scholarly journals Nanopore sequencing and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

2019 ◽  
Author(s):  
Alex N. Salazar ◽  
Arthur R. Gorter de Vries ◽  
Marcel van den Broek ◽  
Nick Brouwers ◽  
Pilar de la Torre Cortès ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Sequence Similarity ◽  
Brewing Yeast ◽  
Linear Evolution ◽  
Pure Cultures ◽  
History Of ◽  
Evolutionary Trajectories ◽  
Group 2 ◽  
Genome Assemblies ◽  
Group 1

AbstractBackgroundThe lager brewing yeast,S. pastorianus, is a hybrid betweenS. cerevisiaeandS. eubayanuswith extensive chromosome aneuploidy.S. pastorianusis subdivided into Group 1 and Group 2 strains, where Group 2 strains have higher copy number and a larger degree of heterozygosity forS. cerevisiaechromosomes. As a result, Group 2 strains were hypothesized to have emerged from a hybridization event distinct from Group 1 strains. Current genome assemblies ofS. pastorianusstrains are incomplete and highly fragmented, limiting our ability to investigate their evolutionary history.ResultsTo fill this gap, we generated a chromosome-level genome assembly of theS. pastorianusstrain CBS 1483 using MinION sequencing and analysed the newly assembled subtelomeric regions and chromosome heterozygosity. To analyse the evolutionary history ofS. pastorianusstrains, we developed Alpaca: a method to compute sequence similarity between genomes without assuming linear evolution. Alpaca revealed high similarities between theS. cerevisiaesubgenomes of Group 1 and 2 strains, and marked differences from sequencedS. cerevisiae strains.ConclusionsOur findings suggest that Group 1 and Group 2 strains originated from a single hybridization involving a heterozygousS. cerevisiaestrain, followed by different evolutionary trajectories. The clear differences between both groups may originate from a severe population bottleneck caused by the isolation of the first pure cultures. Alpaca provides a computationally inexpensive method to analyse evolutionary relationships while considering non-linear evolution such as horizontal gene transfer and sexual reproduction, providing a complementary viewpoint beyond traditional phylogenetic approaches.

scholarly journals Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Alex N. Salazar ◽  
Arthur R. Gorter de Vries ◽  
Marcel van den Broek ◽  
Nick Brouwers ◽  
Pilar de la Torre Cortès ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Sequence Similarity ◽  
Sequencing Data ◽  
Brewing Yeast ◽  
Linear Evolution ◽  
Oxford Nanopore ◽  
Pure Cultures ◽  
Group 2 ◽  
Chromosome Level ◽  
Group 1

Abstract Background The lager brewing yeast, S. pastorianus, is a hybrid between S. cerevisiae and S. eubayanus with extensive chromosome aneuploidy. S. pastorianus is subdivided into Group 1 and Group 2 strains, where Group 2 strains have higher copy number and a larger degree of heterozygosity for S. cerevisiae chromosomes. As a result, Group 2 strains were hypothesized to have emerged from a hybridization event distinct from Group 1 strains. Current genome assemblies of S. pastorianus strains are incomplete and highly fragmented, limiting our ability to investigate their evolutionary history. Results To fill this gap, we generated a chromosome-level genome assembly of the S. pastorianus strain CBS 1483 from Oxford Nanopore MinION DNA sequencing data and analysed the newly assembled subtelomeric regions and chromosome heterozygosity. To analyse the evolutionary history of S. pastorianus strains, we developed Alpaca: a method to compute sequence similarity between genomes without assuming linear evolution. Alpaca revealed high similarities between the S. cerevisiae subgenomes of Group 1 and 2 strains, and marked differences from sequenced S. cerevisiae strains. Conclusions Our findings suggest that Group 1 and Group 2 strains originated from a single hybridization involving a heterozygous S. cerevisiae strain, followed by different evolutionary trajectories. The clear differences between both groups may originate from a severe population bottleneck caused by the isolation of the first pure cultures. Alpaca provides a computationally inexpensive method to analyse evolutionary relationships while considering non-linear evolution such as horizontal gene transfer and sexual reproduction, providing a complementary viewpoint beyond traditional phylogenetic approaches.

