scholarly journals Comparative Genomics of Mycoplasma pneumoniae isolated from Children with Pneumonia: South Korea, 2010-2016

2019 ◽  
Author(s):  
Joon Kee Lee ◽  
Moon-Woo Seong ◽  
Dongjin Shin ◽  
Jong-Il Kim ◽  
Mi Seon Han ◽  
...  
Keyword(s):  
South Korea ◽  
Mycoplasma Pneumoniae ◽  
Gc Content ◽  
Structural Diversity ◽  
Base Pairs ◽  
Tract Infections ◽  
Type 3 ◽  
Phylogenetic Associations

Abstract Background Mycoplasma pneumoniae is a common cause of respiratory tract infections in children and adults. This study applied high-throughput whole genome sequencing (WGS) technologies to analyze the genomes of 30 M. pneumoniae strains isolated from children with pneumonia in South Korea during the two epidemics from 2010 to 2016 in comparison with a global collection of 48 M. pneumoniae strains which includes seven countries ranging from 1944 to 2017. Results The 30 Korean strains had approximately 40% GC content and ranged from 815,686 to 818,669 base pairs, coding for a total of 809 to 828 genes. Overall, BRIG revealed 99% to > 99% similarity among strains. The genomic similarity dropped to approximately 95% in the P1 type 2 strains when aligned to the reference M129 genome, which corresponded to the region of the p1 gene. MAUVE detected four subtype-specific insertions (three in P1 type 1 and one in P1 type 2), of which were all hypothetical proteins except for one tRNA insertion in all P1 type 1 strains. The phylogenetic associations of 30 strains were generally consistent with the multilocus sequence typing results. eBURST analysis demonstrated two clonal complexes which are accordant with the known P1 typing, with higher diversity among P1 type 2 strains. The phylogenetic tree constructed with 78 genomes including 48 genomes outside Korea formed three clusters, in which the sequence type 3 strains from Korea were divided into two P1 type 1 clusters. Conclusions The comparative genome analysis of the 78 M. pneumoniae strains including 30 strains from Korea by WGS reveals structural diversity and phylogenetic associations, even though the similarity across the strains was very high.

scholarly journals Comparative Genomics of Mycoplasma pneumoniae isolated from Children with Pneumonia: South Korea, 2010-2016

2019 ◽  
Author(s):  
Joon Kee Lee ◽  
Eun Hwa Choi ◽  
Moon-Woo Seong ◽  
Youbin Yeon ◽  
Sung Im Cho ◽  
...  
Keyword(s):  
South Korea ◽  
Mycoplasma Pneumoniae ◽  
Gc Content ◽  
Structural Diversity ◽  
Base Pairs ◽  
Tract Infections ◽  
Type 3 ◽  
Phylogenetic Associations

Abstract Background Mycoplasma pneumoniae is a common cause of respiratory tract infections in children and adults. This study applied high-throughput whole genome sequencing (WGS) technologies to analyze the genomes of 30 M. pneumoniae strains isolated from children with pneumonia in South Korea during the two epidemics from 2010 to 2016 in comparison with a global collection of 48 M. pneumoniae strains which includes seven countries ranging from 1944 to 2017. Results The 30 Korean strains had approximately 40% GC content and ranged from 815,686 to 818,669 base pairs, coding for a total of 809 to 828 genes. Overall, BRIG revealed 99% to > 99% similarity among strains. The genomic similarity dropped to approximately 95% in the P1 type 2 strains when aligned to the reference M129 genome, which corresponded to the region of the p1 gene. MAUVE detected four subtype-specific insertions (three in P1 type 1 and one in P1 type 2), of which were all hypothetical proteins except for one tRNA insertion in all P1 type 1 strains. The phylogenetic associations of 30 strains were generally consistent with the multilocus sequence typing results. eBURST analysis demonstrated two clonal complexes which are accordant with the known P1 typing, with higher diversity among P1 type 2 strains. The phylogenetic tree constructed with 78 genomes including 48 genomes outside Korea formed three clusters, in which the sequence type 3 strains from Korea were divided into two P1 type 1 clusters. Conclusions The comparative genome analysis of the 78 M. pneumoniae strains including 30 strains from Korea by WGS reveals structural diversity and phylogenetic associations, even though the similarity across the strains was very high.

