Phylogenomics of the psychoactive mushroom genus Psilocybe and evolution of the psilocybin biosynthetic gene cluster

Psychoactive mushrooms in the genus Psilocybe have immense cultural value and have been used for centuries in Mesoamerica. Despite the recent surge of interest in these mushrooms due to the psychotherapeutic potential of their natural alkaloid psilocybin, their phylogeny and taxonomy remain substantially incomplete. Moreover, the recent elucidation of the psilocybin biosynthetic gene cluster is known for only five of ~165 species of Psilocybe, four of which belong to only one of two major clades. We set out to improve the phylogeny of Psilocybe using shotgun sequencing of fungarium specimens, from which we obtained 71 metagenomes including from 23 types, and conducting phylogenomic analysis of 2,983 single-copy gene families to generate a fully supported phylogeny. Molecular clock analysis suggests the stem lineage of Psilocybe arose ~67 mya and diversified ~56 mya. We also show that psilocybin biosynthesis first arose in Psilocybe, with 4 to 5 possible horizontal transfers to other mushrooms between 40 and 9 mya. Moreover, predicted orthologs of the psilocybin biosynthetic genes revealed two distinct gene orders within the biosynthetic gene cluster that corresponds to a deep split within the genus, possibly a signature of two independent acquisitions of the cluster within Psilocybe.

Immuno-affinity chromatography for purification of IgG from hyper-immune sera raised against 146S fraction of Foot and Mouth Disease Virus for diagnostic purposes

Immunoaffinity chromatography (IAC) is a fundamental isolation and purification tool which is incorporated in a substantial range of therapeutic and diagnostic applications. This study has reappraised the usefulness of immunoaffinity chromatography for the purification of polyclonal antibodies. Protein A based IAC is a convenient and reliable method for purification of IgG, from hyperimmunesera (HIS) raised in experimental animals such as rabbits, guinea pigs and mice to be utilized in pharmaceutics and diagnostics. The 146S fraction of Foot and Mouth Disease virus (FMDV) TCID50=10 5.6 was cultured on a baby hamster kidney cell line 21 (BHK-21), concentrated using salt precipitation method using PEG 6000, purified by size exclusion chromatography (SEC) using Sepharose-30 at 254nm absorbance. Purification of 146S FMDV was analyzed using 12% SDS-PAGE which provided two bands of light and heavy chains. The alum-based vaccine, consisting of ≥10μg of 146S FMDV, was applied in 10 male rabbits and 10 male guinea pigs and two animals of each group were taken as a negative control. The titer of serum was calculated using virus neutralization test. A Protein-A kit (Thermo scientific- 44667, 0528.2) was used to purify HIS raised against 146S FMDV and validated using 12% SDS PAGE in reducing condition. The data demonstrate that protein-A affinity chromatography is an efficient tool for the purification of antibodies from hyper-immune sera raised against 146S FMDV and can be used for the production of diagnostic kits e.g. Enzyme linked immuno-sorbent assay (ELISA) and radioimmunoassay.

A Novel Bead-Capture Nanopore Sequencing Method for Large Structural Rearrangement Detection in Cancer

Rapid, cost-effective genomic stratification of structural rearrangements in cancer is often of vital importance when determining treatment; however, existing diagnostic cytogenetic and molecular testing fails to deliver the required speed when deployed at scale. Next-generation sequencing-based methods are widely used, but these can lack sensitivity and require batching of samples to be cost-effective, with long turnaround times. Here we present a novel method for rearrangement detection from genomic DNA based on third-generation long-read sequencing that overcomes these time and cost issues. The utility of this approach for the genomic stratification of patients with acute myeloid leukemia is shown based on detection of four of the most prevalent structural rearrangements. The method not only determines the precise genomic breakpoint for each expected rearrangement but also discovers and validates novel translocations in one-third of the tested samples, 80% of which involve known oncogenes. This method may prove to be a powerful tool for the diagnosis, genomic stratification, and characterization of cancers.

Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 infection early in the pandemic and the role of unidentified cases in transmission

OBJECTIVES

To analyse nosocomial transmission in the early stages of the coronavirus 2019 (COVID-19) pandemic at a large multisite healthcare institution. Nosocomial incidence is linked with infection control interventions.

METHODS

Viral genome sequence and epidemiological data were analysed for 574 consecutive patients, including 86 nosocomial cases, with a positive PCR test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the first 19 days of the pandemic.

RESULTS

Forty-four putative transmission clusters were found through epidemiological analysis; these included 234 cases and all 86 nosocomial cases. SARS-CoV-2 genome sequences were obtained from 168/234 (72%) of these cases in epidemiological clusters, including 77/86 nosocomial cases (90%). Only 75/168 (45%) of epidemiologically linked, sequenced cases were not refuted by applying genomic data, creating 14 final clusters accounting for 59/77 sequenced nosocomial cases (77%). Viral haplotypes from these clusters were enriched 1-14x (median 4x) compared to the community. Three factors implicated unidentified cases in transmission: (a) community-onset or indeterminate cases were absent in 7/14 clusters (50%), (b) four clusters (29%) had additional evidence of cryptic transmission, and (c) in three clusters (21%) diagnosis of the earliest case was delayed, which may have facilitated transmission. Nosocomial cases decreased to low levels (0-2 per day) despite continuing high numbers of admissions of community-onset SARS-CoV-2 cases (40-50 per day) and before the impact of introducing universal face masks and banning hospital visitors.

CONCLUSION

Genomics was necessary to accurately resolve transmission clusters. Our data support unidentified cases-such as healthcare workers or asymptomatic patients-as important vectors of transmission. Evidence is needed to ascertain whether routine screening increases case ascertainment and limits nosocomial transmission.

Burden-driven feedback control of gene expression

Cells use feedback regulation to ensure robust growth despite fluctuating demands for resources and differing environmental conditions. However, the expression of foreign proteins from engineered constructs is an unnatural burden that cells are not adapted for. Here we combined RNA-seq with an in vivo assay to identify the major transcriptional changes that occur in Escherichia coli when inducible synthetic constructs are expressed. We observed that native promoters related to the heat-shock response activated expression rapidly in response to synthetic expression, regardless of the construct. Using these promoters, we built a dCas9-based feedback-regulation system that automatically adjusts the expression of a synthetic construct in response to burden. Cells equipped with this general-use controller maintained their capacity for native gene expression to ensure robust growth and thus outperformed unregulated cells in terms of protein yield in batch production. This engineered feedback is to our knowledge the first example of a universal, burden-based biomolecular control system and is modular, tunable and portable.

Optimization of saccharification potential of recombinant xylanase from Bacillus licheniformis

Saccharification potential of xylanase enzyme cloned from Bacillus licheniformis into E. coli BL21 (DE3) was evaluated against plant biomass for the production of bioethanol. The expression of cloned gene was studied and conditions were optimized for its large scale production. The parameters effecting enzyme production were examined in a fermenter. Recombinant xylanase has the ability to breakdown birchwood xylan to release xylose as well as the potential to treat plant biomass, such as wheat straw, rice straw, and sugarcane bagass. The saccharification ability of this enzyme was optimized by studying various parameters. The maximum saccharification percentage (84%) was achieved when 20 units of recombinant xylanase were used with 8% sugarcane bagass at 50°C and 120 rpm after 6 hours of incubation. The results indicated that the bioconversion of natural biomass by recombinant xylanase into simple sugars can be used for biofuel (bioethanol) production. This process can replace the use of fossil fuels, and the use of bioethanol can significantly reduce the emission of toxic gases. Future directions regarding pre-treatment of cellulosic and hemicellulosic biomass and other processes that can reduce the cost and enhance the yield of biofuels are briefly discussed.

