Application of citizen science with the nationwide bird census

Citizen science (CS) is the most effective tool for overcoming the limitations of government and/or professional data collection. To compensate for quantitative limitations of the 'Winter Waterbird Census of Korea', we conducted a total of four bird monitoring via CS from 2021 to 2022. To use CS data alongside national data, we studied CS data quality and improvement utilizing (1) digit-based analysis using Benford's law and (2) comparative analysis with national data. In addition, we performed bird community analysis using CS-specific data, demonstrating the necessity of CS. Neither CS nor the national data adhered to Benford's law. Alpha diversity (number of species and Shannon index) was lower, and total beta diversity was higher for the CS data than national data. Regarding the observed bird community, the number of species per family was similar; however, the number of individuals per family/species differed. We also identified the necessity of CS by confirming the possibility of predicting bird communities using CS-specific data. CS was influenced by various factors, including the perceptions of the survey participants and their level of experience. Therefore, conducting CS after systematic training can facilitate the collection of higher-quality data.

Molecular Diet Analysis of Asian Clams for Supplementary Biodiversity Monitoring: A Case Study of Nakdong River Estuary

Environmental DNA (eDNA) extracted from the gut contents of filter feeders can be used to identify biodiversity in aquatic ecosystems. In this study, we used eDNA from the gut contents of the Asian clam Corbicula fluminea to examine biodiversity within estuarine ecosystem. Field sampling was conducted at three points in the Nakdong River Estuary, which is characterised by closed estuarine features resulting from the presence of an estuarine barrage. The collected C. fluminea samples were dissected to separate the gut contents, and the extracted eDNA was amplified using 18S V9 primer targeting all eukaryote-derived DNA. The amplified DNA was sequenced using a next-generation sequencing (NGS) technique, and a BLASTn search was performed based on the National Centre for Biotechnology Information (NCBI) database for taxa identification. We obtained 23 unique operational taxonomic units (OTUs), including fish (approximately 8.70%), copepods (approximately 17.39%), and green algae (approximately 21.74%), representing a wide range of habitats. Furthermore, 8 out of the 20 families were identified through comparisons with reference data from conventional field surveys, and the OTUs of elusive migratory fish were detected. The results support the application of C. fluminea as an eDNA sampler for supplementary biodiversity monitoring.

Complete mitochondrial genome of Ischnura asiatica (Brauer, 1865) assembled from next-generation sequencing data

Ischnura asiatica (Brauer, 1865) is a freshwater damselfly belonging to the family Coenagrionidae that is distributed across most of Korea, primarily in areas with low water flow, such as ponds and wetlands. The complete mitochondrial genome of I. asiatica was sequenced by next-generation sequencing. The circular mitochondrial genome was found to be 15,769 bp long, with of 13 protein-coding, two ribosomal RNA, and 22 transfer RNA genes (GenBank accession no. OM310774). Maximum likelihood, phylogenetic analysis showed that this species clustered with other species belonging to the family Coenagrionidae. This study contributes to the phylogeny of damselflies and other members of the family Coenagrionidae.

OP0027 ASSOCIATION BETWEEN BASELINE CARDIOVASCULAR RISK AND INCIDENCE RATES OF MAJOR ADVERSE CARDIOVASCULAR EVENTS AND MALIGNANCIES IN PATIENTS WITH PSORIATIC ARTHRITIS AND PSORIASIS RECEIVING TOFACITINIB

Background

Common comorbidities of psoriatic arthritis (PsA) and psoriasis (PsO) are cardiovascular (CV) disease and metabolic syndrome (MetS).1,2 Risk of CV disease may be associated with increased risk of future malignancies.3 Tofacitinib is a JAK inhibitor for treatment of PsA and has been investigated for treatment of PsO.

Objectives

To examine baseline (BL) CV risk and its association with incidence rates (IRs) of major adverse CV events (MACE) and malignancies in tofacitinib-treated patients (pts) with PsA and PsO.

Methods

Analysis included data from 3 (Phase [P]3/long-term extension [LTE]) trials of pts with PsA and 7 (P2/3/LTE) trials of pts with PsO receiving ≥1 dose of tofacitinib (5 or 10 mg twice daily). IRs (pts with events/100 pt-yrs) for MACE and malignancies (excluding non-melanoma skin cancer) were stratified by: history of coronary artery disease (HxCAD [≥1 of myocardial infarction, coronary heart disease, coronary artery procedure or stable angina pectoris]); BL 10-yr atherosclerotic CV disease (ASCVD) risk (ASCVD-pooled cohort equations calculator [only in pts without HxCAD]); and BL MetS (≥3 of hypertension, raised triglycerides, reduced high-density lipoprotein cholesterol, high waist circumference or high fasting glucose levels).

Results

Of 783 and 3663 pts with PsA and PsO, total tofacitinib exposure was 2038 and 8950 pt-yrs, and median duration of exposure was 3.0 and 2.4 yrs, respectively. In pts with PsA and PsO, 5.0% and 2.5% had HxCAD, respectively; in those without HxCAD, >20% had intermediate/high BL 10-yr ASCVD risk (Figure 1). At BL, 40.9% and 32.7% of pts with PsA and PsO had MetS, respectively. IRs of MACE were greatest in pts with PsA and PsO who had HxCAD/high BL 10-yr ASCVD risk (Table 1). In the PsA cohort, 5/6 pts with MACE had BL MetS. IRs of malignancies in pts with PsA were greatest in those with intermediate/high BL 10-yr ASCVD risk; 8/9 pts with malignancies in these risk categories had BL MetS (Table 1). In the PsO cohort, IR of malignancies was notably greater in those with high vs low/intermediate BL 10-yr ASCVD risk (Table 1).

