Chapter 1: The Astrobiology Primer 3.0

The Astrobiology Primer 3.0 (ABP3.0) is a concise introduction to the field of astrobiology for students and others who are new to the field of astrobiology. It provides an entry into the broader materials in this supplementary issue of Astrobiology and an overview of the investigations and driving hypotheses that make up this interdisciplinary field. The content of this chapter was adapted from the other 10 articles in this supplementary issue and thus represents the contribution of all the authors who worked on these introductory articles. The content of this chapter is not exhaustive and represents the topics that the authors found to be the most important and compelling in a dynamic and changing field.

Chapter 2: What Is Life?

The question "What is life?" has existed since the beginning of recorded history. However, the scientific and philosophical contexts of this question have changed and been refined as advancements in technology have revealed both fine details and broad connections in the network of life on Earth. Understanding the framework of the question "What is life?" is central to formulating other questions such as "Where else could life be?" and "How do we search for life elsewhere?" While many of these questions are addressed throughout the Astrobiology Primer 3.0, this chapter gives historical context for defining life, highlights conceptual characteristics shared by all life on Earth as well as key features used to describe it, discusses why it matters for astrobiology, and explores both challenges and opportunities for finding an informative operational definition.

Pangenomic Analysis of Nucleo-Cytoplasmic Large DNA Viruses. I: The Phylogenetic Distribution of Conserved Oxygen-Dependent Enzymes Reveals a Capture-Gene Process

The Nucleo-Cytoplasmic Large DNA Viruses (NCLDVs) infect a wide range of eukaryotic species, including amoeba, algae, fish, amphibia, arthropods, birds, and mammals. This group of viruses has linear or circular double-stranded DNA genomes whose size spans approximately one order of magnitude, from 100 to 2500 kbp. The ultimate origin of this peculiar group of viruses remains an open issue. Some have argued that NCLDVs' origin may lie in a bacteriophage ancestor that increased its genome size by subsequent recruitment of eukaryotic and bacterial genes. Others have suggested that NCLDVs families originated from cells that underwent an irreversible process of genome reduction. However, the hypothesis that a number of NCLDVs sequences have been recruited from the host genomes has been largely ignored. In the present work, we have performed pangenomic analyses of each of the seven known NCLDVs families. We show that these families' core- and shell genes have cellular homologs, supporting possible escaping-gene events as part of its evolution. Furthermore, the detection of sequences that belong to two protein families (small chain ribonucleotide reductase and Erv1/Air) and to one superfamily [2OG-Fe(II) oxygenases] that are for distribution in all NCLDVs core and shell clusters encoding for oxygen-dependent enzymes suggests that the highly conserved core these viruses originated after the Proterozoic Great Oxidation Event that transformed the terrestrial atmosphere 2.4-2.3 Ga ago.

Subtle structural differences of nucleotide analogs may impact SARS-CoV-2 RNA-dependent RNA polymerase and exoribonuclease activity

The rapid spread and public health impact of the novel SARS-CoV-2 variants that cause COVID-19 continue to produce major global impacts and social distress. Several vaccines were developed in record time to prevent and limit the spread of the infection, thus playing a pivotal role in controlling the pandemic. Although the repurposing of available drugs attempts to provide therapies of immediate access against COVID-19, there is still a need for developing specific treatments for this disease. Remdesivir, molnupiravir and Paxlovid remain the only evidence-supported antiviral drugs to treat COVID-19 patients, and only in severe cases. To contribute on the search of potential Covid-19 therapeutic agents, we targeted the viral RNA-dependent RNA polymerase (RdRp) and the exoribonuclease (ExoN) following two strategies. First, we modeled and analyzed nucleoside analogs sofosbuvir, remdesivir, favipiravir, ribavirin, and molnupiravir at three key binding sites on the RdRp-ExoN complex. Second, we curated and virtually screened a database containing 517 nucleotide analogs in the same binding sites. Finally, we characterized key interactions and pharmacophoric features presumably involved in viral replication halting at multiple sites. Our results highlight structural modifications that might lead to more potent SARS-CoV-2 inhibitors against an expansive range of variants and provide a collection of nucleotide analogs useful for screening campaigns.