scholarly journals Comparative Genomics of Mycoplasma pneumoniae isolated from Children with Pneumonia: South Korea, 2010-2016

2019 ◽  
Author(s):  
Joon Kee Lee ◽  
Moon-Woo Seong ◽  
Dongjin Shin ◽  
Jong-Il Kim ◽  
Mi Seon Han ◽  
...  
Keyword(s):  
South Korea ◽  
Mycoplasma Pneumoniae ◽  
Gc Content ◽  
Structural Diversity ◽  
Base Pairs ◽  
Tract Infections ◽  
Type 3 ◽  
Phylogenetic Associations

Abstract Background Mycoplasma pneumoniae is a common cause of respiratory tract infections in children and adults. This study applied high-throughput whole genome sequencing (WGS) technologies to analyze the genomes of 30 M. pneumoniae strains isolated from children with pneumonia in South Korea during the two epidemics from 2010 to 2016 in comparison with a global collection of 48 M. pneumoniae strains which includes seven countries ranging from 1944 to 2017. Results The 30 Korean strains had approximately 40% GC content and ranged from 815,686 to 818,669 base pairs, coding for a total of 809 to 828 genes. Overall, BRIG revealed 99% to > 99% similarity among strains. The genomic similarity dropped to approximately 95% in the P1 type 2 strains when aligned to the reference M129 genome, which corresponded to the region of the p1 gene. MAUVE detected four subtype-specific insertions (three in P1 type 1 and one in P1 type 2), of which were all hypothetical proteins except for one tRNA insertion in all P1 type 1 strains. The phylogenetic associations of 30 strains were generally consistent with the multilocus sequence typing results. eBURST analysis demonstrated two clonal complexes which are accordant with the known P1 typing, with higher diversity among P1 type 2 strains. The phylogenetic tree constructed with 78 genomes including 48 genomes outside Korea formed three clusters, in which the sequence type 3 strains from Korea were divided into two P1 type 1 clusters. Conclusions The comparative genome analysis of the 78 M. pneumoniae strains including 30 strains from Korea by WGS reveals structural diversity and phylogenetic associations, even though the similarity across the strains was very high.

scholarly journals Comparative Genomics of Mycoplasma pneumoniae isolated from Children with Pneumonia: South Korea, 2010-2016

2019 ◽  
Author(s):  
Joon Kee Lee ◽  
Moon-Woo Seong ◽  
Dongjin Shin ◽  
Jong-Il Kim ◽  
Mi Seon Han ◽  
...  
Keyword(s):  
South Korea ◽  
Mycoplasma Pneumoniae ◽  
Gc Content ◽  
Structural Diversity ◽  
Base Pairs ◽  
Tract Infections ◽  
Type 3 ◽  
Phylogenetic Associations

Abstract Background Mycoplasma pneumoniae is a common cause of respiratory tract infections in children and adults. This study applied high-throughput whole genome sequencing (WGS) technologies to analyze the genomes of 30 M. pneumoniae strains isolated from children with pneumonia in South Korea during the two epidemics from 2010 to 2016 in comparison with a global collection of 48 M. pneumoniae strains which includes seven countries ranging from 1944 to 2017. Results The 30 Korean strains had approximately 40% GC content and ranged from 815,686 to 818,669 base pairs, coding for a total of 809 to 828 genes. Overall, BRIG revealed 99% to > 99% similarity among strains. The genomic similarity dropped to approximately 95% in the P1 type 2 strains when aligned to the reference M129 genome, which corresponded to the region of the p1 gene. MAUVE detected four subtype-specific insertions (three in P1 type 1 and one in P1 type 2), of which were all hypothetical proteins except for one tRNA insertion in all P1 type 1 strains. The phylogenetic associations of 30 strains were generally consistent with the multilocus sequence typing results. eBURST analysis demonstrated two clonal complexes which are accordant with the known P1 typing, with higher diversity among P1 type 2 strains. The phylogenetic tree constructed with 78 genomes including 48 genomes outside Korea formed three clusters, in which the sequence type 3 strains from Korea were divided into two P1 type 1 clusters. Conclusions The comparative genome analysis of the 78 M. pneumoniae strains including 30 strains from Korea by WGS reveals structural diversity and phylogenetic associations, even though the similarity across the strains was very high.

