bluuebunny/crossref_metadata_2025 huggingface dataset:
Controlling the hypermutation: Exploitation of the MutS protein in Pseudomonas aeruginosa
Authors: Yuan On Yue , Welch Martin
Published: July 2020

Pseudomonas aeruginosa infections commonly develop in individuals with cystic fibrosis (CF), and its adaptation in such an unfavourable condition is always found to be related to hypermutation. In fact, most of the hypermutation is due to the defects in mutS gene which involves in the mismatch repair mechanism, causing the acceleration of mutation rate and adaptive evolution. In order to rheostatically express the MutS protein and achieve “hypomutation” (in which the rate of mutation is lower than that of wild type strain), an exogenous mutS gene with rhamnose-inducible promoter was cloned into MPAO1 mutS::Tn mutant strain. Present findings demonstrate that this system is tightly-controlled and stable, with less rifampicin-resistant mutant frequency and more fluorescence intensity from a GFP-tagged MutS expressing cells were observed when the concentration of the inducer increases. Interestingly, the results from Western blot analysis show that less MutS protein is required to suppress hypermutation in the wild type strain, as compared to our construct that behaves similar to the wild type but obviously needs more MutS expression to achieve such state. This indicates that the exogenous MutS might be lacking of other important protein to work efficiently in mismatch recognition. Therefore, based on our cDNA analysis, we found that fdxA gene next to the mutS gene is in the same operon, which could suggest that they might be functionally related in the DNA repair machinery.
Investigating the effect of Herpes Simplex Virus 1 Latency-Associated Non-Coding RNAs on the Human Neuronal Transcriptome
Authors: Jacobs Amy , Mate Ryan , Fritzsche Martin , O’Hare Peter , Efstathiou Stacey
Published: July 2020

Herpes simplex virus 1 (HSV-1) is a prevalent neurotropic virus that persists for the host’s lifetime due to HSV-1 establishing latency in sensory neurons. During latency, the only abundantly transcribed HSV-1 gene is the latency-associated transcript (LAT), which is processed into the 1.5kb or 2.0kb major LAT intron and several microRNAs. These latency-associated non-coding RNAs (ncRNAs) have been reported to impact the establishment, maintenance and reactivation from latency. However, the molecular mechanisms of these ncRNAs are not fully characterised, especially in the context of human neurons.

This study investigated how the latency-associated ncRNAs affect the human neuronal transcriptome. We developed an experimental system to deliver the latency-associated ncRNAs to human neurons, differentiated from SH-SY5Y neuroblastoma cells. The cells were infected with a replication-defective HSV-1 mutant, in1382, that establishes a quiescent infection in which LAT is strongly expressed. Alternatively, we utilised lentiviruses engineered to express the first 3.1kb of LAT, without or with mutations in splice sites that prevents splicing of the major LAT intron, or five HSV-1 microRNAs, shown to be abundant in latently infected human ganglia.
Following RNA-Seq of uninfected versus infected or transduced SH-SY5Y cells, we identified 178 host genes that had significant differential expression in response to in1382 quiescent infection and lentivirus delivery of LAT or the latency-associated microRNAs. A subset of these were validated by PCR. This work provides insight into possible roles of the latency-associated ncRNAs in neuronal cell biology and latency that could aid future investigations examining how HSV-1 latency affects human neurons.
Identification of Rab GTPases involved in restricting Salmonella Typhi growth in mouse macrophages
Authors: Solano-Collado Virtu , Baldassarre Massimiliano , SpanÒ Stefania
Published: July 2020

Salmonella enterica serovar Typhi (S. Typhi) is a human adapted pathogen and the causative agent of typhoid fever, a life-threatening infection that kills hundred of thousand people every year, being particularly devastating in developing countries. S. Typhi host-restriction is partly due to the Rab32-dependent antimicrobial pathway, which is crucial to prevent the growth of S. Typhi in mouse macrophages. However, the exact mechanisms used by macrophages to kill S. Typhias well as the molecular basis of these mechanisms in the adaptation to the human host are unknown.

In order to identify host genes required to kill S. Typhi, we have performed a targeted short-hairpin RNA (shRNA) screen in primary mouse macrophages, aiming to i) optimize the conditions to perform silencing screenings in primary mouse macrophages and ii) identify novel Rab GTPases involved in S. Typhi host-restriction. For this, pooled shRNAs are used to knockdown gene expression in macrophages using lentiviral-based transduction system. After infection with a fluorescently-labelled S. Typhi strain, macrophages containing different numbers of intracellular bacteria are sorted by flow cytometry and targeted genes identified by next-generation sequencing.

This small-scale screen allowed us to optimize the screening conditions to perform genome-wide screenings in primary macrophages. More importantly, we have identified other Rab GTPases required in mouse macrophages to control S. Typhi survival confirming that this approach can be used to identify genes that macrophages use to control S. Typhi infection and extending our knowledge of the immunity mechanisms controlling the growth of intracellular pathogens.
A novel in vitro urethra model to demonstrate bacterial displacement during urinary catheter insertion
Authors: J. Cortese Yvonne , E. Wagner Victoria , Tierney Morgan , Scully David , M. Devine Declan , Fogarty Andrew
Published: July 2020

Background: There is currently no standard established in vitro model to test the efficacy of intermittent catheters to prevent or control introduction/movement of bacteria into the urethra during device insertion. This study aimed to address this issue by developing a reproducible agar based in vitro urethral model.

