Exploring the transcriptomic data of the Australian paralysis tick, Ixodes holocyclus

Ixodes holocyclus is the paralysis tick commonly found in Australia. I. holocyclus does not cause paralysis in the primary host – bandicoots, but markedly affects secondary hosts such as companion animals, livestock and humans. Holocyclotoxins are the neurotoxin molecules in I. holocyclus responsible for paralysis symptoms. There is a limited understanding of holocyclotoxins due to the difficulties in purifying and expressing these toxins in vitro. Next-generation sequencing technologies were utilised for the first time to generate transcriptome data from two cDNA samples –salivary glands samples collected from female adult ticks engorged on paralysed companion animals and on bandicoots. Contigencoded proteins in each library were annotated according to their best BLAST match against several databases and functionally assigned into six protein categories: housekeeping, transposable elements, pathogen-related, hypothetical, secreted and novel. The “secreted protein” category is comprised of ten protein families: enzymes, protease inhibitors, antigens, mucins, immunity-related, lipocalins, glycinerich, putative secreted, salivary and toxin-like. Comparisons of contig representation between the two libraries reveal the differential expression of tick proteins collected from different hosts. This study provides a preliminary description of the I. holocyclus tick salivary gland transcriptome

Exploring the Transcriptomic Data of the Australian Paralysis Tick, Ixodes Holocyclus

Ixodes holocyclus is the paralysis tickcommonly found in Australia. I. holocyclus does notcause paralysis in the primary host – bandicoots, butmarkedly affects secondary hosts such as companionanimals, livestock and humans. Holocyclotoxins are theneurotoxin molecules in I. holocyclus responsible forparalysis symptoms. There is a limited understanding ofholocyclotoxins due to the difficulties in purifying andexpressing these toxins in vitro. Next-generationsequencing technologies were utilised for the first time togenerate transcriptome data from two cDNA samples –salivary glands samples collected from female adult ticksengorged on paralysed companion animals and onbandicoots. Contig-encoded proteins in each librarywere annotated according to their best BLAST matchagainst several databases and functionally assigned intosix protein categories: housekeeping, transposableelements, pathogen-related, hypothetical, secreted andnovel. The “secreted protein” category is comprised often protein families: enzymes, protease inhibitors,antigens, mucins, immunity-related, lipocalins, glycinerich,putative secreted, salivary and toxin-like.Comparisons of contig representation between the twolibraries reveal the differential expression of tickproteins collected from different hosts. This studyprovides a preliminary description of the I. holocyclustick salivary gland transcriptome

The performance and exhaust emissions of a diesel engine fuelled with Calophyllum inophyllum- palm biodiesel

© 2019 by the authors. Nowadays, increased interest among the scientific community to explore the Calophyllum inophyllum as alternative fuels for diesel engines is observed. This research is about using mixed Calophyllum inophyllum-palm oil biodiesel production and evaluation that biodiesel in a diesel engine. The Calophyllum inophyllum-palm oil methyl ester (CPME) is processed using the following procedure: (1) the crude Calophyllum inophyllum and palm oils are mixed at the same ratio of 50:50 volume %, (2) degumming, (3) acid-catalysed esterification, (4) purification, and (5) alkalinecatalysed transesterification. The results are indeed encouraging which satisfy the international standards, CPME shows the high heating value (37.9 MJ/kg) but lower kinematic viscosity (4.50 mm2/s) due to change the fatty acid methyl ester (FAME) composition compared to Calophyllum inophyllum methyl ester (CIME). The average results show that the blended fuels have higher Brake Specific Fuel Consumption (BSFC) and NOx emissions, lower Brake Thermal Efficiency (BTE), along with CO and HC emissions than diesel fuel over the entire range of speeds. Among the blends, CPME5 offered better performance compared to other fuels. It can be recommended that the CPME blend has great potential as an alternative fuel because of its excellent characteristics, better performance, and less harmful emission than CIME blends

Effects of metal-contaminated soils on the accumulation of heavy metals in gotu kola (Centella asiatica) and the potential health risks: a study in Peninsular Malaysia