Structural Analysis of Monomeric RNA-Dependent Polymerases Revisited

In the past few years, our understanding of the RNA virosphere has changed dramatically due to the growth and spurt of metagenomics, exponentially increasing the number of RNA viral sequences, and providing a better understanding of their range of potential hosts. As of today, the only conserved protein among RNA viruses appears to be the monomeric RNA-dependent RNA polymerase. This enzyme belongs to the right-hand DNA-and RNA polymerases, which also includes reverse transcriptases and eukaryotic replicative DNA polymerases. The ubiquity of this protein in RNA viruses makes it a unique evolutionary marker and an appealing broad-spectrum antiviral target. In this work pairwise structural comparisons of viral RdRps and RTs were performed, including tertiary structures that have been obtained in the last few years. The resulting phylogenetic tree shows that the RdRps from (+)ss- and dsRNA viruses might have been recruited several times throughout the evolution of mobile genetic elements. RTs also display multiple evolutionary routes. We have identified a structural core comprising the entire palm, a large moiety of the fingers and the N-terminal helices of the thumb domain, comprising over 300 conserved residues, including two regions that we have named the “knuckles” and the “hypothenar eminence”. The conservation of an helix bundle in the region preceding the polymerase domain confirms that (−)ss and dsRNA Reoviruses’ polymerases share a recent ancestor. Finally, the inclusion of DNA polymerases into our structural analyses suggests that monomeric RNA-dependent polymerases might have diverged from B-family polymerases.

Two short low complexity regions (LCRs) are hallmark sequences of the Delta SARS-CoV-2 variant spike protein

Low complexity regions (LCRs) are protein sequences formed by a set of compositionally biased residues. LCRs are extremely abundant in cellular proteins and have also been reported in viruses, where they may partake in evasion of the host immune system. Analyses of 28,231 SARS-CoV-2 whole proteomes and of 261,051 spike protein sequences revealed the presence of four extremely conserved LCRs in the spike protein of several SARS-CoV-2 variants. With the exception of Iota, where it is absent, the Spike LCR-1 is present in the signal peptide of 80.57% of the Delta variant sequences, and in other variants of concern and interest. The Spike LCR-2 is highly prevalent (79.87%) in Iota. Two distinctive LCRs are present in the Delta spike protein. The Delta Spike LCR-3 is present in 99.19% of the analyzed sequences, and the Delta Spike LCR-4 in 98.3% of the same set of proteins. These two LCRs are located in the furin cleavage site and HR1 domain, respectively, and may be considered hallmark traits of the Delta variant. The presence of the medically-important point mutations P681R and D950N in these LCRs, combined with the ubiquity of these regions in the highly contagious Delta variant opens the possibility that they may play a role in its rapid spread.

Structural analysis of viral ExoN domains reveals polyphyletic hijacking events

Nidoviruses and arenaviruses are the only known RNA viruses encoding a 3’-5’ exonuclease domain (ExoN). The proofreading activity of the ExoN domain has played a key role in the growth of nidoviral genomes, while in arenaviruses this domain partakes in the suppression of the host innate immune signaling. Sequence and structural homology analyses suggest that these proteins have been hijacked from cellular hosts many times. Analysis of the available nidoviral ExoN sequences reveals a high conservation level comparable to that of the viral RNA-dependent RNA polymerases (RdRp), which are the most conserved viral proteins. Two highly preserved zinc fingers are present in all nidoviral exonucleases, while in the arenaviral protein only one zinc finger can be identified. This is in sharp contrast with the reported lack of zinc fingers in cellular ExoNs, and opens the possibility of therapeutic strategies in the struggle against COVID-19.

