scholarly journals Genome reduction in prokaryotic obligatory intracellular parasites of humans: a comparative analysis

2004 ◽  
Vol 54 (6) ◽  
pp. 1937-1941 ◽  
Author(s):  
Kishore R. Sakharkar ◽  
Pawan Kumar Dhar ◽  
Vincent T. K. Chow
Keyword(s):  
Gene Loss ◽  
Genome Reduction ◽  
Intracellular Parasite ◽  
Comparative Analyses ◽  
Protein Length ◽  
Intracellular Parasites ◽  
Number Of Genes ◽  
Obligatory Intracellular Parasite ◽  
Extreme Specialization ◽  
Over Time

Obligatory intracellular parasites have undergone significant genome reduction by gene loss over time in the context of their obligate associations with the host. The flux, streamlining and elimination of genes in these genomes constitute a selective and ongoing process. Comparative analyses of five completely sequenced obligatory intracellular parasite genomes reveal that these genomes display marked similarities in patterns of protein length and frequency distribution, with substantial sharing of a ‘backbone genome’. From category distribution based on the database of cluster of orthologous groups of proteins (COG), it is clear that habitat is a major factor contributing to genome reduction. It is also observed that, in all five obligatory intracellular parasites, the reduction in number of genes/proteins is greater for proteins with lengths of 200–600 amino acids. These comparative analyses highlight that gene loss is function-dependent, but is independent of protein length. These comparisons enhance our knowledge of the forces that drive the extreme specialization of the bacteria and their association with the host.

scholarly journals Vaccines for Canine Leishmaniasis

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Faeze Foroughi-Parvar ◽  
Gholamreza Hatam
Keyword(s):  
Visceral Leishmaniasis ◽  
Reservoir Host ◽  
Human Infection ◽  
Canine Leishmaniasis ◽  
Effective Vaccine ◽  
Canine Visceral Leishmaniasis ◽  
Intracellular Parasite ◽  
Current Increase ◽  
Obligatory Intracellular Parasite ◽  
Zoonotic Visceral Leishmaniasis

Leishmania infantumis the obligatory intracellular parasite of mammalian macrophages and causes zoonotic visceral leishmaniasis (ZVL). The presence of infected dogs as the main reservoir host of ZVL is regarded as the most important potential risk for human infection. Thus the prevention of canine visceral leishmaniasis (CVL) is essential to stop the current increase of the Mediterranean visceral leishmaniasis. Recently considerable advances in achieving protective immunization of dogs and several important attempts for achieving an effective vaccine against CVL lead to attracting the scientists trust in its important role for eradication of ZVL. This paper highlights the recent advances in vaccination against canine visceral leishmaniasis from 2007 until now.

scholarly journals Sampling and fieldwork practices in Europe: Analysis of methodological documentation from 1,537 surveys in five cross-national projects, 1981-2017

Methodology ◽  
2020 ◽  
Vol 16 (3) ◽  
pp. 186-207
Author(s):  
Piotr Jabkowski ◽  
Marta Kołczyńska
Keyword(s):  
Survey Data ◽  
National Survey ◽  
Comparative Analyses ◽  
National Surveys ◽  
Samples And Sampling ◽  
Survey Methodologies ◽  
Over Time ◽  
Selection Of ◽  
Cross National

This article addresses the comparability of sampling and fieldwork with an analysis of methodological data describing 1,537 national surveys from five major comparative cross-national survey projects in Europe carried out in the period from 1981 to 2017. We describe the variation in the quality of the survey documentation, and in the survey methodologies themselves, focusing on survey procedures with respect to: 1) sampling frames, 2) types of survey samples and sampling designs, 3) within-household selection of target persons in address-based samples, 4) fieldwork execution and 5) fieldwork outcome rates. Our results show substantial differences in sample designs and fieldwork procedures across survey projects, as well as changes within projects over time. This variation invites caution when selecting data for analysis. We conclude with recommendations regarding the use of information about the survey process to select existing survey data for comparative analyses.

Alive or Dead?

2018 ◽  
pp. 19-54
Author(s):  
Ricard Solé ◽  
Santiago F. Elena
Keyword(s):  
Genome Size ◽  
Genome Reduction ◽  
Mutation Rates ◽  
Viral Quasispecies ◽  
Theoretical Terms ◽  
Classical View ◽  
Alan Turing ◽  
Intracellular Parasites ◽  
Molecular Machinery

The classical view of viruses as intracellular parasites requiring available molecular machinery to replicate themselves suggests that they can be considered as some sort of program. In this context, viruses would mainly be considered as encapsulated pieces of software, to be executed by the cellular host hardware. The function that is being executed is a computation, and using this concept will be extremely useful in the exploration of viruses as computational objects. The notion of a general machine capable of performing computations was formalized in theoretical terms by British mathematician Alan Turing. This chapter discusses viruses as replicating machines, viruses as phases of matter, evolving genome reduction, the space of replicators, adaptation at high-mutation rates, viral quasispecies, and critical genome size.