Table 1.

IRs of MACE and malignancies in pts with PsA and PsO receiving tofacitinib, stratified by HxCAD, BL 10-yr ASCVD risk and BL MetS

MACEMalignanciesPsAPsOPsAPsOn/N[n1]IR (95% CI)n/N[n1]IR (95% CI)n/N[n1]IR (95% CI)n/N[n1]IR (95% CI)HxCADYes1/39[0]0.97 (0.02, 5.38)3/93[0]1.49 (0.31, 4.36)0/39[0]0.00 (0.00, 3.52)0/93[0]0.00 (0.00, 1.83)No5/744[5]0.25 (0.08, 0.59)20/3570[10]0.22 (0.13, 0.34)15/744[10]0.75 (0.42, 1.24)60/3570[26]0.66 (0.51, 0.85)BL 10-yr ASCVD risk categoryHigh risk (≥20%)1/35[1]1.26 (0.03, 7.01)7/179[4]1.67 (0.67, 3.43)1/35[1]1.26 (0.03, 7.03)15/179[10]3.57 (2.00, 5.89)Intermediate risk(≥7.5–<20%)2/121[2]0.62 (0.07, 2.23)9/716[6]0.50 (0.23, 0.95)8/121[7]2.46 (1.06, 4.86)23/716[9]1.28 (0.81, 1.92)Borderline risk(≥5–<7.5%)1/91[1]0.42 (0.01, 2.32)2/400[0]0.19 (0.02, 0.67)2/91[1]0.83 (0.10, 3.01)5/400[1]0.47 (0.15, 1.09)Low risk (<5%)1/487[1]0.08 (0.00, 0.42)2/2241[0]0.03 (0.00, 0.13)4/487[1]0.30 (0.08, 0.77)17/2241[6]0.30 (0.17, 0.47)BL MetSYes5/3200.60 (0.20, 1.40)10/11970.34 (0.16, 0.63)10/3201.20 (0.58, 2.21)26/11970.89 (0.58, 1.31)No1/4630.08 (0.00, 0.44)13/24660.20 (0.11, 0.35)5/4630.40 (0.13, 0.92)34/24660.54 (0.37, 0.75)

Follow-up time calculated up to the day of the first event and subject to risk period of 28 days beyond the last dose of study drug.

CI, confidence interval; N, total pts; n, pts with MACE/malignancies; n1, pts with MACE/malignancies and BL MetS.

Conclusion

In tofacitinib-treated pts with PsA and PsO, raised CV risk and MetS at BL were potentially associated with higher IRs of MACE and malignancies. Our findings support assessing CV risk in pts with PsA and PsO and enhanced monitoring for malignancies in those with raised CV risk.

References

[1]Karmacharya et al. Ther Adv Musculoskel Dis 2021; 13: 1-15.

[2]Garshick et al. J Am Coll Cardiol 2021; 77: 1670-1680.

[3]Lau et al. JACC CardioOncol 2021; 3: 48-58.

Acknowledgements

Study sponsored by Pfizer Inc. Medical writing support was provided by Emma Mitchell, CMC Connect, and funded by Pfizer Inc.

Disclosure of Interests

Lars Erik Kristensen Speakers bureau: AbbVie, Amgen, Biogen, Bristol-Myers Squibb, Eli Lilly, Janssen, MSD, Novartis, Pfizer Inc and UCB, Grant/research support from: Biogen, Janssen, Novartis and UCB, Bruce Strober Speakers bureau: AbbVie, Amgen, Eli Lilly, Janssen and Ortho Dermatologics, Consultant of: AbbVie, Almirall, Amgen, Arcutis, Arena, Aristea, Boehringer Ingelheim, Bristol-Myers Squibb, Cara, Celgene, Dermavant, Dermira, Eli Lilly, GlaxoSmithKline, Janssen, Leo, Meiji Seika Pharma, Novartis, Ortho Dermatologics, Pfizer Inc, Regeneron, Sanofi-Genzyme, Sun Pharma and UCB, Denis Poddubnyy Speakers bureau: AbbVie, Bristol-Myers Squibb, Eli Lilly, MSD, Novartis, Pfizer Inc and UCB, Consultant of: AbbVie, BIOCAD, Gilead Sciences, GlaxoSmithKline, Eli Lilly, MSD, Novartis, Pfizer Inc, Samsung Bioepis and UCB, Grant/research support from: AbbVie, MSD, Novartis and Pfizer, Ying Ying Leung Consultant of: AbbVie, Eli Lilly, Janssen and Novartis, Hyejin Jo Consultant of: Pfizer Inc, Employee of: Syneos Health, Kenneth Kwok Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Ivana Vranic Shareholder of: Pfizer Inc, Employee of: Pfizer Ltd, Dona Fleishaker Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Lara Fallon Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Arne Yndestad Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Dafna D Gladman Consultant of: AbbVie, Amgen, Celgene, Eli Lilly, Galapagos, Gilead Sciences, Janssen, Novartis, Pfizer Inc and UCB.

