 214-10,543, respectively, compared to those of 62-95%, 0.65-35%, and 20-1200 by structure-based VS and 55-81%, 0.2-0.7%, and 110-795 by other ligand-based VS tools in screening libraries of >or=1 million compounds. The hit-rates are comparable and the enrichment factors are substantially better than the best results of other VS tools. 24.3-87.6% of the predicted hits are outside the known hit families. SVM appears to be potentially useful for facilitating lead discovery in VS of large compound libraries.

The genetic basic and fine-mapping of a stable quantitative-trait loci for aluminium tolerance in rice

Aluminium (Al) toxicity is a primary cause of low rice productivity in acid soils. We have mapped a number of quantitative-trait loci (QTL) controlling Al tolerance in a recombinant inbred line population derived from a cross between the tolerant japonica cultivar Asominori and the sensitive indica cultivar IR24. Tolerance was assessed on the basis of relative root elongation. QTL were detected on chromosomes 1, 9, and 11, with the percentages of phenotypic variance explained ranging from 13.5 to 17.7%. Alleles from Asominori at all three QTL were associated with increased Al tolerance. qRRE-9 is expressed both in the genetic background of IR24 and in an Asominori/IR24-mixed background. qRRE-9 was reduced to the single recessive Mendelian factor Alt-9. High-resolution genetic and physical maps were constructed for Alt-9 in a BC(3)F(2) population of 1,043 individuals. Alt-9 maps between RM24702 and ID47-2 on chromosome 9, and co-segregates with RM5765.

Halorubrum ejinorense sp. nov., isolated from Lake Ejinor, Inner Mongolia, China

A novel halophilic archaeon, strain EJ-32T, was isolated from water from Lake Ejinor in Inner Mongolia, China. The taxonomy of strain EJ-32T was studied by using a polyphasic approach. On the basis of 16S rRNA gene sequence similarities, strain EJ-32T was shown to be phylogenetically related to Halorubrum coriense (97.9 %), Halorubrum trapanicum (97.9 %), Halorubrum sodomense (97.8 %), Halorubrum tebenquichense (97.8 %), Halorubrum xinjiangense (97.6 %), Halorubrum terrestre (97.4 %), Halorubrum distributum (97.1 %) and Halorubrum saccharovorum (96.4 %). Strain EJ-32T was found to be neutrophilic, non-motile and Gram-negative. It grew in medium containing saturation concentrations of NaCl and did not require magnesium for optimal growth. The G+C content of the DNA is 64.0 mol%. Values for DNA–DNA hybridization with respect to phylogenetically related Halorubrum species were ≤49 %, indicating that EJ-32T constitutes a different genospecies. The data show that strain EJ-32T represents a novel species of the genus Halorubrum, for which the name Halorubrum ejinorense sp. nov. is proposed. The type strain is EJ-32T (=CECT 7194T=CGMCC 1.6782T=JCM 14265T).

Machine learning approaches for predicting compounds that interact with therapeutic and ADMET related proteins

Computational methods for predicting compounds of specific pharmacodynamic and ADMET (absorption, distribution, metabolism, excretion and toxicity) property are useful for facilitating drug discovery and evaluation. Recently, machine learning methods such as neural networks and support vector machines have been explored for predicting inhibitors, antagonists, blockers, agonists, activators and substrates of proteins related to specific therapeutic and ADMET property. These methods are particularly useful for compounds of diverse structures to complement QSAR methods, and for cases of unavailable receptor 3D structure to complement structure-based methods. A number of studies have demonstrated the potential of these methods for predicting such compounds as substrates of P-glycoprotein and cytochrome P450 CYP isoenzymes, inhibitors of protein kinases and CYP isoenzymes, and agonists of serotonin receptor and estrogen receptor. This article is intended to review the strategies, current progresses and underlying difficulties in using machine learning methods for predicting these protein binders and as potential virtual screening tools. Algorithms for proper representation of the structural and physicochemical properties of compounds are also evaluated.