Expression of thermostable β-xylosidase in Escherichia coli for use in saccharification of plant biomass

The present work is aimed to evaluate the saccharification potential of a thermostable β-xylosidase cloned from Bacillus licheniformis into Escherichia coli for production of bioethanol from plant biomass. Recombinant β-xylosidase enzyme possesses the ability of bioconversion of plant biomass like wheat straw, rice straw and sugarcane bagass. By using this approach, plant biomass that mainly constitute cellulose can be converted to reducing sugars that could then be easily converted to bioethanol by simple fermentation process. The production of bioethanol will help to overcome energy requirements due to depleting fossil fuels and will also help to protect environment by reducing greenhouse gas emission. In the end, future directions are briefly mentioned that can be utilized to reduce the cost and increase the yield of biofuels.

Herpes simplex virus zosteriform lesions with adoptive transfer of immune cells: a murine model which mimics human recurrent disease

Existing murine models for cutaneous herpes simplex virus type 1 (HSV-1) infection have limited relevance to recurrent disease in humans, since the infection is usually primary rather than reactivated and infection occurs in the absence of an established immune response. To obtain a reproducible model to study the effects of topical antiviral therapy on recurrent disease we have adapted a mouse model which employs zosteriform spread of HSV-1 in the presence of adoptive transfer of immunity (ATI) which mimics human recrudescent lesions. Mice were infected with HSV-1 by scarification at the lateroventral line of the neck; 2 days later, the mice received adoptive transfer of immune cells from the cervical lymph nodes of syngeneic mice that had been infected in the ear pinna with the same strain of virus 7 days earlier. ATI resulted in a heightened inflammatory response in the target tissues for virus replication. Virus was cleared more quickly from the infected tissues in comparison with mice similarly inoculated without ATI, however, the intensity and duration of the inflammation was greater. The model was then used to test the effect of a topical formulation of foscarnet. The results presented demonstrate that the ATI model can provide useful data concerning the efficacy of topical antiviral chemotherapy in man.

Combinations of antiviral and anti-inflammatory preparations for the topical treatment of herpes simplex virus assessed using a murine zosteriform infection model

Recently we have reported a zosteriform murine infection model which employs the adoptive transfer of immune cells (ATI) to recipient infected mice to produce a disease that mimics human recurrent herpes simplex virus (HSV) disease. Mice were infected with HSV-1 by scarification at the lateroventral line of the neck; 2 days later, the mice received immune cells from HSV-1-infected syngeneic mice. Although virus was cleared more quickly from the target tissues of virus replication in recipient mice, ATI resulted in a heightened inflammatory response and delayed healing. This model was used to test the effects of topical formulations containing foscarnet and/or the anti-inflammatory agent, hydrocortisone. Virus clearance and clinical signs, including ear thickness and zosteriform spread of lesions, were studied. Treatment with 3% foscarnet accelerated virus clearance but had little effect on clinical parameters. By contrast, 0.5% hydrocortisone increased the titre and extended the presence of infectious virus for at least 6 days, although the reduction in clinical signs was greater than that obtained with topical foscarnet. Foscarnet in combination with hydrocortisone produced a marked reduction in clinical signs while virus replication was reduced. These results are discussed in relation to the inflammation and discomfort experienced by patients and a possible role for anti-inflammatory formulations in the treatment of HSV reactivation episodes in man.

EHV-1-induced abortion in mice and its relationship to stage of gestation

The most important consequence of equine herpesvirus-1 (EHV-1) infection is abortion. The object of the present study was to characteristic further a murine EHV-1 abortion model and to make comparisons with the natural host with particular reference to the stage of gestation during which the infection occurs. BALB/c mice at different stages of pregnancy were infected intranasally with EHV-1 (strain AB4); they suffered respiratory distress, weight loss, and other constitutional signs of infection. When the virus was inoculated in the late second or early third week of gestation dead or dying fetuses were aborted, whereas infection between seven and nine days of pregnancy led to fetal death and resorption. During the process of resorption, complications were observed. Virus was frequently isolated from the placentas and occasionally from the tissues of the aborting fetuses, depending on the severity of the infection of the placentas. In some cases, therefore, the inoculation resulted in abortion although the infection was restricted to the placenta. Virus antigen was detected in the placentas, lungs and occasionally in other tissues of the aborting fetuses. The potential of this murine model for testing methods for the diagnosis and control of equine abortion is discussed.