Seasonality and Species Specificity of Submerged Macrophyte Biomass in Shallow Lakes Under the Influence of Climate Warming and Eutrophication

Climate warming and eutrophication caused by anthropogenic activities strongly affect aquatic ecosystems. Submerged macrophytes usually play a key role in shallow lakes and can maintain a stable clear state. It is extremely important to study the effects of climate warming and eutrophication on the growth of submerged macrophytes in shallow lakes. However, the responses of submerged macrophytes to climate warming and eutrophication are still controversial. Additionally, the understanding of the main pathways impacting submerged macrophytes remains to be clarified. In addition, the influence of seasonality on the growth responses of submerged macrophytes to climate warming and eutrophication requires further elucidation. In this study, we conducted a series of mesocosm experiments with four replicates across four seasons to study the effects of rising temperature and nutrient enrichment on the biomass of two submerged macrophytes, Potamogeton crispus and Elodea canadensis. Our results demonstrated the seasonality and species specificity of plant biomass under the influence of climate warming and eutrophication, as well as the main explanatory factors in each season. Consistent with the seasonal results, the overall results showed that E. canadensis biomass was directly increased by rising temperature rather than by nutrient enrichment. Conversely, the overall results showed that P. crispus biomass was indirectly reduced by phosphorus enrichment via the strengthening of competition among primary producers. Distinct physiological and morphological traits may induce species-specific responses of submerged macrophytes to climate warming and eutrophication, indicating that further research should take interspecies differences into account.

AB0248 INFLUENZA ADVERSE EVENTS IN PATIENTS WITH RHEUMATOID ARTHRITIS IN THE TOFACITINIB CLINICAL PROGRAMME

Background:

Patients (pts) with rheumatoid arthritis (RA) have an increased susceptibility to seasonal influenza and its complications.1 In light of the COVID-19 pandemic, there is a need to better understand acute respiratory viral RNA infections, such as influenza, in pts with RA.

Objectives:

To present a comprehensive summary of data on influenza adverse events (AEs) occurring in the tofacitinib RA clinical programme.

Methods:

Influenza AEs were evaluated in pts with RA from 21 Phase (P)1–3b/4 trials and two open-label, long-term extension (LTE) studies from 2005–2019. These were analysed as two cohorts: P2–3b/4 cohort (pts who received tofacitinib 5 or 10 mg twice daily [BID] as monotherapy or with conventional synthetic [cs]DMARDs, adalimumab, methotrexate or placebo, in P2–3b/4 controlled studies) and Overall cohort (pts who received ≥1 tofacitinib dose, as monotherapy or with csDMARDs, in P1–3b/4 and LTE studies; data were summarised by average tofacitinib dose [average tofacitinib 5 or 10 mg BID based on average total daily dose of <15 or ≥15 mg, respectively]). Incidence rates (IRs; unique pts with events/100 pt-years of exposure; censored at day of first event or up to last dose +28 days) were evaluated for influenza AEs, influenza complication AEs, influenza-like illness (all composites of several MedDRA preferred/verbatim terms) and overall influenza AEs (composite of all preferred/verbatim terms included under influenza AEs, influenza complication AEs and influenza-like illness). In the Overall cohort, the incidence of serious non-influenza AEs within 28 days of the start of an overall influenza AE and time taken to resolution of overall influenza AEs by action taken were summarised descriptively.

Results:

In total, 7964 pts were included; 517 (6.5%) pts reported overall influenza AEs, three of which occurred outside the risk period. In the P2–3b/4 cohort (N=6690), IRs for influenza AEs, influenza-like illness and overall influenza AEs generally appeared similar across treatment arms (Figure 1a). In the Overall cohort, IRs for influenza AEs and influenza-like illness were similar between tofacitinib doses (Figure 1b), and IRs for overall influenza AEs were similar between tofacitinib doses and pt age groups (Figure 1c). No influenza complication AEs (eg pneumonia/encephalitis influenzal) were reported in either cohort. Among pts with overall influenza AEs, nine (1.7%) had serious overall influenza AEs (average tofacitinib 5 mg BID, n=6; average tofacitinib 10 mg BID, n=3). Of these pts, eight (1.5%) were hospitalised (average tofacitinib 5 mg BID, n=6; average tofacitinib 10 mg BID, n=2) and two (0.4%) died (average tofacitinib 5 mg BID, n=1; average tofacitinib 10 mg BID, n=1). Both deaths occurred in pts with H1N1 Influenza A. Twelve (2.3%) pts had a serious non-influenza AE within 28 days of the start of the overall influenza AE (average tofacitinib 5 mg BID, n=6; average tofacitinib 10 mg BID, n=6). The most common serious non-influenza AEs (one event each in average tofacitinib 5 and 10 mg BID groups) were acute respiratory distress syndrome and pneumonia. In most pts with overall influenza AEs, no change to tofacitinib treatment was made (70.2%, n=363) or treatment was stopped temporarily (28.2%, n=146) for a mean duration of 11.0 days. The mean number of days to resolution of overall influenza AEs was numerically similar, ranging from 10.4–11.8 days across tofacitinib doses, irrespective of these actions.

