scholarly journals Captivating Perplexities of Spinareovirinae 5′ RNA Caps

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 294
Author(s):  
Justine Kniert ◽  
Qi Feng Lin ◽  
Maya Shmulevitz
Keyword(s):  
Immune Recognition ◽  
Domains Of Life ◽  
The Many ◽  
Rna Capping ◽  
Multiple Domains ◽  
Rna Caps

RNAs with methylated cap structures are present throughout multiple domains of life. Given that cap structures play a myriad of important roles beyond translation, such as stability and immune recognition, it is not surprising that viruses have adopted RNA capping processes for their own benefit throughout co-evolution with their hosts. In fact, that RNAs are capped was first discovered in a member of the Spinareovirinae family, Cypovirus, before these findings were translated to other domains of life. This review revisits long-past knowledge and recent studies on RNA capping among members of Spinareovirinae to help elucidate the perplex processes of RNA capping and functions of RNA cap structures during Spinareovirinae infection. The review brings to light the many uncertainties that remain about the precise capping status, enzymes that facilitate specific steps of capping, and the functions of RNA caps during Spinareovirinae replication.

What Is Creativity?

2018 ◽  
pp. 23-45
Keyword(s):  
Work Environments ◽  
Creative People ◽  
Traditional Work ◽  
The Many ◽  
Multiple Domains ◽  
Creativity And Innovation

The mystique of creativity has many facets. There are conflicting ideas about what creativity means and often there seems to be a lot of misunderstanding about the nature of creative people. The authors believe that creativity has many layers and can be applied across multiple domains to support the workplace and the potential of the workforce. In this chapter, the authors will discuss the definitions of creativity and connections to innovation, identify how the many facets of creativity might impact the workplace and workforce, and some common myths/misconceptions about creativity and innovation that might influence the general perceptions about creative people and their place in traditional work environments. The purpose of this chapter is to explore the perceptions about and meaning of creativity.

scholarly journals Holins in Bacteria, Eukaryotes, and Archaea: Multifunctional Xenologues with Potential Biotechnological and Biomedical Applications

2014 ◽  
Vol 197 (1) ◽  
pp. 7-17 ◽  
Author(s):  
Milton H. Saier ◽  
Bhaskara L. Reddy
Keyword(s):  
Cell Death ◽  
Biomedical Applications ◽  
Cell Lysis ◽  
Gram Negative Bacteria ◽  
Bacterial Genomes ◽  
Future Studies ◽  
Virion Release ◽  
Cytoplasmic Membranes ◽  
Domains Of Life ◽  
The Many

Holins form pores in the cytoplasmic membranes of bacteria for the primary purpose of releasing endolysins that hydrolyze the cell wall and induce cell death. Holins are encoded within bacteriophage genomes, where they promote cell lysis for virion release, and within bacterial genomes, where they serve a diversity of potential or established functions. These include (i) release of gene transfer agents, (ii) facilitation of programs of differentiation such as those that allow sporulation and spore germination, (iii) contribution to biofilm formation, (iv) promotion of responses to stress conditions, and (v) release of toxins and other proteins. There are currently 58 recognized families of holins and putative holins with members exhibiting between 1 and 4 transmembrane α-helical spanners, but many more families have yet to be discovered. Programmed cell death in animals involves holin-like proteins such as Bax and Bak that may have evolved from bacterial holins. Holin homologues have also been identified in archaea, suggesting that these proteins are ubiquitous throughout the three domains of life. Phage-mediated cell lysis of dual-membrane Gram-negative bacteria also depends on outer membrane-disrupting “spanins” that function independently of, but in conjunction with, holins and endolysins. In this minireview, we provide an overview of their modes of action and the first comprehensive summary of the many currently recognized and postulated functions and uses of these cell lysis systems. It is anticipated that future studies will result in the elucidation of many more such functions and the development of additional applications.

scholarly journals Interpreting and integrating big data in the life sciences

2019 ◽  
Author(s):  
Serghei Mangul
Keyword(s):  
Big Data ◽  
Life Science ◽  
Life Sciences ◽  
Reproducible Research ◽  
Computational Techniques ◽  
Omics Data ◽  
Omics Technologies ◽  
Domains Of Life ◽  
The Many ◽  
Review Current