Method: A novel in vitro model and testing method was developed to quantify the displacement of bacterial growth after intermittent catheter insertion.The urethral model consists primarily of a preformed channel within a specifically formulated agar based matrix. The urethra model was inoculated at one side of the channel to act as the urethral meatus, a catheter was then inserted. After incubation the bacteria within the urethra channel was quantified.

Results: Once optimised, the model produced reliable and reproducible results with both E. coli and S. aureus (P≥0.265). The model was used to test three different intermittent catheter types. When compared to the growth control there was a significant difference in bacterial distribution when inserting an uncoated (P≤0.001) or hydrophilic coated (P≤0.009) catheter; there was no significant difference when a prototype catheter was inserted with either bacterial species used (P≥0.423).

Conclusion: These findings support the hypothesis that a single catheter insertion can initiate a catheter-associated urinary tract infection. The in vitro urethra model and associated methodology provide a new research tool for the development and validation of emerging technologies in urological healthcare.
UV irradiation of HSV-1 virions induces the differential recruitment of host intrinsic and innate immune regulators to infecting viral genomes
Authors: Iliev Victor , Orr Anne , McFarlane Steven , Boutell Chris
Published: July 2020

Recognition of virus-derived nucleic acids is a key process in the activation of immune defences to viral infection. However, the spatiotemporal recruitment of host immune regulators to infecting viral DNA (vDNA) genomes remains poorly defined. Here we utilize 5-Ethynyl-2’-deoxycytidine (EdC) nucleotide labelling of WT or UV-irradiated HSV-1 genomes in combination with click chemistry and high-resolution confocal microscopy imaging to investigate the recruitment and proximity of key intracellular immune regulators to infecting vDNA during HSV-1 infection.

We report that UV irradiation of HSV-1 virions restricts vDNA decompaction upon delivery to infected cells. UV treatment reduced the frequency in PML-NB recruitment to nuclear genomes relative to non-irradiated vDNA. These data demonstrate an important role of genome decompaction in the recruitment of intrinsic host factors to nuclear infecting vDNA. Additionally, UV-irradiated HSV-1 genomes favoured a premature cytosolic deposition phenotype, due to ineffective association with microtubules as shown by nocodazole treatment. The cytosolic UV irradiated vDNA showed enhanced association with both cGAS and STING. Interestingly, high-resolution Airyscan imaging identified a consistent unreported 3D interaction between both cGAS and STING, the strength of association of which was enhanced in the context of UV infection. This enhanced recruitment correlated with elevated levels of IFN-β transcription relative to non-irradiated vDNA, despite the presence of non-irradiated cytosolic genomes.

Our data demonstrates that UV irradiation of herpesviruses, a well-established procedure for virus inactivation, has multiple effects on genome structure and sub-cellular localisation that differentially influence the spatiotemporal recruitment of intrinsic and innate host immune regulators to infecting genomes.
Toxigenic Corynebacterium ulcerans: re-emergence of a zoonotic infection
Authors: Enefer Alice , Rose Samuel , Litt David , Gower Charlotte , Foster Geoffrey , Groves Natalie , Said Bengü , Russell Katherine , Chand Meera , Amirthalingam Gayatri , Fry Norman
Published: July 2020

Diphtheria is a potentially life-threatening infection in humans. The three species capable of causing diphtheria are: Corynebacterium diphtheriae, C. ulcerans and C. pseudotuberculosis. Although UK cases are rare, recently there has been an increase in reported toxigenic C. ulceransassociated with companion animals. Potentially toxigenic corynebacteria are sent to the National Reference Laboratory, Public Health England (PHE), London, UK for species confirmation, determination of presence of the diphtheria toxin gene by real-time PCR, and confirmation of toxin expression by the Elek test. We reviewed submissions of C. ulcerans between January 2006 and November 2019.

Fifty-three isolates of toxigenic C. ulcerans were received, 29 from humans and 24 from animals. The most common animal hosts were dogs (15) and cats (7), but isolates were also received from a horse and a captive rhinoceros. Multi-locus sequence typing (MLST) data were derived from whole genome sequencing. In three human cases, C. ulcerans was isolated from companion animals and in all three, typing data supported an epidemiological link between human and animal hosts. The sequence types (STs) for these linked isolates were ST331 (human and dog, human and cat) and ST551 (human and cat).

Although MLST data are limited, the finding of the same ST (ST331) from canine and feline sources indicates that strains can be carried by both hosts.