Conclusion:

This post hoc analysis of influenza AEs across the tofacitinib RA clinical programme, over 14–15 influenza seasons, showed generally similar rates between treatment groups, and between tofacitinib doses and pt age groups. Limitations include varying exposure across treatment arms in the P2–3b/4 cohort. Most influenza AEs were non-serious (98.3%), and were not associated with changes to tofacitinib treatment.

References:

[1]Blumentals et al. BMC Musculoskelet Disord 2012; 13: 158.

Acknowledgements:

Study sponsored by Pfizer Inc. Medical writing support was provided by Kirsten Woollcott, CMC Connect, and funded by Pfizer Inc.

Disclosure of Interests:

Kevin Winthrop Grant/research support from: AbbVie, Bristol-Myers Squibb, Eli Lilly, Galapagos, Gilead Sciences, Pfizer Inc, Roche, UCB, Arne Yndestad Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Dan Henrohn Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Hyejin Jo Consultant of: Pfizer Inc, Employee of: Syneos Health, Sara Marsal Shareholder of: IMIDomics, Consultant of: AbbVie, Celgene, Galapagos, Gilead Sciences, Pfizer Inc, Sandoz, Sanofi, Grant/research support from: AbbVie, Bristol-Myers Squibb, Celgene, Jansen-Cilag, MSD, Novartis, Pfizer Inc, Roche, Sandoz, Sanofi, UCB, María Galindo-Izquierdo Grant/research support from: AbbVie, Eli Lilly, GSK, Janssen-Cilag, Annette Diehl Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Andrea Shapiro Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Stanley B. Cohen Consultant of: AbbVie, Eli Lilly, Genentech, Gilead Sciences, Pfizer Inc, Grant/research support from: AbbVie, Eli Lilly, Genentech, Gilead Sciences, Pfizer Inc

Complete mitochondrial genome of Stictochironomus akizukii (Tokunaga) (Chironomidae, Diptera) assembled from next-generation sequencing data

The complete mitochondrial genome of Stictochironomus akizukii (Tokunaga) was sequenced. The circular mitochondrial genome is 15,052 bp and consists of 13 protein-coding, 3 ribosomal RNAs, and 22 transfer RNA genes (GenBank accession no. MT185679). Results of maximum likelihood analysis showed that this species clustered with other species of the family Chironomidae. This study will contribute to the phylogenetics of genus Stictochironomus and the other genera of Chironomidae.

Warming Effects on Periphyton Community and Abundance in Different Seasons Are Influenced by Nutrient State and Plant Type: A Shallow Lake Mesocosm Study

Periphyton plays an important role in lake ecosystems processes, especially at low and intermediate nutrient levels where periphyton contribution to primary production can be similar to or exceed that of phytoplankton. Knowledge of how periphyton responds to key drivers such as climate change and nutrient enrichment is, therefore, crucial. We conducted a series of mesocosm experiments over four seasons to elucidate the responses of periphyton communities to nutrient (low and high, TN-0.33 mg L-1 TP-7.1 μg L-1 and TN-2.40 mg L-1 TP-165 μg L-1, respectively), temperature (ambient, IPCC A2 scenario and A2 + 50%) and plant type (two submerged macrophytes with different morphological structural complexity: Potamogeton crispus and Elodea canadensis, and their corresponding plastic imitations with similar size and structure). We found a noticeable seasonality in the abundance and composition of periphyton. In spring and summer, periphyton abundances were significantly higher in the turbid-high-nutrient state than in the clear-low-nutrient state, and in summer they were notably higher at ambient temperature than in climate scenario A2 and A2 + 50%. In contrast, periphyton abundances in autumn and winter were not influenced by nutrient and temperature, but they were notably higher on plants with a more complex morphological structure than simple ones. The genus composition of periphyton was significantly affected by nutrient-temperature interactions in all seasons and by plant type in winter. Moreover, periphyton functional composition exhibited noticeable seasonal change and responded strongly to nutrient enrichment and temperature rise in spring, summer, and autumn. Our results suggest that the effect of warming on periphyton abundance and composition in the different seasons varied with nutrient state and host plant type in these mesocosms, and similar results may likely be found under field conditions.

Complete mitochondrial genome of Favonigobius gymnauchen (BLEEKER, 1850) assembled from next-generation sequencing data

The complete mitochondrial genome of Favonigobius gymnauchen was sequenced. The circular mitochondrial genome is 16,480 bp and consists of 13 protein-coding, 2 ribosomal RNAs, and 13 transfer RNA genes (GenBank accession no. MN194589). Results of maximum likelihood analysis showed that this species clustered with other species of the family Gobbidae. This study will contribute to the phylogenetics of genus Favonigobius and the other genera of Gobiidae.

