scholarly journals Plastome phylogenomics and characterization of rare genomic changes as taxonomic markers in plastome groups 1 and 2 Poeae (Pooideae; Poaceae)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6959 ◽  
Author(s):  
Lauren M. Orton ◽  
Sean V. Burke ◽  
Melvin R. Duvall
Keyword(s):  
Strong Support ◽  
Data Matrix ◽  
Phylogenomic Analysis ◽  
Genomic Change ◽  
Genomic Changes ◽  
Plastid Genomes ◽  
Rare Genomic Changes ◽  
Group 2 ◽  
Taxonomic Markers ◽  
Group 1

A phylogenomic analysis of 42 complete plastid genomes (plastomes), including 16 that were newly sequenced, was conducted. Plastomes were sampled from 19 subtribes of Pooideae, to investigate relationships within and between Chloroplast Group 1 (Aveneae) and Group 2 (Poeae) species. Two data partitions: complete plastomes, and a combined plastome and rare genomic change (RGC) data matrix, were analyzed. Overall, 156 non-ambiguous RGC were identified, of which homology was inferred for 38 RGC. Among the 38 RGC identified, six were synapomorphic among the Group 1 subtribes: Aveninae, Agrostidinae, and Anthoxanthinae, (Phalaridinae + Torreyochloinae), and 27 were synapomorphic among the Group 2 subtribes: Loliinae, (Ammochloinae + Parapholiinae + Dactylidinae), Parapholiinae, Dactylidinae, Poinae, and Coleanthinae. Four RGC were determined to be homoplasious in Groups 1 and 2. Two other RGC originated through intrastrand deletion events. The remaining RGC events likely originated through recombination given their size and lack of sequence evidence for other types of mutations. This study also determined that relationships between taxa, even those only weakly supported in previous studies, could be inferred with strong support when utilizing complete plastomes.

scholarly journals Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates

2016 ◽  
Vol 2 (8) ◽  
pp. e1600633 ◽  
Author(s):  
Victor C. Mason ◽  
Gang Li ◽  
Patrick Minx ◽  
Jürgen Schmitz ◽  
Gennady Churakov ◽  
...  
Keyword(s):  
Sequence Data ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Sister Group ◽  
Phylogenomic Analysis ◽  
Isolated Populations ◽  
Conservation Units ◽  
Genetic Changes ◽  
Genomic Changes ◽  
Rare Genomic Changes

Colugos are among the most poorly studied mammals despite their centrality to resolving supraordinal primate relationships. Two described species of these gliding mammals are the sole living members of the order Dermoptera, distributed throughout Southeast Asia. We generated a draft genome sequence for a Sunda colugo and a Philippine colugo reference alignment, and used these to identify colugo-specific genetic changes that were enriched in sensory and musculoskeletal-related genes that likely underlie their nocturnal and gliding adaptations. Phylogenomic analysis and catalogs of rare genomic changes overwhelmingly support the contested hypothesis that colugos are the sister group to primates (Primatomorpha), to the exclusion of treeshrews. We captured ~140 kb of orthologous sequence data from colugo museum specimens sampled across their range and identified large genetic differences between many geographically isolated populations that may result in a >300% increase in the number of recognized colugo species. Our results identify conservation units to mitigate future losses of this enigmatic mammalian order.

scholarly journals Bacillus paralicheniformis sp. nov., isolated from fermented soybean paste

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3487-3492 ◽  
Author(s):  
Christopher A. Dunlap ◽  
Soon-Wo Kwon ◽  
Alejandro P. Rooney ◽  
Soo-Jin Kim
Keyword(s):  
Phylogenetic Analysis ◽  
Genome Sequence ◽  
Draft Genome ◽  
Diaminopimelic Acid ◽  
Phenotypic Characterization ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Bacillus Paralicheniformis ◽  
Group 2 ◽  
Group 1

