Intrinsic factors behind long COVID: III. Persistence of SARS-CoV-2 and its components.

Considerable research has been done in investigating SARS-CoV-2 infection, its characteristics, and host immune response. However, debate is still ongoing over the emergence of post-acute sequelae of SARS-CoV-2 infection (PASC). A multitude of long-lasting symptoms have been reported several weeks after the primary acute SARS-CoV-2 infection that resemble several other viral infections. Thousands of research articles have described various post-COVID-19 conditions. Yet, the evidence around these ongoing health problems, the reasons behind them, and their molecular underpinnings are scarce. These persistent symptoms are also known as long COVID-19. The persistence of SARS-CoV-2 and/or its components in host tissues can lead to long COVID. For example, the presence of viral nucleocapsid protein and RNA was detected in the skin, appendix, and breast tissues of some long COVID patients. The persistence of viral RNA was reported in multiple anatomic sites, including non-respiratory tissues such as the adrenal gland, ocular tissue, small intestine, lymph nodes, myocardium, and sciatic nerve. Distinctive viral spike sequence variants were also found in non-respiratory tissues. Interestingly, prolonged detection of viral subgenomic RNA was observed across all tissues, sometimes in multiple tissues of the same patient, which likely reflects recent but defective viral replication. Moreover, the persistence of SARS-CoV-2 RNA was noticed throughout the brain at autopsy, as late as 230 days following symptom onset among unvaccinated patients who died of severe infection. Here, we review the persistence of SARS-CoV-2 and its components as an intrinsic factor behind long COVID. We also highlight the immunological consequences of this viral persistence.

The Development of a Phytopathogenic Fungi Control Trial: Aspergillus flavus and Aspergillus niger Infection in Jojoba Tissue Culture as a Model.

After introducing the idea of using concentrations equal to or less than the minimum inhibition concentration (MIC) of some active chemical compounds for evacuating microbial cells, different types of microbes were evacuated. The original protocol was given the name sponge-like protocol and then was reduced and modified from a microorganism to another to prepare microbial ghosts for various applications such as immunological applications, drug delivery, and isolation of DNA and protein. Fungal pathogens that infect plants critically affect cost effectiveness, quality, and quantity of their production. They kill plant cells and/or cause plant stress. Plant fungal infections can originate from many sources such as infected soil, seeds, or crop debris causing diseases and quality losses around the world with billions of US dollars annually as costs of the associated productivity loss. This study focused on the application of the sponge-like protocol in protecting in vitro tissue cultures of plants against fungal pathogens. This can be useful for research purposes or may be developed to be introduced in field applications. Aspergillus flavus and Aspergillus niger infection in tissue culture of jojoba (Simmondsia chinensis (Link) Schn.) was used as a model to establish the employment of this protocol to control plant fungal diseases. The best conditions for A. flavus and A. niger ghosts production previously mapped by randomization experimental design (reduced Plackett-Burman experimental design) were used to prepare fungal ghosts. SDS, NaOH, NaHCO3, and H2O2 were used in their MIC (+1 level) or minimum growth concentration (MGC, -1 level) according to the determined optimal experimental design. The release of both of DNA and protein from the fungal cells was evaluated spectrophotometrically at 260nm and 280nm, respectively, as an indicator for cell loss of their cytoplasm. Fungal ghost cells were also examined by transmission electron microscopy. After confirming the preparation of high-quality fungal ghost cells, the same conditions were mimicked to control plant fungal infection. Jojoba grown in tissue culture was sprayed with fungal cells (about 103 CFU) as a control experiment or fungal cells followed by treatment with solution (a) represents the fungal ghost cells formation calculated critical concentration (FGCCC) of SDS, NaOH, and NaHCO3 and then treatment with solution (b) represents H2O2 FGCCC. The plant was examined on day 0 (plant grown before any infection or infection followed by treatment), day 5 (plant at day 5 after infection or infection followed by treatment), and day 10 (plant at day 10 after infection or infection followed by treatment). We observed fungal growth in case of control experiments at days 5 and 10 on the tissue culture medium, as well as plant, and the absence of any fungal growth in case of plant treated with FGCCC even after day 10. We recommend using this FGCCC in the form of chemical spraying formulation to treat the plants aiming to control different plant fungal infections in in vitro tissue culture systems or applied in field.

