Molecular classification and comparative phylogeographic study of insectivorous bat species (Pipisitrellus coromandra) from Punjab, Pakistan

Molecular based identification of bat fauna in Pakistan has been relatively less explored. The current study was therefore planned to report for the first time the molecular classification of insectivorous bats (Pipistrellus coromandra) based on mitochondrion gene (COI) from Punjab, Pakistan. Specimens were collected from five different locations followed by DNA extraction with subsequent gene amplification and sequencing. All samples in the study had shown close identity matches with species (Pipistrellus coromandra) from India and (Pipistrellus tenuis) from Vietnam with percentage identity score of 96.11 and 95.58 respectively except one sequence which only revealed 86.78% identity match on Basic Local Alignment Search Tool (BLAST) and could only be assigned to genus level Pipistrellus sp. The results indicated negligible intra-population genetic distance among collected samples whereas the comparison with species from other countries had shown high intraspecific (P. coromandra) and interspecific (P. tenuis) mean genetic distances. The current study hence successfully proved the efficiency of COI gene as a molecular marker for species identification and in analyzing the patterns of genetic variation with species from other countries.

AB0888-HPR EULAR SJOGREN’S SYNDROME PATIENT REPORTED INDEX-FATIGUE SCORE AND HADS-DEPRESSION SCORE MEDIATE IDENTITY SCORE OF ILLNESS PERCEPTION QUESTIONNAIRE IN PATIENTS WITH PRIMARY SJÖGREN’S SYNDROME

Background:Dryness, fatigue, and pain are common clinical manifestations assessed by EULAR Sjogren’s Syndrome Patient Reported Index (ESSPRI)-Dryness, -Fatigue, -Pain scores in patients with primary Sjögren’s syndrome (pSS). In addition, depression is also seen in these patients owing to the pattern of the chronic disease.Objectives:The aim of the study was to assess the complex interactions among Depression status, Illness Perception, and prominent clinical manifestations evaluated by the ESSPRI (Dryness, Fatigue, and Pain) in patients with pSS.Methods:In this cross-sectional study, 111 patients with pSS (M/F: 5/106; mean age: 52.9 ± 12.01 years) were included. The data were collected by clinical examination and a questionnaire regarding patient reported outcome measures (PROMs). Unstimulated (U-WSFR) and stimulated (S-WSFR) whole saliva flow rates of patients were calculated as ml/min. Hospital Anxiety and Depression Scale (HADS), Illness Perception Questionnaire-R (IPQ-R) and EULAR Sjogren’s Syndrome Patient Reported Index were filled by patients. Increases in HADS score and subgroup scores of ESSPRI (Dryness, Fatigue and Pain) and IPQ-R dimensions regarding Identity, Consequences, and Emotional reflected poor conditions for patients. In addition, patients scored their disease activity (0: inactive-100: the worst activity) by using 100-mm visual analogue scale (VAS). After preliminary analysis, a mediation analysis was used to evaluate the relations among these variables.Results:In the study, ESSPRI-Dryness score (6,27±2,79) was associated with U-WSFR (0,40±0,57) and S-WSFR (1,04±0,86),(r:-0,4 p=0.000; r:-0,3 p=0.004). Moreover, patients reported disease activity score (48,78±26,67) was related to U-WSFR (r: -0,3 p=0.026) as well as Consequence (19,12±5,47) and Emotional (19,54±7,02) scores of IPQ-R questionnaire (r: 0,3 p=0.035; r: 0,3 p=0.014).In IPQ-R questionnaire, Identity score (8,04±3,1) reflecting number of symptoms that patients experienced due to their illness was correlated with scores of ESSPRI-Fatigue (5,29±2,97), ESSPRI-Pain (5,18±3,01), HADS-Anxiety (11,67±5,55), HADS-Depression (9,2±4,98) in the study (p<0.05).In the mediation analysis, Identity score was directly mediated by ESSPRI-Fatigue score (p=0.0093) and indirectly mediated by HADS-Depression score (p=0.0011).A bootstrap analysis with 5000 replications was applied to estimate mediation effect to generate 95% CI. Percentile bootstrap of HADS-Depression was found to be an effective mediator for Identity score based on 5000 bootstrap sample.Conclusion:Both depression status and fatigue affected Identity score reflecting the number of symptoms poorly. Considering this complex relationship in disease activity assessment may positively affect disease outcomes.Disclosure of Interests:None declared