An isolate of a Gram-stain-positive, facultatively anaerobic, motile, rod-shaped, endospore-forming bacterium was recovered from soybean-based fermented paste. Phylogenetic analysis of the 16S rRNA gene indicated that the strain was most closely related to Bacillus sonorensis KCTC-13918T (99.5 % similarity) and Bacillus licheniformis DSM 13T (99.4 %). In phenotypic characterization, the novel strain was found to grow at 15–60 °C and to tolerate up to 10 % (w/v) NaCl. Furthermore, the strain grew in media with pH 6–11 (optimal growth at pH 7.0–8.0). The predominant cellular fatty acids were anteiso-C15 : 0 (37.7 %) and iso-C15 : 0 (31.5 %). The predominant isoprenoid quinone was menaquinone 7 (MK-7). The cell-wall peptidoglycan contained meso-diaminopimelic acid. A draft genome sequence of the strain was completed and used for phylogenetic analysis. Phylogenomic analysis of all published genomes of species in the B. licheniformis group revealed that strains belonging to B. licheniformis clustered into two distinct groups, with group 1 consisting of B. licheniformis DSM 13T and 11 other strains and group 2 consisting of KJ-16T and four other strains. The DNA G+C content of strain KJ-16T was 45.9 % (determined from the genome sequence). Strain KJ-16T and another strain from group 2 were subsequently characterized using a polyphasic taxonomic approach and compared with strains from group 1 and another closely related species of the genus Bacillus. Based upon the consensus of phylogenetic and phenotypic analyses, we conclude that this strain represents a novel species within the genus Bacillus, for which the name Bacillus paralicheniformis sp. nov. is proposed, with type strain KJ-16T ( = KACC 18426T = NRRL B-65293T).

scholarly journals Selection footprints reflect genomic changes associated with breeding efforts in 56 cucumber inbred lines

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Bin Liu ◽  
Dailu Guan ◽  
Xuling Zhai ◽  
Sen Yang ◽  
Shudan Xue ◽  
...  
Keyword(s):  
Selective Breeding ◽  
Agronomic Traits ◽  
Inbred Lines ◽  
Genomic Changes ◽  
Sequence Variations ◽  
Breeding History ◽  
Group 2 ◽  
Or Genes ◽  
Advance Knowledge ◽  
Group 1

AbstractCucumber selective breeding over recent decades has dramatically increased productivity and quality, but the genomic characterizations and changes associated with this breeding history remain unclear. Here, we analyzed the genome resequencing data of 56 artificially selected cucumber inbred lines that exhibit various phenotypes to detect trait-associated sequence variations that reflect breeding improvement. We found that the 56 cucumber lines could be assigned to group 1 and group 2, and the two groups formed a distinctive genetic structure due to the breeding history involving hybridization and selection. Differentially selected regions were identified between group 1 and group 2, with implications for genomic-selection breeding signatures. These regions included known quantitative trait loci or genes that were reported to be associated with agronomic traits. Our results advance knowledge of cucumber genomics, and the 56 selected inbred lines could be good germplasm resources for breeding.

In-vivo evaluation of the effect of cyanoacrylate on prosthetic vascular graft infection – does cyanoacrylate increase the severity of infection?

VASA ◽  
2020 ◽  
Vol 49 (4) ◽  
pp. 281-284
Author(s):  
Atıf Yolgosteren ◽  
Gencehan Kumtepe ◽  
Melda Payaslioglu ◽  
Cuneyt Ozakin
Keyword(s):  
Vascular Graft ◽  
Graft Infection ◽  
Vascular Graft Infection ◽  
Group 4 ◽  
Significant Difference ◽  
Group 3 ◽  
Group 2 ◽  
Prosthetic Vascular Graft Infection ◽  
Group 1

Summary. Background: Prosthetic vascular graft infection (PVGI) is a complication with high mortality. Cyanoacrylate (CA) is an adhesive which has been used in a number of surgical procedures. In this in-vivo study, we aimed to evaluate the relationship between PVGI and CA. Materials and methods: Thirty-two rats were equally divided into four groups. Pouch was formed on back of rats until deep fascia. In group 1, vascular graft with polyethyleneterephthalate (PET) was placed into pouch. In group 2, MRSA strain with a density of 1 ml 0.5 MacFarland was injected into pouch. In group 3, 1 cm 2 vascular graft with PET piece was placed into pouch and MRSA strain with a density of 1 ml 0.5 MacFarland was injected. In group 4, 1 cm 2 vascular graft with PET piece impregnated with N-butyl cyanoacrylate-based adhesive was placed and MRSA strain with a density of 1 ml 0.5 MacFarland was injected. All rats were scarified in 96th hour, culture samples were taken where intervention was performed and were evaluated microbiologically. Bacteria reproducing in each group were numerically evaluated based on colony-forming unit (CFU/ml) and compared by taking their average. Results: MRSA reproduction of 0 CFU/ml in group 1, of 1410 CFU/ml in group 2, of 180 200 CFU/ml in group 3 and of 625 300 CFU/ml in group 4 was present. A statistically significant difference was present between group 1 and group 4 (p < 0.01), between group 2 and group 4 (p < 0.01), between group 3 and group 4 (p < 0.05). In terms of reproduction, no statistically significant difference was found in group 1, group 2, group 3 in themselves. Conclusions: We observed that the rate of infection increased in the cyanoacyrylate group where cyanoacrylate was used. We think that surgeon should be more careful in using CA in vascular surgery.