Effects of phosphonylmethoxyalkyl derivatives studied with a murine model for abortion induced by equine herpesvirus 1

(S)-9-(3-Hydroxy-2-phosphonylmethoxypropyl)adenine (HPMPA) and (S)-9-(3-hydroxy-2-phosphonylmethoxypropyl)cytosine (HPMPC) were tested in a mouse model for equine herpesvirus 1-induced abortion. HPMPA, given twice daily, reduced virus replication, but the compound was embryotoxic. A single dose of HPMPC, however, reduced the incidence of abortion and transfer of virus to the fetuses while producing no obvious toxic effects.

Pathogenesis of equine herpesvirus-1 in specific pathogen-free foals: primary and secondary infections and reactivation

Six specific pathogen-free foals shown to be free of equine herpesvirus-1 and 4 (EHV-1 and -4) and lacking in maternally-derived antibodies were used to investigate the pathogenesis of EHV-1 in horses. Following primary intranasal inoculation with EHV-1 all foals showed signs of a mild, self-limiting upper respiratory tract infection. A leucopenia was observed, comprising both a lymphopenia and neutropenia. Virus was isolated from nasal mucus and buffy coat cells over several days during the clinical episode and after the animals became clinically normal. Notwithstanding the mildness of the clinical disease, virus was not eliminated completely and intravenous administration of dexamethasone resulted in reactivation of latent EHV-1 in animals which had received only a single dose of the virus. In a second infection given to four foals, 61 days after the primary inoculation, no clinical signs were observed, haematological changes were minimal and viraemia was absent.

Reinfection and reactivation of equine herpesvirus-1 in the mouse

Balb/c mice were inoculated with equine herpesvirus-1 (EHV-1) by the intranasal (i.n.) route. Mice developed respiratory signs; virus replication occurred in the respiratory tract and viraemia was detected; some mice died. Recovered mice were given a second inoculation with the same strain 5 months later. Following the second infection no mice died, however, virus replication was again observed in the respiratory tract and viraemia was detected once more. Administration of an antiviral agent during the acute infection prevented mice from developing severe clinical signs and all survived. These mice, and some that had survived an acute infection without chemotherapy, were given a variety of stimuli, for example X-irradiation or corticosteroid injection. Reappearance of infectious virus was detected in approx. 1/3 animals in either the respiratory tract or blood. We speculate on the possible sites of latency in the model.

The acyclic nucleoside analogue penciclovir is a potent inhibitor of equine herpesvirus type 1 (EHV-1) in tissue culture and in a murine model

Equine herpesvirus type 1 (EHV-1) was sensitive to the nucleoside analogue penciclovir (PCV) when tested in tissue culture; the ED50 was 1.6 micrograms/ml. Drug-resistant mutants were selected which were found to be TK-defective and approx. 45-fold less sensitive to PCV compared with the parental strain. PCV was compared with the phosphonyl derivative, HPMPA in mice infected with EHV-1. Both drugs were shown to be effective in vivo, limiting wild-type virus replication in respiratory tissues, and reducing viraemia. The treated mice also showed less clinical signs and reduced histopathology compared with placebo-treated controls. The establishment of latent EHV-1 in the mice, however, was not prevented. The results obtained with mice suggest that antiviral chemotherapy may be practical in the horse and that this possibility is worthy of further investigation in the natural host.

A murine model for studying EHV-1-induced abortion

Balb/c mice were infected with two abortigenic strains of equine herpesvirus-1 (EHV-1) by intranasal inoculation. The inoculation of one strain produced subclinical disease while the other produced a disease characterised by weight loss, constitutional signs, and death in the most severely affected animals. When pregnant mice were infected by the same method of inoculation, one strain of virus produced premature parturition; both strains produced fetal abnormalities. In some cases, virus could be detected in the aborted fetuses by means of virus isolation and immunofluorescent staining.

