scholarly journals Ecology, Structure, and Evolution of Shigella Phages

2020 ◽  
Vol 7 (1) ◽  
pp. 121-141
Author(s):  
Sundharraman Subramanian ◽  
Kristin N. Parent ◽  
Sarah M. Doore
Keyword(s):  
Defense Mechanisms ◽  
Structural Information ◽  
Bacterial Species ◽  
Model Systems ◽  
Isolation And Characterization ◽  
Shigella Species ◽  
Recent Developments ◽  
History Of ◽  
Close Relatives ◽  
Host Evolution

Numerous bacteriophages—viruses of bacteria, also known as phages—have been described for hundreds of bacterial species. The Gram-negative Shigella species are close relatives of Escherichia coli, yet relatively few previously described phages appear to exclusively infect this genus. Recent efforts to isolate Shigella phages have indicated these viruses are surprisingly abundant in the environment and have distinct genomic and structural properties. In addition, at least one model system used for experimental evolution studies has revealed a unique mechanism for developing faster infection cycles. Differences between these bacteriophages and other well-described model systems may mirror differences between their hosts’ ecology and defense mechanisms. In this review, we discuss the history of Shigella phages and recent developments in their isolation and characterization and the structural information available for three model systems, Sf6, Sf14, and HRP29; we also provide an overview of potential selective pressures guiding both Shigella phage and host evolution.

scholarly journals Evolution of the canonical sex chromosomes of the guppy and its relatives

2021 ◽  
Author(s):  
Mark Kirkpatrick ◽  
Jason M Sardell ◽  
Brendan J Pinto ◽  
Groves Dixon ◽  
Catherine L Peichel ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Best Practices ◽  
Sex Chromosomes ◽  
Linkage Mapping ◽  
Poecilia Reticulata ◽  
Model Systems ◽  
History Of ◽  
Suppressed Recombination ◽  
Close Relatives

Abstract The sex chromosomes of the guppy, Poecilia reticulata, and its close relatives are of particular interest: they are much younger than the highly degenerate sex chromosomes of model systems such as humans and Drosophila melanogaster, and they carry many of the genes responsible for the males’ dramatic coloration. Over the last decade, several studies have analyzed these sex chromosomes using a variety of approaches including sequencing genomes and transcriptomes, cytology, and linkage mapping. Conflicting conclusions have emerged, in particular concerning the history of the sex chromosomes and the evolution of suppressed recombination between the X and Y. Here we address these controversies by reviewing the evidence and reanalyzing data. We find no evidence of a nonrecombining sex determining region (SDR) or evolutionary strata in P. reticulata. Further, we find that the data most strongly support the hypothesis that the SDRs of two close relatives of the guppy, P. wingei and Micropoecilia picta, evolved independently after their lineages diverged. We identify possible causes of conflicting results in previous studies and suggest best practices going forward.

scholarly journals Evolution of the canonical sex chromosomes of the guppy and its relatives

2020 ◽  
Author(s):  
M. Kirkpatrick ◽  
G. Dixon ◽  
J.M. Sardell ◽  
M. Schartl ◽  
C. L. Peichel
Keyword(s):  
Drosophila Melanogaster ◽  
Best Practices ◽  
Dosage Compensation ◽  
Sex Chromosomes ◽  
Linkage Mapping ◽  
Poecilia Reticulata ◽  
Model Systems ◽  
History Of ◽  
Suppressed Recombination ◽  
Close Relatives

AbstractThe sex chromosomes of the guppy, Poecilia reticulata, and its close relatives are of particular interest: they are much younger than the highly degenerate sex chromosomes of model systems such as mammals and Drosophila melanogaster, and they carry many of the genes responsible for the males’ dramatic coloration. Over the last decade, several studies have analyzed these sex chromosomes using a variety of approaches including sequencing genomes and transcriptomes, cytology, and linkage mapping. Conflicting conclusions have emerged, in particular concerning the history of the sex chromosomes and the evolution of suppressed recombination between the X and Y. Here we address these controversies by reviewing the evidence and reanalyzing data. We find no support for a nonrecombining sex determining region (SDR) or evolutionary strata in P. reticulata. We confirm that its congener P. picta has evolved dosage compensation across all of its X chromosome. Last, we do not find evidence that the nonrecombining SDRs of P. picta and P. wingei descend from a common ancestral SDR, and suggest instead that suppressed recombination between the X and Y evolved independently after the two species diverged. We identify possible causes of conflicting results in previous studies and suggest best practices going forward.

scholarly journals The Past, Present and Future of Cannabis sativa Tissue Culture

Plants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 185
Author(s):  
Adrian S. Monthony ◽  
Serena R. Page ◽  
Mohsen Hesami ◽  
Andrew Maxwell P. Jones
Keyword(s):  
Tissue Culture ◽  
Disease Virus ◽  
Cannabis Sativa ◽  
Clonal Plants ◽  
Future Directions ◽  
The Past ◽  
Recent Developments ◽  
History Of ◽  
Drug Type

