scholarly journals Evolutionary histories and antimicrobial resistance in Shigella flexneri and Shigella sonnei in Southeast Asia

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Hao Chung The ◽  
Ladaporn Bodhidatta ◽  
Duy Thanh Pham ◽  
Carl J. Mason ◽  
Tuyen Ha Thanh ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Disease Surveillance ◽  
Evolutionary History ◽  
Shigella Flexneri ◽  
Asian Countries ◽  
Genome Sequences ◽  
Evolutionary Trajectory ◽  
History Of ◽  
Susceptibility Patterns ◽  
Clonal Replacement

AbstractConventional disease surveillance for shigellosis in developing country settings relies on serotyping and low-resolution molecular typing, which fails to contextualise the evolutionary history of the genus. Here, we interrogated a collection of 1,804 Shigella whole genome sequences from organisms isolated in four continental Southeast Asian countries (Thailand, Vietnam, Laos, and Cambodia) over three decades to characterise the evolution of both S. flexneri and S. sonnei. We show that S. sonnei and each major S. flexneri serotype are comprised of genetically diverse populations, the majority of which were likely introduced into Southeast Asia in the 1970s–1990s. Intranational and regional dissemination allowed widespread propagation of both species across the region. Our data indicate that the epidemiology of S. sonnei and the major S. flexneri serotypes were characterised by frequent clonal replacement events, coinciding with changing susceptibility patterns against contemporaneous antimicrobials. We conclude that adaptation to antimicrobial pressure was pivotal to the recent evolutionary trajectory of Shigella in Southeast Asia.

scholarly journals Tumor evolutionary directed graphs and the history of chronic lymphocytic leukemia

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Jiguang Wang ◽  
Hossein Khiabanian ◽  
Davide Rossi ◽  
Giulia Fabbri ◽  
Valter Gattei ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Evolutionary History ◽  
Directed Graphs ◽  
Evolutionary Process ◽  
Genetic Alterations ◽  
Lymphocytic Leukemia ◽  
Cross Sectional ◽  
History Of ◽  
Evolutionary Paths ◽  
Clonal Replacement

Cancer is a clonal evolutionary process, caused by successive accumulation of genetic alterations providing milestones of tumor initiation, progression, dissemination, and/or resistance to certain therapeutic regimes. To unravel these milestones we propose a framework, tumor evolutionary directed graphs (TEDG), which is able to characterize the history of genetic alterations by integrating longitudinal and cross-sectional genomic data. We applied TEDG to a chronic lymphocytic leukemia (CLL) cohort of 70 patients spanning 12 years and show that: (a) the evolution of CLL follows a time-ordered process represented as a global flow in TEDG that proceeds from initiating events to late events; (b) there are two distinct and mutually exclusive evolutionary paths of CLL evolution; (c) higher fitness clones are present in later stages of the disease, indicating a progressive clonal replacement with more aggressive clones. Our results suggest that TEDG may constitute an effective framework to recapitulate the evolutionary history of tumors.

Characteristics and evolutionary history of hepatitis B virus quasi-subgenotype B3 in Southeast Asia

2019 ◽  
Vol 273 ◽  
pp. 197762 ◽  
Author(s):  
Jianmei Gao ◽  
Rongxia Zuo ◽  
Jinli Wang ◽  
Tao Shen
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Southeast Asia ◽  
Evolutionary History ◽  
B Virus ◽  
History Of

scholarly journals Viruses Infecting a Freshwater Filamentous Cyanobacterium (Nostocsp.) Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B

mBio ◽  
2016 ◽  
Vol 7 (3) ◽  
Author(s):  
Caroline Chénard ◽  
Jennifer F. Wirth ◽  
Curtis A. Suttle
Keyword(s):  
Dna Polymerase ◽  
Evolutionary History ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Filamentous Cyanobacterium ◽  
Filamentous Cyanobacteria ◽  
Evolutionary Trajectory ◽  
Crispr Array ◽  
History Of ◽  
Pcc 7120