A yellow flag on the horizon: The looming threat of yellow fever to North America

OBJECTIVES

Yellow fever virus historically was a frequent threat to American and European coasts. Medical milestones such as the discovery of mosquitoes as vectors and subsequently an effective vaccine significantly reduced its incidence, in spite of which, thousands of cases of this deathly disease still occur regularly in Sub-Saharan Africa and the Amazonian basin in South America, which are usually not reported. An urban outbreak in Angola, consecutive years of increasing incidence near major Brazilian cities, and imported cases in China, South America and Europe, have brought this virus back to the global spotlight. The aim of this article is to underline that the preventive YFV measures, such as vaccination, need to be carefully revised in order to minimize the risks of new YFV outbreaks, especially in urban or immunologically vulnerable places. Furthermore, this article highlights the diverse factors that have favored the spread of other Aedes spp.-associated arboviral diseases like Dengue, Chikungunya and Zika, to northern latitudes causing epidemics in the United States and Europe, emphasizing the possibility that YFV might follow the path of these viruses unless enhanced surveillance and efficient control systems are urgently initiated.

Are RNA Viruses Candidate Agents for the Next Global Pandemic? A Review

Pathogenic RNA viruses are potentially the most important group involved in zoonotic disease transmission, and they represent a challenge for global disease control. Their biological diversity and rapid adaptive rates have proved to be difficult to overcome and to anticipate by modern medical technology. Also, the anthropogenic change of natural ecosystems and the continuous population growth are driving increased rates of interspecies contacts and the interchange of pathogens that can develop into global pandemics. The combination of molecular, epidemiological, and ecological knowledge of RNA viruses is therefore essential towards the proper control of these emergent pathogens. This review outlines, throughout different levels of complexity, the problems posed by RNA viral diseases, covering some of the molecular mechanisms allowing them to adapt to new host species-and to novel pharmaceutical developments-up to the known ecological processes involved in zoonotic transmission.

Structural Analysis of Monomeric RNA-Dependent Polymerases: Evolutionary and Therapeutic Implications

The crystal structures of monomeric RNA-dependent RNA polymerases and reverse transcriptases of more than 20 different viruses are available in the Protein Data Bank. They all share the characteristic right-hand shape of DNA- and RNA polymerases formed by the fingers, palm and thumb subdomains, and, in many cases, “fingertips” that extend from the fingers towards the thumb subdomain, giving the viral enzyme a closed right-hand appearance. Six conserved structural motifs that contain key residues for the proper functioning of the enzyme have been identified in all these RNA-dependent polymerases. These enzymes share a two divalent metal-ion mechanism of polymerization in which two conserved aspartate residues coordinate the interactions with the metal ions to catalyze the nucleotidyl transfer reaction. The recent availability of crystal structures of polymerases of the Orthomyxoviridae and Bunyaviridae families allowed us to make pairwise comparisons of the tertiary structures of polymerases belonging to the four main RNA viral groups, which has led to a phylogenetic tree in which single-stranded negative RNA viral polymerases have been included for the first time. This has also allowed us to use a homology-based structural prediction approach to develop a general three-dimensional model of the Ebola virus RNA-dependent RNA polymerase. Our model includes several of the conserved structural motifs and residues described in other viral RNA-dependent RNA polymerases that define the catalytic and highly conserved palm subdomain, as well as portions of the fingers and thumb subdomains. The results presented here help to understand the current use and apparent success of antivirals, i.e. Brincidofovir, Lamivudine and Favipiravir, originally aimed at other types of polymerases, to counteract the Ebola virus infection.

Evaluation of the endothelial function in hypertensive patients with 13N-ammonia PET

BACKGROUND

Essential hypertension is one of the main risk factors for the development of coronary artery disease (CAD). Hypertension causes endothelial dysfunction which is considered an early sign for the development of CAD. Positron emission tomography is a non-invasive imaging technique that measures myocardial blood flow (MBF), allowing us to identify patients with endothelial dysfunction.

