Forty years of helminth biochemistry

Parasitology ◽  
2009 ◽  
Vol 136 (12) ◽  
pp. 1633-1642 ◽  
Author(s):  
J. BARRETT
Keyword(s):  
Genome Sequencing ◽  
High Throughput ◽  
Mode Of Action ◽  
Mechanisms Of Resistance ◽  
Catabolic Pathways ◽  
Parasitic Helminths ◽  
Biological Relevance ◽  
New Information ◽  
The Future

SUMMARYThis review describes some of the developments in helminth biochemistry that have taken place over the last 40 years. Since the early 1970s the main anabolic and catabolic pathways in parasitic helminths have been worked out. The mode of action of the majority of anthelmintics is now known, but in many cases the mechanisms of resistance remain elusive. Developments in helminth biochemistry have depended heavily on developments in other areas. High throughput methods such as proteomics, transcriptomics and genome sequencing are now generating vast amounts of new data. The challenge for the future is to interpret and understand the biological relevance of this new information.

Phase emendation of high-throughput genome sequencing

2010 ◽  
Vol 30 (4) ◽  
pp. 1114-1116
Author(s):  
Bing-gang YE ◽  
De-peng WANG ◽  
Jing-xiang LI ◽  
Yan ZHOU ◽  
Xiao-ming WU
Keyword(s):  
Genome Sequencing ◽  
High Throughput

scholarly journals A Roadmap for Genome-Based Phage Taxonomy

Viruses ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 506
Author(s):  
Dann Turner ◽  
Andrew M. Kropinski ◽  
Evelien M. Adriaenssens
Keyword(s):  
Genome Sequencing ◽  
Classification System ◽  
The State ◽  
Family Level ◽  
The Future

Bacteriophage (phage) taxonomy has been in flux since its inception over four decades ago. Genome sequencing has put pressure on the classification system and recent years have seen significant changes to phage taxonomy. Here, we reflect on the state of phage taxonomy and provide a roadmap for the future, including the abolition of the order Caudovirales and the families Myoviridae, Podoviridae, and Siphoviridae. Furthermore, we specify guidelines for the demarcation of species, genus, subfamily and family-level ranks of tailed phage taxonomy.

scholarly journals Experimental evolution of gallium resistance in Escherichia coli

2019 ◽  
Vol 2019 (1) ◽  
pp. 169-180
Author(s):  
Joseph L Graves ◽  
Akamu J Ewunkem ◽  
Jason Ward ◽  
Constance Staley ◽  
Misty D Thomas ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Experimental Evolution ◽  
Molecular Mechanisms ◽  
Gallium Nitrate ◽  
Whole Genome ◽  
Mechanisms Of Resistance ◽  
Genomic Changes ◽  
K 12

Abstract Background and Objectives Metallic antimicrobial materials are of growing interest due to their potential to control pathogenic and multidrug-resistant bacteria. Yet we do not know if utilizing these materials can lead to genetic adaptations that produce even more dangerous bacterial varieties. Methodology Here we utilize experimental evolution to produce strains of Escherichia coli K-12 MG1655 resistant to, the iron analog, gallium nitrate (Ga(NO3)3). Whole genome sequencing was utilized to determine genomic changes associated with gallium resistance. Computational modeling was utilized to propose potential molecular mechanisms of resistance. Results By day 10 of evolution, increased gallium resistance was evident in populations cultured in medium containing a sublethal concentration of gallium. Furthermore, these populations showed increased resistance to ionic silver and iron (III), but not iron (II) and no increase in traditional antibiotic resistance compared with controls and the ancestral strain. In contrast, the control populations showed increased resistance to rifampicin relative to the gallium-resistant and ancestral population. Genomic analysis identified hard selective sweeps of mutations in several genes in the gallium (III)-resistant lines including: fecA (iron citrate outer membrane transporter), insl1 (IS30 tranposase) one intergenic mutations arsC →/→ yhiS; (arsenate reductase/pseudogene) and in one pseudogene yedN ←; (iapH/yopM family). Two additional significant intergenic polymorphisms were found at frequencies > 0.500 in fepD ←/→ entS (iron-enterobactin transporter subunit/enterobactin exporter, iron-regulated) and yfgF ←/→ yfgG (cyclic-di-GMP phosphodiesterase, anaerobic/uncharacterized protein). The control populations displayed mutations in the rpoB gene, a gene associated with rifampicin resistance. Conclusions This study corroborates recent results observed in experiments utilizing pathogenic Pseudomonas strains that also showed that Gram-negative bacteria can rapidly evolve resistance to an atom that mimics an essential micronutrient and shows the pleiotropic consequences associated with this adaptation. Lay summary We utilize experimental evolution to produce strains of Escherichia coli K-12 MG1655 resistant to, the iron analog, gallium nitrate (Ga(NO3)3). Whole genome sequencing was utilized to determine genomic changes associated with gallium resistance. Computational modeling was utilized to propose potential molecular mechanisms of resistance.

scholarly journals Genome sequencing of linezolid-resistant Streptococcus pneumoniae mutants reveals novel mechanisms of resistance

2009 ◽  
Vol 19 (7) ◽  
pp. 1214-1223 ◽  
Author(s):  
J. Feng ◽  
A. Lupien ◽  
H. Gingras ◽  
J. Wasserscheid ◽  
K. Dewar ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Genome Sequencing ◽  
Mechanisms Of Resistance

DNA-Directed Patterning for Versatile Validation and Characterization of a Lipid-Based Nanoparticle Model of SARS-CoV-2