scholarly journals A novel polymer of tubulin forms the conoid of Toxoplasma gondii

2002 ◽  
Vol 156 (6) ◽  
pp. 1039-1050 ◽  
Author(s):  
Ke Hu ◽  
David S. Roos ◽  
John M. Murray
Keyword(s):  
Toxoplasma Gondii ◽  
Cell Shape ◽  
Microscopic Analysis ◽  
Laboratory Model ◽  
Human Pathogen ◽  
Intracellular Parasite ◽  
Electron Microscopic ◽  
Obligatory Intracellular Parasite ◽  
Late Stages ◽  
Rapid Incorporation

Toxoplasma gondii is an obligatory intracellular parasite, an important human pathogen, and a convenient laboratory model for many other human and veterinary pathogens in the phylum Apicomplexa, such as Plasmodium, Eimeria, and Cryptosporidia. 22 subpellicular microtubules form a scaffold that defines the cell shape of T. gondii. Its cytoskeleton also includes an intricate apical structure consisting of the conoid, two intraconoid microtubules, and two polar rings. The conoid is a 380-nm diameter motile organelle, consisting of fibers wound into a spiral like a compressed spring. FRAP analysis of transgenic T. gondii expressing YFP-α-tubulin reveals that the conoid fibers are assembled by rapid incorporation of tubulin subunits during early, but not late, stages of cell division. Electron microscopic analysis shows that in the mature conoid, tubulin is arranged into a novel polymer form that is quite different from typical microtubules.

scholarly journals Bacterial Genes Outnumber Archaeal Genes in Eukaryotic Genomes

2020 ◽  
Vol 12 (4) ◽  
pp. 282-292 ◽  
Author(s):  
Julia Brueckner ◽  
William F Martin
Keyword(s):  
Gene Loss ◽  
Protein Sequences ◽  
Metabolic Processes ◽  
Encephalitozoon Intestinalis ◽  
Human Parasite ◽  
Intracellular Parasites ◽  
Genetic Information Processing ◽  
Bacterial Genes ◽  
Eukaryotic Genomes ◽  
Eukaryote Genome

Abstract Eukaryotes are typically depicted as descendants of archaea, but their genomes are evolutionary chimeras with genes stemming from archaea and bacteria. Which prokaryotic heritage predominates? Here, we have clustered 19,050,992 protein sequences from 5,443 bacteria and 212 archaea with 3,420,731 protein sequences from 150 eukaryotes spanning six eukaryotic supergroups. By downsampling, we obtain estimates for the bacterial and archaeal proportions. Eukaryotic genomes possess a bacterial majority of genes. On average, the majority of bacterial genes is 56% overall, 53% in eukaryotes that never possessed plastids, and 61% in photosynthetic eukaryotic lineages, where the cyanobacterial ancestor of plastids contributed additional genes to the eukaryotic lineage. Intracellular parasites, which undergo reductive evolution in adaptation to the nutrient rich environment of the cells that they infect, relinquish bacterial genes for metabolic processes. Such adaptive gene loss is most pronounced in the human parasite Encephalitozoon intestinalis with 86% archaeal and 14% bacterial derived genes. The most bacterial eukaryote genome sampled is rice, with 67% bacterial and 33% archaeal genes. The functional dichotomy, initially described for yeast, of archaeal genes being involved in genetic information processing and bacterial genes being involved in metabolic processes is conserved across all eukaryotic supergroups.

scholarly journals Genome Reduction Is Associated with Bacterial Pathogenicity across Different Scales of Temporal and Ecological Divergence

2020 ◽  
Author(s):  
Gemma G R Murray ◽  
Jane Charlesworth ◽  
Eric L Miller ◽  
Michael J Casey ◽  
Catrin T Lloyd ◽  
...  
Keyword(s):  
Gene Loss ◽  
Gc Content ◽  
Genome Reduction ◽  
Metabolic Capacity ◽  
Host Restriction ◽  
Common Features ◽  
Bacterial Pathogenicity ◽  
Reduced Genome ◽  
Bacterial Endosymbionts ◽  
Genetic Clusters

Abstract Emerging bacterial pathogens threaten global health and food security, and so it is important to ask whether these transitions to pathogenicity have any common features. We present a systematic study of the claim that pathogenicity is associated with genome reduction and gene loss. We compare broad-scale patterns across all bacteria, with detailed analyses of Streptococcus suis, an emerging zoonotic pathogen of pigs, which has undergone multiple transitions between disease and carriage forms. We find that pathogenicity is consistently associated with reduced genome size across three scales of divergence (between species within genera, and between and within genetic clusters of S. suis). Although genome reduction is also found in mutualist and commensal bacterial endosymbionts, genome reduction in pathogens cannot be solely attributed to the features of their ecology that they share with these species, that is, host restriction or intracellularity. Moreover, other typical correlates of genome reduction in endosymbionts (reduced metabolic capacity, reduced GC content, and the transient expansion of nonfunctional elements) are not consistently observed in pathogens. Together, our results indicate that genome reduction is a consistent correlate of pathogenicity in bacteria.