METHODS AND RESULTS

19 patients without comorbidities recently diagnosed hypertensive, as well as 21 healthy volunteers were studied. A three-phase (rest, cold pressor test, and adenosine-induced hyperemia) (13)N-ammonia PET was performed, and MBF was measured. Endothelial-Dependent Vasodilation Index, ΔMBF, and coronary flow reserve (CFR) were calculated for each patient. Hypertensive patients had a significantly higher systolic and diastolic blood pressures compared with the control group (134.6 ± 11.7/86.4 ± 10.6 mm Hg and 106.0 ± 11.8/71.4 ± 6.6 mm Hg, respectively, P < .001). The ENDEVI (1.28 ± 0.26 vs 1.79 ± 0.30, P < .001), the ΔMBF (0.81 ± 0.50 vs 0.25 ± 0.21, P < .001) and the CFR (2.18 ± 0.88 vs 3.17 ± 0.68, P = .001) were significantly lower in the hypertensive patients compared to the control group, 84% of the former group had endothelial dysfunction i.e., ENDEVI < 1.5 and 58% had vasomotor abnormalities, i.e., CFR < 2.5.

CONCLUSIONS

In this study, we showed that recently diagnosed hypertensive patients have coronary endothelial dysfunction and vasomotor disturbances which are early signs for the development of CAD.

Automatic alignment of myocardial perfusion PET and 64-slice coronary CT angiography on hybrid PET/CT

BACKGROUND

Hybrid PET/CT allows for acquisition of cardiac PET and coronary CT angiography (CCTA) in one session. However, PET and CCTA are acquired with differing breathing protocols and require software registration. We aimed to validate automatic correction for breathing misalignment between PET and CCTA acquired on hybrid scanner.

METHODS

Single-session hybrid PET/CT studies of rest/stress (13)N-ammonia PET and CCTA in 32 consecutive patients were considered. Automated registration of PET left ventricular (LV) surfaces with CCTA volumes was evaluated by comparing with expert manual alignment by two observers.

RESULTS

The average initial misalignments between the position of LV on PET and CCTA were 27.2 ± 11.8, 13.3 ± 11.5, and 14.3 ± 9.1 mm in x, y, and z axes on rest, and 26.3 ± 10.2, 11.1 ± 9.5, and 11.7 ± 7.1 mm in x, y, and z axes on stress, respectively. The automated PET-CCTA co-registration had 95% agreement as judged visually. Compared with expert manual alignment, the translation errors of the algorithm were 5.3 ± 2.8 mm (rest) and 6.0 ± 3.5 mm (stress). 3D visualization of combined coronary vessel anatomy and hypoperfusion from PET could be made without further manual adjustments.

CONCLUSION

Software co-registration of CCTA and PET myocardial perfusion imaging on hybrid PET/CT scanners is necessary, but can be performed automatically, facilitating integrated 3D display on PET/CT.

Comparison of clinical tools for measurements of regional stress and rest myocardial blood flow assessed with 13N-ammonia PET/CT

Several models for the quantitative analysis of myocardial blood flow (MBF) at stress and rest and myocardial flow reserve (MFR) with (13)N-ammonia myocardial perfusion PET have been implemented for clinical use. We aimed to compare quantitative results obtained from 3 software tools (QPET, syngo MBF, and PMOD), which perform PET MBF quantification with either a 2-compartment model (QPET and syngo MBF) or a 1-compartment model (PMOD).

METHODS

We considered 33 adenosine stress and rest (13)N-ammonia studies (22 men and 11 women). Average age was 54.5 ± 15 y, and average body mass index was 26 ± 4.2. Eighteen patients had a very low likelihood of disease, with no chest pain, normal relative perfusion results, and normal function. All data were obtained on a PET/CT scanner in list mode with CT attenuation maps. Sixteen dynamic frames were reconstructed (twelve 10-s, two 30-s, one 1-min, and one 6-min frames). Global and regional stress and rest MBF and MFR values were obtained with each tool. Left ventricular contours and input function region were obtained automatically in system QPET and syngo MBF and manually in PMOD.

RESULTS

The flow values and MFR values were highly correlated among the 3 packages (R(2) ranging from 0.88 to 0.92 for global values and from 0.78 to 0.94 for regional values. Mean reference MFR values were similar for QPET, syngo MBF, and PMOD (3.39 ± 1.22, 3.41 ± 0.76, and 3.66 ± 1.19, respectively) by 1-way ANOVA (P = 0.74). The lowest MFR in very low likelihood patients in any given vascular territory was 2.25 for QPET, 2.13 for syngo MBF, and 2.23 for PMOD.