Management of diphtheria cases is an important public health issue. Typing data can support epidemiological linkage and identify possible sources, allowing the potential intervention and treatment of animals thus avoiding onward transmission.
Understanding the evolution of Mycobacterium tuberculosis lineages using an integrated genomics and metabolomics approach
Authors: Cheyne Ashleigh , Broda Agnieszka , Krishnan Nitya , Robertson Brian , Kaforou Myrsini , Larrouy-Maumus Gerald
Published: July 2020

Despite being the number one cause of death from an infectious disease, little is known of the 7 phylogenetic lineages of Mycobacterium tuberculosis (Mtb). These lineages are thought to have adapted differently to their human hosts, as they are geographically localised. As a result, they show variation at the phenotype level, such as virulence and the ability to develop antibiotic resistance, and at a genomic level, such as in single nucleotide polymorphisms (SNPs). We have linked the differences in SNPs between lineages to differences in metabolites (i.e. what is ultimately produced by a cell). Through multi-omic integration of these datasets we have discovered lineage-specific metabolomic changes, potentially as a result of genomic adaptation. The differences between lineages will provide insight into new biological pathways to target and manipulate in future research.
Use of probiotic bacteria to selectively modulate Candida albicans virulence in biofilms
Authors: Cummins Thomas , Hughes Megan , Marchesi Julian , Morse Daniel
Published: July 2020

Candida albicans is an opportunistic fungal pathogen present in the oral cavities of up to two-thirds of people. Despite typically existing as a commensal microorganism, it has pathogenic potential, particularly in older, immunocompromised individuals. A common Candida-associated infection is denture-associated stomatitis (DS), which presents clinically as areas of erythema on the palatal mucosa, and discomfort for the denture-wearer. In vitro, previous work has shown that the expression of C. albicans virulence factors varies according to its interactions with other oral microorganisms.

Mature single- and mixed-species biofilms (with Candida and several strains of common oral bacteria) were grown on poly(methyl methacrylate) (PMMA) coupons, representing dentures. Additionally, to some coupons, individual probiotic strains were added. Total RNA was extracted, reverse transcribed and putative virulence gene expression was determined by RT-qPCR relative to ACT1, a housekeeping gene. Biofilm-infection assays of FADU and TR146 epithelial cell lines were also performed by pre-culturing cells, then adding single- or mixed-species inocula overnight. Quantification of cell damage determined by lactate dehydrogenase assay.

Biofilm co-culture with the addition of certain probiotic strains downregulated C. albicans virulence genes in both short-term and long-term mixed-species biofilms.
With an increasing aged population that is heavily reliant on the use of antibiotics that can negatively affect the microbiota of patients, there is a requirement to look at the benefits of prophylactics, from both an economic and patient well-being viewpoint. The results show the realistic possibility of using probiotics to prevent or restrict development of Candida-associated oral diseases.
The Missing Link: Developing a pipeline for accelerated antibiotic discovery from Streptomyces through linking ‘omics data
Authors: Scobie Darren , Hjorleifsson Grimur , Herron Paul , Rogers Simon , Duncan Katherine
Published: July 2020

The genus Streptomyces has proven to be a rich reservoir of specialized metabolites, accounting for 80% of all microbially produced antibiotics including chloramphenicol and nystatin from S. venezuelae and S. noursei respectively. However, the discovery of novel microbial chemistry is still greatly needed to combat antimicrobial resistance. Comparative metabolomics, using platforms such as Global Natural Products Social Molecular Networking (GNPS), as well as tools such as antiSMASH and BiGSCAPE have aided the mining of biosynthetic gene clusters (BGC’s) across datasets but comparing the chemistry to the encoding biosynthetic gene clusters is a significant bottleneck.

In this study, ten Streptomyces strains were selected, based on phylogeny and availability of genome sequence. The strains were cultured on 6 types of Actinomycete-specific media to maximise metabolite diversity. Liquid Chromatography tandem Mass Spectrometry (LC-MS/MS) was used to obtain spectral data from crude metabolite extracts enabling comparative metabolomics analysis via the GNPS platform. As the genome sequences were publicly available, genome mining of BGC’s was achieved using antiSMASH resulting in 260 BGC’s across the ten strains. This revealed 53 gene cluster families when analysed using BiGSCAPE, the largest encoding for 8 metabolites.

In future, both biosynthetic (BGC’s) and chemistry (parent ions) datasets will be computationally linked based on strain presence/absence. The development of standardised datasets that enable cross-‘omics comparison will aid prioritisation of novel antibiotics, especially when combined with bioactivity data.
Recombination between African and Asian lineages of Zika virus in vitro and its consequences for viral phenotype
Authors: Dermendjieva Michaela , Donald Claire , Kohl Alain , Evans David
Published: July 2020

Recombination is a process of extensive genetic exchange that is known to contribute to virus evolution and has been frequently observed in positive-sense RNA viruses. Zika virus (ZIKV) is an emerging arbovirus of the family Flaviviridae with two distinct lineages – African and Asian. While some phylogenetic evidence suggests that recombination in the envelope-encoding region of the ZIKV genome has occurred during evolution, there has been no experimental evidence for ZIKV recombination to date. We conducted co-infections of mammalian and insect cells, using the prototype African ZIKV strain (MR766) and an Asian isolate from the 2015-16 ZIKV outbreak in Brazil (BeH819015), and used a recombinant-specific PCR assay to detect recombinant sequences from total cell RNA extracts. In brief, a 564bp fragment spanning the boundary between the structural and the non-structural genes of the viral genome was amplified using a primer pair consisting of an Asian-specific and an African-specific primer. A total of 24 individual sequences were screened. All were in-frame recombinants and they formed 10 unique junctions. Several of the detected recombinant sequences were chosen for construction of full-length infectious clones to test the viability and phenotype of the recombinant viruses. This study represents the first isolation of recombinant ZIKV sequences from co-infected cultured cells and demonstrates the capacity of ZIKV to recombine in an experimental system. Further investigation is required to better understand the evolutionary potential of this mechanism and its putative role in the emergence of ZIKV.
An image-based screening system for the study of Mycobacterium avium persistence and drug discovery
Authors: Nagalekshmi Karthika , O’Kane Cecilia , Schroeder Gunnar
Published: July 2020

Mycobacterium avium infects human macrophages causing opportunistic infections. A steady increase of these infections over the past four decades and resistance to common anti-mycobacterial drugs, create an urgent need for new treatments; however, drug discovery is held back by a lack of knowledge about how M. avium replicates or persists in host cells.