Recent advances in omics technologies have led to the broad applicability of computational techniques across various domains of life science and medical research. These technologies provide an unprecedented opportunity to collect omics data from hundreds of thousands of individuals and to study gene-disease association without the aid of prior assumptions about the trait biology. Despite the many advantages of modern omics technologies, interpretations of big data produced by such technologies require advanced computational algorithms. Below I outline key challenges that biomedical researches are facing when interpreting and integrating big omics data. I discuss the reproducibility aspect of big data analysis in the life sciences and review current practices in reproducible research. Finally, I explain the skills which biomedical researchers need to acquire in order to independently analyze big omics data.

scholarly journals Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression

2019 ◽  
Vol 48 (1) ◽  
pp. 121-163 ◽  
Author(s):  
Rob Phillips ◽  
Nathan M. Belliveau ◽  
Griffin Chure ◽  
Hernan G. Garcia ◽  
Manuel Razo-Mejia ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Dna Sequences ◽  
Binding Sites ◽  
Regulatory Sequence ◽  
Theoretical Predictions ◽  
Domains Of Life ◽  
History Of ◽  
Predictive Understanding ◽  
The Many

It is tempting to believe that we now own the genome. The ability to read and rewrite it at will has ushered in a stunning period in the history of science. Nonetheless, there is an Achilles’ heel exposed by all of the genomic data that has accrued: We still do not know how to interpret them. Many genes are subject to sophisticated programs of transcriptional regulation, mediated by DNA sequences that harbor binding sites for transcription factors, which can up- or down-regulate gene expression depending upon environmental conditions. This gives rise to an input–output function describing how the level of expression depends upon the parameters of the regulated gene—for instance, on the number and type of binding sites in its regulatory sequence. In recent years, the ability to make precision measurements of expression, coupled with the ability to make increasingly sophisticated theoretical predictions, has enabled an explicit dialogue between theory and experiment that holds the promise of covering this genomic Achilles’ heel. The goal is to reach a predictive understanding of transcriptional regulation that makes it possible to calculate gene expression levels from DNA regulatory sequence. This review focuses on the canonical simple repression motif to ask how well the models that have been used to characterize it actually work. We consider a hierarchy of increasingly sophisticated experiments in which the minimal parameter set learned at one level is applied to make quantitative predictions at the next. We show that these careful quantitative dissections provide a template for a predictive understanding of the many more complex regulatory arrangements found across all domains of life.

Twin-Singleton Comparisons Across Multiple Domains of Life

2021 ◽  
pp. 51-71
Author(s):  
Gonneke Willemsen ◽  
Veronika Odintsova ◽  
Eco de Geus ◽  
Dorret I. Boomsma
Keyword(s):  
Domains Of Life ◽  
Multiple Domains

Treatment of Chronic Pain

2021 ◽  
pp. 141-156
Author(s):  
John D. Otis
Keyword(s):  
Chronic Pain ◽  
Gold Standard ◽  
Subjective Experience ◽  
Pain Treatment ◽  
Psychological Treatment ◽  
Negative Mood ◽  
Cognitive Behavioral ◽  
Psychological Treatments ◽  
Domains Of Life ◽  
The Many

Chronic pain is a highly prevalent condition that causes substantial impairment in many domains of life. Recent advances in pain research have elucidated the many biological, psychological, and social factors that can contribute to and impact the subjective experience of pain. In addition to treating patients using medications to manage pain, psychological treatments have now been developed and tested and found to significantly improve the severity of pain and the negative mood that often accompanies pain, as well as disability and impairment. Cognitive behavioral approaches are now considered the “gold standard” psychological treatment for pain. To maximize their efficacy, however, these treatments are not implemented rigidly; rather, they are tailored to the particular needs of the patient. This chapter covers the essential treatment components for pain and offers therapists ideas for effectively tailoring treatment to individual patients, so that pain treatment can be implemented flexibly, but with fidelity.

scholarly journals An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism

2020 ◽  
Author(s):  
Mitchell G. Thompson ◽  
Jacquelyn M. Blake-Hedges ◽  
Jose Henrique Pereira ◽  
John A. Hangasky ◽  
Michael S. Belcher ◽  
...  
Keyword(s):  
Physiological Function ◽  
Germination Rate ◽  
Structural Similarity ◽  
Free Form ◽  
Dependent Manner ◽  
Bacterial Fermentation ◽  
Sequence Identity ◽  
Domains Of Life ◽  
Multiple Domains ◽  
Lysine Catabolism