The agent associated with blue dwarf disease in wheat represents a new phytoplasma taxon, ‘Candidatus Phytoplasma tritici’

Wheat blue dwarf (WBD) is one of the most economically damaging cereal crop diseases in northwestern PR China. The agent associated with the WBD disease is a phytoplasma affiliated with the aster yellows (AY) group, subgroup C (16SrI-C). Since phytoplasma strains within the AY group are ecologically and genetically diverse, it has been conceived that the AY phytoplasma group may consist of more than one species. This communication presents evidence to demonstrate that, while each of the two 16 rRNA genes of the WBD phytoplasma shares >97.5 % sequence similarity with that of the ‘Candidatus Phytoplasma asteris’ reference strain, the WBD phytoplasma clearly represents an ecologically separated lineage: the WBD phytoplasma not only has its unique transmitting vector (Psammotettix striatus) but also elicits a distinctive symptom in its predominant plant host (wheat). In addition, the WBD phytoplasma possesses molecular characteristics that further manifest its significant divergence from ‘Ca. P. asteris’. Such molecular characteristics include lineage-specific antigenic membrane proteins and a lower than 95 % genome-wide average nucleotide identity score with ‘Ca. P. asteris’. These ecological, molecular and genomic evidences justify the recognition of the WBD phytoplasma as a novel taxon, ‘Candidatus Phytoplasma tritici’.

Duganella callida sp. nov., a novel addition to the Duganella genus, isolated from the soil of a cultivated maize field

A Gram-negative, rod-shaped bacterium, strain Duganella callida DN04T, was isolated from the soil of a maize field in North Carolina, USA. Based on the 16S rRNA gene sequence, the most similar Duganella species are D. sacchari Sac-22T, D. ginsengisoli DCY83T, and D. radicis Sac-41T with a 97.8, 97.6, or 96.9 % sequence similarity, respectively. We compared the biochemical phenotype of DN04T to D. sacchari Sac-22T and D. zoogloeoides 115T and other reference strains from different genera within the Oxalobacteraceae and while the biochemical profile of DN04T is most similar to D. sacchari Sac-22T and other Duganella and Massilia strains, there are also distinct differences. DN04T can for example utilize turanose, N-acetyl-d-glucosamine, inosine, and l-pyroglutamic acid. The four fatty acids found in the highest percentages were C15 : 0 iso (24.6 %), C15 : 1 isoG (19.4 %), C17 : 0 iso3-OH (16.8 %), and summed feature 3 (C16:1 ⍵7c and/or C16:1 ⍵6c) (12.5 %). We also applied whole genome sequencing to determine if DN04T is a novel species. The most similar AAI (average amino acid identity) score was 70.8 % ( Massilia plicata NZ CP038026T), and the most similar ANI (average nucleotide identity) score was 84.8 % ( D. radicis KCTC 22382T), which indicates that DN04T is a novel species. The genome-to-genome-distance calculation (GGDC) revealed a DDH of 28.3 % to D. radicis KCTC 22382T, which is much lower than the new species threshold. Based on the morphological, phenotypic, and genomic differences, we propose Duganella callida sp. nov. as a novel species within the Duganella genus (type strain DN04T=NRRL B-65552T=LMG 31736T).