We implemented an image-based assay using a fluorescence dilution (FD) system to measure M. avium replication and persistence. M. avium strain 104 carrying a plasmid encoding GFP and TurboFP635 under constitutive and inducible promoters, respectively, is induced prior to infection of THP1 macrophages and the fluorescent signals are tracked over time in the absence of the inducer. Loss of the TurboFP635 signal while GFP signal is maintained, identifies replicating and retention of both signals non-replicating bacteria.

In the absence of inducer, the M. avium 104 FD strain replicated in the macrophages, leading to increasing numbers of GFP-expressing intracellular bacteria and concomitant loss of TurboFP635 signal in >90% of the infected cells after 24 hours. Upon re-induction, these bacteria expressed TurboFP635, suggesting they are metabolically active and alive. We observed the presence of a small non replicating population that persisted over 96 hours pi. We applied our assay to compare the effect of a panel of anti-mycobacterial drugs, revealing different effects on killing, intracellular replication and induction of persisting, non-replicating bacteria, illustrating the power of this system to facilitate the dissection of the biology of persistence and anti-mycobacterial drug discovery in the future.
Investigation of Pseudomonas aeruginosa biofilm formation within washing machines using novel nanosensor technology
Authors: Blunk Birte , Camara Miguel , Williams Paul , Aylott Jonathan , Hardie Kim
Published: July 2020

Biofilms are communities of microorganisms that attach to various surfaces and are widely associated with infections. Our investigation is focussed on a current and growing concern: the formation of biofilms in washing machines. Many countries wash clothes at reduced temperatures (30°C to 40°C) rather than at higher temperatures above 60°C that would kill the bacteria. Survival of the bacteria is associated with biofouling, malodour and an increased infection risk due to the distribution of human pathogens such as Pseudomonas aeruginosa, one of the predominant bacteria found in washing machines.

Little is known about environmental microniches present in biofilms. Here, we focus on the pH variation throughout P. aeruginosa biofilms knowing that the pH can influence biofilm formation and could be an important aspect for the prevention of biofilms. We use novel pH-sensitive optical nanosensors that penetrate P. aeruginosa biofilms and emit fluorescence in response to pH variation. Using time lapse imaging, pH changes were tracked in real time at a single cell level which will ultimately facilitate monitoring of environmental changes induced as biocides penetrate biofilms. We also look at the isolation and identification of P. aeruginosa from household washing machines. Whole genome analysis was performed to identify different genomic features relevant to antimicrobial resistance (AMR) and biofilm formation. Furthermore, testing of different washing detergent formulations revealed a range of abilities to disrupt biofilm formation or kill P. aeruginosa, which will facilitate the development of more effective washing agents to limit the emergence of AMR within biofilms.
Increasing production of the antibiotic-abyssomicin C in Micromonospora maris
Authors: Zhong Yanhua , Stach Jem , Hall Michael
Published: July 2020

Abyssomicin C is a polyketide antibiotic produced by Micromonospora maris AB-18-032. Previous work on abyssomicin C indicated that it inhibits growth of infectious pathogens such as Methicillin-resistant S. aureus (MRSA) and vancomycin-resistant S. aureus (VRSA). It does this by suppressing para-aminobenzoic acid (pABA) synthesis, which is required for folic acid biosynthesis in bacteria. This makes abyssomicin C an appealing antibiotic drug, as it is specific only to bacteria. However, its yield in chemical synthesis (4 %) and biosynthesis (60.0 mg/L) are low. Ribosome engineering, through the selection of streptomycin-resistant and rifampin-resistant mutants, of M. maris may result in strains with a higher titer of production. After screening by bioassay and sequencing, the mutant genes in six Ochi mutants were identified. Of these mutants, four of them are able to produce a higher titer of abyssomicin C. The other two strains were detected to produce the other secondary metabolite.
AMR Escherichia coli and its temporal and spatial variability within the aquatic environment
Authors: Odell Amelia , Eady Paul , Dixon Ronald
Published: July 2020

Phenotypic and genotypic identification methods have been used to determine the temporal and spatial dynamics of AMR-Escherichia coli in a mainly rural watercourse that receives WWTP-effluent compared to a parallel river which does not. We aimed to investigate the incidence of plasmid-mediated mcr-1and β-lactamase-genes in E. coli recovered from both water and Asellus aquaticus samples throughout two-calendar-years.

Samples of the water and A. aquaticus were recovered from the relevant locations each month. CHROMagar ESBL agar was used throughout to isolate and identify ESBL-E. coli. The presence of AMR-genes was confirmed using the ‘BSAC’ antibiotic-disk-synergy method and PCR analysis to confirm the presence of mcr-1and ESBL-genes. The CHROMagar ESBL agar was found to be 99.7% (n=578) accurate when confirmed with a PCR analysis of the ESBL-genes. Seventy-six-point-six percent (n=449) of the isolated ESBL-E. coli were correctly identified as ESBL-producing organisms using the ‘BSAC’ method. Interestingly 61.9% (n=358) of the ESBL-E. coli were also found to carry the mcr-1 gene.