scholarly journals Analysis of 56,348 Genomes Identifies the Relationship between Antibiotic and Metal Resistance and the Spread of Multidrug-Resistant Non-Typhoidal Salmonella

2021 ◽  
Vol 9 (7) ◽  
pp. 1468
Author(s):  
Gavin J. Fenske ◽  
Joy Scaria
Keyword(s):  
Antibiotic Resistance ◽  
Foodborne Pathogen ◽  
Antibiotic Resistance Genes ◽  
Multidrug Resistant ◽  
Metal Resistance ◽  
Group 3 ◽  
Group 2 ◽  
Occurrence Matrix ◽  
Genome Assemblies ◽  
Group 1

Salmonella enterica is common foodborne pathogen that generates both enteric and systemic infections in hosts. Antibiotic resistance is common is certain serovars of the pathogen and of great concern to public health. Recent reports have documented the co-occurrence of metal resistance with antibiotic resistance in one serovar of S. enterica. Therefore, we sought to identify possible co-occurrence in a large genomic dataset. Genome assemblies of 56,348 strains of S. enterica comprising 20 major serovars were downloaded from NCBI. The downloaded assemblies were quality controlled and in silico serotyped to ensure consistency and avoid improper annotation from public databases. Metal and antibiotic resistance genes were identified in the genomes as well as plasmid replicons. Co-occurrent genes were identified by constructing a co-occurrence matrix and grouping said matrix using k-means clustering. Three groups of co-occurrent genes were identified using k-means clustering. Group 1 was comprised of the pco and sil operons that confer resistance to copper and silver, respectively. Group 1 was distributed across four serovars. Group 2 contained the majority of the genes and little to no co-occurrence was observed. Metal and antibiotic co-occurrence was identified in group 3 that contained genes conferring resistance to: arsenic, mercury, beta-lactams, sulfonamides, and tetracyclines. Group 3 genes were also associated with an IncQ1 class plasmid replicon. Metal and antibiotic co-occurrence from group 3 genes is mostly isolated to one clade of S. enterica I 4,[5],12:i:-.

Myeloid neoplasms in the setting of chronic lymphocytic leukaemia/chronic lymphocytic leukaemia-like disease: a clinicopathological study of 66 cases comparing cases with prior history of treatment to those without

2021 ◽  
pp. jclinpath-2020-207334
Author(s):  
Catherine Luedke ◽  
Yue Zhao ◽  
Jenna McCracken ◽  
Jake Maule ◽  
Lian-He Yang ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukaemia ◽  
Lymphocytic Leukaemia ◽  
The Other ◽  
Prior History ◽  
Myeloid Neoplasm ◽  
Myeloid Neoplasms ◽  
History Of ◽  
Cytogenetic Profile ◽  
Group 2 ◽  
Group 1

AimsMyeloid neoplasms occur in the setting of chronic lymphocytic leukaemia (CLL)/CLL-like disease. The underlying pathogenesis has not been elucidated.MethodsRetrospectively analysed 66 cases of myeloid neoplasms in patients with CLL/CLL-like disease.ResultsOf these, 33 patients (group 1) had received treatment for CLL/CLL-like disease, while the other 33 patients (group 2) had either concurrent diagnoses or untreated CLL/CLL-like disease before identifying myeloid neoplasms. The two categories had distinct features in clinical presentation, spectrum of myeloid neoplasm, morphology, cytogenetic profile and clinical outcome. Compared with group 2, group 1 demonstrated a younger age at the diagnosis of myeloid neoplasm (median, 65 vs 71 years), a higher fraction of myelodysplastic syndrome (64% vs 36%; OR: 3.1; p<0.05), a higher rate of adverse unbalanced cytogenetic abnormalities, including complex changes, −5/5q- and/or −7/7q- (83% vs 28%; OR: 13.1; p<0.001) and a shorter overall survival (median, 12 vs 44 months; p<0.05).ConclusionsMyeloid neoplasm in the setting of CLL/CLL-like disease can be divided into two categories, one with prior treatment for CLL/CLL-like disease and the other without. CLL-type treatment may accelerate myeloid leukaemogenesis. The risk is estimated to be 13-fold higher in patients with treatment than those without. The causative agent could be attributed to fludarabine in combination with alkylators, based on the latency of myeloid leukaemogenesis and the cytogenetic profile.

