The Need for a Wellbeing Tool for Children

Well-being is characterized by a measure of overall quality of life that spans cognitive, behavioral, emotional, and social functions. As a multi-dimensional concept, its measurement is vital for the evaluation of mental and physical development. Well-being was immensely disrupted by the COVID-19 pandemic and enforced isolation measures, resulting in challenged mental, physical, and emotional health of children. Prior studies pertaining to the impacts on the youth population include an increase in sedentary behaviors, social isolation, and more severe symptoms of stress, anxiety and depression. A lack of physical activity and social distancing could lead to numerous psychosocial and physical implications. Research findings demonstrate the need for a focus on child wellbeing post pandemic. There is currently no existing tool to assess child wellbeing. The Wellbeing Tool that we propose is an instrument that will measure overall quality of life, utilizing pictures and simple language suitable for young children to easily comprehend. The Wellbeing Tool is beneficial to assess the emotional, physical, and mental health of children in a standardized way, especially in times of extreme stress and poor health due to external factors. Results from this study can be utilized to raise awareness of the negative effects of quarantine and isolation and to develop interventions that address challenges of mental health in youth.https://orb.binghamton.edu/research_days_posters_2022/1016/thumbnail.jp

Table 1: Chloroplast genomes of the parasitic and non-parasitic plants used in the case study.

Whole genome alignments and comparative analysis are key methods in the quest of unraveling the dynamics of genome evolution. Interactive visualization and exploration of the generated alignments, annotations, and phylogenetic data are important steps in the interpretation of the initial results. Limitations of existing software inspired us to develop our new tool AliTV, which provides interactive visualization of whole genome alignments. AliTV reads multiple whole genome alignments or automatically generates alignments from the provided data. Optional feature annotations and phylo- genetic information are supported. The user-friendly, web-browser based and highly customizable interface allows rapid exploration and manipulation of the visualized data as well as the export of publication-ready high-quality figures. AliTV is freely available at https://github.com/AliTVTeam/AliTV

ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage

ProPortal (http://proportal.mit.edu/) is a database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus. Our goal is to provide a source of cross-referenced data across multiple scales of biological organization—from the genome to the ecosystem—embracing the full diversity of ecotypic variation within this microbial taxon, its sister group, Synechococcus and phage that infect them. The site currently contains the genomes of 13 Prochlorococcus strains, 11 Synechococcus strains and 28 cyanophage strains that infect one or both groups. Cyanobacterial and cyanophage genes are clustered into orthologous groups that can be accessed by keyword search or through a genome browser. Users can also identify orthologous gene clusters shared by cyanobacterial and cyanophage genomes. Gene expression data for Prochlorococcus ecotypes MED4 and MIT9313 allow users to identify genes that are up or downregulated in response to environmental stressors. In addition, the transcriptome in synchronized cells grown on a 24-h light–dark cycle reveals the choreography of gene expression in cells in a ‘natural’ state. Metagenomic sequences from the Global Ocean Survey from Prochlorococcus, Synechococcus and phage genomes are archived so users can examine the differences between populations from diverse habitats. Finally, an example of cyanobacterial population data from the field is included

The Infinitely Many Genes Model for the Distributed Genome of Bacteria

The distributed genome hypothesis states that the gene pool of a bacterial taxon is much more complex than that found in a single individual genome. However, the possible fitness advantage, why such genomic diversity is maintained, whether this variation is largely adaptive or neutral, and why these distinct individuals can coexist, remains poorly understood. Here, we present the infinitely many genes (IMG) model, which is a quantitative, evolutionary model for the distributed genome. It is based on a genealogy of individual genomes and the possibility of gene gain (from an unbounded reservoir of novel genes, e.g., by horizontal gene transfer from distant taxa) and gene loss, for example, by pseudogenization and deletion of genes, during reproduction. By implementing these mechanisms, the IMG model differs from existing concepts for the distributed genome, which cannot differentiate between neutral evolution and adaptation as drivers of the observed genomic diversity. Using the IMG model, we tested whether the distributed genome of 22 full genomes of picocyanobacteria (Prochlorococcus and Synechococcus) shows signs of adaptation or neutrality. We calculated the effective population size of Prochlorococcus at 1.01 × 1011 and predicted 18 distinct clades for this population, only six of which have been isolated and cultured thus far. We predicted that the Prochlorococcus pangenome contains 57,792 genes and found that the evolution of the distributed genome of Prochlorococcus was possibly neutral, whereas that of Synechococcus and the combined sample shows a clear deviation from neutrality

