Comparative analysis of mitochondrial genomes in Ceratocystis fimbriata complex across diverse hosts

The decline ofAcacia mangiumWilld. in Malaysia, especially in Sabah since 2010, is primarily due to Ceratocystiswilt and canker disease (CWCD) caused by theCeratocystis fimbriataEllis & Halst. complex. This study was aimed to investigate the mitochondrial genome architecture of two differentC. fimbriatacomplex isolates from Malaysia: one fromA. mangiumin Pahang (FRIM1162) and another fromEucalyptus pellitain Sarawak (FRIM1441). This research employed Next-Generation Sequencing (NGS) to contrast genomes from diverse hosts with nine additional mitochondrial sequences, identifying significant genetic diversity and mutational hotspots in the mitochondrial genome alignment. The mitochondrial genome-based phylogenetic analysis revealed a significant genetic relationship between the studied isolates and theC. fimbriatacomplex in the South American Subclade, indicating that theC. fimbriatacomplex discovered in Malaysia isC. manginecans. The comparative mitochondrial genome demonstrates the adaptability of the complex due to mobile genetic components and genomic rearrangements in the studiedfungal isolates. This research enhances our knowledge of the genetic diversity and evolutionary patterns within theC. fimbriatacomplex, aiding in a deeper understanding of fungal disease development and host adaption processes. The acquired insights are crucial for creating specific management strategies for CWCD, improving the overall understanding of fungal disease evolution and control.

Association of vaspin rs2236242 with type 2 diabetes mellitus and obesity: a meta-analysis of case-control studies

Background

Elevated circulating vaspin levels is linked with type 2 diabetes mellitus (T2DM) and obesity. The genetic basis of the association between vaspin rs2236242 and T2DM and obesity is still being investigated. We executed a meta-analysis to evaluate the magnitude of effect caused by vaspin rs2236242 on T2DM and obesity.

Methods

We searched Pubmed, Embase, MEDLINE, Scopus, Web of Science, and Google Scholar for relevant articles published up to 19 February 2022. Data were extracted and summary estimates of the association between vaspin rs2236242 and T2DM and obesity were assessed. Odds ratios (ORs) and confidence intervals (CIs) were used to measure the effect.

Results

This meta-analysis included 2206 cases and 2715 controls in the T2DM cohort, meanwhile 271 cases and 444 controls in the obesity cohort. The pooled estimates revealed no link between vaspin rs2236242 and T2DM, but allele-A was significantly higher in the controls of the obesity cohort, showing that this single nucleotide polymorphism (SNP) has a reduced obesity risk effect. Sensitivity analysis revealed no studies that would modify the estimates or the heterogeneity. Begg and Mazumdar's and Egger's tests indicated no substantial publication bias.

Conclusion

Our meta-analysis provides evidence of significant association between vaspin rs2236242 and reduced risk of obesity but not T2DM.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40200-022-01119-8.

Highly divergent regions in the complete plastome sequences of Aquilaria are suitable for DNA barcoding applications including identifying species origin of agarwood products

Members of Aquilaria Lam. (Thymelaeaceae) are evergreen trees that are widely distributed in the Indomalesia region. Aquilaria is highly prized for its unique scented resin, agarwood, which is often the subject of unlawful trade activities. Survival of the tree is heavily threatened by destructive harvesting and agarwood poaching, leading to its protection under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Unfortunately, an efficient species identification method, which is crucial to aid in the conservation efforts of Aquilaria is lacking. Here, we described our search for a suitable specific DNA barcode for Aquilaria species using eight complete plastome sequences. We identified five highly variable regions (HVR) (matK-rps16, ndhF-rpl32, psbJ-petA, trnD, and trnT-trnL) in the plastomes. These regions were further analyzed using the neighbor-joining (NJ) method to assess their ability at discriminating the eight species. Coupled with in silico primer design, two potential barcoding regions, psbJ-petA and trnT-trnL, were identified. Their strengths in species delimitation were evaluated individually and in combination, via DNA barcoding analysis. Our findings showed that the combined dataset, psbJ-petA + trnT-trnL, effectively resolved members of the genus Aquilaria by clustering all species into their respective clades. In addition, we demonstrated that the newly proposed DNA barcode was capable at identifying the species of origin of six commercial agarwood samples that were included as unknown samples. Such achievement offers a new technical advancement, useful in the combat against illicit agarwood trades and in assisting the conservation of these valuable species in natural populations.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03479-1.

Impact of urinary calcium excretion on kidney, bone, and cardiovascular systems in patients with bone biopsy proven osteoporosis: a longitudinal long-term follow-up study

The impact of urine calcium on kidney, bone, and cardiovascular systems in osteoporosis is not well-known. In this 7-year-follow-up study, high urine calcium did not affect kidney function but increased risk of kidney stones, while low urine calcium increased cardiovascular diseases. Maintaining normal urine calcium is beneficial for bone health.

PURPOSE

Hypercalciuria is common in patients with osteoporosis. However, the long-term effect of urinary calcium excretion (UCaE) on patients' health is not well-examined. The current study aims to assess the impact of UCaE on kidney, bone, and cardiovascular outcomes in patients with bone biopsy proven osteoporosis.

METHODS

Longitudinal study of all patients with osteoporosis who underwent bone biopsy and 24-h urine collection between 2008 and 2015 in the University of Kentucky. DXA scans, serum markers, kidney function, and cardiovascular events were recorded until last clinic visit in 2021. Exclusion criteria were secondary osteoporosis or conditions that might substantially impact UCaE. The significant results in univariate analysis were confirmed in multi-variable regression models involving clinically important covariates that might impact patients' outcomes.

