The vital role of exercise and nutrition in COVID-19 rehabilitation: synergizing strength.

Since the outset of the COVID-19 pandemic, the global healthcare community has faced the challenge of understanding and addressing the ongoing and multi-faceted SARS-CoV-2 infection outcomes. As millions of individuals worldwide continue to navigate the complexities of post-hospitalization recovery, reinfection rates, and the increasing prevalence of Long-COVID symptoms, comprehensive COVID-19 rehabilitation strategies are greatly needed. Previous studies have highlighted the potential synergy between exercise and nutrition, suggesting that their integration into patient rehabilitation programs may yield improved clinical outcomes for survivors of COVID-19. Our group aimed to consolidate existing knowledge following the implementation of patient, intervention, comparison, and outcome (PICO) search strategies on the distinct and combined impacts of exercise and nutrition interventions in facilitating the recovery of COVID-19 patients following hospitalization, with a specific focus on their implications for both public health and clinical practice. The incorporation of targeted nutritional strategies alongside exercise-based programs may expedite patient recovery, ultimately promoting independence in performing activities of daily living (ADLs). Nonetheless, an imperative for expanded scientific inquiry remains, particularly in the realm of combined interventions. This mini-review underscores the compelling prospects offered by an amalgamated approach, advocating for the seamless integration of exercise and nutrition as integral components of post-hospitalization COVID-19 rehabilitation. The pursuit of a comprehensive understanding of the synergistic effects and effectiveness of exercise and nutrition stands as a crucial objective in advancing patient care and refining recovery strategies in the wake of this enduring global health crisis.

ORFanID: A web-based search engine for the discovery and identification of orphan and taxonomically restricted genes.

With the numerous genomes sequenced today, it has been revealed that a noteworthy percentage of genes in a given taxon of organisms in the phylogenetic tree of life do not have orthologous sequences in other taxa. These sequences are commonly referred to as "orphans" or "ORFans" if found as single occurrences in a single species or as "taxonomically restricted genes" (TRGs) when found at higher taxonomic levels. Quantitative and collective studies of these genes are necessary for understanding their biological origins. However, the current software for identifying orphan genes is limited in its functionality, database search range, and very complex algorithmically. Thus, researchers studying orphan genes must harvest their data from many disparate sources. ORFanID is a graphical web-based search engine that facilitates the efficient identification of both orphan genes and TRGs at all taxonomic levels, from DNA or amino acid sequences in the NCBI database cluster and other large bioinformatics repositories. The software allows users to identify genes that are unique to any taxonomic rank, from species to domain, using NCBI systematic classifiers. It provides control over NCBI database search parameters, and the results are presented in a spreadsheet as well as a graphical display. The tables in the software are sortable, and results can be filtered using the fuzzy search functionality. The visual presentation can be expanded and collapsed by the taxonomic tree to its various branches. Example results from searches on five species and gene expression data from specific orphan genes are provided in the Supplementary Information.

Phage-encoded cationic antimicrobial peptide required for lysis.

Most phages of Gram-negative hosts encode spanins for disruption of the outer membrane, the last step in host lysis. However, bioinformatic analysis indicates that ∼15% of these phages lack a spanin gene, suggesting they have an alternate way of disrupting the OM. Here, we show that the T7-like coliphage phiKT causes the explosive cell lysis associated with spanin activity despite not encoding spanins. A putative lysis cassette cloned from the phiKT late gene region includes the hypothetical novel gene 28 located between the holin and endolysin genes and supports inducible lysis in E. coli K-12. Moreover, induction of an isogenic construct lacking gene 28 resulted in divalent cation-stabilized spherical cells rather than lysis, implicating gp28 in OM disruption. Additionally, gp28 was shown to complement the lysis defect of a spanin-null λ lysogen. Gene 28 encodes a 56-amino acid cationic protein with predicted amphipathic helical structure and is membrane-associated after lysis. Urea and KCl washes did not release gp28 from the particulate, suggesting a strong hydrophobic membrane interaction. Fluorescence microscopy supports membrane localization of the gp28 protein prior to lysis. Gp28 is similar in size, charge, predicted fold, and membrane association to the human cathelicidin antimicrobial peptide LL-37. Synthesized gp28 behaved similar to LL-37 in standard assays mixing peptide and cells to measure bactericidal and inhibitory effects. Taken together, these results indicate that phiKT gp28 is a phage-encoded cationic antimicrobial peptide that disrupts bacterial outer membranes during host lysis and thus establishes a new class of phage lysis proteins, the disruptins. Significance We provide evidence that phiKT produces an antimicrobial peptide for outer membrane disruption during lysis. This protein, designated as a disruptin, is a new paradigm for phage lysis and has no similarities to other known lysis genes. Although many mechanisms have been proposed for the function of antimicrobial peptides, there is no consensus on the molecular basis of membrane disruption. Additionally, there is no established genetic system to support such studies. Therefore, the phiKT disruptin may represent the first genetically tractable antimicrobial peptide, facilitating mechanistic analyses.