The influence of continuous local wound infusion on postoperative pain in patients undergoing transfemoral amputation

VASA ◽  
2015 ◽  
Vol 44 (5) ◽  
pp. 381-386 ◽  
Author(s):  
Christian Uhl ◽  
Thomas Betz ◽  
Andrea Rupp ◽  
Markus Steinbauer ◽  
Ingolf Töpel
Keyword(s):  
Pain Management ◽  
Pilot Study ◽  
Local Anaesthetic ◽  
Phantom Pain ◽  
Transfemoral Amputation ◽  
Postoperative Wound ◽  
Stump Pain ◽  
Management Protocol ◽  
Group 2 ◽  
Group 1

Abstract. Summary: Background: This pilot study was set up to examine the effects of a continuous postoperative wound infusion system with a local anaesthetic on perioperative pain and the consumption of analgesics. Patients and methods: We included 42 patients in this prospective observational pilot study. Patients were divided into two groups. One group was treated in accordance with the WHO standard pain management protocol and in addition to that received a continuous local wound infusion treatment (Group 1). Group 2 was treated with analgesics in accordance with the WHO standard pain management protocol, exclusively. Results: The study demonstrated a significantly reduced postoperative VAS score for stump pain in Group 1 for the first 5 days. Furthermore, the intake of opiates was significantly reduced in Group 1 (day 1, Group 1: 42.1 vs. Group 2: 73.5, p = 0.010; day 2, Group 1: 27.7 vs. Group 2: 52.5, p = 0.012; day 3, Group 1: 23.9 vs. Group 2: 53.5, p = 0.002; day 4, Group 1: 15.7 vs. Group 2: 48.3, p = 0.003; day 5, Group 1 13.3 vs. Group 2: 49.9, p = 0.001). There were no significant differences between the two groups, neither in phantom pain intensity at discharge nor postoperative complications and death. Conclusions: Continuous postoperative wound infusion with a local anaesthetic in combination with a standard pain management protocol can reduce both stump pain and opiate intake in patients who have undergone transfemoral amputation. Phantom pain was not significantly affected.

Abnormal Haemostasis and Blood Viscosity in Malignant Hypertension

1984 ◽  
Vol 52 (03) ◽  
pp. 253-255 ◽  
Author(s):  
C Isles ◽  
G D O Lowe ◽  
B M Rankin ◽  
C D Forbes ◽  
N Lucie ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Blood Viscosity ◽  
Renal Damage ◽  
Antithrombin Iii ◽  
Plasma Viscosity ◽  
Malignant Hypertension ◽  
Fibrin Deposition ◽  
Group 3 ◽  
Group 2 ◽  
Group 1

SummaryWe have previously shown abnormalities of haemostasis suggestive of intravascular coagulation in patients with malignant hypertension, a condition associated with retinopathy and renal fibrin deposition. To determine whether such abnormalities are specific to malignant hypertension, we have measured several haemostatic and haemorheological variables in 18 patients with malignant hypertension (Group 1), 18 matched healthy controls (Group 2), and 18 patients with non-malignant hypertension (Group 3) matched for renal pathology, blood pressure and serum creatinine with Group 1. Both Groups 1 and 3 had increased mean levels of fibrinogen, factor VIIIc, beta-thrombo- globulin, plasma viscosity and blood viscosity (corrected for haematocrit); and decreased mean levels of haematocrit, antithrombin III and platelet count. Mean levels of fast antiplasmin and alpha2-macroglobulin were elevated in Group 1 but not in Group 3. We conclude that most blood abnormalities are not specific to malignant hypertension; are also present in patients with non-malignant hypertension who have similar levels of blood pressure and renal damage; and might result from renal damage as well as promoting further renal damage by enhancing fibrin deposition. However increased levels of fibrinolytic inhibitors in malignant hypertension merit further investigation in relation to removal of renal fibrin.