RESULTS

Study included 230 patients with mean follow-up of 7.2 ± 2.9 years. The mean age was 61 years, and the mean eGFR at baseline was 85 ± 19 ml/min/1.73 m². Low bone turnover (LBT) was present in 57% and high bone turnover (HBT) in 43% of patients. Hypercalciuria was found in one-third of patients with no difference between LTB and HTB. UCaE correlated positively with eGFR but did not affect the rate of eGFR decline over time. Higher UCaE predicted kidney stones development. We observed U-shaped effect of UCaE on bone health. Hypercalciuria predicted loss of BMD at all sites, but also hypocalciuria was associated with higher loss in total hip BMD. Upper limb fractures were the most observed fractures, and their incidence was higher in patients with hyper- or hypo-calciuria. Lower UCaE independently predicted development of major adverse cardiac events (MACE) and cardiovascular disease (CVD).

CONCLUSION

UCaE correlated with eGFR but it did not affect the change of eGFR over time. Patients with normal UCaE had lower incidence of upper limb fractures and less reduction in BMD. Low UCaE predicted MACE and CVD.

S-100 Negative Granular Cell Tumor of Oral Cavity with Aggressive Clinical Behavior

Introduction/Objective

Granular cell tumors (GCTs) are neoplasms with neuroectodermal (Schwann cell) differentiation that is typically benign and cured by surgical excision. These tumors characteristically display strong expression of S-100 protein. Similar tumors without expression of S-100 protein are called “S-100 negative granular cell tumors.” The few reported cases of S-100 negative GCT in the oral cavity describe indolent clinical behavior. We report a case of a 49-year-old male with recurrent S-100 negative GCT in the oral cavity.

Methods/Case Report

The patient presented initially with a mass in the hard palate, which was resected and diagnosed as an S-100 negative GCT. One year later, the patient developed severe epistaxis and anemia (hemoglobin 7.2 g/dL). A large tumor of the hard palate was the source of bleeding. It was resected and diagnosed as recurrent S-100 negative GCT. Histologically, this tumor consists of small nests of epithelioid to spindled cells with moderately abundant granular eosinophilic cytoplasm, round central nuclei with vesicular chromatin and distinct eosinophilic nucleoli, and significant mitotic activity. The cells are immunoreactive for SOX10 and negative for S-100, melan-A, keratin AE1/AE3, p40, synaptophysin, smooth muscle actin, desmin, and myogenin.

Results (if a Case Study enter NA)

N/A

Conclusion

S-100 negative GCTs are rare, and only a few case reports describe their involvement in the oral cavity. We report this case because of its rarity and aggressive clinical behavior. Recognition of this entity and its potential for locally aggressive growth is important. Management of this tumor by complete excision seems advisable.

Tropical and subtropical Asia's valued tree species under threat

Tree diversity in Asia's tropical and subtropical forests is central to nature-based solutions. Species vulnerability to multiple threats, which affect provision of ecosystem services, is poorly understood. We conducted a region-wide, spatially explicit assessment of the vulnerability of 63 socioeconomically important tree species to overexploitation, fire, overgrazing, habitat conversion, and climate change. Trees were selected for assessment from national priority lists, and selections were validated by an expert network representing 20 countries. We used Maxent suitability modeling to predict species distribution ranges, freely accessible spatial data sets to map threat exposures, and functional traits to estimate threat sensitivities. Species-specific vulnerability maps were created as the product of exposure maps and sensitivity estimates. Based on vulnerability to current threats and climate change, we identified priority areas for conservation and restoration. Overall, 74% of the most important areas for conservation of these trees fell outside protected areas, and all species were severely threatened across an average of 47% of their native ranges. The most imminent threats were overexploitation and habitat conversion; populations were severely threatened by these factors in an average of 24% and 16% of their ranges, respectively. Our model predicted limited overall climate change impacts, although some study species were likely to lose over 15% of their habitat by 2050 due to climate change. We pinpointed specific natural areas in Borneo rain forests as hotspots for in situ conservation of forest genetic resources, more than 82% of which fell outside designated protected areas. We also identified degraded areas in Western Ghats, Indochina dry forests, and Sumatran rain forests as hotspots for restoration, where planting or assisted natural regeneration will help conserve these species, and croplands in southern India and Thailand as potentially important agroforestry options. Our results highlight the need for regionally coordinated action for effective conservation and restoration.

Malignant Gastrointestinal Neuroectodermal Tumor: a case report and a review of the literature

Introduction/Objective

Malignant gastrointestinal neuroectodermal tumor (GNET) is a rare soft tissue tumor arising in the wall of the gastrointestinal tract. The GNET was first described as an osteoclast rich tumor of the gastrointestinal tract with features resembling clear cell sarcoma, with only few cases reported in the literature.

Methods/Case Report

We report a case of a 71-year-old man with a past medical history of hypertension, hyperlipidemia, and benign prostatic hyperplasia presented with complaints of dyspnea, dizziness, fatigue, black stools, and a recent syncopal episode. Laboratory testing revealed anemia (HB 5.4 g/dL). Esophagogastroduodenoscopy demonstrated a submucosal gastric mass. An abdominal CT scan confirmed a 7.8 cm mass along the gastric cardia and fundus.