scholarly journals Comparative genomics of Mycoplasma pneumoniae isolated from children with pneumonia: South Korea, 2010–2016

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Joon Kee Lee ◽  
Moon-Woo Seong ◽  
Dongjin Shin ◽  
Jong-Il Kim ◽  
Mi Seon Han ◽  
...  
Keyword(s):  
South Korea ◽  
Mycoplasma Pneumoniae ◽  
Gc Content ◽  
Structural Diversity ◽  
Whole Genome ◽  
Base Pairs ◽  
Tract Infections ◽  
Phylogenetic Associations

Abstract Background Mycoplasma pneumoniae is a common cause of respiratory tract infections in children and adults. This study applied high-throughput whole genome sequencing (WGS) technologies to analyze the genomes of 30 M. pneumoniae strains isolated from children with pneumonia in South Korea during the two epidemics from 2010 to 2016 in comparison with a global collection of 48 M. pneumoniae strains which includes seven countries ranging from 1944 to 2017. Results The 30 Korean strains had approximately 40% GC content and ranged from 815,686 to 818,669 base pairs, coding for a total of 809 to 828 genes. Overall, BRIG revealed 99% to > 99% similarity among strains. The genomic similarity dropped to approximately 95% in the P1 type 2 strains when aligned to the reference M129 genome, which corresponded to the region of the p1 gene. MAUVE detected four subtype-specific insertions (three in P1 type 1 and one in P1 type 2), of which were all hypothetical proteins except one tRNA insertion in all P1 type 1 strains. The phylogenetic associations of 30 strains were generally consistent with the multilocus sequence typing results. The phylogenetic tree constructed with 78 genomes including 30 genomes from Korea formed two clusters and further divided into two sub-clusters. eBURST analysis revealed two clonal complexes according to P1 typing results showing higher diversity among P1 type 2 strains. Conclusions The comparative whole genome approach was able to define high genetic identity, unique structural diversity, and phylogenetic associations among the 78 M. pneumoniae strains isolated worldwide.

scholarly journals 638. Comparative Genomics of Mycoplasma pneumoniae Isolated From Children with Pneumonia: South Korea, 2010–2016

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S295-S295
Author(s):  
Hoan J Lee ◽  
Joon Kee Lee ◽  
Yun Young Choi ◽  
Ji Young Park ◽  
Moon-Woo Seong ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
South Korea ◽  
Mycoplasma Pneumoniae ◽  
Gc Content ◽  
Genomic Analysis ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Whole Genome

Abstract Background This study applied high-throughput whole-genome sequencing (WGS) technologies to investigate the comparative genomics of 30 M. pneumoniae strains isolated from children with pneumonia in South Korea during two epidemics from 2010 to 2016 in comparison with a global collection of 48 Mycoplasma pneumoniae strains which includes seven countries ranging from 1944 to 2017. Methods A total number of 30 M. pneumoniae strains were selected for whole-genome sequence analysis from two epidemics, 2010–2012 and 2014–2016. Next-generation sequencing (NGS) of all M. pneumoniae strains was performed using the Illumina MiSeq desktop sequencer. Comparative genomic analysis was performed using BLAST Ring Image Generator (BRIG), MAUVE, MAFFT, CLC Phylogeny Module, SnpEff, and Pathosystems Resource Integration Center (PATRIC). Results The 30 Korean strains had approximately 40% GC content and ranged from 815,686 to 818,669 base pairs, coding for a total of 809 to 828 genes. Overall, BRIG revealed 99% to>99% similarity among strains. The genomic similarity dropped to approximately 95% in the P1 type 2 strains when aligned to the reference M129 genome, which corresponded to the region of the p1 gene. MAUVE detected four subtype-specific of which were all hypothetical proteins except for one tRNA insertion in all P1 type 1 strains. eBURST analysis demonstrated two clonal complexes which are accordant with the known P1 typing, with higher diversity among P1 type 2 strains. The phylogenetic tree constructed with 78 genomes including 48 genomes outside Korea, formed three clusters, in which the sequence type 3 strains from Korea were divided into two P1 type 1 clusters. Conclusion The comparative genomics of the 78 M. pneumoniae strains including 30 strains from Korea by WGS reveals structural diversity and phylogenetic associations, even though the similarity across the strains was very high. Disclosures All authors: No reported disclosures.