ABSTRACT  Here we present the first genomic characterization of viruses infectingNostoc, a genus of ecologically important cyanobacteria that are widespread in freshwater. Cyanophages A-1 and N-1 were isolated in the 1970s and infectNostocsp. strain PCC 7210 but remained genomically uncharacterized. Their 68,304- and 64,960-bp genomes are strikingly different from those of other sequenced cyanophages. Many putative genes that code for proteins with known functions are similar to those found in filamentous cyanobacteria, showing a long evolutionary history in their host. Cyanophage N-1 encodes a CRISPR array that is transcribed during infection and is similar to the DR5 family of CRISPRs commonly found in cyanobacteria. The presence of a host-related CRISPR array in a cyanophage suggests that the phage can transfer the CRISPR among related cyanobacteria and thereby provide resistance to infection with competing phages. Both viruses also encode a distinct DNA polymerase B that is closely related to those found in plasmids ofCyanothecesp. strain PCC 7424,Nostocsp. strain PCC 7120, andAnabaena variabilisATCC 29413. These polymerases form a distinct evolutionary group that is more closely related to DNA polymerases of proteobacteria than to those of other viruses. This suggests that the polymerase was acquired from a proteobacterium by an ancestral virus and transferred to the cyanobacterial plasmid. Many other open reading frames are similar to a prophage-like element in the genome ofNostocsp. strain PCC 7524. TheNostoccyanophages reveal a history of gene transfers between filamentous cyanobacteria and their viruses that have helped to forge the evolutionary trajectory of this previously unrecognized group of phages.IMPORTANCEFilamentous cyanobacteria belonging to the genusNostocare widespread and ecologically important in freshwater, yet little is known about the genomic content of their viruses. Here we report the first genomic analysis of cyanophages infecting filamentous freshwater cyanobacteria, revealing that their gene content is unlike that of other cyanophages. In addition to sharing many gene homologues with freshwater cyanobacteria, cyanophage N-1 encodes a CRISPR array and expresses it upon infection. Also, both viruses contain a DNA polymerase B-encoding gene with high similarity to genes found in proteobacterial plasmids of filamentous cyanobacteria. The observation that phages can acquire CRISPRs from their hosts suggests that phages can also move them among hosts, thereby conferring resistance to competing phages. The presence in these cyanophages of CRISPR and DNA polymerase B sequences, as well as a suite of other host-related genes, illustrates the long and complex evolutionary history of these viruses and their hosts.

scholarly journals HO CHI MINH’S MULTICULTURAL THOUGHTS

2019 ◽  
Vol 4 (2) ◽  
Author(s):  
Yang Jingqing
Keyword(s):  
Southeast Asia ◽  
Best Practice ◽  
Western World ◽  
Asian Countries ◽  
Geographical Isolation ◽  
National Unity ◽  
Depth Analysis ◽  
History Of ◽  
Independence Movements ◽  
Southeast Asian Countries

Ho Chi Minh is one of influential personages in the history of Vietnam. His thoughts became the crucial guideline in the anti-colonial, anti-imperialist and independence movements of Vietnam. So far, quite a few scholars have conducted in-depth analysis of Ho Chi Minh‟s thoughts from the perspectives of politics, sociology and philosophy, but few scholars have studied Ho‟s thoughts from the perspective of multiculturalism. Given that multiculturalism is a theory that firstly put forward by western scholars in the western world, whether the theory is applicable to traditional and communitarian oriental world has become a hot topic in academic circles. From the perspective of morality, the elements of liberty, equality and justice of multiculturalism have the function of anti-colonialism and anti-imperialism in Southeast Asian countries including Vietnam. In the colonial times, French deliberately isolated Vietnamese ethnic groups through ideological control and geographical isolation, but under the guideline of Ho Chi Minh‟s thought, the Vietnamese broken the barrier of colonial and successfully achieve national unity and ethnic unity. This paper intends to prove that multiculturalism has the function of anti-colonialism and anti-imperialism by researching the Ho Chi Minh‟s multicultural thoughts, which is the best practice of western multiculturalism in southeast Asia.

scholarly journals Urgent Need for Field Surveys of Coronaviruses in Southeast Asia to Understand the SARS-CoV-2 Phylogeny and Risk Assessment for the Future Outbreaks

2020 ◽  
Author(s):  
Murat Seyran ◽  
Sk Sarif Hassan ◽  
Vladimir N. Uversky ◽  
Pabitra Pal Choudhury ◽  
Bruce D. Uhal ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Evolutionary History ◽  
Statistical Approach ◽  
Intermediate Hosts ◽  
Field Surveys ◽  
Standard Quality ◽  
History Of ◽  
Related Group ◽  
Sampling Problems

Phylogeny is a statistical approach displaying the evolutionary history of a genetically related group of organisms with the fundamental prerequisite of the utilization of a significant sample size that could represent the whole population under investigation. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) phylogeny analyses are based on a single isolate of BatCoVs, which is not a sufficient representation of genetically related CoVs. For instance, the unique Bat-CoV RaTG13 sequence that is genetically associated with SARS-CoV-2 was isolated from Yunnan, China, in 2013. To date, no other RaTG13 sequence has been obtained in a different time (temporal), place (spatial), or other host condition. Data scarcity of Bat-CoVs sequences raises concern on the several fundamental experimental and biostatistical aspects, e.g. repeatability of the sequences and intraspecies variation of critical genes, such as the receptor-binding domain of Spike protein. Sunda pangolin has been proposed as the intermediate host and source of SARS-CoV-2, but no Pangolin-CoV isolates have been isolated in Southeast Asia, where Sunda pangolins inhabit. Most Pangolin-CoVs were isolated from deceased pangolins, that were captured during illegal animal trafficking into China, hence raising questions about the reliability and quality of such isolates. Pangolin-CoV sampling problems are also evident in the deposited sequences that are of sub-standard quality. Therefore, there is urgent need for survey the Bat-CoVs and possible intermediate hosts, such as pangolins and civets in Southeast Asia. These surveys are required to investigate the genomic source of SARS-CoV-2 and assess possible future risks for new outbreaks. The current SARS-CoV-2 phylogeny with unacceptably limited numbers of Bat-CoVs and Pangolin-CoVs sequences not sufficient and technically not appropriate for reliable phylogenic analysis.