Total Knee Arthroplasty after Previous Ipsilateral Hip Arthroplasty Showed Lower Clinical Outcomes and Higher Leg Length Discrepancy Perception

2020 ◽  
Author(s):  
Han-Jun Lee ◽  
Seong Hwan Kim ◽  
Nicolas Pujol ◽  
Yong-Beom Park
Keyword(s):  
Clinical Outcomes ◽  
Hip Arthroplasty ◽  
Leg Length ◽  
Function Score ◽  
Patient’S Satisfaction ◽  
Length Discrepancy ◽  
Total Knee ◽  
Group 2 ◽  
Ks Function ◽  
Group 1

AbstractThe purpose of this study is to compare perception of leg length discrepancy (LLD) and clinical results of total knee arthroplasties (TKA) in patients with or without previous ipsilateral hip arthroplasty. Between 2008 and 2015, navigation-assisted TKA was performed in 43 patients with previous hip arthroplasty after hip fracture. After 1:3 propensity score matching was performed, 108 patients of primary navigation-assisted TKA (group 1) and 36 patients with hip arthroplasty (group 2) were included. Knee Society (KS) scores, Western Ontario and McMaster Universities Index (WOMAC) scores, and patients' satisfaction including perception of LLD were evaluated. Radiographic evaluation included mechanical axis, component position, and LLD. Logistic regression analysis was performed to find the factors that affect the clinical outcomes. No significant differences in radiologic and clinical evaluations, except for KS function score, patient's satisfaction and LLD (p< 0.001), were detected between the groups. LLD and its perception were significantly higher in group 2 (1.8 ± 3.4 mm in group 1 and 9.7 ± 4.1 mm in group 2, p = 0.000). Risk factors for the low KS function score were found as LLD (odds ratio [OR]: 1.403, p = 0.008) and previous hip arthroplasty itself (OR: 15.755, p = 0.002), but much higher OR was found in previous hip arthroplasty. Although the outcomes of TKA in patients with ipsilateral hip arthroplasty are comparable to those of primary TKA, LLD was high and patient's satisfaction and functional outcomes were low in patients with previous ipsilateral hip arthroplasty. Care should be taken when considering TKA in patients with previous hip arthroplasty. This is a Level III, case control study.

Clinical and Radiological Changes after use of Alpha-1 Blocker Therapy in Patients of Posterior Urethral Valve with Bladder Neck Hypertrophy

JMS SKIMS ◽  
2009 ◽  
Vol 12 (1) ◽  
pp. 3-7
Author(s):  
Aejaz A Baba ◽  
Bajpai Minu
Keyword(s):  
Bladder Neck ◽  
Posterior Urethral Valve ◽  
Posterior Urethral Valves ◽  
Blocker Therapy ◽  
Urethral Valve ◽  
Novel Method ◽  
Radiological Changes ◽  
Group 2 ◽  
Mean Time ◽  
Group 1

Background: We evaluated the effects of alpha-1 blocker therapy on clinical and radiological abnormalities in patients of posterior urethral valve with bladder neck hypertrophy. Materials and Methods: A total of 74 patients with posterior urethral valves were seen at our department between 2003 and 2007. Out of these 24 had radiological evidence of bladder neck hypertrophy. Those patients with bladder neck hypertrophy who were seen before June 2006 and did not receive alpha-1 blocker (prazocin) therapy after valve ablation were assigned to group 1 (n=10). Group 2 consisted of 14 age matched patients with bladder neck hypertrophy and comparable prognostic factors who received alpha-1 blocker therapy after valve ablation (n=14). Micturating cystourethrography (MCU) was done periodically and a novel method used to calculate bladder neck hypertrophy. Trends in symptoms and radiological changes were evaluated throughout follow-up. Results: Mean patient age at presentation was 3.02±2.68 years in group 1 and 3.12±3.4 years in group 2. Bladder neck hypertrophy decreased from 2.3±1.0 to 2.0±0.5 in a mean time of 52.0 (34-52) weeks in group 1 where as it decreased from 2.2±0.5 to 1.6±0.3 in a mean time of 32.0 (22-52) weeks. Symptomatically patients in group 2 who received alpha-1 blocker therapy after valve ablation were better and had quick resolution of bladder neck hypertrophy. Conclusions: Use of alpha-1 blocker therapy in patients of posterior urethral valve with bladder neck hypertrophy helps in quick resolution of bladder neck hypertrophy. J Med Sci 2009;12(1):3-7.