Centella asiatica is a commonly used medicinal plant in Malaysia. As heavy metal accumulation in medicinal plants which are highly consumed by human is a serious issue, thus the assessment of heavy metals in C. asiatica is important for the safety of consumers. In this study, the heavy metal accumulation in C. asiatica and the potential health risks were investigated. Samples of C. asiatica and surface soils were collected from nine different sites around Peninsular Malaysia. The concentration of six heavy metals namely Cd, Cu, Ni, Fe, Pb and Zn were determined by air-acetylene flame atomic absorption spectrophotometer (AAS). The degree of anthropogenic influence was assessed by calculating the enrichment factor (EF) and index of geoaccumulation (Igeo). The heavy metal uptake into the plant was estimated through the calculation of translocation factor (TF), bioconcentration factor (BCF) and correlation study. Estimated daily intakes (EDI) and target hazard quotients (THQ) were used to determine the potential health risk of consuming C. asiatica. The results showed that the overall surface soil was polluted by Cd, Cu and Pb, while the uptake of Zn and Ni by the plants was high. The value of EDI and THQ showed that the potential of Pb toxicity in C. asiatica was high as well. As heavy metal accumulation was confirmed in C. asiatica, daily consumption of the plant derived from polluted sites in Malaysia was not recommended

Therapeutic issues in HIV/HCV-coinfected patients

The importance of treating hepatitis C virus (HCV)-associated morbidities in a growing population of patients coinfected with human immunodeficiency virus (HIV) has increased since the introduction of highly active antiretroviral therapy. As a result, investigative attention is turning to HCV-related liver disease and treatment-associated issues in coinfection. HIV/HCV-coinfected patients have higher HCV RNA loads and show more rapid progression of fibrosis than do monoinfected patients. Combination therapy with pegylated interferon plus ribavirin (RBV) is the standard of care for HCV in coinfected patients. Therapy slows fibrosis progression, but toxicity prevents identification of the most effective RBV dose. Coinfected patients have about a threefold greater risk of antiretroviral therapy-associated hepatotoxicity than patients with HIV only. Other challenges include anaemia, mitochondrial toxicity, drug–drug interactions and leucopenia. Thus, chronic hepatitis C should be treated in HIV/HCV-coinfected patients, but steps must be taken to prevent and treat potential toxicities. The first European Consensus Conference on the Treatment of Chronic Hepatitis B and C in HIV Co-infected Patients was held March 2005 in Paris to address these issues. This article reviews the peer-reviewed literature and expert opinion published from 1990 to 2005, and compares results with presentations and recommendations from the Consensus Conference to best present current issues in coinfection

Proteomic Analysis of Neisseria gonorrhoeae Biofilms Shows Shift to Anaerobic Respiration and Changes in Nutrient Transport and Outermembrane Proteins

Neisseria gonorrhoeae, the causative agent of gonorrhea, can form biofilms in vitro and in vivo. In biofilms, the organism is more resistant to antibiotic treatment and can serve as a reservoir for chronic infection. We have used stable isotope labeling by amino acids in cell culture (SILAC) to compare protein expression in biofilm and planktonic organisms. Two parallel populations of N. gonorrhoeae strain 1291, which is an arginine auxotroph, were grown for 48 h in continuous-flow chambers over glass, one supplemented with 13C6-arginine for planktonic organisms and the other with unlabeled arginine for biofilm growth. The biofilm and planktonic cells were harvested and lysed separately, and fractionated into three sequential protein extracts. Corresponding heavy (H) planktonic and light (L) biofilm protein extracts were mixed and separated by 1D SDS-PAGE gels, and samples were extensively analyzed by liquid chromatography-mass spectrometry. Overall, 757 proteins were identified, and 152 unique proteins met a 1.5-fold cutoff threshold for differential expression with p-values <0.05. Comparing biofilm to planktonic organisms, this set included 73 upregulated and 54 downregulated proteins. Nearly a third of the upregulated proteins were involved in energy metabolism, with cell envelope proteins making up the next largest group. Of the downregulated proteins, the largest groups were involved in protein synthesis and energy metabolism. These proteomics results were compared with our previously reported results from transcriptional profiling of gonococcal biofilms using microarrays. Nitrite reductase and cytochrome c peroxidase, key enzymes required for anaerobic growth, were detected as highly upregulated in both the proteomic and transcriptomic datasets. These and other protein expression changes observed in the present study were consistent with a shift to anaerobic respiration in gonococcal biofilms, although changes in membrane proteins not explicitly related to this shift may have other functions