Isolation of equine herpesvirus-1 mutants in the presence of (S)-9-(3-hydroxy-2-phosphonylmethoxypropyl)adenine: demonstration of resistance in vitro and in vivo

The compound (S)-9-(3-hydroxy-2-phosphonylmethoxypropyl)adenine (HPMPA) had been previously shown to be highly effective in treatment of EHV-1 in a murine model for the equine disease. This paper describes the isolation of a series of mutants resistant to the drug. Resistance was demonstrated in cell culture and one mutant was tested in a murine model. The resistant mutant was pathogenic for mice; infectious virus was recovered from respiratory tissues and blood at levels similar to the parental virus. However, the mutant showed a significant degree of resistance in vivo, thus proving the virus-specific mode of action of the antiviral compound.

The raising of equine colostrum-deprived foals; maintenance and assessment of specific pathogen (EHV-1/4) free status

Over a period of two years, a total of 22 full term foals from Welsh Mountain pony mares were raised in conditions that were free from infection by Equid herpesvirus (EHV-1/4). Parturition dates were predicted by monitoring colostrum electrolytes, and the mares allowed to foal naturally under supervision or following induction with intravenous oxytocin. Immediately following birth, foals were separated from their dams and transferred to a specially built, positive pressure isolation unit. They were given antibiotic prophylaxis and fed bovine colostrum during the first 24 h, and then mare's milk replacer until weaned. Out of 22 specific pathogen free (SPF) foals one that had not been given antibiotic prophylaxis died of an E. coli septicaemia aged eight days. Two foals developed a streptococcal upper respiratory tract infection, which responded to antibiotic therapy and did not spread to the rest of the herd. A self limiting upper respiratory tract infection was seen in a fourth foal and mild diarrhoea was observed in six foals. Physical development in all SPF foals appeared normal and behavioural patterns resembled those of conventional handreared foals. Newborn foals were held in a separate quarantine area, within the isolation unit, and checked extensively for evidence of EHV-1/4 infection, before being transferred to the main holding unit. Periodic checks were then made for EHV-1/4 over a period ranging from 2 to 4 months; none of the SPF foals showed evidence of infection with EHV-1/4 in terms of clinical disease, virus isolation, sero-conversion or specific lymphocyte transformation.

The pathogenesis of equine herpesvirus type 1 in the mouse: a new model for studying host responses to the infection

An infection was established in adult BALB/c mice by means of intranasal inoculation of the AB4 strain of equine herpesvirus type 1 (EHV-1). The acute infection was confined to the respiratory tract and blood. Virus was shown to replicate in the nasal mucosa, trachea and lung for several days producing clinical signs of disease. Viraemia was also detected and a small proportion of peripheral blood cells contained virus at the peak of the infection. Histological and electron microscopic evidence were obtained which proved that productive virus replication occurred in the ciliated epithelial cells lining the bronchi and in pneumocytes in the lung, resulting in the destruction of these cells. Both humoral and cell-mediated responses to the infection were detected and monitored. By means of immunoprophylaxis or chemotherapy it was possible to modify the course of the infection. This infection model has many striking features in common with that observed in the natural host and the observations suggest that the mouse is a convenient and relevant model in which to study both host responses to EHV-1 infection and modification of the pathogenesis by means of immunoprophylaxis or therapy.

Effective chemotherapy of equine herpesvirus 1 by phosphonylmethoxyalkyl derivatives of adenine demonstrated in a novel murine model for the disease

Equine herpesvirus 1 was established in adult mice by means of intranasal inoculation. A disease developed that showed several features closely resembling the infection in the natural host. These included the restriction of virus replication to the respiratory tract and blood, the replication of virus in ciliated mucosa, and development of viremia for several days during the acute phase of the infection. Infected mice were treated with the antiviral agent (S)-9-(3-hydroxy-2-phosphonylmethoxypropyl)adenine. A marked effect was observed on virus replication in the respiratory tract when chemotherapy was commenced 1 day before virus inoculation; it also cleared the viremia and reversed the progression of clinical signs. When chemotherapy was commenced 1 day after virus inoculation, a moderate, though less marked effect was observed. The efficacy of this drug in the murine infection correlated with activity of the drug against equine herpesvirus 1 in cell cultures. The prospects for chemotherapy in the natural host are discussed in the light of these findings.