scholarly journals Conservation analysis of SARS-CoV-2 spike suggests complicated viral adaptation history from bat to human

2020 ◽  
Vol 2020 (1) ◽  
pp. 290-303
Author(s):  
Kuan Cheok Lei ◽  
Xiaohua Douglas Zhang
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Mutation Analysis ◽  
Evolutionary History ◽  
Sequence Similarity ◽  
Similarity Analysis ◽  
Current Form ◽  
Conservation Analysis ◽  
Spike Sequences ◽  
History Of ◽  
Spike Sequence

Abstract Background The current coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome (SARS)-CoV-2, has become the most devastating public health emergency in the 21st century and one of the most influential plagues in history. Studies on the origin of SARS-CoV-2 have generally agreed that the virus probably comes from bat, closely related to a bat CoV named BCoV-RaTG13 taken from horseshoe bat (Rhinolophus affinis), with Malayan pangolin (Manis javanica) being a plausible intermediate host. However, due to the relatively low number of SARS-CoV-2-related strains available in public domain, the evolutionary history remains unclear. Methodology Nine hundred ninety-five coronavirus sequences from NCBI Genbank and GISAID were obtained and multiple sequence alignment was carried out to categorize SARS-CoV-2 related groups. Spike sequences were analyzed using similarity analysis and conservation analyses. Mutation analysis was used to identify variations within receptor-binding domain (RBD) in spike for SARS-CoV-2-related strains. Results We identified a family of SARS-CoV-2-related strains, including the closest relatives, bat CoV RaTG13 and pangolin CoV strains. Sequence similarity analysis and conservation analysis on spike sequence identified that N-terminal domain, RBD and S2 subunit display different degrees of conservation with several coronavirus strains. Mutation analysis on contact sites in SARS-CoV-2 RBD reveals that human-susceptibility probably emerges in pangolin. Conclusion and implication We conclude that the spike sequence of SARS-CoV-2 is the result of multiple recombination events during its transmission from bat to human, and we propose a framework of evolutionary history that resolve the relationship of BCoV-RaTG13 and pangolin coronaviruses with SARS-CoV-2. Lay Summary This study analyses whole-genome and spike sequences of coronavirus from NCBI using phylogenetic and conservation analyses to reconstruct the evolutionary history of severe acute respiratory syndrome (SARS)-CoV-2 and proposes an evolutionary history of spike in the progenitors of SARS-CoV-2 from bat to human through mammal hosts before they recombine into the current form.

Role of biometric characteristics of the uterine junctional zone in fertility outcomes in patients with adenomyosis

2021 ◽  
Vol 70 (3) ◽  
pp. 41-50
Author(s):  
Ekaterina K. Orekhova ◽  
Olga A. Zhandarova ◽  
Igor Yu. Kogan
Keyword(s):  
Magnetic Resonance Imaging ◽  
Magnetic Resonance ◽  
Pregnancy Outcomes ◽  
Adverse Pregnancy Outcomes ◽  
Resonance Imaging ◽  
Junctional Zone ◽  
History Of ◽  
Group 2 ◽  
Adverse Pregnancy ◽  
Group 1