Full Mouth Rehabilitation with Implant-Supported Prostheses for Severe Periodontitis: A Case Report

Oral rehabilitation for a patient with severe loss of alveolar bone and soft tissue resulting from severe periodontitis presents a challenge to clinicians. Replacing loosening natural teeth with fixed prostheses supported by dental implants often requires either gingival surgery or bone grafting. The outcome of the bone grafting is sometimes unpredictable and requires longer healing time and/ or multiple surgeries. The presence of periodontal inflammation and periapical lesions often delay the placement of bone grafts as well as dental implants. Here we present a clinical case of a patient undergone full mouth reconstruction with implant-supported fixed prostheses. We demonstrated that early placement of implants (three weeks after extractions) with minimal bone grafting may be an alternative to conventional bone grafting followed by implant placement. We believe that primary stability during implant placement may contribute to our success. In addition, composite resin gingival material may be indicated in cases of large fixed implant prostheses as an alternative to pink porcelain

Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome

Transposable elements (TEs) have no longer been totally considered as “junk DNA” for quite a time since the continual discoveries of their multifunctional roles in eukaryote genomes. As one of the most important and abundant TEs that still active in human genome, Alu, a SINE family, has demonstrated its indispensable regulatory functions at sequence level, but its spatial roles are still unclear. Technologies based on 3C(chromosomeconformation capture) have revealed the mysterious three-dimensional structure of chromatin, and make it possible to study the distal chromatin interaction in the genome. To find the role TE playing in distal regulation in human genome, we compiled the new released Hi-C data, TE annotation, histone marker annotations, and the genome-wide methylation data to operate correlation analysis, and found that the density of Alu elements showed a strong positive correlation with the level of chromatin interactions (hESC: r=0.9, P<2.2×1016; IMR90 fibroblasts: r = 0.94, P < 2.2 × 1016) and also have a significant positive correlation withsomeremote functional DNA elements like enhancers and promoters (Enhancer: hESC: r=0.997, P=2.3×10−4; IMR90: r=0.934, P=2×10−2; Promoter: hESC: r = 0.995, P = 3.8 × 10−4; IMR90: r = 0.996, P = 3.2 × 10−4). Further investigation involving GC content and methylation status showed the GC content of Alu covered sequences shared a similar pattern with that of the overall sequence, suggesting that Alu elements also function as the GC nucleotide and CpG site provider. In all, our results suggest that the Alu elements may act as an alternative parameter to evaluate the Hi-C data, which is confirmed by the correlation analysis of Alu elements and histone markers. Moreover, the GC-rich Alu sequence can bring high GC content and methylation flexibility to the regions with more distal chromatin contact, regulating the transcription of tissue-specific genes

The AURORA pilot study for molecular screening of patients with advanced breast cancer–a study of the breast international group

Several studies have demonstrated the feasibility of molecular screening of tumour samples for matching patients with cancer to targeted therapies. However, most of them have been carried out at institutional or national level. Herein, we report on the pilot phase of AURORA (NCT02102165), a European multinational collaborative molecular screening initiative for advanced breast cancer patients. Forty-one patients were prospectively enroled at four participating centres across Europe. Metastatic tumours were biopsied and profiled using an Ion Torrent sequencing platform at a central facility. Sequencing results were obtained for 63% of the patients in real-time with variable turnaround time stemming from delays between patient consent and biopsy. At least one clinically actionable mutation was identified in 73% of patients. We used the Illumina sequencing technology for orthogonal validation and achieved an average of 66% concordance of substitution calls per patient. Additionally, copy number aberrations inferred from the Ion Torrent sequencing were compared to single nucleotide polymorphism arrays and found to be 59% concordant on average. Although this study demonstrates that powerful next generation genomic techniques are logistically ready for international molecular screening programs in routine clinical settings, technical challenges remain to be addressed in order to ensure the accuracy and clinical utility of the genomic data.info:eu-repo/semantics/publishe