Preoperative Platelet to Lymphocyte Ratio Is Associated with Early Morbidity and Mortality after Coronary Artery Bypass Grafting

2015 ◽  
Vol 18 (6) ◽  
pp. 255 ◽  
Author(s):  
Hüseyin Şaşkın ◽  
Çagrı Düzyol ◽  
Kazım Serhan Özcan ◽  
Rezan Aksoy ◽  
Mustafa Idiz
Keyword(s):  
Coronary Artery ◽  
Coronary Artery Bypass Grafting ◽  
Coronary Artery Bypass ◽  
Artery Bypass ◽  
Bypass Grafting ◽  
Platelet To Lymphocyte Ratio ◽  
Artery Bypass Grafting ◽  
Lymphocyte Ratio ◽  
Group 2 ◽  
Group 1

<strong>Objective:</strong> To investigate the association of platelet to lymphocyte ratio to mortality and morbidity after coronary artery bypass grafting operation.<br /><strong>Methods:</strong> We evaluated records of 916 patients who underwent coronary artery bypass grafting operation between January 2009 and May 2014 retrospectively. Patients were grouped as Group 1 (n = 604) if the platelet to lymphocyte ratio was above 142 and Group 2 (n = 312) if platelet to lymphocyte ratio was below 142.<br /><strong>Results:</strong> The number of patients who developed a neurologic event during the hospital stay and in the first postoperative month was 7 (1.2%) in Group 1 and 12 (3.8%) in Group 2 for which the difference was statistically significant (P = .007). Early term mortality occurred in 3 patients (0.5%) in Group 1 and in 10 patients (3.2%) in Group 2 for which the difference was statistically highly significant (P = .001). In univariate and multivariate regression analysis, the preoperative platelet to lymphocyte ratio was determined as an independent risk factor for occurrence of atrial fibrillation in the early postoperative period, reoperation for sternum dehiscence, occurrence of a neurologic event, prolonged stay in the hospital and mortality.<br /><strong>Conclusion:</strong> In this study, elevated levels of platelet to lymphocyte ratio were associated with mortality and morbidity after coronary artery bypass grafting operation.

Immediate and long-term results of the first line chemotherapy in patients with metastatic triple negative breast cancer. Final analysis of randomized study

2020 ◽  
pp. 75-80
Author(s):  
S.A. Lyalkin ◽  
◽  
L.A. Syvak ◽  
N.O. Verevkina ◽  
◽  
...  
Keyword(s):  
Breast Cancer ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Randomized Study ◽  
Progression Free Survival ◽  
First Line ◽  
Free Survival ◽  
Group 2 ◽  
Line Chemotherapy ◽  
Group 1

The objective: was to evaluate the efficacy of the first line chemotherapy in patients with metastatic triple negative breast cancer (TNBC). Materials and methods. Open randomized study was performed including 122 patients with metastatic TNBC. The efficacy and safety of the first line chemotherapy of regimens АТ (n=59) – group 1, patients received doxorubicine 60 мг/м2 and paclitaxel 175 мг/м2 and ТР (n=63) – group 2, patients received paclitaxel 175 мг/м2 and carboplatin AUC 5 were evaluated. Results. The median duration of response was 9.5 months (4.5–13.25 months) in patients received AT regimen and 8.5 months (4.7–12.25 months), in TP regimen; no statistically significant differences were observed, р=0.836. The median progression free survival was 7 months (95% CI 5–26 months) in group 1 and 7.5 months (95% CI 6–35 months) in group 2, p=0.85. Both chemotherapy regimens (AT and TP) had mild or moderate toxicity profiles (grade 1 or 2 in most patients). No significant difference in gastrointestinal toxicity was observed. The incidence of grade 3–4 neutropenia was higher in patients of group 2 (TP regimen): 42.8% versus 27% (р<0.05). Conclusions. Both regimens of chemotherapy (AT and TP) are appropriate to use in the first line setting in patients with metastatic TNBC. Key words: metastatic triple negative breast cancer, chemotherapy, progression free survival, chemotherapy toxicity.

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