Results (if a Case Study enter NA)

Biopsy rendered a gastrointestinal neuroectodermal tumor (GNET). Microscopically, the tumor cells were spindle with eosinophilic cytoplasm and arranged in fascicules. They were positive for CD56, CD99, and Fli-1, synaptophysin, and negative for chromogranin, TTF-1, SMA, desmin, CD34, EMA, pan-cytokeratin, and lymphoid markers. Two months later, further imaging confirmed metastasis to the liver and spleen. GNETs typically arise within the muscularis propria of the gastrointestinal tract and often extend into the submucosa and subserosa.

Conclusion

The most important differential of GNET is the clear cell sarcoma of the gastrointestinal tract (CCS-GI). Both share similar morphological as well as molecular features and show S100 positivity; however, the lack of melanocytic differentiation in GNET distinguishes it from CCS-GI. Both typically show rearrangements of the EWSR1 gene, with t(12;22) (q13;q12) EWSR1-ATF1 or t(2;22)(q34;q12) EWSR1-CREB1 fusions. Pathologists should be aware of GNET diagnostic entity due to its aggressive behavior and high rate of recurrence and mortality even after complete resection.

Cell viability and electrical response of breast cancer cell treated in aqueous graphene oxide solution deposition on interdigitated electrode

Breast cancer is one of the most reported cancers that can lead to death. Despite the advances in diagnosis and treatment procedures, the possibility of cancer recurrences is still high in many cases. With that in consideration, researchers from all over the world are showing interest in the unique features of Graphene oxide (GO), such as its excellent and versatile physicochemical properties, to explore further its potential and benefits towards breast cancer cell treatment. In this study, the cell viability and electrical response of GO, in terms of resistivity and impedance towards the breast cancer cells (MCF7) and normal breast cells (MCF10a), were investigated by varying the pH and concentration of GO. Firstly, the numbers of MCF7 and MCF10a were measured after being treated with GO for 24 and 48 h. Next, the electrical responses of these cells were evaluated by using interdigitated gold electrodes (IDEs) that are connected to an LCR meter. Based on the results obtained, as the pH of GO increased from pH 5 to pH 7, the number of viable MCF7 cells decreased while the number of viable MCF10a slightly increased after the incubation period of 48 h. Similarly, the MCF7 also experienced higher cytotoxicity effects when treated with GO concentrations of more than 25 µg/mL. The findings from the electrical characterization of the cells observed that the number of viable cells has corresponded to the impedance of the cells. The electrical impedance of MCF7 decreased as the number of highly insulating viable cell membranes decreased. But in contrast, the electrical impedance of MCF10a increased as the number of highly insulating viable cell membranes increased. Hence, it can be deduced that the GO with higher pH and concentration influence the MCF7 cancer cell line and MCF10a normal breast cell.

1268 Pathology Pick up Rate in Routine Preoperative Endoscopy and its Impact on Patients Undergoing Gastric Bypass Surgery

Aim

Preoperative OGD in patients undergoing bariatric surgery, has been a subject for debate for decades. The aim of this study is to evaluate the pathology pick up rate in routine preoperative endoscopy in patients undergoing Gastric Bypass surgery (LRYGB) in our unit.

Method

Retrospective review of patients’ records who underwent LRYBG in our unit from February 2009 to March 2020. Patients were divided into two groups according to the presence or absence of symptoms prior to bariatric surgery: Group A (Asymptomatic) and Group B (Symptomatic). Data from prospectively kept electronic OGD reports, CLO test results, histology reports and the changes in management plan were collected and analysed.

Results

114 patients were included in the analysis, 85 (74.56%) were in group A and 29 in group B. OGD detected pathology in 34 patients in group A and 21 in group B (p = 0.004). Those included hiatus hernia (HH) (17.65% group A, 44.83% group B, p = 0.006); stomach ulcer (7.06% group A, 3.45% group B, p = 0.676), H.pylori infection (12.86% group A, 29.41% group B). This led to change of management in 22 patients in group A and 12 of group B (p = 0.157) excluding PPI prescription. Those changes included H.pylori eradication (10.59% group A, 17.24% group B, p = 0.153), HH repair (3.53% group A, 24.14% group B, p = 0.002). There was no cancellation or change in bariatric surgery offered in both groups.

Conclusions

Preoperative OGD has only significantly impacted the bariatric patient’s pathway in symptomatic patients. However, in Asymptomatic patients, OGD could be replaced by cheaper and non-invasive alternatives.

The complete chloroplast genome of Walla Patta, Gyrinops walla (Thymelaeaceae), an agarwood-producing tree species from Sri Lanka

Gyrinops walla is an important agarwood-producing tree and threatened species from Sri Lanka. Herein, we assembled and characterized the complete chloroplast (cp) genome of G. walla as a genomic resource for conservation purposes. The 175,130 bp long genome is comprised of 87,376 bp large single-copy (LSC) and 3316 bp small single-copy (SSC) regions, which are separated by two inverted repeat (IR) region, each with a size of 42,291 bp. A total of 140 genes were predicted for the cp genome, which includes 94 protein-coding, 38 tRNA, and eight rRNA genes. Phylogenetic analysis showed that G. walla is fully resolved in a sister position to Aquilaria in the family Thymelaeaceae. The data provided will be useful for study on the molecular phylogenetics and evolution of Thymelaeaceae in the future.