scholarly journals ‘Simple’ Oligopyridine Complexes – Sources of Unexpected Structural Diversity

2020 ◽  
Vol 73 (6) ◽  
pp. 390 ◽  
Author(s):  
Edwin C. Constable ◽  
Catherine E. Housecroft
Keyword(s):  
Structural Diversity ◽  
Heterocyclic Ligands ◽  
Bridging Ligands ◽  
Face To Face ◽  
Main Group Metal ◽  
Polymeric Solid ◽  
Type 3 ◽  
Solid State Structures

The simple formulae often presented for main-group metal complexes of oligopyridines (typically 2,2′-bipyridine, 1,10-phenanthroline, and 2,2′:6′,2″-terpyridine) hide a wide variety of polymeric solid-state structures. We present an overview of these structures and reveal a plethora of 1D chains, including ladder assemblies, and 2D networks. In most assemblies, the polymeric backbone or network is defined by the metal atoms and bridging ligands other than oligopyridines. The heterocyclic ligands typically feature as peripheral decorations, often engaging in face-to-face supramolecular π-stacking interactions which define the assembly of the crystal. In 1D coordination polymers, three types of decoration predominate which we have defined as Type 1 (all the oligopyridines on the same side and π-stacked), Type 2 (alternating arrangement of oligopyridines), and Type 3 (a pairwise alternating structure).

FUNCTIONAL STATUS AND ADAPTIVE POTENTIAL IN FOREIGN STUDENTS WITH DIFFERENT TYPES OF VEGETATIVE REGULATION DURING TUITION

2020 ◽  
pp. 118-126
Author(s):  
A.M. Satarkulova
Keyword(s):  
Heart Rate ◽  
Foreign Students ◽  
Autonomic Regulation ◽  
The Body ◽  
Functional Changes ◽  
Different Types ◽  
Type 3 ◽  
Adaptive Abilities