Auto-induction expression of human consensus interferon-alpha in Escherichia coli.

BACKGROUND: Isopropyl-ß-D-1-thiolgalactopyranoside (IPTG)-inducible expression of recombinant proteins in E. coli is commonly used and effective. Nevertheless, unintended induction was encountered as a problem when using these bacterial expression systems, generating cultures that give reduced or variable protein yields. Auto-induction allows for production of much higher target protein yield and cell mass than conventional procedures using induction with IPTG without monitoring cell growth then adding IPTG at the appropriate cell density. This method involves special media recipes that promote growth to high density and automatically induce expression of target protein from T7 promoter. Consensus interferon is a synthetic artificially engineered interferon having an amino acid sequence that is a rough average of the sequences of all natural human alpha interferon subtypes and has greater potency than other interferons even the pegylated versions. The purpose of this study was high-level expression of human consensus interferon-alpha (cIFN-α) in E. coli using an auto-induction protocol. The cIFN-α gene was cloned into pET101/D-TOPO expression vector under the T7 promoter transcriptional regulation. Expression was optimized with respect to temperature and length of incubation in shake flask cultures. The antiviral potency and anticancer activity of cIFN-α were evaluated in comparison to IFN-α2a. RESULTS: The expressed cIFN-α protein in auto-induction T7 system was found mostly in soluble fraction of the cell lysate (about 70% of yield in total cell lysate) after lowering incubation temperature to 25°C or 30°C. Protein expression was maximal after 24 h incubation at 25°C or 30°C. After purification via single-step chromatography using DEAE-Sepharose, the yield was 270 mg/L in shake flask E. coli cultures which is much higher than IPTG-inducible T7 expression system and other systems according to available data. The synthesized cIFN-α was biologically active as confirmed by its anticancer and antiviral effects and was significantly more potent than IFN-α2a. CONCLUSIONS: The auto-induction process was reliable and convenient for production of cIFN-α protein in E. coli, and can be adapted for large-scale therapeutic protein production.

Therapeutic alpha-interferons protein: structure, production, and biosimilar.

In 2007, the world solemnized the golden jubilee of the discovery of interferon (IFN). Interferon is a small protein messenger called a pluripotent cytokine, produced by several cells of the host in response to various biological as well as synthetic stimuli. There are three major classes of interferons in humans: IFN-alpha, IFN-beta, and IFN-gamma. As a treatment option, interferon-alpha (IFN-α) is the most effective one. IFN-α has proved to be effective as an antiviral therapy and tumor-fighting drug in the past two decades. Meanwhile, great progress has been achieved in establishing IFN-α as the first choice of antiviral therapy for chronic hepatitis C virus (HCV) patients. Recently, novel pegylated IFN-α2 products with extended in vivo half-lives and consensus interferon, an artificially engineered type I interferon, have been developed to substantially improve treatment regimes for HCV patients. Undesirable acute and chronic side effects in addition to immunogenicity of therapeutic IFN products remain constraints to conquer for further improvements in clinical applications of IFN. It is certainly expected that more research will be conducted in the future, not only to face these challenges but also to extend the range of IFN products and their clinical targets. The objective herein is to review the current therapeutic alpha-interferons production, formulation technologies, and prospective future for the original entity and its biogeneric version.

Fungi as a Source of Edible Proteins and Animal Feed.

It is expected that the world population will reach 9 billion by 2050. Thus, meat, dairy or plant-based protein sources will fail to meet global demand. New solutions must be offered to find innovative and alternative protein sources. As a natural gift, edible wild mushrooms growing in the wet and shadow places and can be picked by hand have been used as a food. From searching mushrooms in the forests and producing single cell proteins (SCP) in small scales to mega production, academia, United Nations Organizations, industries, political makers and others, play significant roles. Fermented traditional foods have also been reinvestigated. For example, kefir, miso, and tempeh, are an excellent source for fungal isolates for protein production. Fungi have unique criteria of consuming various inexpensive wastes as sources of carbon and energy for producing biomass, protein concentrate or amino acids with a minimal requirement of other environmental resources (e.g., light and water). Fungal fermented foods and SCP are consumed either intentionally or unintentionally in our daily meals and have many applications in food and feed industries. This review addresses fungi as an alternative source of edible proteins and animal feed, focusing mainly on SCP, edible mushrooms, fungal fermented foods, and the safety of their consumption.