BACKGROUND: The uterine junctional zone is the inner part of the myometrium. Dysfunction of the zone may underlie the pathogenesis of adenomyosis and its clinical manifestations, while biometric characteristics of the zone are currently considered as promising early diagnostic criteria for this disease. Adenomyosis has traditionally been associated with parity and intrauterine interventions, primarily in older patients. However, modern imaging tools often allow diagnosing the disease in young patients with infertility and an unburdened gynecological history. It is assumed that the detection of changes in the structure and function of the uterine junctional zone in adenomyosis can be the basis for predicting fertility outcomes and complications of pregnancy, as well as for the development of promising therapeutic strategies at the pregravid stage. AIM: The aim of this study was to assess the influence of biometric characteristics of the uterine junctional zone on pregnancy outcomes, depending on the parity and intrauterine interventions in patients with adenomyosis. MATERIALS AND METHODS: This prospective study included 102 patients aged 2239 years old with ultrasound features of adenomyosis who were going to conceive. The patients were divided into two groups: Group 1 (n = 58) consisted of nulliparous patients with no history of previous intrauterine interventions, and Group 2 (n = 44) comprised multipara women with a history of labor and / or intrauterine interventions. Using magnetic resonance imaging, we evaluated minimal, average and maximal junctional zone thicknesses, junctional zone deferential and a ratio of junctional zone thickness to myometrium thickness. Thresholds of biometric characteristics of the uterine junctional zone for adverse pregnancy outcomes were estimated. RESULTS: The frequencies of pregnancy and retrochorial hematoma in patients of Groups 1 and 2 in the first trimester of pregnancy did not differ significantly and amounted to 43.1% and 38.6%, 13.8% and 22.7%, respectively, p 0.05. Adverse pregnancy outcomes were diagnosed in 63.8% of patients in Group 1 and in 68.2% of patients in Group 2, p 0.05. In Group 1, the frequency of retrochorial hematoma depended on the initial junctional zone deferential, as well as on the initial average and maximal junctional zone thicknesses, junctional zone deferentials and ratios of junctional zone thickness to myometrium thickness, which, with an adverse pregnancy outcome, were 1.72.5 times higher than those in patients with a favorable outcome, p 0.05. In Group 2, adverse pregnancy outcomes were recorded with significantly higher values of average and maximal junctional zone thicknesses and junctional zone deferential. ROC curves were constructed using data of logistic regression analysis based on biometric characteristics of the uterine junctional zone to predict spontaneous abortion and infertility in patients with adenomyosis. CONCLUSIONS: Fertility outcomes in patients with adenomyosis depend on a complex of biometric characteristics of the uterine junctional zone as determined by magnetic resonance imaging.

scholarly journals The Threshold of Admission Glycemia as a Predictor of Adverse Events in Diabetic and Non-Diabetic Patients with Acute Coronary Syndrome

2009 ◽  
Vol 3 ◽  
pp. CMC.S2289 ◽  
Author(s):  
Taysir S. Garadah ◽  
Salah Kassab ◽  
Qasim M. Al-Shboul ◽  
Abdulhai Alawadi
Keyword(s):  
Acute Coronary Syndrome ◽  
Adverse Events ◽  
Diabetic Patients ◽  
Stress Hyperglycemia ◽  
Coronary Syndrome ◽  
History Of ◽  
Group 3 ◽  
Group 2 ◽  
High Level ◽  
Group 1

Recent studies indicated a high prevalence of hyperglycemia in non-diabetic patients presenting with acute coronary syndrome (ACS). However, the threshold of admission glucose (AG) as a predictor of adverse events in ACS is unclear. Objective The aim of this study was to assess the threshold of admission glucose (AG) as a predictor of adverse events including Major Acute Cardiac Events (MACE) and mortality, during the first week of admitting patients presenting with ACS. Material and Methods The data of 551 patients with ACS were extracted and evaluated. Patients were stratified according to their blood glucose on admission into three groups: group 1: <7 mmol/L (n = 200, 36.3%) and group 2: >7 mmol/L and <15 mmol/L (n = 178, 32.3%) and group 3: ≥15 mmol/L (n = 173, 31.4%). Stress hyperglycemia was arbitrarily defined as AG levels > 7 mmol/L (group 2 and 3). Patients with ACS were sub-divided into two groups: patients with unstable angina (UA, n = 285) and those with ST segment elevation myocardial Infarction (STEMI, n = 266) and data were analyzed separately using multiple regression analysis. Results The mean age of patients was 59.7 ± 14.8 years and 63% were males. The overall mortality in the population was 8.5% (5.4% in STEMI and 3.1% in UA) patients. In STEMI patients, the odds ratio of stress hyperglycemia as predictor of mortality in group 3 compared with group 1 was 3.3 (CI 0.99-10.98, P < 0.05), while in group 2 compared with group 1 was 2.4 (CI: 0.75-8.07, P = 0.065) after adjustment for age and sex. Similarly, in UA patients, the odds ratio of stress hyperglycemia in group 3 compared with group 1 was 2.7 (CI 0.37-18.98, P < 0.05), while in group 2 compared with group 1 was 2.4 (CI: 0.4-15.2, P = 0.344) after adjustment for age and sex. The incidence of more than 2 MACE in both STEMI and UA patients was higher in group 3 compared with the other two groups. Regression analysis showed that history of DM, high level of LDL cholesterol, high level of HbA1c, and anterior infarction were significant predictors of adverse events while other risk factors such as BMI, history of hypertension and smoking were of no significance. Conclusion This study indicates that the stress hyperglycemia on admission is a powerful predictor of increased major adverse events and hospital mortality in patients with acute coronary syndrome.