The assessment and dynamic control over students’ status is a very important task. It allows timely detection of prenosological status prior to pathology and health maintenance in students. The objective of the paper is to assess the adaptive abilities of the body, to analyze changes in heart rate variability indicators in students with various types of autonomic regulation, to identify prenosological status and precursory pathological symptoms. Materials and Methods. The study enrolled 302 students from India, aged 21.54±1.43. Programming complex «Psychophysiologist» was used to register the main HRV parameters within 5 minutes. Health status was evaluated according to the index of functional changes and the scale of functional states. Results. N.I. Shlyk (2009) distinguished two groups of students with different types of autonomic regulation: type 1 (53 %) with moderate and type 2 (5 %) with marked characteristics of central regulation profile, type 3 (35 %) with moderate and type 4 (7 %) with marked characteristics of autonomous regulation profile. Main parameters of HRV and adaptation potential were defined for each student.All the parameters characterized functional and health status. Conclusions. It was shown that 82 % of trial subjects (type 1), 53 % (type 2), 94 % (type 3) and 95 % (type 4) demonstrated satisfactory adaptation and their physiological processes were at an optimal level. 18 % of students (type 1) demonstrated reduced adaptive abilities of the body. Moreover, they were under moderate stress. 47 % of subjects (type 2) were also under a significant stress, which was proven by excessively high SI, low SDNN and TP, and an increased index of functional changes. 5 % of students (type 4) revealed dysfunctional characteristics in the heart rhythm, peculiar to pathology. Keywords: foreign students, heart rate variability, types of autonomic regulation, adaptation potential, functional status. Оценка состояния студентов и динамический контроль за ним является важной задачей, поскольку позволяет своевременно выявлять у студентов донозологические состояния, предшествующие патологии, и способствовать сохранению здоровья. Цель. Оценка адаптивных возможностей организма, анализ изменений показателей вариабельности сердечного ритма у студентов с различными типами вегетативной регуляции, выявление донозологических состояний и ранних признаков патологии. Материалы и методы. В исследовании участвовало 302 студента в возрасте 21,54+1,43 года из Индии. Регистрировались основные параметры ВСР в течение 5 мин с использованием программно-аппаратного комплекса «Психофизиолог». Состояние и уровень здоровья оценивались по индексу функциональных изменений и шкале функциональных состояний. Результаты. По способу, предложенному Н.И. Шлык, выделены группы студентов с различными типами вегетативной регуляции: I (53 %) и II типы (5 %) – с умеренным и выраженным преобладанием центрального контура регуляции соответственно, III (35 %) и IV типы (7 %) – с умеренным и выраженным преобладанием автономного контура регуляции соответственно. У каждого из студентов определены основные параметры ВСР и адаптационного потенциала, характеризующие функциональное состояние и уровень здоровья. Выводы. Показано, что для 82 % обследуемых с I типом, 53 % со II типом, 94 % c III типом и 95 % с IV типом регуляции характерно состояние удовлетворительной адаптации, физиологические процессы сохраняются на оптимальном уровне. В группе студентов I типа у 18 % студентов адаптивные возможности организма снижены, выявлено состояние умеренного напряжения. У 47 % обследуемых II типа также зафиксировано состояние резко выраженного напряжения, индикатором которого является чрезмерно высокое значение SI, низкие величины SDNN и ТP, повышенное значение индекса функциональных изменений. В группе студентов с IV типом у 5 % учащихсяв регуляции ритма сердца выявлены дисфункциональные признаки, характерные для патологии. Ключевые слова: иностранные студенты, вариабельность сердечного ритма, типы вегетативной регуляции, адаптационный потенциал, функциональное состояние.

POLIOMYELITIS IN CANADIAN ESKIMOS: LABORATORY STUDIES. V. TYPE 1 AND TYPE 3 POLIOMYELITIS ANTIBODY LEVELS IN BAFFIN ISLAND ESKIMOS

1954 ◽  
Vol 32 (1) ◽  
pp. 119-125
Author(s):  
W. Wood ◽  
Eina M. Clark ◽  
F. T. Shimada ◽  
A. J. Rhodes
Keyword(s):  
Medical Records ◽  
Baffin Island ◽  
Tissue Cultures ◽  
Laboratory Studies ◽  
Poliomyelitis Virus ◽  
Antibody Titers ◽  
Antibody Levels ◽  
Type 3

Studies on the basic immunology of poliomyelitis in Canadian Eskimos have been continued. Some 87 sera collected from Eskimos at Pangnirtung, Baffin Island, have been examined for the presence of Type 1 and Type 3 poliomyelitis antibody by quantitative tests in tissue cultures. The same sera were previously examined for Type 2 antibody by quantitative tests in mice. The results of the three determinations are now presented together for comparison. These sera came from Eskimos aged 2 to 72 years of age. None of the Eskimos showed any evidence of paralysis. Examination of the medical records did not suggest that any paralytic disease had been present in this part of Baffin Island. Very few of the sera showed the presence of poliomyelitis antibody; thus, Type 1 antibody was demonstrated in the sera of 8%, Type 2 antibody in the sera of 9%, and Type 3 antibody in the sera of 14%. No significant number of Eskimos below the age of 45 years had acquired poliomyelitis antibody. The antibody titers mostly ranged between 10−1.0 and 10−2.0, and were significantly lower than the titers customarily found in recently paralyzed cases. These findings suggest that poliomyelitis infection occurred in Pangnirtung Eskimos many years before the date on which the samples were taken (1951). These results point to the worldwide prevalence of the three types of poliomyelitis virus.