Genomes of marine cyanopodoviruses reveal multiple origins of diversity

The marine cyanobacteria Prochlorococcus and Synechococcus are highly abundant in the global oceans, as are the cyanophage with which they co-evolve. While genomic analyses have been relatively extensive for cyanomyoviruses, only three cyanopodoviruses isolated on marine cyanobacteria have been sequenced. Here we present nine new cyanopodovirus genomes, and analyse them in the context of the broader group. The genomes range from 42.2 to 47.7 kb, with G+C contents consistent with those of their hosts. They share 12 core genes, and the pan-genome is not close to being fully sampled. The genomes contain three variable island regions, with the most hypervariable genes concentrated at one end of the genome. Concatenated core-gene phylogeny clusters all but one of the phage into three distinct groups (MPP-A and two discrete clades within MPP-B). The outlier, P-RSP2, has the smallest genome and lacks RNA polymerase, a hallmark of the Autographivirinae subfamily. The phage in group MPP-B contain photosynthesis and carbon metabolism associated genes, while group MPP-A and the outlier P-RSP2 do not, suggesting different constraints on their lytic cycles. Four of the phage encode integrases and three have a host integration signature. Metagenomic analyses reveal that cyanopodoviruses may be more abundant in the oceans than previously thought.National Science Foundation (U.S.). Center for Microbial Oceanography: Research and Education (Grant OCE-042560)National Science Foundation (U.S.). Center for Microbial Oceanography: Research and Education (Grant EF 0424599

Transcriptome dynamics of a broad host-range cyanophage and its hosts

Cyanobacteria are highly abundant in the oceans and are constantly exposed to lytic viruses. The T4-like cyanomyoviruses are abundant in the marine environment and have broad host-ranges relative to other cyanophages. It is currently unknown whether broad host-range phages specifically tailor their infection program for each host, or employ the same program irrespective of the host infected. Also unknown is how different hosts respond to infection by the same phage. Here we used microarray and RNA-seq analyses to investigate the interaction between the Syn9 T4-like cyanophage and three phylogenetically, ecologically and genomically distinct marine Synechococcus strains: WH7803, WH8102 and WH8109. Strikingly, Syn9 led a nearly identical infection and transcriptional program in all three hosts. Different to previous assumptions for T4-like cyanophages, three temporally regulated gene expression classes were observed. Furthermore, a novel regulatory element controlled early-gene transcription, and host-like promoters drove middle gene transcription, different to the regulatory paradigm for T4. Similar results were found for the P-TIM40 phage during infection of Prochlorococcus NATL2A. Moreover, genomic and metagenomic analyses indicate that these regulatory elements are abundant and conserved among T4-like cyanophages. In contrast to the near-identical transcriptional program employed by Syn9, host responses to infection involved host-specific genes primarily located in hypervariable genomic islands, substantiating islands as a major axis of phage-cyanobacteria interactions. Our findings suggest that the ability of broad host-range phages to infect multiple hosts is more likely dependent on the effectiveness of host defense strategies than on differential tailoring of the infection process by the phage