Molecular Mechanisms Lead to Sex-Specific COVID-19 Prognosis and Targeted Therapies.

Clinical and epidemiological studies have identified male sex as an important risk factor for COVID-19 clinical outcomes and mortality. This raises the question as to how this risk factor can be addressed in the prognosis, clinical management, and the treatment of patients with Coronavirus disease 2019 (COVID-19). Currently, there are no guidelines or protocols to help alter the course of sex-specific COVID-19 prognosis, especially in severe disease presentations. This is partly due to the lack of research studies characterizing the differences in male vs. female host response to the severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) infection and a lack of a well-rounded understanding of the molecular mechanisms involved. Here, we discuss three distinct but interconnected molecular-level differences in males and females that likely play an essential role in the COVID-19 prognosis. We review interactions of SARS-CoV-2 with host cell angiotensin-converting enzyme 2 (ACE2) in the viral entry between males vs. females and discuss the differential regulation of the renin-angiotensin system (RAS) between the two sexes. Next, we present immune response disparities and how immune function and endocrine regulation may render males increasingly vulnerable to severe COVID-19. We describe the interconnected roles of these three regulatory systems in males and females in response to SARS-CoV-2 infection. Finally, we highlight the clinical implications of these mechanisms to patients with COVID-19 and propose putative targeted therapies that can help reduce COVID-19 severity in those critically ill.

Biopsychosocial and Spiritual Implications of Patients With COVID-19 Dying in Isolation.

Critically ill patients with the Coronavirus disease 2019 (COVID-19) are dying in isolation without the comfort of their family or other social support in unprecedented numbers. Recently, healthcare teams at COVID-19 epicenters have been inundated with critically ill patients. Patients isolated for COVID-19 have had no contact with their family or loved ones and may have likely experienced death without closure. This situation highlights concerns about patients' psychological and spiritual well-being with COVID-19 and their families, as they permanently part ways. While palliative care has advanced to adequately address these patients' needs, the COVID-19 pandemic presents several barriers that force healthcare teams to deprioritize these essential aspects of patient care. The severe acute respiratory syndrome (SARS) outbreak in 2003 gave us a glimpse of these challenges as these patients were also isolated in hospitals. Here, we discuss the importance of the biopsychosocial spiritual model in end-of-life care and its implications on patients dying with COVID-19. Furthermore, we outline an integrative approach to address the unique and holistic needs of critically ill patients dying with COVID-19. These include intentional and increased coordination with trained palliative care staff, early and frequent goals of care including discussion of end-of-life plans, broader use of technology to improve connectedness, and shared decision making with patients' families.

Early COVID-19 Interventions Failed to Replicate 1918 St. Louis vs. Philadelphia Outcomes in the United States.

The Coronavirus disease 2019 (COVID-19) pandemic has elicited an abrupt pause in the United States in multiple sectors of commerce and social activity. As the US faces this health crisis, the magnitude and rigor of their initial public health response was unprecedented. As a response, the entire nation shutdown at the state-level for the duration of a ~1-3 months. These public health interventions, however, were not arbitrarily decided, but rather, implemented as a result of evidence-based practices. These practices were a result of lessons learned during the 1918 influenza pandemic and the city-level non-pharmaceutical interventions (NPIs) taken across the US. During the 1918 pandemic, two model cities, St. Louis, MO, and Philadelphia, PA, carried out two different approaches to address the spreading disease, which resulted in two distinctly different outcomes. Our group has evaluated the state-level public health response adopted by states across the US, with a focus on New York, California, Florida, and Texas, and compared the effectiveness of reducing the spread of COVID-19. Our assessments show that while the states mentioned above benefited from the implementations of early preventative measures, they inadequately replicated the desired outcomes observed in St. Louis during the 1918 crisis. Our study indicates that there are other factors, including health disparities that may influence the effectiveness of public health interventions applied. Identifying more specific health determinants may help implement targeted interventions aimed at preventing the spread of COVID-19 and improving health equity.