A73 PERFORMANCE OF ASGE AND ESGE CRITERIA FOR RISK STRATIFICATION FOR CHOLEDOCHOLITHIASIS IN A REAL-WORLD SETTING

Background

Choledocholithiasis (CDL) is a common clinical entity and can lead to serious complications, such as pancreatitis or ascending cholangitis. Endoscopic retrograde cholangio-pancreatography (ERCP) is generally the first-line procedure for definitive management of CDL. ERCP has well-established adverse events. Given the risks, patients can be stratified by likelihood of finding CDL on ERCP, thus potentially avoiding an unnecessary procedure in low probability patients. There are three commonly used criteria for this – the American Society for Gastrointestinal Endoscopy (ASGE) 2010 criteria, the ASGE 2019 criteria, and the European Society of Gastrointestinal Endoscopy (ESGE) 2019 criteria. These criteria use a mixture of biliary imaging, clinical condition, and liver biochemistry to stratify patients into low, intermediate, and high probability for CDL.

Aims

To test the performance characteristics of the ASGE 2010, ASGE 2019, and ESGE 2019 criteria for probability of CDL on a real-world sample.

Methods

We identified all adult patients who had ERCP done at our local centre for suspected CDL between 2012/01/01 and 2018/10/07. A sample of 1000 cases were chosen. We obtained the patients’ pre-procedural liver biochemistries, pre-procedural imaging in the preceding 6 months, and their ERCP reports. We used a semi-automated algorithm to determine confirmation of CDL. We inferred clinical gallstone pancreatitis using the surrogate of serum lipase at or greater than three times upper limit of normal. We could not capture clinical ascending cholangitis from the collected data. We stratified each patient according to the three guidelines and calculated their performance characteristics.

Results

After manually reviewing visits with incomplete ERCP or repeat ERCP, we analyzed 879 ERCP visits. There were 622 with stone or sludge found on ERCP. The performance characteristics of the high-probability and intermediate-probability criteria of the three guidelines are listed in the table below.

Conclusions

Our results for the 2010 ASGE guidelines high probability patients are in keeping with previous validation studies. There have been only one validation study each of the 2019 ASGE guidelines and the 2019 ESGE guidelines, and our results are different in sensitivity and negative predictive value. Future directions in refining these risk stratification tools are needed, and our project in ongoing in assessing the additional value of trends in liver biochemistry.

Funding Agencies

None

Comparison of eight complete chloroplast genomes of the endangered Aquilaria tree species (Thymelaeaceae) and their phylogenetic relationships

Aquilaria tree species are naturally distributed in the Indomalesian region and are protected against over-exploitation. They produce a fragrant non-timber product of high economic value, agarwood. Ambiguous species delimitation and limited genetic information within Aquilaria are among the impediments to conservation efforts. In this study, we conducted comparative analysis on eight Aquilaria species complete chloroplast (cp) genomes, of which seven were newly sequenced using Illumina HiSeq X Ten platform followed by de novo assembly. Aquilaria cp genomes possess a typical quadripartite structure including gene order and genomic structure. The length of each of the cp genome is about 174 kbp and encoded between 89 and 92 proteins, 38 tRNAs, and 8 rRNAs, with 27 duplicated in the IR (inverted repeat) region. Besides, 832 repeats (forward, reverse, palindrome and complement repeats) and nine highly variable regions were also identified. The phylogenetic analysis suggests that the topology structure of Aquilaria cp genomes were well presented with strong support values based on the cp genomes data set and matches their geographic distribution pattern. In summary, the complete cp genomes will facilitate development of species-specific molecular tools to discriminate Aquilaria species and resolve the evolutionary relationships of members of the Thymelaeaceae family.

Cross-amplification of microsatellite markers across agarwood-producing species of the Aquilarieae tribe (Thymelaeaceae)

Tree species in the Aquilarieae tribe of the Thymelaeaceae family produce agarwood, a natural product highly valued for its fragrance, but the species are under threat due to indiscriminate harvesting. For conservation of these species, molecular techniques such as DNA profiling have been used. In this study, we assessed cross-amplification of microsatellite markers, initially developed for three Aquilaria species (A. crassna, A. malaccensis, and A. sinensis), on ten other agarwood-producing species, including members of Aquilaria (A. beccariana, A. hirta, A. microcarpa, A. rostrata, A. rugosa, A. subintegra, and A. yunnanensis) and Gyrinops (G. caudata, G. versteegii, and G. walla), both from the Aquilarieae tribe. Primers for 18 out of the 30 microsatellite markers successfully amplified bands of expected sizes in 1 sample each of at least 10 species. These were further used to genotype 74 individuals representing all the 13 studied species, yielding 13 cross-amplifiable markers, of which only 1 being polymorphic across all species. At each locus, the number of alleles ranged from 7 to 23, indicating a rather high variability. Four markers had relatively high species discrimination power. Our results demonstrated that genetic fingerprinting can be an effective tool in helping to manage agarwood genetic resources by potentially supporting the chain-of-custody of agarwood and its products in the market.

A272 THE CANADIAN DIRECT OBSERVATION OF PROCEDURAL SKILLS (CANDOPS) TOOL FOR ENDOSCOPIC RETROGRADE CHOLANGIOPANCREATOGRAPHY: A MULTI-CENTRE PROSPECTIVE STUDY

Background

Previous studies have demonstrated that many graduating trainees may not have all of the skills needed to independently practice endoscopic retrograde cholangiopancreatography (ERCP) safely and effectively. As a part of competency-based learning curriculum development, it is essential to provide formative feedback to trainees and ensure they acquire the knowledge and skills for independent practice.

Aims

To assess the performance of advanced endoscopy trainees across Canada using the Canadian Direct Observation of Procedural Skills (CanDOPS) ERCP assessment tool. Procedural items evaluated include both technical (cannulation, sphincterotomy, stone extraction, tissue sampling, and stent placement) and non-technical (leadership, communication and teamwork, judgment and decision making) skills.