Our data shows that AMR levels were highest at the WWTP-effluent throughout the two-years for both water and A. aquaticus samples. The incidence of AMR-E. coli 1km downstream of the effluent discharge was equivalent to the parallel river sites, suggesting that the dispersal of AMR from the WWTP-effluent is limited, although AMR-E. coli were found in relatively high numbers at the WWTP-effluent. We argue that the presence of AMR in the freshwater invertebrate A. aquaticus could represent an important route by which AMR can spread from the aquatic environment to the terrestrial environment.
Anoxygenic phototroph pufLM gene sequences derived from tropical aquatic sampling sites: Diversity, distribution, and phylogenetics
Authors: Padilla Crespo Elizabeth , Gordils Lois , Ramirez Xelimar , Michael Ceballos Ruben
Published: July 2020

Purple sulfur bacteria (PSB) and purple non-sulfur bacteria (PNSB) are characterized by their ability to perform anoxygenic photosynthesis. PSB and PNSB are ubiquitously found in coastal waters, enclosed lagoons, stagnant water, mangrove soils, estuaries, and similar environments. In this study, we examine microbial diversity in PSB enrichments derived from a variety of tropical sampling sites (e.g., Thailand, Puerto Rico) associated with shrimp ponds, coastal mangroves, fresh water ponds, and Nymphaeaceae (i.e., water lily) plant tissue. Since 16S rRNA-based analyses are inadequate to describe the diversity of phototrophic bacteria, other biomarkers (e.g., pufLM) are used to construct phylogenies and elucidate biogeography. Our samples indicate that the majority of sequences associated with freshwater pond PSB were related to known marine, halophilic, or salt-tolerant PSB (e.g., Marichromatium, Allochromatium, Thiococcus, and Thiohalocapsa). Phylotypes not closely-associated with known species of PSB (or PNSB) were also found. PNSB gene sequences, which appear to be related to Rhodopseudomonas and Rhodoplanes, were mostly found in freshwater samples and from Nymphaeaceae plant tissues, suggesting a difference in the ecology and distribution of these two broader bacterial groups. This difference is likely due to differences in habitat such as physical (e.g., temperature) and chemical parameters (e.g., salinity). Our preliminary analyses demonstrate a rich diversity of anoxygenic phototrophic bacteria from tropical sampling sites. Few studies have described the diversity of purple bacteria in tropical environments using full pufLM gene sequences. Employing next-generation sequencing (NGS) appears to provide greater resolution towards a deeper understanding of the global diversity and distribution of these anoxygenic phototrophs.
From waste to bioplastics: bio-based conversion of volatile fatty acids to polyhydroxyalkanoates
Authors: Perez-Zabaleta Mariel , Khatami Kasra , Cetecioglu Zeynep
Published: July 2020

Production of polyhydroxyalkanoates (PHAs) as bio-alternative to petroleum-based plastics is an important field in the biorefinery to move forward in the development of the circular economy. PHAs are bioplastics stored inside microbial cells as carbon reservoirs and can be produced from a broad range of renewable resources such as waste streams. One important waste stream is food waste that can be converted into volatile fatty acids (VFAs) by anaerobic digestion. The produced effluent from food waste is not only rich in VFAs but also, other nutrients such as nitrogen and phosphorus that can be used by the microorganisms to produce PHAs. The aim of this research is to convert VFAs produced from food waste into PHAs, in which two approaches have been studied. The first approach was to use microbial mixed cultures (MMCs) while the second used microbial pure cultures.

The MMCs were enriched in sequencing batch bioreactor cultivations, where nitrogen and carbon starvation were combined to enhance the selection phase. PHA accumulation of the selected cultures was studied in nitrogen-limited fed-batch cultivations. The second approach studied five different PHA producing bacteria: Cupriavidus necator, Burkholderia cepacea, Bacillus megaterium, Bacillus cereus and Bacillus cereus. To select the most promising bacteria, synthetic medium with the same VFAs composition as in MMCs study was used for pre-screening experiments. Both, pure and mixed culture studies, resulted in the production of PHAs containing (R)-3-hydroxybutyrate, (R)-3-hydroxyvalerate and (R)-3-hydroxyhexanoate as monomers and VFAs were consumed with a high rate by the microorganisms.
Elucidation of environment dependent antibiotic resistance mechanisms
Authors: Machado Henrique , Seif Yara , Dillon Nicholas , Tsunemoto Hannah , Pogliano Joseph , Nizet Victor , O. Palsson Berhnard , Lyngby Kgs.
Published: July 2020

The propensity of pathogens to evolve resistance to antibiotics used in clinical infectious disease therapeutics has been an increasing concern in recent decades. Acquisition of resistance often translates into treatment failure and puts patients at risk of serious adverse outcomes. Current laboratory testing of antibiotic susceptibility does not account for the different microenvironments that bacteria encounter within the human body, providing results that often do not translate into the clinic. Our goal is to better understand evolutionary strategies employed by Staphylococcus aureus in development of resistance in distinct environments.