scholarly journals Evidence of ancient papillomavirus recombination

2006 ◽  
Vol 87 (9) ◽  
pp. 2527-2531 ◽  
Author(s):  
Arvind Varsani ◽  
Eric van der Walt ◽  
Livio Heath ◽  
Edward P. Rybicki ◽  
Anna Lise Williamson ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Papillomavirus ◽  
Evolutionary History ◽  
Full Genome ◽  
Genome Sequences ◽  
Aids Epidemic ◽  
Immunodeficiency Virus ◽  
History Of ◽  
Hpv Types ◽  
Open Question

An open question amongst papillomavirus taxonomists is whether recombination has featured in the evolutionary history of these viruses. Since the onset of the global AIDS epidemic, the question is somewhat less academic, because immune-compromised human immunodeficiency virus patients are often co-infected with extraordinarily diverse mixtures of human papillomavirus (HPV) types. It is expected that these conditions may facilitate the emergence of HPV recombinants, some of which might have novel pathogenic properties. Here, a range of rigorous analyses is applied to full-genome sequences of papillomaviruses to provide convincing statistical and phylogenetic evidence that evolutionarily relevant papillomavirus recombination can occur.

Trends in new species discovery of Orthoptera (Insecta) from Southeast Asia

Zootaxa ◽  
2017 ◽  
Vol 4238 (1) ◽  
pp. 127 ◽  
Author(s):  
MING KAI TAN ◽  
JIHEA CHOI ◽  
NIVEDITA SHANKAR
Keyword(s):  
Information System ◽  
New Species ◽  
Southeast Asia ◽  
Colonial History ◽  
Asian Countries ◽  
Type Specimens ◽  
Species Discovery ◽  
History Of ◽  
Time Periods ◽  
Southeast Asian Countries

The orthopterans are diverse insects and play important roles in the ecosystem as well as having “love-hate relationship” with humans. Documentation of diversity in Southeast Asia has long history but remains incomplete. Using information of type specimens and Geographic Information System (GIS) techniques, we investigated the following questions on new species discovery for the region, specifically: (1) How are new species discoveries of orthopterans distributed in Southeast Asia? (2) How have new species discoveries changed with time? (3) How do new species discoveries relate to the countries of the type depositories? We found that new species discoveries, relative to sampling, are fragmentary in Southeast Asia and changes with different time periods. We also find type depositories tightly linked to the human (colonial) history of Southeast Asian countries. We provide some recommendations and hope that this can help to accelerate the study of orthopteran diversity in the region. 

scholarly journals Insertion Sequence Diversity in Archaea

2007 ◽  
Vol 71 (1) ◽  
pp. 121-157 ◽  
Author(s):  
J. Filée ◽  
P. Siguier ◽  
M. Chandler
Keyword(s):  
Evolutionary History ◽  
Insertion Sequence ◽  
Prokaryotic Genome ◽  
Methanogenic Archaea ◽  
Insertion Sequences ◽  
Genome Sequences ◽  
The Public ◽  
Extensive Analysis ◽  
History Of ◽  
Families First

SUMMARY Insertion sequences (ISs) can constitute an important component of prokaryotic (bacterial and archaeal) genomes. Over 1,500 individual ISs are included at present in the ISfinder database (www-is.biotoul.fr ), and these represent only a small portion of those in the available prokaryotic genome sequences and those that are being discovered in ongoing sequencing projects. In spite of this diversity, the transposition mechanisms of only a few of these ubiquitous mobile genetic elements are known, and these are all restricted to those present in bacteria. This review presents an overview of ISs within the archaeal kingdom. We first provide a general historical summary of the known properties and behaviors of archaeal ISs. We then consider how transposition might be regulated in some cases by small antisense RNAs and by termination codon readthrough. This is followed by an extensive analysis of the IS content in the sequenced archaeal genomes present in the public databases as of June 2006, which provides an overview of their distribution among the major archaeal classes and species. We show that the diversity of archaeal ISs is very great and comparable to that of bacteria. We compare archaeal ISs to known bacterial ISs and find that most are clearly members of families first described for bacteria. Several cases of lateral gene transfer between bacteria and archaea are clearly documented, notably for methanogenic archaea. However, several archaeal ISs do not have bacterial equivalents but can be grouped into Archaea-specific groups or families. In addition to ISs, we identify and list nonautonomous IS-derived elements, such as miniature inverted-repeat transposable elements. Finally, we present a possible scenario for the evolutionary history of ISs in the Archaea.

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