A De Novo Optimized Cell-Free System for the Expression of Soluble and Active Human Tumor Necrosis Factor-Alpha.

Cell-free (in vitro) expression is a robust alternative platform to the cell-based (in vivo) system for recombinant protein production. Tumor necrosis factor-alpha (TNF-α) is an effective pro-inflammatory cytokine with pleiotropic effects. The aim of the current study was de novo optimized expression of soluble and active human TNF-α by an in vitro method in an E. coli-based cell-free protein synthesis (CFPS) system and its biological activity evaluation. The codon-optimized synthetic human TNF-α gene was constructed by a two-step PCR, cloned into pET101/D-TOPO vector and then expressed by the E. coli CFPS system. Cell-free expression of the soluble protein was optimized using a response surface methodology (RSM). The anticancer activity of purified human TNF-α was assessed against three human cancer cell lines: Caco-2, HepG-2 and MCF-7. Data from RSM revealed that the lowest value (7.2 µg/mL) of cell-free production of recombinant human TNF-α (rhTNF-α) was obtained at a certain incubation time (6 h) and incubation temperature (20 °C), while the highest value (350 µg/mL) was recorded at 4 h and 35 °C. This rhTNF-α showed a significant anticancer potency. Our findings suggest a cell-free expression system as an alternative platform for producing soluble and functionally active recombinant TNF-α for further research and clinical trials.

The anti-cancer activity of human consensus interferon-alpha synthesized in cell-free system.

The cell-free method is suitable for rapid and economical production of therapeutic proteins, since it is an open system, which allows us to control the reaction microenvironment to promote folding, solubility of proteins and maximize the protein yield. Consensus interferon is a newly developed type I interferon, a rapid-acting version of interferon that appears more potent than the currently approved pegylated version. Our work aimed to synthesize human consensus interferon-alpha (cIFN-α) in cell-free protein expression system of Escherichia coli cells origin. The cloned cIFN-α gene in pET101/D-TOPO expression system was used in cell-free IFN production. The system was tested by using a standard construct, GFP (green fluorescent protein) gene was cloned into pIVEX2.3 vector; this gene and our gene, both are under the T7 promoter transcriptional control. The synthesis of active cIFN-α gradually increased from 2 to 6 h of the reaction, also reducing the temperature of incubation to ≤ 30°C maximized its solubility. After purification on nickel-nitrilotriacetate acid (Ni-NTA) resin, the yield of cIFN-α was 400 µg/ml cell-free reaction solution. The resultant cIFN-α was fully biologically active as demonstrated by its anti-cancer effect and immunoassay signals.

Recent Approaches towards Control of Fungal Diseases in Plants: An Updated Review.

Recent research demonstrates that the number of virulent phytopathogenic fungi continually grows, which leads to significant economic losses worldwide. Various procedures are currently available for the rapid detection and control of phytopathogenic fungi. Since 1940, chemical and synthetic fungicides were typically used to control phytopathogenic fungi. However, the substantial increase in development of fungal resistance to these fungicides in addition to negative effects caused by synthetic fungicides on the health of animals, human beings, and the environment results in the exploration of various new approaches and green strategies of fungal control by scientists from all over the world. In this review, the development of new approaches for controlling fungal diseases in plants is discussed. We argue that an effort should be made to bring these recent technologies to the farmer level.

De novo expression and antibacterial potential of four lactoferricin peptides in cell-free protein synthesis system.

For the first time, we produced four lactoferricin (LFcin) peptides by a cell-free (in vitro) method. These short antimicrobial peptides were expressed in an E. coli cell-free protein synthesis (CFPS) system and the bioactivity of the produced peptides was demonstrated. Additionally, we designed a novel synthetic consensus peptide (ConLFcin). The genes of bovine Lfcin (bLFcin), human Lfcin (hLFcin), camel Lfcin (cLFcin), and ConLFcin were cloned into pET101/D-TOPO vector then peptides were synthesized in vitro by E. coli CFPS system. The antibacterial activity of these synthesized peptides was evaluated against Escherichia coli, Salmonella typhi, Pseudomonas aeruginosa, Staphylococcus aureus, and methicillin-resistant Staphylococcus aureus (MRSA). The four cell-free synthesized peptides showed significant antibacterial potency at minimum inhibitory concentration (MIC) values between 1.25 and 10 µg/mL. cLFcin and ConLFcin showed higher antibacterial effects than bLFcin and hLFcin. Thus, cell-free expression system is an ideal system for rapid expression of functionally active short bioactive peptides.

