Development of Industrial Strain, Medium Characteristics and Biochemical Pathways

While most advances in the study of the origin of life on Earth (OoLoE) are piecemeal, tested against the laws of chemistry and physics, ultimately the goal is to develop an overall scenario for life’s origin(s). However, the dimensionality of non-equilibrium chemical systems, from the range of possible boundary conditions and chemical interactions, renders the application of chemical and physical laws difficult. Here we outline a set of simple criteria for evaluating OoLoE scenarios. These include the need for containment, steady energy and material flows, and structured spatial heterogeneity from the outset. The Principle of Continuity, the fact that all life today was derived from first life, suggests favoring scenarios with fewer non-analog (not seen in life today) to analog (seen in life today) transitions in the inferred first biochemical pathways. Top-down data also indicate that a complex metabolism predated ribozymes and enzymes, and that full cellular autonomy and motility occurred post-LUCA. Using these criteria, we find the alkaline hydrothermal vent microchamber complex scenario with a late evolving exploitation of the natural occurring pH (or Na+ gradient) by ATP synthase the most compelling. However, there are as yet so many unknowns, we also advocate for the continued development of as many plausible scenarios as possible.

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Our Evolving Understanding of ME/CFS

Medicina ◽

10.3390/medicina57030200 ◽

2021 ◽

Vol 57 (3) ◽

pp. 200 ◽

Cited By ~ 1

Author(s):

Kenneth J. Friedman ◽

Modra Murovska ◽

Derek F. H. Pheby ◽

Paweł Zalewski

Keyword(s):

Active Phase ◽

Case Definitions ◽

Diagnostic Laboratory ◽

Biochemical Pathways ◽

Patient Organizations ◽

Clinical Consequences ◽

Potential Benefits ◽

Multiple Case ◽

Use Of The Internet ◽

The Uk

The potential benefits of the scientific insights gleaned from years of treating ME/CFS for the emerging symptoms of COVID-19, and in particular Longhaul- or Longhauler-COVID-19 are discussed in this opinion article. Longhaul COVID-19 is the current name being given to the long-term sequelae (symptoms lasting beyond 6 weeks) of SARS-CoV-2 infection. Multiple case definitions for ME/CFS exist, but post-exertional malaise (PEM) is currently emerging as the ‘hallmark’ symptom. The inability to identify a unique trigger of ME/CFS, as well as the inability to identify a specific, diagnostic laboratory test, led many physicians to conclude that the illness was psychosomatic or non-existent. However, recent research in the US and the UK, championed by patient organizations and their use of the internet and social media, suggest underlying pathophysiologies, e.g., oxidative stress and mitochondrial dysfunction. The similarity and overlap of ME/CFS and Longhaul COVID-19 symptoms suggest to us similar pathological processes. We put forward a unifying hypothesis that explains the precipitating events such as viral triggers and other documented exposures: For their overlap in symptoms, ME/CFS and Longhaul COVID-19 should be described as Post Active Phase of Infection Syndromes (PAPIS). We further propose that the underlying biochemical pathways and pathophysiological processes of similar symptoms are similar regardless of the initiating trigger. Exploration of the biochemical pathways and pathophysiological processes should yield effective therapies for these conditions and others that may exhibit these symptoms. ME/CFS patients have suffered far too long. Longhaul COVD-19 patients should not be subject to a similar fate. We caution that failure to meet the now combined challenges of ME/CFS and Longhaul COVID-19 will impose serious socioeconomic as well as clinical consequences for patients, the families of patients, and society as a whole.

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General Unified Microbiome Profiling Pipeline (GUMPP) for Large Scale, Streamlined and Reproducible Analysis of Bacterial 16S rRNA Data to Predicted Microbial Metagenomes, Enzymatic Reactions and Metabolic Pathways

Metabolites ◽

10.3390/metabo11060336 ◽

2021 ◽

Vol 11 (6) ◽

pp. 336

Author(s):

Boštjan Murovec ◽

Leon Deutsch ◽

Blaž Stres

Keyword(s):

16S Rrna ◽

Metabolic Pathways ◽

Large Scale ◽

Enzymatic Reactions ◽

Operational Taxonomic Units ◽

Biochemical Pathways ◽

Meaningful Information ◽

Novel Biomarkers ◽

Reproducible Analysis ◽

Microbiome Profiling

General Unified Microbiome Profiling Pipeline (GUMPP) was developed for large scale, streamlined and reproducible analysis of bacterial 16S rRNA data and prediction of microbial metagenomes, enzymatic reactions and metabolic pathways from amplicon data. GUMPP workflow introduces reproducible data analyses at each of the three levels of resolution (genus; operational taxonomic units (OTUs); amplicon sequence variants (ASVs)). The ability to support reproducible analyses enables production of datasets that ultimately identify the biochemical pathways characteristic of disease pathology. These datasets coupled to biostatistics and mathematical approaches of machine learning can play a significant role in extraction of truly significant and meaningful information from a wide set of 16S rRNA datasets. The adoption of GUMPP in the gut-microbiota related research enables focusing on the generation of novel biomarkers that can lead to the development of mechanistic hypotheses applicable to the development of novel therapies in personalized medicine.

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Individual performances and biochemical pathways as altered by field-realistic exposures of current-use fungicides and their mixtures in a non-target species, Gammarus fossarum

Chemosphere ◽

10.1016/j.chemosphere.2021.130277 ◽

2021 ◽

Vol 277 ◽

pp. 130277

Author(s):

Jérémie D. Lebrun ◽

Kelly De Jesus ◽

Julien Tournebize

Keyword(s):

Target Species ◽

Gammarus Fossarum ◽

Biochemical Pathways

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Cytokines as Biomarkers and Their Respective Clinical Cutoff Levels

International Journal of Inflammation ◽

10.1155/2017/4309485 ◽

2017 ◽

Vol 2017 ◽

pp. 1-11 ◽

Cited By ~ 51

Author(s):

Rebecca N. Monastero ◽

Srinivas Pentyala

Keyword(s):

Tumor Necrosis ◽

Inflammatory Diseases ◽

Low Cost ◽

The Body ◽

Tumor Necrosis Factors ◽

Biochemical Pathways ◽

Downstream Effects ◽

Future Work ◽

Receiver Operator Characteristics ◽

Cutoff Levels

Cytokines, including interleukins, interferons, tumor necrosis factors, and chemokines, have a variety of pro- and anti-inflammatory effects in the body through a number of biochemical pathways and interactions. Stimuli, actions, interactions, and downstream effects of cytokines have been investigated in more depth in recent years, and clinical research has also been conducted to implicate cytokines in causal patterns in certain diseases. However, particular cutoffs of cytokines as biomarkers for disease processes have not been well studied, and this warrants future work to potentially improve diagnoses for diseases with inflammatory markers. A limited number of studies in this area are reviewed, considering diseases correlated with abnormal cytokine profiles, as well as specific cutoffs at which cytokines have been deemed clinically useful for diagnosing those diseases through Receiver Operator Characteristics modeling. In light of studies such as those discussed in this review, cytokine testing has the potential to support diagnosis due to its lack of invasiveness and low cost, compared to other common types of testing for infections and inflammatory diseases.

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