AbstractDue to low abundance in many staple food crops, the essential amino acid lysine must be produced industrially to meet global food supply needs. Despite intensive study, manipulation, and agricultural importance, the steps of plant lysine catabolism beyond the 2-oxoadipate (2OA) intermediate remain undescribed. Recently we described a missing step in the D-lysine catabolic pathway of the bacterium Pseudomonas putida in which 2OA is converted to D-2-hydroxyglutarate (D2HG) via hydroxyglutarate synthase (HglS), an enzyme belonging to the previously uncharacterized DUF1338 protein family. Here we solve the structure of HglS to 1.1Å resolution in the substrate-free form and in complex with 2OA. Structural similarity to hydroxymandelate synthase suggested a successive decarboxylation and intramolecular hydroxylation mechanism forming 2HG in a Fe(II)- and O2-dependent manner, which is validated experimentally. 2OA specificity was mediated by a single arginine (R74), highly conserved across nearly all DUF1338 family proteins, including in 76% of plant enzymes. In Arabidopsis thaliana, a DUF1338 homolog is coexpressed with known lysine catabolism enzymes, and mutants show significant germination rate defects consistent with disrupted lysine catabolism. Structural and biochemical analysis of the Oryza sativa homolog FLO7 revealed identical activity to HglS despite low sequence identity. Our results suggest that nearly all DUF1338 containing enzymes likely catalyze the same biochemical reaction, exerting the same physiological function across bacteria and eukaryotes.SignificanceTo meet human demands, millions of tons of lysine are produced by bacterial fermentation annually due to its low abundance in staple crops. Here, we show the last missing step of lysine catabolism in nearly all plant endosperms is likely catalyzed by an iron-dependant DUF1338-containing enzyme homologous to the bacterial hydroxyglutarate synthase. Structural and bioninformatic analyses of DUF1338-containing enzymes showed high conservation of critical catalytic and specificity-conferring residues across multiple domains of life despite low sequence identity. These results suggest that the DUF1338 family evolved a specific physiological function within lysine catabolism across multiple domains of life.

scholarly journals Black Lives Matter: A Theological Response to Racism’s Impact on the Black Body in the United States

2017 ◽  
Vol 43 (1) ◽  
pp. 28-45
Author(s):  
Christine M. Mitchell ◽  
David R. Williams
Keyword(s):  
United States ◽  
Predominantly White ◽  
Black Body ◽  
The United States ◽  
The Body ◽  
Black Lives Matter ◽  
National Conversation ◽  
The Many ◽  
The Life Course ◽  
Multiple Domains

After the killing of 18-year-old Michael Brown by police in Ferguson, Missouri in August 2014, there has been a renewed movement in the United States and across the world in support of black lives. The movement, under the guiding framework of Black Lives Matter, has resulted in a national conversation on police brutality and racism, and the violent effects these have on the black body. Using the framework of black theological thought on the body, this paper identifies the many ways that racism, as Ta-Nehisi Coates writes, “lands, with great violence, upon the body” across multiple domains and levels throughout history and across the life course. The paper closes with some initial recommendations for historically predominantly white churches to offer an anti-racist response to this violence, as informed by black theology.

Interpreting and integrating big data in the life sciences

2019 ◽  
Vol 3 (4) ◽  
pp. 335-341 ◽  
Author(s):  
Serghei Mangul
Keyword(s):  
Big Data ◽  
Life Science ◽  
Life Sciences ◽  
Reproducible Research ◽  
Computational Techniques ◽  
Omics Data ◽  
Omics Technologies ◽  
Domains Of Life ◽  
The Many ◽  
Review Current

Abstract Recent advances in omics technologies have led to the broad applicability of computational techniques across various domains of life science and medical research. These technologies provide an unprecedented opportunity to collect the omics data from hundreds of thousands of individuals and to study the gene–disease association without the aid of prior assumptions about the trait biology. Despite the many advantages of modern omics technologies, interpretations of big data produced by such technologies require advanced computational algorithms. I outline key challenges that biomedical researches are facing when interpreting and integrating big omics data. I discuss the reproducibility aspect of big data analysis in the life sciences and review current practices in reproducible research. Finally, I explain the skills that biomedical researchers need to acquire to independently analyze big omics data.

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