Gracilibacillus oryzae sp. nov., isolated from rice seeds

A Gram-stain-positive, facultatively anaerobic, endospore-forming bacterium, designated strain TD8T, was isolated from surface-sterilized rice seeds (Oryza sativa L.). Phylogenetic analysis of the 16S rRNA gene indicated that strain TD8T should be placed within the genus Gracilibacillus (95.2–99.0 % sequence similarity); it exhibited highest similarities to Gracilibacillus ureilyticus CGMCC 1.7727T (99.0 %), ‘ Gracilibacillus xinjiangensis ’ CGMCC 1.12449T (98.9 %) and Gracilibacillus dipsosauri CGMCC 1.3642T (97.5 %). Chemotaxonomic analysis showed that menaquinone-7 (MK-7) was the major isoprenoid quinone. Diphosphatidylglycerol, phosphatidylglycerol and one unidentified phospholipid were the major cellular polar lipids, and the major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, C16 : 0 and iso-C16 : 0, which supported the allocation of the strain to the genus Gracilibacillus . The digital DNA–DNA hybridization value between strain TD8T and Gracilibacillus ureilyticus CGMCC 1.7727T was lower than 70 % (22.60 %), and the average nucleotide identity score was 79.54±5.09 %, suggesting that strain TD8T represented a novel species in the genus Gracilibacillus . The genomic DNA G+C content was 37.5 %. Based on physiological and biochemical characteristics and genotypic data, strain TD8T represents a novel species of the genus Gracilibacillus , for which the name Gracilibacillus oryzae sp. nov. is proposed. The type strain is TD8T (=ACCC 61556T=CICC 24889T=JCM 33537T).

Increased Chondrocytic Gene Expression Is Associated With Improved Repair Tissue Quality and Graft Survival in Patients After Autologous Chondrocyte Implantation

Background: Assays to quantitate the quality of autologous chondrocyte implants have recently become available. However, the correlation of the assay score with radiological and clinical outcomes has not been established. Purpose/Hypothesis: The purpose was to assess the influence of cell identity (chondrocyte/synoviocyte gene expression ratio) and viability on patient-reported outcome measures, graft survival, and repair tissue quality. It was hypothesized that greater cell product quality as assessed through an identity assay and cell viability is associated with superior outcomes after autologous chondrocyte implantation (ACI) for symptomatic cartilage defects. Study Design: Cohort study; Level of evidence, 3. Methods: Seventy-nine patients with a minimum follow-up of 2 years were included in this study. Of these, 67 patients were available for imaging assessment utilizing the Magnetic Resonance Observation of Cartilage Repair Tissue (MOCART) scoring system. Patients were assigned to groups either below or above the cohort’s mean based on their individual cell identity score and viability percentage. Results: Patients were predominantly female (57.7%) with a mean age of 30.0 ± 9.3 years. No differences were seen between Knee injury and Osteoarthritis Outcome Score, Lysholm, Tegner, or International Knee Documentation Committee Subjective Knee Evaluation Form within the viability and cell identity groups at a final follow-up of 3.8 ± 1.4 years after ACI ( P > .05). In a subset of patients, the mean MOCART score was 68.3 ± 15.6 at an average magnetic resonance imaging follow-up of 17.7 ± 9.56 months. Low cell identity was significantly associated with the degree of defect filling ( P = .025), integration of border zone ( P = .01), effusion ( P = .024), and ACI graft failure ( P = .002). Patients with above-average cell identity scores had a significantly higher survival rate at 5-year follow-up compared with patients with below-average scores (95.8% vs 64.7%; P = .013). Cell viability did not influence MOCART subscales or graft failure (all P > .05). Cell viability and identity showed no significant correlation with each other ( r = −0.045; P = .694). Conclusion: Cell identity was significantly correlated with structural repair quality and graft survival after second-generation ACI for symptomatic chondral lesions in the knee. While improved imaging outcome and higher graft survivorship were associated with a higher individual cell identity score indicating a higher chondrocyte/synoviocyte gene expression ratio in the final cell product, clinical outcome did not correlate with the identity score.