Bacteriostatic and Bactericidal Activities of Camel Lactoferrins Against Salmonella enterica Serovar Typhi.

Lactoferrin is an iron-binding glycoprotein present in various secretions (e.g., milk, tears, saliva, pancreatic juice), which performs multiple functions, with one of them being the antimicrobial defense. Purified camel lactoferrins (cLfs) from different Saudi camel clans, as well as human and bovine lactoferrins (hLf or bLf) were tested as antimicrobial agents against Salmonella enterica serovar Typhi (S. Typhi). All cLfs showed superior antibacterial potentials relative to hLf or bLf, while there was no noticeable difference in the antimicrobial capabilities between the cLfs from different camel clans. We observed synergy between the inhibitory activities of Lfs and antibiotics against bacterial growth. Expression of numerous bacterial proteins was affected by the treatment with Lf and its combinations, giving insight into the molecular mechanisms of the Lf action. Furthermore, several bacterial proteins were shown to interact with cLf-biotin. Scanning and transmission electron microscopy revealed the presence of obvious extracellular and intracellular changes after S. Typhi treatment by antibiotic (carbenicillin) or cLf alone, and in combination. The effects of antibiotics and Lf were synergistic, supporting the potential of the use of Lf-antibiotic combinations.

Immunogenicity comparison of lactoferrin purified from Saudi Arabia camel clans milk.

Secretory lactoferrins play a crucial rolls at mucosal surfaces as not only antimicrobial molecules in primate as well as human, but as physiological protein. Its multiple functions extended to be one of immunogen could elicited autoimmune disorders. Purified camel lactoferrin (cLfs) from different Saudi camel clans were shown to be a potent immunogen when injected into rabbit. Four rabbit were subcutaneously immunized with different camel clans lactoferrin/Freunds adjuvant. Anti-cLfs potency titration was reach 1:32000 and did not significantly differences between different cLfs. The cross-reactivity level of different anti-Lfs were highly significant, specially between cLfs and bLf/hLf.

Synergistic Killing of Pathogenic Escherichia coli Using Camel Lactoferrin from Different Saudi Camel Clans and Various Antibiotics.

Current study aimed to analyze the synergistic killing of pathogenic Escherichia coli using camel lactoferrin from different Saudi camel clans and various antibiotics. Methods: using multiple microbiological and protein analysis techniques, the results were shown that the purified camel lactoferrins (cLfs) from different Saudi camel have strong antimicrobial potentials against two strains of E. coli. Although all cLfs were superior relative to human or bovine lactoferrins (hLf or bLf), there was no noticeable difference in the antimicrobial potentials of cLfs from different camel clans. The effects of antibiotics and cLfs were synergistic, indicating the superiority of using cLf-antibiotic combinations against E. coli growth. Since these combinations possessed distinguished synergy profiles, it is likely that they can be used to enhance the low efficacy of antibiotics, as well as to control the problems associated with bacterial resistance. Furthermore, these combinations can reduce the cost of cure of bacterial infections, especially in the developing countries. The analysis of the molecular mechanisms of lactoferrin action revealed that expression of several E. coli proteins was affected by the treatment with these antibacterial factors. Several proteins of different molecular weights interacting with cLf-biotin were found. Scanning and transmission electron microscopy analysis revealed the presence of noticeable morphological changes associated with the treatment of E. coli strains by antibiotic carbenicillin or cLf alone, and in combination. Camel lactoferrin has superior potential killing of E. coli over bovine and human lactoferrin, and this potential can be further synergistically enhanced of cLF is combined with antibiotics.

Efficacy comparison of gel-based, membrane and glass array techniques to detect human antibodies isotypes among the Egyptian HCV-patients.