Responses of fish assemblage structure to large-scale weir construction in riverine ecosystems

Worldwide, increasing amounts of dams and weirs have been established in rivers in recent decades, often with drastic effects on their ecosystems. Between late 2009 and 2011, 16 large-scale dams were built in the main channels of the four largest rivers in South Korea, eight of these along the main channel of Nakdong River (300 km, 520 km in total). We studied the effect of these constructions on the fish community in the riparian zone based on intensive fish field surveys conducted in the littoral zone during 2007-2017, analysis of fishermen's catch data and molecular analysis of the diet of the keystone species, largemouth bass (Micropterus salmoides). Our results, based on RDA and GLM analyses, showed that environmental characteristics and fish species composition changed significantly with dam construction. Total fish abundance and biomass decreased after the start of the weir construction and fish richness decreased with time. The abundance and biomass of exotic fish decreased during construction but recovered afterwards, leading to higher proportions of exotics. Dominance and Shannon indices did not change significantly from before to after construction, while the Evenness index showed a significant decreasing trend. A comparison of the diet composition of largemouth bass showed decreasing genetic variation after construction. The changes in Functional Feeding Group (FFG) of the benthic communities at the study sites did not coincide with FFG changes in the prey items of largemouth bass, indicating a transition in feeding mode from before to after construction. In conclusion, the endemic and native fish species were most sensitive and showed lower resilience to disturbance by the large-scale dam construction than the translocated and exotic species, and the lake-like ecosystems after construction markedly improved the competitive capacity of these exotic fish over the native and endemic species in the riparian zone of the river.

Explicit Characterization of Spatial Heterogeneity Based on Water Quality, Sediment Contamination, and Ichthyofauna in a Riverine-to-Coastal Zone

Our study aims to identify the spatial characteristics of water quality and sediment conditions in relation to fisheries resources, since the productivity of fisheries resources is closely related to the ambient conditions of the resource areas. We collected water quality samples and sediment contaminants from twenty-one sites at Gwangyang Bay, Korea, in the summer of 2018. Our study sites covered the area from the Seomjin River estuary to the inner and outer bays. To spatially characterize physicochemical features of Gwangyang Bay, we used Self-Organizing Map (SOM), which is known as a robust and powerful tool of unsupervised neural networks for pattern recognition. The present environmental conditions of Gwangyang Bay were spatially characterized according to four different attributes of water quality and sediment contamination. From the results, we put emphasis on several interesting points: (i) the SOM manifests the dominant physicochemical attributes of each geographical zone associated with the patterns of water quality and sediment contamination; (ii) fish populations appear to be closely associated with their food sources (e.g., shrimps and crabs) as well as the ambient physicochemical conditions; and (iii) in the context of public health and ecosystem services, the SOM result can potentially offer guidance for fish consumption associated with sediment heavy metal contamination. The present study may have limitations in representing general features of Gwangyang Bay, given the inability of snapshot data to characterize a complex ecosystem. In this regard, consistent sampling and investigation are needed to capture spatial variation and to delineate the temporal dynamics of water quality, sediment contamination, and fish populations. However, the SOM application is helpful and useful as a first approximation of an environmental assessment for the effective management of fisheries resources.

Complete mitochondrial genome of the freshwater bryozoan Pectinatella magnifica (Phylactolaemata: Plumatellida) assembled from next-generation sequencing data

The complete mitochondrial genome of the freshwater bryozoan Pectinatella magnifica was sequenced. The circular mitochondrial genome is 17,539 bp and consists of 13 protein-coding, two ribosomal RNA, and 22 transfer RNA genes (GenBank accession no. MG546680). The Bayesian comparative analysis of molecular evolution rates revealed no acceleration of the mitochondrial DNA (mtDNA) evolution of P. magnifica. Results of maximum likelihood analysis showed that this species clustered with other species of the phylum Bryozoa.

Extracellular ATP Induces Calcium Signaling in Odontoblasts

Odontoblasts form dentin at the outermost surface of tooth pulp. An increasing level of evidence in recent years, along with their locational advantage, implicates odontoblasts as a secondary role as sensory or immune cells. Extracellular adenosine triphosphate (ATP) is a well-characterized signaling molecule in the neuronal and immune systems, and its potential involvement in interodontoblast communications was recently demonstrated. In an effort to elaborate the ATP-mediated signaling pathway in odontoblasts, the current study performed single-cell reverse transcription polymerase chain reaction (RT-PCR) and immunofluorescent detection to investigate the expression of ATP receptors related to calcium signal in odontoblasts from incisal teeth of 8- to 10-wk-old rats, and demonstrated an in vitro response to ATP application via calcium imaging experiments. While whole tissue RT-PCR analysis detected P2Y₂, P2Y₄, and all 7 subtypes (P2X₁ to P2X₇) in tooth pulp, single-cell RT-PCR analysis of acutely isolated rat odontoblasts revealed P2Y₂, P2Y₄, P2X₂, P2X₄, P2X₆, and P2X₇ expression in only a subset (23% to 47%) of cells tested, with no evidence for P2X₁, P2X₃, and P2X₅ expression. An increase of intracellular Ca²⁺ concentration in response to 100μM ATP, which was repeated after pretreatment of thapsigargin or under the Ca²⁺-free condition, suggested function of both ionotropic and metabotropic ATP receptors in odontoblasts. The enhancement of ATP-induced calcium response by ivermectin and inhibition by 5-(3-bromophenyl)-1,3-dihydro-2H-benzofuro[3,2-e]-1,4-diazepin-2-one (5-BDBD) confirmed a functional P2X₄ subtype in odontoblasts. Positive calcium response to 2',3'-O-(benzoyl-4-benzoyl)-ATP (BzATP) and negative response to α,β-methylene ATP suggested P2X₂, P2X₄, and P2X₇ as functional subunits in rat odontoblasts. Single-cell RT-PCR analysis of the cells with confirmed calcium response and immunofluorescent detection further corroborated the expression of P2X₄ and P2X₇ in odontoblasts. Overall, this study demonstrated heterogeneous expression of calcium-related ATP receptor subtypes in subsets of individual odontoblasts, suggesting extracellular ATP as a potential signal mediator for odontoblastic functions.