Systematic Review and Meta-Analysis of Sex-Specific COVID-19 Clinical Outcomes.

To successfully mitigate the extraordinary devastation caused by the Coronavirus disease 2019 (COVID-19) pandemic, it is crucial to identify important risk factors for this disease. One such neglected health determinant is the sex of the patient. This is an essential clinical characteristic, as it can factor into a patient's clinical management and preventative measures. Some clinical studies have shown disparities in the proportion between males and females that have more severe clinical outcomes or, subsequently, die from this disease. However, this association has not been unequivocally established. Thus, the purpose of this investigation was to examine the association between male sex and COVID-19 severity. We systematically reviewed the literature, identified studies that matched predetermined selection criteria, and performed a meta-analysis to evaluate the proportion of males among four disease severity categories. Appropriate assessment strategies were implemented to assess and minimize potential biases. The results of this meta-analysis indicated that males constituted a significantly higher proportion of those who had adverse clinical outcomes and died from COVID-19. As the coronavirus spread from the East to the West, male sex remained a consistent risk factor. Our results support the establishment of the male sex as an important risk factor for this disease. Early identification and appropriate medical care for males with lab-confirmed COVID-19 may substantially change the course of clinical prognosis, resulting in greater numbers of lives saved.

Molecular Nanomachines Can Destroy Tissue or Kill Multicellular Eukaryotes.

Light-activated molecular nanomachines (MNMs) can be used to drill holes into prokaryotic (bacterial) cell walls and the membrane of eukaryotic cells, including mammalian cancer cells, by their fast rotational movement, leading to cell death. We examined how these MNMs function in multicellular organisms and investigated their use for treatment and eradication of specific diseases by causing damage to certain tissues and small organisms. Three model eukaryotic species, Caenorhabditis elegans, Daphnia pulex, and Mus musculus (mouse), were evaluated. These organisms were exposed to light-activated fast-rotating MNMs and their physiological and pathological changes were studied in detail. Slow rotating MNMs were used to control for the effects of rotation rate. We demonstrate that fast-rotating MNMs caused depigmentation and 70% mortality in C. elegans while reducing the movement as well as heart rate and causing tissue damage in Daphnia. Topically applied light-activated MNMs on mouse skin caused ulceration and microlesions in the epithelial tissue, allowing MNMs to localize into deeper epidermal tissue. Overall, this study shows that the nanomechanical action of light-activated MNMs is effective against multicellular organisms, disrupting cell membranes and damaging tissue in vivo. Customized MNMs that target specific tissues for therapy combined with spatial and temporal control could have broad clinical applications in a variety of benign and malignant disease states including treatment of cancer, parasites, bacteria, and diseased tissues.

Molecular Nanomachines Disrupt Bacterial Cell Wall, Increasing Sensitivity of Extensively Drug-Resistant Klebsiella pneumoniae to Meropenem.

Multidrug resistance in pathogenic bacteria is an increasing problem in patient care and public health. Molecular nanomachines (MNMs) have the ability to open cell membranes using nanomechanical action. We hypothesized that MNMs could be used as antibacterial agents by drilling into bacterial cell walls and increasing susceptibility of drug-resistant bacteria to recently ineffective antibiotics. We exposed extensively drug-resistant Klebsiella pneumoniae to light-activated MNMs and found that MNMs increase the susceptibility to Meropenem. MNMs with Meropenem can effectively kill K. pneumoniae that are considered Meropenem-resistant. We examined the mechanisms of MNM action using permeability assays and transmission electron microscopy, finding that MNMs disrupt the cell wall of extensively drug-resistant K. pneumoniae, exposing the bacteria to Meropenem. These observations suggest that MNMs could be used to make conventional antibiotics more efficacious against multi-drug-resistant pathogens.

Hetero-Multivalency of Pseudomonas aeruginosa Lectin LecA Binding to Model Membranes.

A single glycan-lectin interaction is often weak and semi-specific. Multiple binding domains in a single lectin can bind with multiple glycan molecules simultaneously, making it difficult for the classic "lock-and-key" model to explain these interactions. We demonstrated that hetero-multivalency, a homo-oligomeric protein simultaneously binding to at least two types of ligands, influences LecA (a Pseudomonas aeruginosa adhesin)-glycolipid recognition. We also observed enhanced binding between P. aeruginosa and mixed glycolipid liposomes. Interestingly, strong ligands could activate weaker binding ligands leading to higher LecA binding capacity. This hetero-multivalency is probably mediated via a simple mechanism, Reduction of Dimensionality (RD). To understand the influence of RD, we also modeled LecA's two-step binding process with membranes using a kinetic Monte Carlo simulation. The simulation identified the frequency of low-affinity ligand encounters with bound LecA and the bound LecA's retention of the low-affinity ligand as essential parameters for triggering hetero-multivalent binding, agreeing with experimental observations. The hetero-multivalency can alter lectin binding properties, including avidities, capacities, and kinetics, and therefore, it likely occurs in various multivalent binding systems. Using hetero-multivalency concept, we also offered a new strategy to design high-affinity drug carriers for targeted drug delivery.