Hepatitis C virus is a major public health problem leading to cirrhosis and increased risk for development of hepatocellular carcinoma, both leading indications for liver transplantation. Egypt has the highest prevalence of hepatitis C of worldwide. Anti-HCV antibody is usually detected by enzyme immunoassay (EIA). Microarray analysis of 8 Anti-HCV antibody isotypes and 5 HCV peptides considered separately on 5 different matrixes was carried out on 50 hepatitis C Egyptian patients. The optimal substrate kind was chosen based on the greatest amount of antibody bonded with the minimal background. Mercaptosilane activated slides, agarose-slides and polyvinylidene difluoride membranes were the best substrates, while polyacrylamide and nitrocellulose membrane were less sensitive. IgM isotype gave the weakest signals in all patients whatever the substrate type used for antibody immobilization while IgG (total) and its subtypes IgG2, IgG3 and IgG(4) gave the strongest signals with most of the substrates follows by IgA(1), IgG(1) and total IgA, respectively. The results demonstrate that IgG2, IgG3 and IgG(4) are the dominant IgG subtypes, which may indicate that HCV patient immune response shift toward Th-2 immunity. The microarrays permitted the simultaneous serodetection of hepatitis C virus core and envelope peptides by using corresponding rabbit anti-peptides. Hepatitis C virus core and envelope peptides 1, 2, 3, 4 and 5 showed strong signals on all the used substrates except for polyacrylamide slides and nitrocellulose membranes.

Development of nanoparticle adjuvants to potentiate the immune response against diphtheria toxoid.

BACKGROUND: Over the years, diphtheria was known as contagious fatal infection caused by Corynebacterium diphtheria that affects upper respiratory system. The spread of diphtheria epidemic disease is best prevented by vaccination with diphtheria toxoid vaccine. Aluminum adjuvants were reported to stimulate the immune responses to killed and subunit vaccines. OBJECTIVE: Our study aimed to minimize adjuvant particles size, to gain insight of resulting immunity titer and impact on immune response antibody subtypes. METHODS: Aluminum salts and calcium phosphate adjuvants were prepared, followed by micro/nanoparticle adjuvants preparation. After formulation of diphtheria vaccine from diphtheria toxoid and developed adjuvants, we evaluated efficacy of these prepared vaccines based on their impact on immune response via measuring antibodies titer, antibodies isotyping and cytokines profile in immunized mice. RESULTS: A noteworthy increase in immunological parameters was observed; antibodies titer was higher in serum of mice injected with nanoparticle adjuvants-containing vaccine than mice injected with standard adjuvant-containing vaccine and commercial vaccine. Aluminum compounds adjuvants (nanoparticles and microparticles formulation) and microparticles calcium phosphate adjuvant induce TH2 response, while nanoparticles calcium phosphate and microparticles aluminum compounds adjuvants stimulate TH1 response. CONCLUSIONS: Different treatments to our adjuvant preparations (nanoparticles and microparticles formulation) had a considerable impact on vaccine immunogenicity.

Functionality of intrinsic disorder in tumor necrosis factor-α and its receptors.

Tumor necrosis factor-α (TNF-α) is a pleiotropic inflammatory cytokine that exerts potent cytotoxic effects on solid tumor cells, while not affecting their normal counterparts. It is also known that TNF-α exerts many of its biological functions via interaction with specific receptors. To understand the potential roles of intrinsic disorder in the functioning of this important cytokine, we explored the peculiarities of intrinsic disorder distribution in human TNF-α and its homologs from various species, ranging from zebrafish to chimpanzee. We also studied the peculiarities of intrinsic disorder distribution in human TNF-α receptors, TNFR1 and TNFR2. Analysis revealed that cytoplasmic domains of TNF-α and its receptors are expected to be highly disordered. Furthermore, although the sequence identities of analyzed TNF-α homologs range from 99.57% (between human and chimpanzee proteins) to 22.33% (between frog and fish proteins), their intrinsic disorder profiles are characterized by a remarkable similarity. These observations indicate that the peculiarities of distribution of the intrinsic disorder propensity within the amino acid sequences are evolutionary conserved, and therefore could be of functional importance for this family of proteins. We also show that disordered and flexible regions of human TNF-α and its TNFR1 and TNFR2 receptors are crucial for some of their biological activities.

Influence of camel milk on the hepatitis C virus burden of infected patients.