Multi-threading the generation of Burrows-Wheeler Alignment

Along with recent progress in next-generation sequencing technology, it has become easier to process larger amounts of genome sequencing data at a lower cost. The most time-consuming step of next-generation sequencing data analysis involves the mapping of read data into a reference genome. Although the Burrows-Wheeler Alignment (BWA) tool is one of the most widely used open-source software tools for aligning read sequences, it still has a limitation in that it does not fully support a multi-thread mechanism during the alignment generation step. In this article, we propose a BWA-MT tool based on BWA that supports multi-thread mechanisms for processing alignment generation. To evaluate BWA-MT, we used an evaluation system equipped with 24 cores and 128 GB of memory. As workloads, we used the hg19 human genome reference sequence and sequences of various read sizes from the 1 to 40 M spots. In our evaluation, BWA-MT showed a maximum of 3.66-times better performance, and generated the same Sequence Alignment/Map result file as that of BWA. Although the ability to speed up the procedure might be dependent on computing resources, we confirmed that BWA-MT is a highly effective and fast alignment tool.

Discovering hidden biodiversity: the use of complementary monitoring of fish diet based on DNA barcoding in freshwater ecosystems

Ecological monitoring contributes to the understanding of complex ecosystem functions. The diets of fish reflect the surrounding environment and habitats and may, therefore, act as useful integrating indicators of environmental status. It is, however, often difficult to visually identify items in gut contents to species level due to digestion of soft‐bodied prey beyond visual recognition, but new tools rendering this possible are now becoming available. We used a molecular approach to determine the species identities of consumed diet items of an introduced generalist feeder, brown trout (Salmo trutta), in 10 Tasmanian lakes and compared the results with those obtained from visual quantification of stomach contents. We obtained 44 unique taxa (OTUs) belonging to five phyla, including seven classes, using the barcode of life approach from cytochrome oxidase I (COI). Compared with visual quantification, DNA analysis showed greater accuracy, yielding a 1.4‐fold higher number of OTUs. Rarefaction curve analysis showed saturation of visually inspected taxa, while the curves from the DNA barcode did not saturate. The OTUs with the highest proportions of haplotypes were the families of terrestrial insects Formicidae, Chrysomelidae, and Torbidae and the freshwater Chironomidae. Haplotype occurrence per lake was negatively correlated with lake depth and transparency. Nearly all haplotypes were only found in one fish gut from a single lake. Our results indicate that DNA barcoding of fish diets is a useful and complementary method for discovering hidden biodiversity.

Investigation of bioaccumulation and biotransformation of polybrominated diphenyl ethers, hydroxylated and methoxylated derivatives in varying trophic level freshwater fishes

The concentrations and distributions of polybrominated diphenyl ethers (PBDEs) and their hydroxylated and methoxylated derivatives (OH- and MeO-BDEs) were determined in seven representative fish species from a river in the Republic of Korea. The PBDEs and their derivatives were found to be accumulated in the internal organs of the fish to different extents. PBDEs were preferentially accumulated in the internal organs rather than muscle tissue, and especially, showed increasing accumulation tendencies with increasing bromination level in liver. The OH-BDEs and MeO-BDEs were preferentially accumulated in the liver and gastrointestinal tract, respectively. MeO-BDE concentrations were found to increase according to relative trophic level, suggesting that the PBDE derivatives can be biomagnified to a greater extent than the parent PBDEs in freshwater food webs. In a comparison with the dissolved analyte concentrations in the water that were measured by using semi-permeable membrane devices, the greater uptake of non-ortho substituted MeO-BDEs by fish was observed.

Application of DNA barcoding for identification of freshwater carnivorous fish diets: Is number of prey items dependent on size class for Micropterus salmoides?

Understanding predator–prey interactions is a major challenge in ecological studies. In particular, the accurate identification of prey is a fundamental requirement in elucidating food-web structure. This study took a molecular approach in determining the species identity of consumed prey items of a freshwater carnivorous fish (largemouth bass, Micropterus salmoides), according to their size class. Thirty randomly selected gut samples were categorized into three size classes, based on the total length of the bass. Using the universal primer for the mtDNA cytochrome oxidase I (COI) region, polymerase chain reaction (PCR) amplification was performed on unidentified gut contents and then sequenced after cloning. Two gut samples were completely empty, and DNA materials from 27 of 28 gut samples were successfully amplified by PCR (success rate: 96.4%). Sequence database navigation yielded a total of 308 clones, containing DNA from 26 prey items. They comprised four phyla, including seven classes, 12 orders, and 12 families based on BLAST and BOLD database searches. The results indicate that largemouth bass show selective preferences in prey item consumption as they mature. These results corroborate a hypothesis, presence of ontogenetic diet shift, derived through other methodological approaches. Despite the practical limitations inherent in DNA barcoding analysis, high-resolution (i.e., species level) identification was possible, and the predation patterns of predators of different sizes were identifiable. The utilization of this method is strongly recommended for determining specific predator–prey relationships in complex freshwater ecosystems.