We used adaptive laboratory evolution (ALE) to generate isogenic strains resistant to several antibiotics. Different media were used to mimic distinct environments and multi-omics approaches applied in the understanding of resistance mechanisms.

Evolved strains presented phenotypes similar to those observed in clinical resistant isolates. Mutational analysis indicated that resistance was specific and condition-dependent. Distinct mutations led to resistance phenotypes under a particular environmental condition, but these mutations did not necessarily translate into resistance under a different environmental condition. Furthermore, resistant strains possessed distinct transcriptional landscapes, even when the same systems were mutated, suggesting that similar evolutionary paths translate into distinct resistance mechanisms.

We identified several resistance mechanisms employed by S. aureus that were not only environment-dependent, but also environment specific. Additionally, we showed that ALE can be applied in pathogens of interest to study antibiotic resistance evolution and prediction of clinical resistance mechanisms, as supported by the significant overlap of mutations identified via ALE and those reported in clinical isolates.
Can m6A-modified RNA be used as an Anti-Viral Target?
Authors: Barker Amy M. , RÖder Konstantin , Pasquali Samuela , Foster Richard , Whitehouse Adrian
Published: July 2020

Kaposi’s sarcoma-associated herpesvirus (KSHV) is a DNA virus associated with several HIV-associated malignancies.

Like all herpesviruses, KSHV has a biphasic life cycle encompassing a latent state and lytic replication. The KSHV replication and transcription activator viral protein, encoded from open reading frame 50 (ORF50), is the key viral protein which drives the switch between the latent and lytic phases (Guito and Lukac, 2012). We have recently demonstrated that KSHV manipulates the host cell N6-methyl adenosine (m6A) RNA modification pathway to enhance viral gene expression. Specifically, we have shown that the KSHV ORF50 transcript is m6A methylated, allowing the recruitment of the m6A reader protein, Staphylococcal nuclease domain-containing protein 1 (SND-1), resulting in the stabilisation of the ORF50 transcript and efficient KSHV lytic replication (Baquero-Perez et al. 2019).

Further analysis of the m6A modified site with the ORF50 transcript has identified an RNA stem-loop, termed ORF50-1, which is a m6A-modified 43-mer, essential for SND-1 binding, thought to occur in a secondary structure/ sequence-dependent manner. Taking this into consideration, novel ligands have been assessed as effective anti-viral reagents. The importance of A versus m6A within the lytic phase of KSHV’s lifecycle will be investigated by combining in silicoscreening with biophysical techniques and cell based assays.
Effectiveness of COCOA, a COVID-19 contact notification application, in Japan
Authors: Kurita Junko , Sugawara Tamie , Ohkusa Yasushi
Published: July 2020

Background

COCOA, a contact reporting application in Japan, was launched at the end of June 2020.

Object

We assessed effectiveness of COCOA.

Method

After developing a simple susceptible–infected–recovery model with COCOA and voluntary restrictions against going out (VRG), we assumed that COCOA can reduce infectiousness by 10–50% points through self-quarantine at home after receiving notification from COCOA.

Results

COCOA alone is insufficient to halt an outbreak. Even if the entire population were to use COCOA, the reproduction number would be 1.31. However, if VRG were 15%, about half of the maximum VRG effectiveness under the emergency state declaration, then 10% COCOA use by a population can reduce the reproduction number to less than one.

Conclusion

Significant effects of COCOA for reducing the reproduction number were found. However, without VRG, COCOA alone is insufficient to control an outbreak.
Covid-19 and dysregulated cerebral perfusion: observations with multimodal MRI
Authors: Henry-Feugeas Marie-Cécile , Gaudemer Augustin , Lescure Xavier , Dossier Antoine , Sonneville Romain , Ehmer Carsten , Choquet Christophe , Israel Theresa , Simon Agathe Raynaud , Borie Raphael , Amarenco Pierre , Khalil Antoine
Published: July 2020

The pathogenesis of encephalopathy-associated Covid-19 is still unclear. Multimodal brain MRI in 25 Covid-19 patients with neurological symptoms revealed angiographic and brain perfusion changes suggesting an under-recognized dysregulated brain perfusion not identified by morphological neuroimaging alone. Endothelial dysfunction, a key pathomechanism of dysregulated brain perfusion, may contribute to central-nervous-system disturbances in Covid-19.
COVID-19 incidence and R decreased on the Isle of Wight after the launch of the Test, Trace, Isolate programme
Authors: Kendall Michelle , Milsom Luke , Abeler-Dörner Lucie , Wymant Chris , Ferretti Luca , Briers Mark , Holmes Chris , Bonsall David , Abeler Johannes , Fraser Christophe
Published: July 2020