Hepatitis C virus (HCV) infection represents a world health problem and no protective vaccine or effective drug currently exists. For economic reasons, many patients use traditional medicines to control the infection. In Egypt, camel milk is one of the traditional medicines widely consumed by patients infected with HCV. The present study aimed to evaluate the efficacy of camel milk in the treatment of patients infected with HCV. Whole camel milk from a local farm was administered to patients for 4 months (250 ml/day/patient). Patient sera were collected prior to and following camel milk drinking, and three markers were set-up for sera-evaluation. The three markers indicating the effect of camel milk on HCV infection were: Liver function assays [alanine aminotransferase (ALT) and aspartate aminotransferase (AST)]; a viral load assay; and anti-HCV antibodies profile and isotyping against synthetic HCV epitopes. Camel milk demonstrated the ability to improve general fatigue, health and liver function (ALT and AST levels); ALT was reduced in ~88% of patients and AST was reduced in all patients subsequent to drinking camel milk for four months. The majority of patients responded positively to camel milk treatment; RNA viral load decreased in 13 out of the 17 patients (76.47%) and one patient exhibited undetected viremia following camel milk treatment. The anti-HCV antibodies profile and isotyping were significantly decreased (P<0.05) in immunoglobulin (Ig)G1 following treatment in 70-76% of patients. However, the treatment was ineffective in 23.53% of patients who experienced no reduction in RNA viral load following treatment with camel milk. In conclusion, whole camel milk treatment demonstrated efficacy in vivo; the viral load in the majority of patient sera was reduced and the IgG isotype profile was converted to Th1 immunity.

Significant antibacterial activity and synergistic effects of camel lactoferrin with antibiotics against methicillin-resistant Staphylococcus aureus (MRSA).

Methicillin-resistant Staphylococcus aureus (MRSA) causes major healthcare problems in many countries, as it is present as several hospital- and community-associated strains. Hospital-associated MRSA is one of the most prevalent nosocomial pathogens throughout the world and infections caused by community-acquired MRSA are rising. This emphasizes the need for new and efficient anti-MRSA agents. We evaluated the antibacterial effects of camel lactoferrin (cLf) and human lactoferrin (hLf) alone and in combination with several antibiotics against MRSA. Antimicrobials were tested against MRSA and an S. aureus control strain by the agar disc diffusion method. The minimum inhibitory concentration (MIC) was determined for antimicrobials by the broth microdilution method. Synergy between cLf or hLf and antibiotics was examined by checkerboard and time-kill assays. The agar disc diffusion assay showed that MRSA growth was inhibited by cLf at 0.25-3 mg/ml and hLf at 1-3 mg/ml. cLf demonstrated 3 times higher inhibitory activity against MRSA than hLf in terms of MIC values (250 vs. 750 µg/ml, respectively). Biotinylated cLf was recognized by two membrane proteins of MRSA, 66-67 KDa. Combinations of cLf or hLf and oxacillin or vancomycin at sub-MIC levels enhanced in vitro antibacterial activity against MRSA compared with each agent alone.

Human consensus interferons: Bridging the natural and artificial cytokines with intrinsic disorder.

The consensus interferons are artificially engineered proteins that combine most of the therapeutic features of natural human α-interferons and show high anti-cancer and anti-viral activities. Egyptian patients infected with hepatitis C virus (HCV) genotype 4 show lower responses to interferon (IFN) therapy than the distributed worldwide patients infected with the other HCV genotypes. Numerous studies have reported that patients with hepatitis C who have not responded to a previous standard IFN-alpha therapy or those who relapsed following treatment cessation may benefit from retreatment with consensus IFN-α (cIFN-α). IFNs-α are shown here to have functionally important disordered regions. Furthermore, a strong correlation is established between the peculiarities of disorder profiles of these proteins and their known structural features. Intrinsic disorder profiles of existing cIFNs-α possess remarkable similarity to the consensus disorder profile calculated as averaged disorder predispositions of all human IFNs-α. If the peculiarities of disorder distribution within the protein sequence are related to protein functionality, then comparison of the disorder profiles of artificial cIFNs (query profiles) with the averaged disorder predisposition profile of human IFNs-α (target profile) can be used in the design of novel cIFNs. The goal here would be to achieve a close similarity between the query and target profiles by manipulating the cIFN sequence.