scholarly journals Management of a pediatric burn center during the covid-19 pandemic

2021 ◽  
Author(s):  
Ahmet Erturk ◽  
Sabri Demir ◽  
Can İhsan Oztorun ◽  
Elif Emel Erten ◽  
Dogus Guney ◽  
...  
Keyword(s):  
Length Of Stay ◽  
Total Body Surface Area ◽  
Center Staff ◽  
Staff Members ◽  
Burn Center ◽  
History Of ◽  
Group 2 ◽  
Travel Abroad ◽  
Pcr Test ◽  
Group 1

Abstract The aim of this study was to evaluate the results of an algorithm that was created to prevent coronavirus disease-2019 (COVID-19) transmission during the management of children with burns in a tertiary pediatric burn center. Children admitted to the burn center between May 2020 and November 2020 were prospectively evaluated for cause, burn depth, total body surface area (TBSA), length of stay, symptoms suggesting COVID-19, suspicious contact history, history of travel abroad, and COVID-19 polymerase chain reaction (PCR) test results. Patients were divided into two groups: unsuspected (Group 1) and suspected (Group 2), depending on any history of suspicious contact, travel abroad, and/or presence of symptoms. A total of 101 patients were enrolled in the study, which included 59 boys (58.4%) and 42 girls (41.6%). Group 1 included 79 (78.2%) patients, and Group 2 consisted of 22 (21.8%) patients. The most common cause of the burns was scald injuries (74.2%). The mean age, TBSA, and length of stay were 4.5 years, 12.0%, and 13.2 days, respectively. Four patients (3.9%) had a positive PCR test (two patients in each group). Comparing groups, males were more commonly found in Group 2 (p=0.042), but no differences were found for the other variables. No patients or burn center staff members developed COVID-19 during the course of hospitalization. In conclusion, every child should be tested for COVID-19 upon admission to a burn unit, and a modified algorithm should be constructed for the handling and management of pediatric burn patients.

Growth differentiation factor 15 associations with clinical features of chronic heart failure with midrange ejection fraction and preserved ejection fraction depending on the history of myocardial infarction

Kardiologiia ◽  
2021 ◽  
Vol 61 (5) ◽  
pp. 59-64
Author(s):  
E. A. Kuzheleva ◽  
A. A. Garganeeva ◽  
V. A. Aleksandrenko ◽  
V. A. Fedyunina ◽  
O. N. Ogurkova
Keyword(s):  
Myocardial Infarction ◽  
Ejection Fraction ◽  
Stroke Volume ◽  
Inflammatory Marker ◽  
Left Ventricular Ejection ◽  
Growth Differentiation Factor 15 ◽  
Differentiation Factor ◽  
History Of ◽  
Group 2 ◽  
Group 1