Inorganic phosphate induces mammalian growth plate chondrocyte apoptosis in a mitochondrial pathway involving nitric oxide and JNK MAP kinase

Chondrocytes in the hypertrophic zone of the growth plate undergo apoptosis during endochondral bone development via mechanisms that involve inorganic phosphate (Pi) and nitric oxide (NO). Recent evidence suggests that Pi-dependent NO production plays a role in apoptosis of cells in the resting zone as well. This study examined the mechanism by which Pi induces NO production and the signaling pathways by which NO mediates its effects on apoptosis in these cells. Pi decreased the number of viable cells based on MTT activity; the number of TUNEL-positive cells and the level of DNA fragmentation were increased, indicating an increase in apoptosis. Blocking NO production using the NO synthase (NOS) inhibitor L: -NAME or cells from eNOS(-/-) mice blocked Pi-induced chondrocyte apoptosis, indicating that NO production is necessary. NO donors NOC-18 and SNOG both induced chondrocyte apoptosis. SNOG also upregulated p53 expression, the Bax/Bcl-2 expression ratio, and cytochrome c release from mitochondria, as well as caspase-3 activity, indicating that NO induces apoptosis via a mitochondrial pathway. Inhibition of JNK, but not of p38 or ERK1/2, MAP kinase was able to block NO-induced apoptosis, indicating that JNK is necessary in this pathway. Pi elevates NO production via eNOS in resting zone chondrocytes, which leads to a mitochondrial apoptosis pathway dependent on JNK.

Molecular characterization of the human ABO blood group orthologus system in pigs

The selection and use of animals with blood group 0 in the process of transplanting pig organs or tissues into humans can positively contribute to the control of acute immune rejection due to differences in blood groups. Exon-specific PCRs for the porcine blood group A transferase gene against genomic DNA from either blood group A or 0 animals resulted in the amplification failure of the A0 blood group gene exon 8 from blood group 0 animals. To characterize the genetic abnormality in the genome of blood group 0 animals, we screened bacterial artificial chromosome (BAC) clones from a Korean native pig BAC library which had the blood group 0 allele, and carried out shotgun sequencing. The analysis showed that the 0 allele has a large deletion between exon 7 of the A0 blood group gene and the neighbouring SURF6. We also showed that the ABO blood group antigens in humans and the A0 blood group antigens in pigs are coded by mutations within the orthologous glycosyltransferase gene. In addition, we developed a multiplex genotyping method for the porcine A0 blood group gene.

Assessment of referral patterns for CT KUB in a tertiary setting

The purpose of this study was to assess the referral patterns and the use of unenhanced renal tract CT (CT KUB) for investigating patients presenting with clinically suspected renal colic. We retrospectively reviewed 500 consecutive CT KUB studies requested for suspected renal colic carried out at a single institution between December 2006 and July 2007. Follow-up radiology reports and discharge summaries on the hospital clinical Intranet were also reviewed. Studies were analysed for characteristics including patient demographics, referring clinical team, time of referral, final diagnosis and requirement for further imaging. The majority of requests were from Emergency (ED) or Urology Departments (49%, 245 out of 500, and 37%, 186 out of 500, respectively). The positive rate for urolithiasis was 67% (337 out of 500), the negative rate was 25% (123 out of 500), and 8% (40 out of 500) of patients had alternative significant findings. Female patients were more likely to have a negative study than male patients (35 versus 20%, P < 0.0001) and more likely to have alternative significant pathology (12 versus 6%, P < 0.0001). Patients referred by specialities other than Urology and ED were more likely to be female and have a negative or alternative finding (P < 0.0001). CT KUB is a widely used first method of investigation for patients with suspected renal colic with a high positive predictive value allowing rapid diagnosis and intervention. However, given the high rate of negative or alternative findings on CT KUB in young women, especially those referred by specialities other than ED or Urology, ultrasound should be considered as an alternative imaging method to minimise unnecessary radiation exposure.

The in vitro effects of dehydroepiandrosterone on human osteoarthritic chondrocytes

OBJECTIVE

To investigate the in vitro effects of dehydroepiandrosterone (DHEA) on human osteoarthritic chondrocytes.

DESIGN

Chondrocytes isolated from human osteoarthritic knee cartilage were three-dimensionally cultured in alginate beads, except for cell proliferation experiment. Cells were treated with DHEA in the presence or absence of IL-1beta. The effects on chondrocytes were analyzed using a 3-(4,5-dimethylthiazol-2yl)-5-(3-carboxymethoxy-phenyl)-2-(4-sulfophenyl)-2H-tetrazolium inner salt (MTS) assay (for chondrocyte proliferation), a dimethylmethylene blue (DMB) assay (for glycosaminoglycan (GAG) synthesis), and an indole assay (for DNA amount). Gene expressions of type I and II collagen, metalloproteinase-1 and -3 (MMP-1 and -3), and tissue inhibitor of metalloproteinase-1 (TIMP-1) as well as the IL-1beta-induced gene expressions of MMP-1 and -3 were analyzed by reverse transcription-polymerase chain reaction (RT-PCR). The protein synthesis of MMP-1 and -3 and TIMP-1 was determined by Western blotting.