The Caenorhabditis elegans p38 MAPK Gene plays a key role in protection from mycobacteria.

Mitogen-activated protein kinases (MAPK) are critical mediators of cellular responses to pathogens and are activated in response to infection, but investigation is difficult in multi-cell hosts due to developmental lethality of mutations. Mycobacterium marinum (Mm) is an established model for tuberculosis, a disease afflicting nearly one-third of the world's population. We found that Mm-infected Caenorhabditis elegans display >80% mortality, but nonpathogenic M. smegmatis cause <15% mortality. C. elegans display pathological changes when infected with Mm, whereas Mm mutants produce lower mortality, suggesting that C. elegans is a promising virulence model for detailed genetic analysis. C. elegans MAPK mutants are hypersusceptible to mycobacterial infection; however, the C. elegans TOL-like, TGF-ß and insulin-like pathway genes do not play important roles in susceptibility. We show that pathogenic mycobacteria inhibit MAPK-mediated protection through the MAPK phosphatase gene and demonstrate that C. elegans provide a genetically tractable pathogenicity model of both the host and pathogen.

Coliform and Escherichia coli contamination of desserts served in public restaurants from Guadalajara, Mexico, and Houston, Texas.

Bacterial enteropathogens acquired from contaminated food are the principal causes of travelers' diarrhea (TD). We evaluated desserts obtained from popular restaurants in the tourist city of Guadalajara, Mexico, and Houston, Texas, to determine coliform and Escherichia coli contamination levels and presence of diarrheagenic E. coli known to be important in TD. Contamination for all organisms was seen for desserts served in Guadalajara restaurants. Desserts should be considered as potentially risky foods for development of TD among international visitors to developing regions of the world.

Improvement in detection of enterotoxigenic Escherichia coli in patients with travelers' diarrhea by increasing the number of E. coli colonies tested.

No cause of one-third of travelers' diarrhea (TD) cases can be detected despite microbiologic assessment. We propose that these pathogen-negative TD cases include undetected enterotoxigenic Escherichia coli (ETEC). As a standard in diagnostic microbiology, samples of five E. coli colonies were tested to detect ETEC from stool cultures. We compared the sensitivities and the number of ETEC detected by 20 colonies with those of 5, 10, and 15 colonies. The percent detection of ETEC with five E. coli colonies was significantly different from that using 20 E. coli colonies. Of the 116 subjects studied, the number positive for ETEC for 5, 10, 15 and 20 colonies tested were 22 (19.0%), 37 (31.9%), 45 (38.8%) and 46 (39.7%), respectively. Based on our results, we recommend the testing of at least 10 E. coli colonies for optimum detection of ETEC in patients with TD.

Repeated temperature fluctuation extends the life span of Caenorhabditis elegans in a daf-16-dependent fashion.

Thermocyclers were utilized to regularly shift nematodes between 12 degrees C and 25 degrees C throughout their life spans. When wild-type worms (N2) were "thermocycled" between 12 degrees C and 25 degrees C at 10-min intervals they lived almost as long as those that were incubated constantly at 12 degrees C. Shifting at 1-min or 1-h intervals lessened this effect. Similar results were observed for the long-lived mutants daf-2, eat-2 and clk-1, each of which prolongs life span through different mechanisms. In contrast, the life span of a daf-16 mutant was not prolonged by thermocycling worms, indicating that the effect is mediated by an insulin-like signaling pathway. To elucidate the molecular basis for the life span extension, two transgenic strains were employed in which heat shock proteins (HSPs) drove expression of the green fluorescent protein (GFP) gene. As expected, both HSPs were expressed at significantly higher levels in animals grown at 25 degrees C. Moreover, HSP expression in the thermocycled worms approximated that of animals grown at 25 degrees C more so than animals grown at 12 degrees C. This suggests that incubation at the higher temperatures for short time intervals induced stress-responsive gene expression that led to significant life span extension.