2021 ◽  
Author(s):  
Molly Kozminsky ◽  
Thomas Carey ◽  
Lydia L. Sohn
Keyword(s):  
High Throughput ◽  
Glass Substrate ◽  
Rapid Development ◽  
Neutralizing Antibody ◽  
S Protein ◽  
Biological Relevance ◽  
The Face ◽  
Great Control ◽  
Tetraspanin Cd63

Lipid-based nanoparticles have risen to the forefront of the COVID-19 pandemic—from encapsulation of vaccine components to modeling the virus, itself. Their rapid development in the face of the volatile nature of the pandemic requires high-throughput, highly flexible methods for characterization. DNA-directed patterning is a versatile method to immobilize and segregate lipid-based nanoparticles for subsequent analysis. DNA-directed patterning selectively conjugates oligonucleotides onto a glass substrate and then hybridizes them to complementary oligonucleotides tagged to the liposomes, thereby patterning them with great control and precision. The power of this method is demonstrated by characterizing a novel recapitulative lipid-based nanoparticle model of SARS-CoV-2 —S-liposomes— which present the SARS-CoV-2 spike (S) protein on their surfaces. Patterning of a mixture of S-liposomes and liposomes that display the tetraspanin CD63 into discrete regions of a substrate is used to show that ACE2 specifically binds to S-liposomes. Importantly, DNA-directed patterning of S-liposomes is used to verify the performance of a commercially available neutralizing antibody against the S protein. Ultimately, the introduction of S-liposomes to ACE2-expressing cells demonstrates the biological relevance of DNA-directed patterning. Overall, DNA-directed patterning enables a wide variety of custom assays for the characterization of any lipid-based nanoparticle.

Looking backward to the future: Counter-memory as oppositional knowledge-production in the Israeli–Palestinian conflict

2016 ◽  
Vol 65 (1) ◽  
pp. 54-72 ◽  
Author(s):  
Yifat Gutman
Keyword(s):  
Knowledge Production ◽  
Historical Narrative ◽  
Temporal Shift ◽  
Palestinian Refugees ◽  
The Past ◽  
Historical Justice ◽  
New Information ◽  
The Future ◽  
Peace Activism ◽  
Activist Groups

This article examines a strategy of peace activism that gained visibility in the last decades: memory activism. Memory activists manifest a temporal shift in transnational politics: first the past, then the future. Affiliated with the globally-circulating paradigm of historical justice, memory activist groups assume that a new understanding of the past could lead to a new perception of present problems and project alternative solutions for the future. Based on ethnographic fieldwork and discourse analysis among memory activists of the 1948 war in Israel since 2001, the article examines the activist production of counter-memory during active conflict. Using Coy et al.’s typology of oppositional knowledge-production, the article shows how the largest group of memory activism in Israel produced ‘new’ information on the war, critically assessed the dominant historical narrative, offered an alternative shared narrative, and began to envision practical solutions for Palestinian refugees. However, the analysis raises additional concerns that reach beyond the scope of the typology, primarily regarding the unequal power relations that exist not only between the dominant and activist production of oppositional knowledge, but also among activists.

scholarly journals Is our perception of the spread of COVID-19 inherently inaccurate?

2021 ◽  
Author(s):  
Alexander Maier
Keyword(s):  
Decision Making ◽  
Subjective Perception ◽  
Logarithmic Function ◽  
Original Formulation ◽  
Global Crisis ◽  
New Information ◽  
The World ◽  
Non Linear ◽  
The Future ◽  
Linear Nature

One of the most fundamental insights into the nature of our subjective perception of the world around us is that it is not veridical. In other words, we tend to not perceive information about the world around us accurately. Instead, our brains interpret new information through a host of innate and learned mechanisms that can introduce bias and distortions One of the best studied mechanisms that guide – and distort – our perception is the psychophysical Weber-Fechner law. According to this empirically derived, mathematically formulated law we tend to put more emphasis on smaller deviations in size while underestimating larger changes. The original formulation of the Weber-Fechner law takes the shape of a logarithmic function and is commonly applied to somatosensory perception such as the weight of an object. However, later work showed that the Weber-Fechner law can be generalized and describe a large variety of perceived changes in magnitude that even go beyond the sensory domain. Here we investigate the hypothesis that our perception of data associated with the spread of COVID-19 and similar pandemics is governed by the same psychophysical laws. Based on several recently published studies, we demonstrate that the Weber-Fechner law can be shown to directly affect the decision-making of officials in response to this global crisis as well as the greater public at large. We discuss how heightened awareness of the non-linear nature of subjective perception could help alleviate problematic judgements in similar situations in the future.

Rapid, high throughput library preparation of SARS-CoV2 using Illumina’s DNA Prep Library Preparation Kit v2

2022 ◽  
Author(s):  
Jason Nguyen ◽  
Rebecca Hickman ◽  
Tracy Lee ◽  
Natalie Prystajecky ◽  
John Tyson
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
High Throughput ◽  
Illumina Miseq ◽  
Whole Genome ◽  
Library Preparation ◽  
Dna Libraries ◽  
Reaction Volumes ◽  
Single Size ◽  
Stop Buffer

This procedure provides instructions on how to prepare DNA libraries for whole genome sequencing on an Illumina MiSeq or NextSeq using Illumina’s DNA Prep Library Preparation Kit scaled to half reaction volumes with modifications to the post-PCR procedures; tagmentation stop buffer and associated washes are removed and libraries are pooled post PCR then a single size selection is performed. This protocol is used to sequence SARS-CoV-2 using the cDNA/PCR protocol: https://dx.doi.org/10.17504/protocols.io.b3viqn4e

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