The recent legalization of Cannabis sativa L. in many regions has revealed a need for effective propagation and biotechnologies for the species. Micropropagation affords researchers and producers methods to rapidly propagate insect-/disease-/virus-free clonal plants and store germplasm and forms the basis for other biotechnologies. Despite this need, research in the area is limited due to the long history of prohibitions and restrictions. Existing literature has multiple limitations: many publications use hemp as a proxy for drug-type Cannabis when it is well established that there is significant genotype specificity; studies using drug-type cultivars are predominantly optimized using a single cultivar; most protocols have not been replicated by independent groups, and some attempts demonstrate a lack of reproducibility across genotypes. Due to culture decline and other problems, the multiplication phase of micropropagation (Stage 2) has not been fully developed in many reports. This review will provide a brief background on the history and botany of Cannabis as well as a comprehensive and critical summary of Cannabis tissue culture. Special attention will be paid to current challenges faced by researchers, the limitations of existing Cannabis micropropagation studies, and recent developments and future directions of Cannabis tissue culture technologies.

Transforming Historical Objectivism into Historical Hermeneutics: From “Historical Illness” to Properly Lived Historicality

2019 ◽  
Vol 61 (4) ◽  
pp. 490-515
Author(s):  
Thomas Tops
Keyword(s):  
Reception History ◽  
Biblical Studies ◽  
Historical Study ◽  
Necessary Condition ◽  
New Paradigm ◽  
History Of Interpretation ◽  
Critical Methodology ◽  
Recent Developments ◽  
History Of ◽  
Biblical Texts

Summary The present study analyses recent criticisms against the use of modern-historical methodologies in Biblical Studies. These methodologies abstract from the historical horizon of the researcher. In order to relate properly to the historicality of the researcher, historical objectivism needs to be transformed into historical hermeneutics. Recent developments in the historical methodology of biblical scholars are unable to reckon with the historicality of the researcher due to the partial or incorrect implementation of Gadamer’s views on reception history. I analyse the views of Nietzsche, Kierkegaard, and Gadamer on historicality and contend that the study of reception history is a necessary condition for conducting historical study from within the limits of our historicality. Reception history should not be a distinct methodological step to study the “Nachleben” of biblical texts, but needs to clarify how the understanding of these texts is already effected by their history of interpretation. The awareness of the presuppositions that have guided previous interpretations of biblical texts enables us to be confronted by their alterity. This confrontation calls for a synthesis between reception-historical and historical-critical methodology that introduces a new paradigm for conducting historical study in Biblical Studies in dialogue with other theological disciplines.

Why Diamonds Really are a Girl's Best Friend: Another American Narrative

Daedalus ◽  
2012 ◽  
Vol 141 (1) ◽  
pp. 89-100
Author(s):  
Linda K. Kerber
Keyword(s):  
The United States ◽  
Cultural Practice ◽  
Legal Tradition ◽  
Domestic Relations ◽  
Recent Developments ◽  
American Law ◽  
History Of ◽  
The Republic ◽  
1960S And 1970S ◽  
The 1960S

The old law of domestic relations and the system known as coverture have shaped marriage practices in the United States and have limited women's membership in the constitutional community. This system of law predates the Revolution, but it lingers in U.S. legal tradition even today. After describing coverture and the old law of domestic relations, this essay considers how the received narrative of women's place in U.S. history often obscures the story of women's and men's efforts to overthrow this oppressive regime, and also the story of the continuing efforts of men and some women to stabilize and protect it. The essay also questions the paradoxes built into American law: for example, how do we reconcile the strictures of coverture with the founders' care in defining rights-holders as “persons” rather than “men”? Citing a number of court cases from the early days of the republic to the present, the essay describes the 1960s and 1970s shift in legal interpretation of women's rights and obligations. However, recent developments – in abortion laws, for example – invite inquiry as to how full the change is that we have accomplished. The history of coverture and the way it affects legal, political, and cultural practice today is another American narrative that needs to be better understood.

scholarly journals Simulation of bonding effects in HRTEM images of light element materials

2011 ◽  
Vol 2 ◽  
pp. 394-404 ◽  
Author(s):  
Simon Kurasch ◽  
Jannik C Meyer ◽  
Daniela Künzel ◽  
Axel Groß ◽  
Ute Kaiser
Keyword(s):  
Density Functional ◽  
Structural Information ◽  
Hexagonal Boron Nitride ◽  
Light Element ◽  
Model Systems ◽  
Single Atom ◽  
Transmission Electron ◽  
Relative Contrast ◽  
Oxygen Substitution ◽  
Simulation Scheme