Salsuginibacillus kocurii gen. nov., sp. nov., a moderately halophilic bacterium from soda-lake sediment

A Gram-positive, endospore-forming, alkali-tolerant, moderately halophilic bacterium, designated strain CH9dT, was isolated from the sediment of Lake Chagannor in the Inner Mongolia Autonomous Region, China. The cells were rod-shaped and motile. Isolate CH9dT grew at pH 5.8–10.0 (optimally at pH 8.5), at salinities of 3–20 % (w/v) marine salts (optimally at 10.0 %, w/v) and between 20 and 50 °C (optimally at 37 °C). The cell wall contained meso-diaminopimelic acid and the major respiratory isoprenoid quinone was MK-7. The predominant cellular fatty acids of strain CH9dT were anteiso-C15 : 0, anteiso-C17 : 0, iso-C17 : 0 and iso-C15 : 0 and its polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and two unknown phospholipids. The G+C content of the DNA was 44.7 mol%. Strain CH9dT exhibited a 16S rRNA gene sequence similarity value of only 91 % with respect to Thalassobacillus devorans DSM 16966T and showed values below 91 % with respect to members of the genera Bacillus, Halobacillus and Marinococcus. Strain CH9dT could be clearly differentiated from its closest phylogenetic neighbours on the basis of several phenotypic, genotypic and chemotaxonomic features. Therefore, data from the polyphasic study support the placement of strain CH9dT in a novel genus and species, for which the name Salsuginibacillus kocurii gen. nov., sp. nov. is proposed. The type strain is CH9dT (=CCM 7365T=CECT 7154T=CGMCC 1.6287T=DSM 18087T).

Halopiger xanaduensis gen. nov., sp. nov., an extremely halophilic archaeon isolated from saline Lake Shangmatala in Inner Mongolia, China

Strain SH-6(T) was isolated from the sediment of Lake Shangmatala, a saline lake in Inner Mongolia (China). Cells were pleomorphic. The organism was neutrophilic and required at least 2.5 M (15 %) NaCl, but not MgCl(2), for growth; optimal growth occurred at 4.3 M (25 %) NaCl. The G+C content of its DNA was 63.1 mol%. 16S rRNA gene sequence analysis revealed that strain SH-6(T) is a member of the family Halobacteriaceae, but there was a low level of similarity with other members of this family. Highest sequence similarity (94.6 %) was obtained with the 16S rRNA genes of the type strains of Natronolimnobius innermongolicus and Natronolimnobius baerhuensis. Polar lipid analyses revealed that strain SH-6(T) contains phosphatidylglycerol and phosphatidylglyceromethylphosphate, derived from both C(20)C(20) and C(20)C(25) glycerol diethers together with the glycolipid S(2)-DGD-1. On the basis of the data obtained, the new isolate could not be classified in any recognized genus. Strain SH-6(T) is thus considered to represent a novel species in a new genus within the family Halobacteriaceae, order Halobacteriales, for which the name Halopiger xanaduensis gen. nov., sp. nov. is proposed. The type strain of Halopiger xanaduensis is SH-6(T) (=CECT 7173(T)=CGMCC 1.6379(T)=JCM 14033(T)).

Prediction of factor Xa inhibitors by machine learning methods

Factor Xa (FXa) inhibitors have been explored as anticoagulants for treatment and prevention of thrombotic diseases. Molecular docking, pharmacophore, quantitative structure-activity relationships, and support vector machines (SVM) have been used for computer prediction of FXa inhibitors. These methods achieve promising prediction accuracies of 69-80% for FXa inhibitors and 85-99% for non-inhibitors. Prediction performance, particularly for inhibitors, may be further improved by exploring methods applicable to more diverse range of compounds and by using more appropriate set of molecular descriptors. We tested the capability of several machine learning methods (C4.5 decision tree, k-nearest neighbor, probabilistic neural network, and support vector machine) by using a much more diverse set of 1098 compounds (360 inhibitors and 738 non-inhibitors) than those in other studies. A feature selection method was used for selecting molecular descriptors appropriate for distinguishing FXa inhibitors and non-inhibitors. The prediction accuracies of these methods are 89.1-97.5% for FXa inhibitors and 92.3-98.1% for non-inhibitors. In particular, compared to other studies, support vector machine gives a substantially improved accuracy of 94.6% for FXa non-inhibitors and maintains a comparable accuracy of 98.1% for inhibitors, based-on a more rigorous test with more diverse range of compounds. Our study suggests that machine learning methods such as SVM are useful for facilitating the prediction of FXa inhibitors.