Toward Personalized Treatment for Patients with Low von Willebrand Factor and Quantitative von Willebrand Disease

2021 ◽  
Vol 47 (02) ◽  
pp. 192-200
Author(s):  
James S. O'Donnell
Keyword(s):  
Von Willebrand Factor ◽  
Bleeding Risk ◽  
Von Willebrand Disease ◽  
Personalized Treatment ◽  
Treatment Plans ◽  
Type 3 ◽  
Von Willebrand ◽  
Willebrand Factor

AbstractThe biological mechanisms involved in the pathogenesis of type 2 and type 3 von Willebrand disease (VWD) have been studied extensively. In contrast, although accounting for the majority of VWD cases, the pathobiology underlying partial quantitative VWD has remained somewhat elusive. However, important insights have been attained following several recent cohort studies that have investigated mechanisms in patients with type 1 VWD and low von Willebrand factor (VWF), respectively. These studies have demonstrated that reduced plasma VWF levels may result from either (1) decreased VWF biosynthesis and/or secretion in endothelial cells and (2) pathological increased VWF clearance. In addition, it has become clear that some patients with only mild to moderate reductions in plasma VWF levels in the 30 to 50 IU/dL range may have significant bleeding phenotypes. Importantly in these low VWF patients, bleeding risk fails to correlate with plasma VWF levels and inheritance is typically independent of the VWF gene. Although plasma VWF levels may increase to > 50 IU/dL with progressive aging or pregnancy in these subjects, emerging data suggest that this apparent normalization in VWF levels does not necessarily equate to a complete correction in bleeding phenotype in patients with partial quantitative VWD. In this review, these recent advances in our understanding of quantitative VWD pathogenesis are discussed. Furthermore, the translational implications of these emerging findings are considered, particularly with respect to designing personalized treatment plans for VWD patients undergoing elective procedures.

scholarly journals Optimally growing initial errors of El Niño events in the CESM

2021 ◽  
Author(s):  
Hui Xu ◽  
Lei Chen ◽  
Wansuo Duan
Keyword(s):  
El Niño ◽  
El Nino ◽  
Equatorial Pacific ◽  
Initial Error ◽  
Initial Errors ◽  
El Niño Events ◽  
Type 3 ◽  
El Nino Events

AbstractThe optimally growing initial errors (OGEs) of El Niño events are found in the Community Earth System Model (CESM) by the conditional nonlinear optimal perturbation (CNOP) method. Based on the characteristics of low-dimensional attractors for ENSO (El Niño Southern Oscillation) systems, we apply singular vector decomposition (SVD) to reduce the dimensions of optimization problems and calculate the CNOP in a truncated phase space by the differential evolution (DE) algorithm. In the CESM, we obtain three types of OGEs of El Niño events with different intensities and diversities and call them type-1, type-2 and type-3 initial errors. Among them, the type-1 initial error is characterized by negative SSTA errors in the equatorial Pacific accompanied by a negative west–east slope of subsurface temperature from the subsurface to the surface in the equatorial central-eastern Pacific. The type-2 initial error is similar to the type-1 initial error but with the opposite sign. The type-3 initial error behaves as a basin-wide dipolar pattern of tropical sea temperature errors from the sea surface to the subsurface, with positive errors in the upper layers of the equatorial eastern Pacific and negative errors in the lower layers of the equatorial western Pacific. For the type-1 (type-2) initial error, the negative (positive) temperature errors in the eastern equatorial Pacific develop locally into a mature La Niña (El Niño)-like mode. For the type-3 initial error, the negative errors in the lower layers of the western equatorial Pacific propagate eastward with Kelvin waves and are intensified in the eastern equatorial Pacific. Although the type-1 and type-3 initial errors have different spatial patterns and dynamic growing mechanisms, both cause El Niño events to be underpredicted as neutral states or La Niña events. However, the type-2 initial error makes a moderate El Niño event to be predicted as an extremely strong event.

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