Methods

We conducted a prospective national multi-centre prospective study. Advanced endoscopy trainees with at least two years of gastroenterology training or five years of general surgery in North America and minimal experience performing ERCPs (less than 100 ERCP procedures) were invited to participate. The CanDOPS tool was used to measure every fifth ERCP performed by trainees over a 12-month fellowship training period. ERCPs were evaluated by experienced staff endoscopists at each study site under standard clinical protocol. Cumulative sum (CUSUM) analyses were used to generate learning curves.

Results

The data from five Canadian sites and 11 trainees participated in the study. A total of 261ERCP evaluations were completed. Median number of evaluations by site and trainee was 49 (IQR 31–76) and 15 (IQR 11–45). Median number of cases trainees performed prior to their ERCP training was 50 (IQR 25–400). There was a significant improvement in almost all scores over time, including selective cannulation, sphincterotomy, biliary stenting and all non-technical skills (P<0.01). CUSUM analyses using acceptable and unacceptable failure rates of 20% and 50% demonstrated trainees achieved competency for most measures in their final month of their training. Competency in tissue sampling was not achieved within a one-year training period.

Conclusions

This is the first ERCP performance evaluation tool that examines multiple technical and non-technical aspects of the procedure. Although trainee ERCP skills do improve during their training period, there exists a notable variability in time to competency for the different skills measured using the CanDOPS tool. Large prospective research is required to determine if competency is achieved using more stringent definitions of ERCP competency and to determine factors associated with reaching competency.

Funding Agencies

None

A279 EUS-GUIDED BILIARY DRAINAGE IN MALIGNANT DISTAL BILIARY OBSTRUCTION: AN INTERNATIONAL SURVEY TO IDENTIFY BARRIERS OF TECHNOLOGY IMPLEMENTATION

Background

Endoscopic ultrasound-guided biliary drainage (EUS-BD) is a promising alternative to endoscopic retrograde cholangiopancreatography (ERCP) in malignant distal biliary obstruction (MDBO). Recent small randomized controlled trials comparing EUS-BD with ERCP suggest that EUS-BD achieves a similar technical success rate and safety profile while potentially being associated with lower rates of stent dysfunction However, its application in clinical practice has been impeded by various undefined barriers.

Aims

To evaluate the current practice of EUS-BD and the determinants for its clinical implementation in MDBO.

Methods

An online survey was generated using Google Forms. Five endoscopy societies have distributed the survey as of October 10th, 2019. Survey questions measured participant characteristics, EUS-BD in different clinical scenarios, and potential barriers to implementation. Descriptive statistics were calculated using frequencies, chi-square statistics were used for inferential analysis, and a standard step-wise multivariable analysis was performed to identify independent variables for and against the use of EUS-BD.

Results

To date, 102 physicians have participated in the survey (response rate 7.97%). The majority of participants are from North America (39.2%), Asia (31.4%), and Europe (19.6%). Most participants are gastroenterologists with formal therapeutic endoscopy training (66.7%), though only 28.4% have received EUS-BD training. In unresectable cancer, 85.1% of respondents favoured EUS-BD over percutaneous biliary drainage following ERCP failure (p<0.0001), while in borderline resectable disease, 72.3% preferred EUS-BD. On multivariable analysis, male gender, formal training in EUS-BD, and unresectable cancer were independent variables for the use of EUS-BD. Conversely, independent discouraging factors for EUS-BD included fear of adverse events, limited high-quality data, lack of local expertise, and inadequate access to EUS technology.

Conclusions

In this international survey, it appears that EUS-BD is gaining traction, especially in the setting of unresectable disease following ERCP failure. However, barriers to implementation include the lack of high-quality data, fear for adverse events, limited experts in the field, and inadequate access to EUS technology. This suggest the need for high-quality clinical trials, increased endoscopist training in this field, and further technology development in EUS-BD in order to increase its uptake in clinical practice.

Funding Agencies

None

Diversity and characterization of lignocellulolytic fungi isolated from oil palm empty fruit bunch, and identification of influencing factors of natural composting process

Oil palm empty fruit bunch (EFB) is the most significant waste generated from the agricultural industry in Malaysia. Composting is one of the potential approaches to utilize EFB. However, composting of EFB is a time-consuming process, thus impractical for industrial application. The composting process can be shortened by introducing competent fungi into an optimal EFB composting system. This study was conducted to isolate and identify competent fungi that can naturally compost EFB. Samplings were carried out at eight different time points over a 20-weeks experimental period. The physical properties of EFB samples such as pH, residual oil content, and moisture content were measured and the EFB composting process that was indicated by the contents of cellulose, hemicellulose, and lignin were assessed. The fungal growth, distribution, and lignocellulolytic enzyme activities were evaluated. The results indicated that the changes in physical properties of EFB were correlated to the fungal growth. The gradual reduction in moisture content and residual oil, and the increment in pH values in EFB samples throughout the experimental period resulted in reduced fungal growth and diversity. Such phenomenon delayed EFB composting process as revealed by the changes in EFB lignin, hemicellulose, and cellulose contents. The most dominant and resilient fungi (Lichtheimia ramosa and Neurospora crassa) survived up to 16 weeks and were capable of producing various lignocellulolytic enzymes. Further understanding of these factors that would contribute to effective EFB composting could be useful for future industrial applications.