RESULTS

The treatment of chondrocytes with DHEA did not affect chondrocyte proliferation or GAG synthesis up to 100 micro M of concentration. The gene expression of type II collagen increased in a dose-dependent manner, while that of type I decreased. DHEA suppressed the expression of MMP-1 significantly at concentrations exceeding 50 micro M. The gene expression of MMP-3 was also suppressed, but this was without statistical significance. The expression of TIMP-1 was significantly increased by DHEA at concentrations exceeding 10 micro M. The effects of DHEA on the gene expressions of MMP-1 and -3 were more prominent in the presence of IL-1beta, in which DHEA suppressed not only MMP-1, but also MMP-3 at the lower concentrations, 10 and 50 micro M, respectively. Western blotting results were in agreement with RT-PCR, which indicates that DHEA acts at the gene transcription level.

CONCLUSIONS

Our study demonstrates that DHEA has no toxic effect on chondrocytes up to 100 micro M of concentration and has an ability to modulate the imbalance between MMPs and TIMP-1 during OA at the transcription level, which suggest that it has a protective role against articular cartilage loss.

Endothelial NOS-dependent activation of c-Jun NH(2)- terminal kinase by oxidized low-density lipoprotein

Oxidized low-density lipoprotein (oxLDL) is known to activate a number of signal transduction pathways in endothelial cells. Among these are the c-Jun NH(2)-terminal kinase (JNK), also known as stress-activated protein kinase, and extracellular signal-regulated kinase (ERK). These mitogen-activated protein kinases (MAP kinase) determine cell survival in response to environmental stress. Interestingly, JNK signaling involves redox-sensitive mechanisms and is activated by reactive oxygen and nitrogen species derived from both NADPH oxidases, nitric oxide synthases (NOS), peroxides, and oxidized low-density lipoprotein (oxLDL). The role of endothelial NOS (eNOS) in the activation of JNK in response to oxLDL has not been examined. Herein, we show that on exposure of endothelial cells to oxLDL, both ERK and JNK are activated through independent signal transduction pathways. A key role of eNOS activation through a phosphatidylinositol-3-kinase-dependent mechanism leading to phosphorylation of eNOS is demonstrated for oxLDL-dependent activation of JNK. Moreover, we show that activation of ERK by oxLDL is critical in protection against the cytotoxicity of oxLDL.

Protein kinase B/Akt activates c-Jun NH(2)-terminal kinase by increasing NO production in response to shear stress

Laminar shear stress activates c-Jun NH(2)-terminal kinase (JNK) by the mechanisms involving both nitric oxide (NO) and phosphatidylinositide 3-kinase (PI3K). Because protein kinase B (Akt), a downstream effector of PI3K, has been shown to phosphorylate and activate endothelial NO synthase, we hypothesized that Akt regulates shear-dependent activation of JNK by stimulating NO production. Here, we examined the role of Akt in shear-dependent NO production and JNK activation by expressing a dominant negative Akt mutant (Akt(AA)) and a constitutively active mutant (Akt(Myr)) in bovine aortic endothelial cells (BAEC). As expected, pretreatment of BAEC with the PI3K inhibitor (wortmannin) prevented shear-dependent stimulation of Akt and NO production. Transient expression of Akt(AA) in BAEC by using a recombinant adenoviral construct inhibited the shear-dependent stimulation of NO production and JNK activation. However, transient expression of Akt(Myr) by using a recombinant adenoviral construct did not induce JNK activation. This is consistent with our previous finding that NO is required, but not sufficient on its own, to activate JNK in response to shear stress. These results and our previous findings strongly suggest that shear stress triggers activation of PI3K, Akt, and endothelial NO synthase, leading to production of NO, which (along with O(2-), which is also produced by shear) activates Ras-JNK pathway. The regulation of Akt, NO, and JNK by shear stress is likely to play a critical role in its antiatherogenic effects.

Development of virtual environment for treating acrophobia

Virtual Reality (VR) is a new technology that makes humans communicate with computer. It allows the user to see, hear, feel and interact in a three-dimensional virtual world created graphically. Virtual Reality Therapy (VRT), based on this sophisticated technology, has been recently used in the treatment of subjects diagnosed with acrophobia, a disorder that is characterized by marked anxiety upon exposure to heights, avoidance of heights, and a resulting interference in functioning. Conventional virtual reality system for the treatment of acrophobia has a limitation in scope that it is based on over-costly devices or somewhat unrealistic graphic scene. The goal of this study was to develop a inexpensive and more realistic virtual environment for the exposure therapy of acrophobia. We constructed two types virtual environment. One is constituted a bungee-jump tower in the middle of a city. It includes the open lift surrounded by props beside tower that allowed the patient to feel sense of heights. Another is composed of diving boards which have various heights. It provides a view of a lower diving board and people swimming in the pool to serve the patient stimuli upon exposure to heights.