In May 2020 the UK introduced a Test, Trace, Isolate programme in response to the COVID-19 pandemic. The programme was first rolled out on the Isle of Wight and included Version 1 of the NHS contact tracing app. We used COVID-19 daily case data to infer incidence of new infections and estimate the reproduction number R for each of 150 Upper Tier Local Authorities in England, and at the National level, before and after the launch of the programme on the Isle of Wight. We used Bayesian and Maximum-Likelihood methods to estimate R, and compared the Isle of Wight to other areas using a synthetic control method. We observed significant decreases in incidence and R on the Isle of Wight immediately after the launch. These results are robust across each of our approaches. Our results show that the sub-epidemic on the Isle of Wight was controlled significantly more effectively than the sub-epidemics of most other Upper Tier Local Authorities, changing from having the third highest reproduction number R (of 150) before the intervention to the tenth lowest afterwards. The data is not yet available to establish a causal link. However, the findings highlight the need for further research to determine the causes of this reduction, as these might translate into local and national non-pharmaceutical intervention strategies in the period before a treatment or vaccination becomes available.
Optogenetic control of small GTPases reveals RhoA-mediated intracellular calcium signaling
Authors: Inaba Hironori , Miao Qianqian , Nakata Takao
Published: July 2020

Rho/Ras family small GTPases are known to regulate numerous cellular processes, including cytoskeletal reorganization, cell proliferation, and cell differentiation. These processes are also controlled by Ca2+, and consequently, crosstalk between these signals is considered likely. However, systematic quantitative evaluation is not yet reported. Thus, we constructed optogenetic tools to control the activity of small GTPases (RhoA, Rac1, Cdc42, Ras, Rap, and Ral) using an improved light-inducible dimer system (iLID). Using these optogenetic tools, we investigated calcium mobilization immediately after small GTPase activation. Unexpectedly, we found that a transient intracellular calcium elevation was specifically induced by RhoA activation in RPE1 and HeLa cells. These findings were confirmed in all the cell lines tested in this study. Of note, molecular mechanisms were identified to be different among cell types. In RPE1 and HeLa cells, RhoA activated phospholipase C epsilon (PLCε) at the plasma membrane, which in turn induced Ca2+release from the endoplasmic reticulum (ER). The RhoA-PLCε axis induced calcium-dependent NFAT nuclear translocation, suggesting it does activate intracellular calcium signaling.
Analyzing cannabinoid-induced abnormal behavior in a zebrafish model
Authors: Hasumi Akihiro , Maeda Hideyuki , Yoshida Ken-ichi
Published: July 2020

This study investigated the locomotor activity and responses under stressful conditions to assess marijuana-induced abnormal behavior in zebrafish larvae (Danio rerio), as an alternative to the standard rodent model. To induce the desired symptoms, cannabidiol and WIN55,212-2, two chemical components derived from marijuana plants, were used. A repeated light and dark test was used to assess how drug exposure influenced locomotive responses. Subjects were examined after moderate cannabidiol and WIN55,212-2 exposure and 24 h after relocation into untreated water. Cannabidiol did not produce a dose-dependent inhibitory effect on locomotor activity; 0.5 and 10 μg/mL cannabidiol decreased total distance and velocity, and 10 μg/mL cannabidiol attenuated responses in the darkness. No differences between the control and cannabidiol-treated groups were apparent after 24 h in fresh water. WIN55,212-2 at 0.5 and 1 μg/mL almost completely stopped fish activity even in darkness and at 10 μg/mL induced mortality. Spending 24 h in fresh water almost reversed drug-induced immobilization, even in WIN55,212-2-treated groups. Subjects were evaluated for responses to additional cannabidiol after WIN55,212-2 exposure. Cannabidiol attenuated WIN55,212-2-induced abnormal immobilization, whereas commensurate doses of cannabidiol and WIN55,212-2 produced a mixed response. In conclusion, the behavioral effects of marijuana depend on the ratio of the two different cannabinoid properties. The repeated light and dark test might be a suitable method for drug-induced behavioral assay.
A Deep Semi-Supervised Framework for Accurate Modelling of Orphan Sequences
Authors: Moffat Lewis , Jones David T.
Published: July 2020

Accurate modelling of a single orphan protein sequence in the absence of homology information has remained a challenge for several decades. Although not as performant as their homology-based counterparts, single-sequence bioinformatic methods are not constrained by the requirement of evolutionary information and so have a swathe of applications and uses. By taking a bioinformatics approach to semi-supervised machine learning we develop Profile Augmentation of Single Sequences (PASS), a simple but powerful framework for developing accurate single-sequence methods. To demonstrate the effectiveness of PASS we apply it to the mature field of secondary structure prediction. In doing so we develop S4PRED, the successor to the open-source PSIPRED-Single method, which achieves an unprecedentedQ3score of 75.3% on the standard CB513 test. PASS provides a blueprint for the development of a new generation of predictive methods, advancing our ability to model individual protein sequences.
The prevalence of antibodies to SARS-CoV-2 among blood donors in China
Authors: Chang Le , Hou Wangheng , Zhao Lei , Zhang Yali , Wang Yanbin , Wu Linfeng , Xu Tingting , Wang Lilin , Wang Juan , Ma Jian , Wang Lan , Zhao Junpeng , Xu Jing , Dong Juan , Yan Ying , Yang Ru , Li Yu , Guo Fei , Cheng Wenjuan , Su Yingying , Zeng Jinfeng , Han Wei , Cheng Tong , Zhang Jun , Yuan Quan , Xia Ningshao , Wang Lunan
Published: July 2020

Objectives

The prevalence of antibodies to SARS-CoV-2 among blood donors in China remains unknown. To reveal the missing information, we investigated the seroprevalence of SARS-CoV-2 antibodies among blood donors in the cities of Wuhan, Shenzhen, and Shijiazhuang of China.