scholarly journals Stage-Specific and Selective Delivery of Caged Azidosugars into the Intracellular Parasite Toxoplasma gondii by Using an Esterase-Ester Pair Technique

mSphere ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Tadakimi Tomita ◽  
Hua Wang ◽  
Peng Wu ◽  
Louis M. Weiss
Keyword(s):  
Toxoplasma Gondii ◽  
Small Molecules ◽  
Click Chemistry ◽  
Cell Biology ◽  
Host Cells ◽  
Intracellular Parasite ◽  
Content Type ◽  
Intracellular Parasites ◽  
Specific Manner ◽  
Selective Delivery

ABSTRACT Toxoplasma gondii is an obligate intracellular parasite that chronically infects up to a third of the human population. The parasites persist in the form of cysts in the central nervous system and serve as a reservoir for the reactivation of toxoplasmic encephalitis. The cyst wall is known to have abundant O-linked N-acetylgalactosamine glycans, but the existing metabolic labeling methods do not allow selective labeling of intracellular parasite glycoproteins without labeling of host glycans. In this study, we have integrated Cu(I)-catalyzed bioorthogonal click chemistry with a specific esterase-ester pair system in order to selectively deliver azidosugars to the intracellular parasites. We demonstrated that α-cyclopropyl modified GalNAz was cleaved by porcine liver esterase produced in the parasites but not in the host cells. Our proof-of-concept study demonstrates the feasibility and potential of this esterase-ester click chemistry approach for the selective delivery of small molecules in a stage-specific manner. IMPORTANCE Selective delivery of small molecules into intracellular parasites is particularly problematic due to the presence of multiple membranes and surrounding host cells. We have devised a method that can deliver caged molecules into an intracellular parasite, Toxoplasma gondii, that express an uncaging enzyme in a stage-specific manner without affecting host cell biology. This system provides a valuable tool for studying many intracellular parasites.

scholarly journals Genome reduction is associated with bacterial pathogenicity across different scales of temporal and ecological divergence

2020 ◽  
Author(s):  
Gemma G. R. Murray ◽  
Jane Charlesworth ◽  
Eric L. Miller ◽  
Michael J. Casey ◽  
Catrin T. Lloyd ◽  
...  
Keyword(s):  
Gene Loss ◽  
Gc Content ◽  
Predictive Marker ◽  
Genome Reduction ◽  
Metabolic Capacity ◽  
Host Restriction ◽  
Bacterial Pathogenicity ◽  
Reduced Genome ◽  
Bacterial Endosymbionts ◽  
Genetic Clusters

AbstractEmerging bacterial pathogens threaten global health and food security, and so it is important to ask whether these transitions to pathogenicity have any common features. We present a systematic study of the claim that pathogenicity is associated with genome reduction and gene loss. We compare broad-scale patterns across all bacteria, with detailed analyses of Streptococcus suis, a zoonotic pathogen of pigs, which has undergone multiple transitions between disease and carriage forms. We find that pathogenicity is consistently associated with reduced genome size across three scales of divergence (between species within genera, and between and within genetic clusters of S. suis). While genome reduction is most often associated with bacterial endosymbionts, other correlates of symbiosis (reduced metabolic capacity, GC content, and the expansion of non-coding elements) are not found consistently in pathogens, and genome reduction in pathogens cannot be attributed to changes in intracellularity or host restriction. Together, our results indicate that genome reduction is a predictive marker of pathogenicity in bacteria, and that the causes and consequences of genome reduction in pathogens are sometimes distinct from those in endosymbionts.

Comparative Studies of Policy Dynamics

2011 ◽  
Vol 44 (8) ◽  
pp. 947-972 ◽  
Author(s):  
Frank R. Baumgartner ◽  
Bryan D. Jones ◽  
John Wilkerson
Keyword(s):  
Public Policy ◽  
Policy Change ◽  
Classification System ◽  
Comparative Studies ◽  
Special Issue ◽  
Comparative Analyses ◽  
Time Period ◽  
Policy Dynamics ◽  
Over Time ◽  
New Infrastructure

Major new understandings of policy change are emerging from a program to measure attention to policies across nations using the same instrument. Participants in this special issue have created new indicators of government activities in 11 countries over several decades. Each database is comprehensive in that it includes information about every activity of its type (e.g., laws, bills, parliamentary questions, prime ministerial speeches) for the time period covered, typically several decades. These databases are linked by a common policy topic classification system, which allows new types of analyses of public policy dynamics over time. The authors introduce the theoretical and practical questions addressed in the volume, explain the nature of the work completed, and suggest some of the ways that this new infrastructure may allow new types of comparative analyses of public policy, institutions, and outcomes. In particular, the authors challenge political scientists to incorporate policy variability into their analyses and to move far beyond the search for partisan and electoral explanations of policy change.

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