Aim    To analyze associations between levels of the inflammatory marker, growth differentiation factor 15 (GDF-15), and echocardiographic indexes in CHF patients with mid-range and preserved left ventricular ejection fraction (LV EF) depending on the history of myocardial infarction (MI).Material and methods    This study included 34 CHF patients with preserved and mid-range LV EF after MI (group 1, n=19) and without a history of MI (group 2, n=15). Serum concentration of GDF-15 was measured with enzyme immunoassay (BioVendor, Czech Republic). Statistical analysis was performed with STATISTICA 10.0.Results    Patients of the study groups were age-matched [62 (58;67) and 64 (60;70) years, p=0.2] but differed in the gender; group 1 consisted of men only (100 %) whereas in group 2, the proportion of men was 53.3 % (p=0.001). Median concentration of GDF-15 was 2385 (2274; 2632.5) and 1997 (1534;2691) pg/ml in groups 1 and 2, respectively (p=0.09). Patients without MI showed a moderate negative correlation between LV EF and GDF-15 concentration (r= – 0.51, p=0.050) and a pronounced correlation between GDF-15 and LV stroke volume (r= –0.722, p=0.002). For patients after MI, a correlation between the level of GDF-15 and the degree of systolic dysfunction was not found (р>0.05).Conclusion    Blood concentration of the inflammatory marker, GDF-15, correlates with LV EF and stroke volume in CHF patients with preserved or mid-range LV EF and without a history of MI while no such correlations were observed for patients with a history of MI. 

Abstract WP380: Thyrotoxicosis is Associated With Worse In-Hospital Mortality in Patients With Ischemic Stroke

Stroke ◽  
2020 ◽  
Vol 51 (Suppl_1) ◽  
Author(s):  
Sakiru O Isa ◽  
Olajide Buhari ◽  
Hameem Changezi
Keyword(s):  
Ischemic Stroke ◽  
Hospital Mortality ◽  
Length Of Hospital Stay ◽  
The Body ◽  
Significant Difference ◽  
History Of ◽  
Group 3 ◽  
Group 2 ◽  
Time Of Presentation ◽  
Group 1

Introduction: Hyperthyroidism increases the basal metabolic rate and affects most systems in the body. Patients with hyperthyroidism have been shown to have a higher incidence of ischemic stroke. There is a paucity of information regarding its effects on the short-term outcomes of patients admitted with ischemic stroke. Hypothesis: Hyperthyroidism is associated with worse in-hospital outcomes in patients admitted for ischemic stroke. Methods: We queried the National Inpatient Sample to identify adult patients(aged 18 and above) admitted for ischemic stroke between January 2011 and December 2014. We compared those with a history of hyperthyroidism (group 1) and thyrotoxicosis on admission (group 2) with the rest of the patients (group 3). The main outcome was in-hospital mortality. Secondary outcomes included the length of hospital stay and cost of hospitalization. We used the logistic regression model and adjusted for baseline characteristics and co-morbidities. Results: There were 643,786 patients in the study, 0.44% had a history of hyperthyroidism, and 0.01% had thyrotoxicosis at the time of presentation. The odd of mortality in group 1 compared to group 3 was 0.89, 95% CI 0.75-1.05, p=0.16 while in group 2 compared to group 3, it was 2.42, 95% CI 1.29-4.52, p<0.006. The mean length of stay was also longer in group 2 with a mean difference of 8.06, 95% CI 4.74 - 11.39, p<0.0001. Conclusion: From the study, there was no significant difference in in-hospital mortality between patients with previously diagnosed hyperthyroidism and those without diagnosed hyperthyroidism. Patients who had thyrotoxicosis on admission, on the other hand, had worse outcomes compared to patients without thyrotoxicosis.

Dysregulatory visceropathies in patients with uterine endometriosis and recurrent endometrial hyperplasia

1986 ◽  
Vol 67 (5) ◽  
pp. 347-349
Author(s):  
N. I. Petrushkova
Keyword(s):  
Endometrial Hyperplasia ◽  
Digestive System ◽  
Practical Significance ◽  
Control Group ◽  
Liver And Pancreas ◽  
Rational Therapy ◽  
History Of ◽  
Group 2 ◽  
Digestive Glands ◽  
Group 1

The study of neurohormonal-visceral relationships in patients with uterine endometriosis is of practical significance in the development of rational therapy and prevention of this complex and rather frequent pathology. This study was aimed to investigate the functional state of the digestive glands of the stomach, intestines, liver and pancreas in 152 patients with uterine internal endometriosis (Group 1) and in 50 patients with recurrent endometrial hyperplasia (Group 2). Twenty healthy women were the control group. Patients with no history of diseases of the digestive system were selected for the examination.

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