CONCLUSION

Different implementations of 1- and 2-compartment models demonstrate an excellent correlation in MFR for each vascular territory, with similar mean MFR values.

[The importance of multi-imaging diagnosis in cardiology]

Cardiovascular imaging is one of the disciplines in cardiology with the most recent advances. This means that the teaching of Cardiology must evolve in the same way. In 2009, the American College of Cardiology published a statement, which points out that all of the cardiology residents must have basic training in every one of the cardiovascular imaging modalities available. Ischemic heart disease is the main cause of death in the world, including Mexico. Up to 43% of the patients that suffered a myocardial infarction and up to 31% of the patients with sudden cardiac death had an almost normal nuclear myocardial perfusion study in the year before the event, thus evidencing the importance of a multi-imaging approach. With the better understanding of the pathophysiological processes of coronary artery disease, new techniques have been developed that allows the detection of this disease almost from the beginning, through the detection of endothelial dysfunction by Positron Emission Tomography. Later on, when the patient develops diffuse atherosclerosis, we can rely on the use of de coronary calcium score and the detection of atherosclerotic plaques with coronary computed tomography angiography. To detect the presence of myocardial ischemia, two methods are widely used: echocardiography and nuclear medicine. Other options to identify myocardial ischemia are magnetic resonance imaging and computed tomography, due to the development of the "Dual Source" and "Flash" technologies. After an acute coronary event, cardiovascular imaging is useful for risk stratification and detection of myocardial viability, being the positron emission tomography the gold standard.

Effect of ezetimibe-simvastatine over endothelial dysfunction in dyslipidemic patients: assessment by 13N-ammonia positron emission tomography

BACKGROUND

Dyslipidemias constitute an independent risk factor for the development of atherogenesis and they also predispose to the development of endothelial dysfunction (ED). Using PET with (13)N-ammonia, it is possible to quantify myocardial blood flow (MBF) in mL/min/g and to quantitatively evaluate ED. With the use of lipid lowering therapy it is possible to reduce ED and increase the MBF and the endothelial-dependent vasodilation index (ENDEVI). In this study, we aimed to evaluate with (13)N-ammonia PET the benefic effects of the combined treatment ezetimibe/simvastatine on the endothelial function of dyslipidemic patients after 8 weeks of treatment.

MATERIAL AND METHODS

Fourteen consecutive patients with dyslipidemia diagnosis and 17 healthy volunteers were studied with a three phase [rest, Cold Pressor Test (CPT), and adenosine-induced hyperemia] (13)N-ammonia PET for MBF quantification assessment. A second PET study was performed in the dyslipidemic group after 8 weeks of treatment with ezetimibe/simvastatine (10/40 mg). Myocardial flow reserve (MFR), ENDEVI, and %ΔMBF were calculated.

RESULTS

Total cholesterol, LDL cholesterol, HDL cholesterol, and triglycerides concentrations were markedly altered in the dyslipidemic group and after 8 weeks of treatment these values improved. Dyslipidemic patients showed endothelial dysfunction when compared with the control group, (MFR 2.79 ± 0.94 vs 3.15 ± 0.48, P < 0.05 ; ENDEVI 1.28 ± 0.25 vs 1.53 ± 0.24, P < 0.05; and %ΔMBF 29.08 ± 24.62 vs 53 ± 24.60%, P < 0.05, respectively). After 8 weeks of treatment, we found a significant increase in all the endothelial function markers (MFR: 3.14 ± 0.86, P < 0.05, ENDEVI 1.65 ± 0.23, P < 0.05; %ΔMBF: 65.21 ± 23.43, P < 0.05).

CONCLUSIONS

Dyslipidemic patients show endothelial dysfunction measured with (13)N-ammonia PET. Treatment with ezetimibe/simvastatine was effective improving the lipid profile as well as the endothelial function of these patients. PET may be a useful tool to monitor vascular reactivity and regression/progression of coronary atherosclerosis after pharmacologic interventions.