The accuracy of multislice high-resolution transmission electron microscopy (HRTEM) simulation can be improved by calculating the scattering potential using density functional theory (DFT) Gemming, T.; Möbus, G.; Exner, M.; Ernst, F.; Rühle, M. J. Microsc. 1998, 190, 89–98. doi:10.1046/j.1365-2818.1998.3110863.xDeng, B.; Marks, L. D. Acta Crystallogr., Sect. A 2006, 62, 208–216. doi:10.1107/S010876730601004X. This approach accounts for the fact that electrons in the specimen are redistributed according to their local chemical environment. This influences the scattering process and alters the absolute and relative contrast in the final image. For light element materials with well defined geometry, such as graphene and hexagonal boron nitride monolayers, the DFT based simulation scheme turned out to be necessary to prevent misinterpretation of weak signals, such as the identification of nitrogen substitutions in a graphene network. Furthermore, this implies that the HRTEM image does not only contain structural information (atom positions and atomic numbers). Instead, information on the electron charge distribution can be gained in addition. In order to produce meaningful results, the new input parameters need to be chosen carefully. Here we present details of the simulation process and discuss the influence of the main parameters on the final result. Furthermore we apply the simulation scheme to three model systems: A single atom boron and a single atom oxygen substitution in graphene and an oxygen adatom on graphene.

Collaborative Research Funding

2014 ◽  
Vol 36 (4) ◽  
Author(s):  
Markus Behnke ◽  
Laura McConnell ◽  
Chris Ober
Keyword(s):  
International Collaboration ◽  
Research Funding ◽  
International Committee ◽  
Research Projects ◽  
Scientific Success ◽  
Funding Sources ◽  
Chemistry Research ◽  
National Organizations ◽  
Recent Developments ◽  
History Of

Within a changing research world, international collaboration has become even more important in achieving scientific success. Given the increased need and desire for multinational research, the actors are forced to identify appropriate funding sources. Whereas, science knows no international boundaries, support for scientific research, including in chemical sciences, is mostly provided by the national funding organizations. This is particularly true for the chemical sciences, where most research projects are relatively small in size and with respect to the number of involved PIs. Traditionally, national organizations are reluctant to provide funds to non-domestic researchers, and in practice, funding truly international research projects can be a real challenge for a variety of technical and bureaucratic reasons. In an effort to change this, an international Committee on Chemistry Research Funding (CCRF)—backed by several leading funding organizations—was established by IUPAC in December 2007 to promote increased international collaboration and networking in the global chemistry community. The following report gives a short overview on the history of IUPAC’s involvement in service for chemistry research funding and on the most recent developments.

scholarly journals A Cryptic Non-Inducible Prophage Confers Phage-Immunity on the Streptococcus thermophilus M17PTZA496

Viruses ◽  
2018 ◽  
Vol 11 (1) ◽  
pp. 7 ◽  
Author(s):  
Vinícius da Silva Duarte ◽  
Sabrina Giaretta ◽  
Stefano Campanaro ◽  
Laura Treu ◽  
Andrea Armani ◽  
...  
Keyword(s):  
Mitomycin C ◽  
Defense Mechanisms ◽  
Large Subunit ◽  
Bacterial Species ◽  
Dairy Industry ◽  
Model Organism ◽  
Streptococcus Thermophilus ◽  
Starter Cultures ◽  
Economic Losses ◽  
Important Species

Streptococcus thermophilus is considered one of the most important species for the dairy industry. Due to their diffusion in dairy environments, bacteriophages can represent a threat to this widely used bacterial species. Despite the presence of a CRISPR-Cas system in the S. thermophilus genome, some lysogenic strains harbor cryptic prophages that can increase the phage-host resistance defense. This characteristic was identified in the dairy strain S. thermophilus M17PTZA496, which contains two integrated prophages 51.8 and 28.3 Kb long, respectively. In the present study, defense mechanisms, such as a lipoprotein-encoding gene and Siphovirus Gp157, the last associated to the presence of a noncoding viral DNA element, were identified in the prophage M17PTZA496 genome. The ability to overexpress genes involved in these defense mechanisms under specific stressful conditions, such as phage attack, has been demonstrated. Despite the addition of increasing amounts of Mitomycin C, M17PTZA496 was found to be non-inducible. However, the transcriptional activity of the phage terminase large subunit was detected in the presence of the antagonist phage vB_SthS-VA460 and of Mitomycin C. The discovery of an additional immune mechanism, associated with bacteriophage-insensitive strains, is of utmost importance, for technological applications and industrial processes. To our knowledge, this is the first study reporting the capability of a prophage integrated into the S. thermophilus genome expressing different phage defense mechanisms. Bacteriophages are widespread entities that constantly threaten starter cultures in the dairy industry. In cheese and yogurt manufacturing, the lysis of Streptococcus thermophilus cultures by viral attacks can lead to huge economic losses. Nowadays S. thermophilus is considered a well-stablished model organism for the study of natural adaptive immunity (CRISPR-Cas) against phage and plasmids, however, the identification of novel bacteriophage-resistance mechanisms, in this species, is strongly desirable. Here, we demonstrated that the presence of a non-inducible prophage confers phage-immunity to an S. thermophilus strain, by the presence of ltp and a viral noncoding region. S. thermophilus M17PTZA496 arises as an unconventional model to study phage resistance and potentially represents an alternative starter strain for dairy productions.

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