Time-based LC-MS/MS analysis provides insights into early responses to mechanical wounding, a major trigger to agarwood formation in Aquilaria malaccensis Lam

Mechanical wounding is the major trigger for the formation of agarwood in the tropical tree taxon Aquilaria. To understand the molecular mechanism by which Aquilaria reacts to wounding, we applied a proteomics approach using liquid chromatography electrospray-ionization coupled with tandem mass spectrometry (LC-MS/MS) coupled with bioinformatics analysis and principal component analysis. Protein samples were extracted from wood tissues collected from drilled wounds on the stems of five-year old Aquilaria malaccensis. Samples were collected at different time-points of 0, 2, 6, 12, and 24 h after mechanical wounding for protein identification. Venn diagram analysis showed that 564 out of 2227 identified proteins were time-point specific proteins. GO analysis using the REViGO software (including functional proteins) supported these findings. In total, 20 wound-response proteins and one unknown protein were identified as having important roles in the signaling response to wounding, response to stress, activation of plant defense systems, and plant regeneration. The detected biological processes include brassinosteroid stimulus, polyamine catabolism, hypersensitive response, response to cadmium ions, response to oxidative stress, and malate metabolism, suggesting that the wounded trees must have undergone major plant cell damage. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that several wound-response proteins were involved in agarwood formation. Our proteomics data thus provide useful information for understanding the wound response mechanisms that trigger agarwood formation.

Mechanical wounding triggers agarwood synthesis pathways in Aquilaria malaccensis.

The complete chloroplast genome sequence of Chengal (Neobalanocarpus heimii, Dipterocarpaceae), a durable tropical hardwood

Known for its durable timber quality, Neobalanocarpus heimii (King) Ashton is a highly sought after tree species endemic to the Malay Peninsula. Due to its scarcity and high value, the tree is classified under the IUCN Red List categories of Vulnerable. In this study, we assembled the complete chloroplast (cp) genome of N. heimii using data from high-throughput Illumina sequencing. The Chengal cp genome is 151,191 bp in size and includes two inverted repeat regions of 23,721 bp each, which is separated by a large single copy region of 83,801 bp and a small single copy region of 19,948 bp. A total of 130 genes were predicted, including 37 tRNA, 8 rRNA, and 85 protein-coding genes. Phylogenetic analysis placed N. heimii within the order Malvales.

The complete chloroplast genome of Aquilaria malaccensis Lam. (Thymelaeaceae), an important and threatened agarwood-producing tree species

Known for its valuable agarwood, Aquilaria malaccensis Lam. is an evergreen tropical forest tree species endemic to the Indo-malesian region. Indiscriminate damaging and harvesting of the trees in the wild have resulted in it being listed in the CITES Appendix II for controlled trade and in the IUCN Red List as ‘Vulnerable (VU)’. In this study, the complete chloroplast genome of A. malaccensis was assembled using data from high-throughput Illumina sequencing. The chloroplast genome was 174,832 bp in size, which included two inverted repeat regions of 42,091 bp each, separated by a large single copy region of 87,302 bp and a small single copy region of 3,348 bp. A total of 139 genes were predicted, including 39 tRNA, 8 rRNA, and 92 protein-coding genes. Phylogenetic analysis placed A. malaccensis within the family Thymelaeaceae. The chloroplast genome sequence of A. malaccensis offers a useful resource for future studies on the taxonomy and conservation of the threatened Aquilaria trees.

Diversity and Characterization of Endophytic Fungi Isolated From the Tropical Mangrove Species, Rhizophora mucronata, and Identification of Potential Antagonists Against the Soil-Borne Fungus, Fusarium solani

Rhizophora mucronata is an important ecosystem entity of the Malaysian mangrove forest. Since the species grows in a harsh environment, any organism that is isolated from this species would be of huge interest due to its potential in having novel bioactive compounds. In the present work, we isolated, identified and characterized, a total of 78 fungal isolates harboring inside the leaf tissues of R. mucronata. Molecular identification using the nuclear ribosomal DNA internal transcribe spacer (ITS) sequences returned with high similarity matches to known sequences in the GenBank. Maximum likelihood analysis revealed the phylogenetic relationship of all isolates from this study. Most of the dominating fungal endophytes were from the genera Pestalotiopsis, followed by Alternaria and Cladosporium. Six isolates representing the genera Alternaria, Fusarium, Nigrospora, Pestalotiopsis, Phoma, and Xylaria, were further screened for their antagonism activities. Dual culture test assay revealed their inhibition percentages against the phytopathogenic fungus Fusarium solani between 45-66%, and 0.8-23% when using non-volatile test assay. Of the six isolates, only Fusarium lateritium and Xylaria sp. showed antibacterial activities against the pathogenic bacteria, Bacillus subtilis, Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus, with the Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC) ranging from 0.5 to 2 mg/mL. The DPPH radical scavenging assay recorded a high level of antioxidant activity in Xylaria sp., 3-fold above that of F. lateritium. We demonstrate for the first time, two members belonging to the endophytic fungal community in the tropical mangrove species that have potential use as antagonists and antibacterial agents for future biotechnological applications.