FASTCAR: Rapid alignment-free prediction of sequence alignment identity scores using self-supervised general linear models

MotivationPairwise alignment is a predominant algorithm in the field of bioinformatics. This algorithm is quadratic — slow especially on long sequences. Many applications utilize identity scores without the corresponding alignments. For these applications, we propose FASTCAR. It produces identity scores for pairs of DNA sequences using alignment-free methods and two self-supervised general linear models.ResultsFor the first time, the new tool can predict the pair-wise identity score in linear time and space. On two large-scale sequence databases, FASTCAR provided the best compromise between sensitivity and precision while being faster than BLAST by 40% and faster than USEARCH by 6–10 times. Further, FASTCAR is capable of producing the pair-wise identity scores of long DNA sequences — millions-of-nucleotides-long bacterial genomes; this task cannot be accomplished by any alignment-based tool.AvailabilityFASTCAR is available at https://github.com/TulsaBioinformaticsToolsmith/FASTCAR and as the Supplementary Dataset [email protected] informationSupplementary data are available online.

Acculturation attitudes and urban-related identity of internal migrants in three largest cities of Turkey

This present study explored the acculturation strategies and urban related identity of Turk and Kurd internal migrants moved from different regions of Turkey to Istanbul, Ankara and Izmir. In terms of acculturation strategies, assimilation was found to be the most preferred acculturation attitude among Turks whereas separation was found to be most endorsed acculturation attitude among Kurds. Concerning urban-related identity mean scores, Turks reported higher urban-related identity scores than Kurds. Furthermore the internal migrants in Izmir reported higher urban-related identity score than the migrants living in Istanbul and Ankara. The results of the hierarchical multiple regression analysis revealed that gender, length of residence and migration type were the significant predictors of integration preference of Kurds.

IDENTIFICATION OF NOVEL BACTERIAL SPECIES CAPABLE OF DEGRADING DALAPON USING 16S RRNA SEQUENCING

2,2-dichloropropionic acid (2,2DCP) is used as herbicide in agricultural industry and it is one of the halogenated organic compounds distributed widely in the world causing contamination. In this study, a bacterial strain isolated from contaminated soil where halogenated pesticides applied in Universiti Teknologi Malaysia and it was named “JHA1”. Bacterium JHA1 was able to utilize 2,2 dichloropropionate 2,2-DCP or (Dalapon) as a source of carbon and energy. Based on 16S rRNA analysis, the isolate showed 87% identity to Terrabacter terrae strain PPLB. The identity score was lower than 98% so that it was suggested to be new organisms that worth for further investigations if it will be proven that this is novel. Therefore, current isolate was designated as Terrabacter terrae JHA1. The isolate grew in the minimal media containing 10 mM, 15 mM, 20 mM and 25 mM of 2,2- DCP as the sole energy and carbon source and the best growth rate was in 20 mM as the optimum concentration of 2,2-DCP while bacterial growth was inhibited in medium with 30 mM 2,2-DCP.

M ethanocaldococcus bathoardescens sp. nov., a hyperthermophilic methanogen isolated from a volcanically active deep-sea hydrothermal vent

A hyperthermophilic methanogen, strain JH146T, was isolated from 26 °C hydrothermal vent fluid emanating from a crack in basaltic rock at Marker 113 vent, Axial Seamount in the northeastern Pacific Ocean. It was identified as an obligate anaerobe that uses only H2 and CO2 for growth. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain is more than 97 % similar to other species of the genus Methanocaldococcus . Therefore, overall genome relatedness index analyses were performed to establish that strain JH146T represents a novel species. For each analysis, strain JH146T was most similar to Methanocaldococcus sp. FS406-22, which can fix N2 and also comes from Marker 113 vent. However, strain JH146T differs from strain FS406-22 in that it cannot fix N2. The average nucleotide identity score for strain JH146T was 87 %, the genome-to-genome direct comparison score was 33–55 % and the species identification score was 93 %. For each analysis, strain JH146T was below the species delineation cut-off. Full-genome gene synteny analysis showed that strain JH146T and strain FS406-22 have 97 % genome synteny, but strain JH146T was missing the operons necessary for N2 fixation and assimilatory nitrate reduction that are present in strain FS406-22. Based on its whole genome sequence, strain JH146T is suggested to represent a novel species of the genus Methanocaldococcus for which the name Methanocaldococcus bathoardescens is proposed. The type strain is JH146T ( = DSM 27223T = KACC 18232T).