Polyclonality of Concurrent Natural Populations of Alteromonas macleodii

We have analyzed a natural population of the marine bacterium, Alteromonas macleodii, from a single sample of seawater to evaluate the genomic diversity present. We performed full genome sequencing of four isolates and 161 metagenomic fosmid clones, all of which were assigned to A. macleodii by sequence similarity. Out of the four strain genomes, A. macleodii deep ecotype (AltDE1) represented a different genome, whereas AltDE2 and AltDE3 were identical to the previously described AltDE. Although the core genome (∼80%) had an average nucleotide identity of 98.51%, both AltDE and AltDE1 contained flexible genomic islands (fGIs), that is, genomic islands present in both genomes in the same genomic context but having different gene content. Some of the fGIs encode cell surface receptors known to be phage recognition targets, such as the O-chain of the lipopolysaccharide, whereas others have genes involved in physiological traits (e.g., nutrient transport, degradation, and metal resistance) denoting microniche specialization. The presence in metagenomic fosmids of genomic fragments differing from the sequenced strain genomes, together with the presence of new fGIs, indicates that there are at least two more A. macleodii clones present. The availability of three or more sequences overlapping the same genomic region also allowed us to estimate the frequency and distribution of recombination events among these different clones, indicating that these clustered near the genomic islands. The results indicate that this natural A. macleodii population has multiple clones with a potential for different phage susceptibility and exploitation of resources, within a seemingly unstructured habitat

Evolutionary consequences of viral resistance in the marine picoeukaryote Ostreococcus tauri

In marine environments, eukaryotic marine microalgae coexist with the viruses that infect them. Marine microalgae are the main primary producers in the oceans and are at the base of the marine food web. Viruses play important roles in top-down control of algae populations, cycling of organic matter, and as evolutionary drivers of their hosts. Algae must adapt in response to the strong selection pressure that viruses impose for resistance to infection. In addition to biotic selection pressures such as viral infections, algae must also adapt to their abiotic environment. Global climate change is affecting temperature, salinity, pH, light and nutrient concentrations in the oceans, particularly in surface waters, where microalgae live. Currently, little is known about how consistent the effects of viruses on their hosts are, whether the cost of host resistance varies across environments, and whether there is a trade-off between maintaining resistance to viruses and adapting to other environmental changes. The marine picoeukaryote Ostreococcus tauri is abundant in Mediterranean lagoons, where it experiences large fluctuations in environmental conditions and co-occurs with lytic viruses (Ostreococcus tauri viruses – OtVs). Viral infection causes lysis of susceptible (S) cells, however a small proportion of cells are resistant (R) and avoid lysis. Some resistant O. tauri populations can coexist with infectious viruses, and it has been proposed that these viruses are produced by a minority of susceptible cells within a mainly resistant population. These populations are referred to as resistant producers (RP). Virus production in RP populations is unstable and eventually they shift to R populations. I used O. tauri and one of its viruses, OtV5, as a model system to investigate whether cells that are susceptible or resistant to virus infection adapt to environmental change differently and whether there is a cost of being resistant. For the first time, I evolved susceptible and resistant hosts of a marine alga separately under a range of environments and directly compared their plastic and evolved responses. I showed that resistant populations of O. tauri maintained their resistance for more than 200 generations in the absence of viruses across all environments, indicating that the resistance mechanism is difficult to reverse. Furthermore, I did not detect a cost of being resistant, as measured by population growth rate and competitive ability. Virus production in RP populations stopped in all environments and all populations became R. In addition, I found that virus production in RP O. tauri populations can fluctuate before completely ceasing, and that phosphate affected the length of time it took for virus production to stop. These results, combined with mathematical modelling of O. tauri infection dynamics, provide support for the prediction that RP populations consist of a mixed population of susceptible and resistant cells. By examining multiple environments and resistance types, we can better understand first, how microalgae populations adapt to environmental change and second, the ecological and evolutionary consequences of maintaining resistance to viruses in common marine picoeukaryotes

Biogeographic Variation in Host Range Phenotypes and Taxonomic Composition of Marine Cyanophage Isolates

This Document is Protected by copyright and was first published by Frontiers. All rights reserved. it is reproduced with permission.Funding for this research was provided by the Gordon and Betty Moore Foundation, the National Science Foundation (OCE-1332740 and OCE-1029684 to MM; OCE-1005388 and OCE-1031783 to JM) and a NOAA NERRS Graduate Research Fellowship (Estuarine Reserves Division, Office of Ocean and Coastal Resource Management, National Oceanic and Atmospheric Administration) to CH