Phylogenetic Relatedness of Several Agarwood-Producing Taxa (Thymelaeaceae) from Indonesia

Indonesia is home to several tree taxa that are harvested for agarwood. This highly valuable oleoresin ironically was the cause for some species to become vulnerable due to gluttonous human activity. However, information on the genetic diversity of these endangered trees is limited. In this study, 28 specimens representing eight species from two genera, Aquilaria and Gyrinops, were collected from ex-situ and in-situ populations in Indonesia. Phylogenetic analysis conducted on DNA sequences of the nuclear ribosomal internal transcribed spacer (ITS) and the trnL-trnF intergenic spacer regions, revealed that Aquilaria and Gyrinops are paraphyletic when Aquilaria cumingiana is excluded. The phylogenetic analysis for ITS and trnL-trnF showed capability to categorise agarwood-producing species based on their regions: East Indonesia and West Indonesia, using Wallace’s Line as the divider. In addition, we discuss challenges in species identification and taxonomy of agarwood-producing genera, and their conservation efforts in Indonesia.

Genome Size, Molecular Phylogeny, and Evolutionary History of the Tribe Aquilarieae (Thymelaeaceae), the Natural Source of Agarwood

The tribe Aquilarieae of the family Thymelaeaceae consists of two genera, Aquilaria and Gyrinops, with a total of 30 species, distributed from northeast India, through southeast Asia and the south of China, to Papua New Guinea. They are an important botanical resource for fragrant agarwood, a prized product derived from injured or infected stems of these species. The aim of this study was to estimate the genome size of selected Aquilaria species and comprehend the evolutionary history of Aquilarieae speciation through molecular phylogeny. Five non-coding chloroplast DNA regions and a nuclear region were sequenced from 12 Aquilaria and three Gyrinops species. Phylogenetic trees constructed using combined chloroplast DNA sequences revealed relationships of the studied 15 members in Aquilarieae, while nuclear ribosomal DNA internal transcribed spacer (ITS) sequences showed a paraphyletic relationship between Aquilaria species from Indochina and Malesian. We exposed, for the first time, the estimated divergence time for Aquilarieae speciation, which was speculated to happen during the Miocene Epoch. The ancestral split and biogeographic pattern of studied species were discussed. Results showed no large variation in the 2C-values for the five Aquilaria species (1.35-2.23 pg). Further investigation into the genome size may provide additional information regarding ancestral traits and its evolution history.

Historical epidemiology of hepatitis C virus in select countries-volume 4

Due to the introduction of newer, more efficacious treatment options, there is a pressing need for policy makers and public health officials to develop or adapt national hepatitis C virus (HCV) control strategies to the changing epidemiological landscape. To do so, detailed, country-specific data are needed to characterize the burden of chronic HCV infection. In this study of 17 countries, a literature review of published and unpublished data on HCV prevalence, viraemia, genotype, age and gender distribution, liver transplants and diagnosis and treatment rates was conducted, and inputs were validated by expert consensus in each country. Viraemic prevalence in this study ranged from 0.2% in Hong Kong to 2.4% in Taiwan, while the largest viraemic populations were in Nigeria (2 597 000 cases) and Taiwan (569 000 cases). Diagnosis, treatment and liver transplant rates varied widely across the countries included in this analysis, as did the availability of reliable data. Addressing data gaps will be critical for the development of future strategies to manage and minimize the disease burden of hepatitis C.

The present and future disease burden of hepatitis C virus infections with today's treatment paradigm: Volume 4

Factors influencing the morbidity and mortality associated with viremic hepatitis C virus (HCV) infection change over time and place, making it difficult to compare reported estimates. Models were developed for 17 countries (Bahrain, Bulgaria, Cameroon, Colombia, Croatia, Dominican Republic, Ethiopia, Ghana, Hong Kong, Jordan, Kazakhstan, Malaysia, Morocco, Nigeria, Qatar and Taiwan) to quantify and characterize the viremic population as well as forecast the changes in the infected population and the corresponding disease burden from 2015 to 2030. Model inputs were agreed upon through expert consensus, and a standardized methodology was followed to allow for comparison across countries. The viremic prevalence is expected to remain constant or decline in all but four countries (Ethiopia, Ghana, Jordan and Oman); however, HCV-related morbidity and mortality will increase in all countries except Qatar and Taiwan. In Qatar, the high-treatment rate will contribute to a reduction in total cases and HCV-related morbidity by 2030. In the remaining countries, however, the current treatment paradigm will be insufficient to achieve large reductions in HCV-related morbidity and mortality.

Strategies to manage hepatitis C virus infection disease burden-Volume 4

The hepatitis C virus (HCV) epidemic was forecasted through 2030 for 17 countries in Africa, Asia, Europe, Latin America and the Middle East, and interventions for achieving the Global Health Sector Strategy on viral hepatitis targets-"WHO Targets" (65% reduction in HCV-related deaths, 90% reduction in new infections and 90% of infections diagnosed by 2030) were considered. Scaling up treatment and diagnosis rates over time would be required to achieve these targets in all but one country, even with the introduction of high SVR therapies. The scenarios developed to achieve the WHO Targets in all countries studied assumed the implementation of national policies to prevent new infections and to diagnose current infections through screening.

Plant cytochrome P450s: nomenclature and involvement in natural product biosynthesis

Cytochrome P450s constitute the largest family of enzymatic proteins in plants acting on various endogenous and xenobiotic molecules. They are monooxygenases that insert one oxygen atom into inert hydrophobic molecules to make them more reactive and hydro-soluble. Besides for physiological functions, the extremely versatile cytochrome P450 biocatalysts are highly demanded in the fields of biotechnology, medicine, and phytoremediation. The nature of reactions catalyzed by P450s is irreversible, which makes these enzymes attractions in the evolution of plant metabolic pathways. P450s are prime targets in metabolic engineering approaches for improving plant defense against insects and pathogens and for production of secondary metabolites such as the anti-neoplastic drugs taxol or indole alkaloids. The emerging examples of P450 involvement in natural product synthesis in traditional medicinal plant species are becoming increasingly interesting, as they provide new alternatives to modern medicines. In view of the divergent roles of P450s, we review their classification and nomenclature, functions and evolution, role in biosynthesis of secondary metabolites, and use as tools in pharmacology.

DNA Barcoding of the Endangered Aquilaria (Thymelaeaceae) and Its Application in Species Authentication of Agarwood Products Traded in the Market

The identification of Aquilaria species from their resinous non-wood product, the agarwood, is challenging as conventional techniques alone are unable to ascertain the species origin. Aquilaria is a highly protected species due to the excessive exploitation of its precious agarwood. Here, we applied the DNA barcoding technique to generate barcode sequences for Aquilaria species and later applied the barcodes to identify the source species of agarwood found in the market. We developed a reference DNA barcode library using eight candidate barcode loci (matK, rbcL, rpoB, rpoC1, psbA-trnH, trnL-trnF, ITS, and ITS2) amplified from 24 leaf accessions of seven Aquilaria species obtained from living trees. Our results indicated that all single barcodes can be easily amplified and sequenced with the selected primers. The combination of trnL-trnF+ITS and trnL-trnF+ITS2 yielded the greatest species resolution using the least number of loci combination, while matK+trnL-trnF+ITS showed potential in detecting the geographical origins of Aquilaria species. We propose trnL-trnF+ITS2 as the best candidate barcode for Aquilaria as ITS2 has a shorter sequence length compared to ITS, which eases PCR amplification especially when using degraded DNA samples such as those extracted from processed agarwood products. A blind test conducted on eight agarwood samples in different forms using the proposed barcode combination proved successful in their identification up to the species level. Such potential of DNA barcoding in identifying the source species of agarwood will contribute to the international timber trade control, by providing an effective method for species identification and product authentication.

Asian-Pacific clinical practice guidelines on the management of hepatitis B: a 2015 update

Worldwide, some 240 million people have chronic hepatitis B virus (HBV), with the highest rates of infection in Africa and Asia. Our understanding of the natural history of HBV infection and the potential for therapy of the resultant disease is continuously improving. New data have become available since the previous APASL guidelines for management of HBV infection were published in 2012. The objective of this manuscript is to update the recommendations for the optimal management of chronic HBV infection. The 2015 guidelines were developed by a panel of Asian experts chosen by the APASL. The clinical practice guidelines are based on evidence from existing publications or, if evidence was unavailable, on the experts' personal experience and opinion after deliberations. Manuscripts and abstracts of important meetings published through January 2015 have been evaluated. This guideline covers the full spectrum of care of patients infected with hepatitis B, including new terminology, natural history, screening, vaccination, counseling, diagnosis, assessment of the stage of liver disease, the indications, timing, choice and duration of single or combination of antiviral drugs, screening for HCC, management in special situations like childhood, pregnancy, coinfections, renal impairment and pre- and post-liver transplant, and policy guidelines. However, areas of uncertainty still exist, and clinicians, patients, and public health authorities must therefore continue to make choices on the basis of the evolving evidence. The final clinical practice guidelines and recommendations are presented here, along with the relevant background information.

Regulatory role of GSK3β in the activation of NF-κB and modulation of cytokine levels in Burkholderia pseudomallei-infected PBMC isolated from streptozotocin-induced diabetic animals

Increased susceptibility of diabetics to melioidosis, a disease caused by the Burkholderia pseudomallei bacterium is believed to be attributed to dysfunction of the innate immune system. However, the underlying mechanism of the innate susceptibility is not well-understood. Glycogen synthase kinase-3β (GSK3β) plays an important role in the innate inflammatory response caused by bacterial pathogens. The present study was conducted to investigate the effects of GSK3β inhibition by LiCl on levels of pro- and anti-inflammatory cytokines; and the activity of transcription factor NF-κB in B. pseudomallei-infected peripheral blood mononuclear cells (PBMC) derived from diabetic-induced and normal Sprague Dawley rats. In addition, the effects of LiCl on intracellular bacterial counts were also investigated. Infection of PBMC from diabetic and normal rats with B. pseudomallei resulted in elevated levels of cytokines (TNF-α, IL-12 and IL-10) and phosphorylation of NF-κB in both cell types. Intracellular bacterial counts decreased with time in both cell types during infection. However bacterial clearance was less prominent in diabetic PBMC. Burkholderia pseudomallei infection also caused inactivation (Ser9 phosphorylation) of GSK3β in normal PBMC, an effect absent in infected diabetic PBMC. Inhibition of GSK3β by LiCl lowered the levels of pro-inflammatory cytokines (TNF-α and IL-12) in both normal and diabetic PBMC. Similarly, phosphorylated NF- κB (pNF-κB) levels in both cell types were decreased with LiCl treatment. Also, LiCl was able to significantly decrease the intracellular bacterial count in normal as well as diabetic PBMC. Interestingly, the levels of anti-inflammatory cytokine IL-10 in both normal and diabetic PBMC were further elevated with GSK3β inhibition. More importantly, GSK3β in infected diabetic PBMC was inactivated as in their non-diabetic counterparts upon LiCl treatment. Taken together, our results suggest that inhibition of dysregulated GSK3β in diabetic PBMC resulted in the inactivation of NF-κB and modulation of inflammatory cytokine levels. This is evidence that dysregulation of GSK3β is a contributing factor in the molecular basis of innate dysfunction and susceptibility of diabetic host to melioidosis infection.