Design

Cross-sectional study

Setting

Three blood centers, located in the central, south and north China, respectively, recruiting from January to April 2020.

Participants

38,144 healthy blood donors donated in Wuhan, Shenzhen and Shijiazhuang were enrolled, who were all met the criteria for blood donation during the COVID-19 pandemic in China.

Main outcome measures

Specific antibodies against SARS-CoV-2 including total antibody (TAb), IgG antibody against receptor-binding domain of spike protein (IgG-RBD) and nucleoprotein (IgG-N), and IgM. Pseudotype lentivirus-based neutralization test was performed on all TAb-positive samples. In addition, anonymous personal demographic information, including gender, age, ethnicity, occupation and educational level, and blood type were collected.

Results

A total of 519 samples from 410 donors were confirmed by neutralization tests. The SARS-CoV-2 seroprevalence among blood donors was 2.29% (407/17,794, 95%CI: 2.08% to 2.52%) in Wuhan, 0.029% (2/6,810, 95%CI: 0.0081% to 0.11%) in Shenzhen, and 0.0074% (1/13,540, 95%CI: 0.0013% to 0.042%) in Shijiazhuang, respectively. The earliest emergence of SARS-CoV-2 seropositivity in blood donors was identified on January 20, 2020 in Wuhan. The weekly prevalence of SARS-CoV-2 antibodies in Wuhan’s blood donors changed dynamically and were 0.08% (95%CI: 0.02% to 0.28%) during January 15 to 22 (before city lockdown), 3.08% (95%CI: 2.67% to 3.55%) during January 23 to April 7 (city quarantine period) and 2.33% (95%CI: 2.06% to 2.63%) during April 8 to 30 (after lockdown easing). Female and older-age were identified to be independent risk factors for SARS-CoV-2 seropositivity among donors in Wuhan.

Conclusions

The prevalence of antibodies to SARS-CoV-2 among blood donors in China was low, even in Wuhan city. According to our data, the earliest emergence of SARS-CoV-2 in Wuhan’s donors should not earlier than January, 2020. As most of the population of China remained uninfected during the early wave of COVID-19 pandemic, effective public health measures are still certainly required to block viral spread before a vaccine is widely available.
Predicting primer and panel off-target rate in QIAseq targeted DNA panels using convolutional neural networks
Authors: Xu Chang , Padmanabhan Raghavendra , Reinecke Frank , DiCarlo John , Wang Yexun
Published: July 2020

In QIAseq targeted DNA panels, synthetic primers (short single-strand DNA sequences) are used for target enrichment via complementary DNA binding. Off-target priming could occur in this process when a primer binds to some loci where the DNA sequences are identical or very similar to the target template. These off-target DNA segments go through the rest of the workflow, wasting sequencing resources in unwanted regions. Off-target cannot be avoided if some segments of the target region are repetitive throughout the genome, nor can it be quantified until after sequencing. But if off-target rates can be prospectively predicted, scientists can make informed decisions about investment on high off-target panels.

We developedpordle(predictingoff-target rate withdeep learning andepcr07), a convolutional neural network (CNN) model to predict off-target binding events of a given primer. The neural network was trained using 10 QIAseq DNA panels with 29,274 unique primers and then tested on an independent QIAseq panel with 7,576 primers. The model predicted a 10.5% off-target rate for the test panel, a -0.1% bias from the true value of 10.6%. The model successfully selected the better primer (in terms of off-target rate) for 89.2% of 3,835 pairs of close-by primers in the test panel whose off-target rates differ by at least 10%. The order-preserving property may help panel developers select the optimal primer from a group of candidates, which is a common task in panel design.
Development and application of a cultivation platform for mammalian suspension cell lines with single-cell resolution (MaSC)
Authors: Schmitz Julian , Täuber Sarah , Westerwalbesloh Christoph , von Lieres Eric , Noll Thomas , Grünberger Alexander
Published: July 2020

In bioproduction processes cellular heterogeneity can cause unpredictable process outcomes or even provoke process failure. Still, cellular heterogeneity is not examined systematically in bioprocess research and development. One reason for this shortcoming are the applied average bulk analyses, which are not able to detect cell-to-cell differences. In this work we present a microfluidic tool for single-cell cultivation of mammalian suspension cells (MaSC). The design of our platform allows long-term cultivation at highly controllable environments. As model system CHO K1 cells were cultivated over 150 h. Growth behavior was analyzed on single-cell level and resulted in growth rates between 0.85 – 1.16 d-1, which are comparable to classical cultivation approaches such as shake flask and labscale bioreactor. At the same time, heterogeneous growth and division behavior, e.g., unequal division time, as well as rare cellular events like polynucleation or reversed mitosis were observed, which would have remained undetected in a standard population analysis based on average measurements. Therefore, MaSC will open the door for systematic single-cell analysis of mammalian suspension cells. Possible fields of application represent basic research topics like cell-to-cell heterogeneity studies, clonal stability, pharmaceutical drug screening and stem cell research, as well as bioprocess related topics such as media development and novel scale-down approaches.
A general-purpose mechanism of visual feature association in visual word identification and beyond
Authors: Vidal Yamil , Viviani Eva , Zoccolan Davide , Crepaldi Davide
Published: July 2020

Writing systems are a recent cultural invention, which makes it unlikely that specific cognitive mechanisms have developed through selective pressure for reading itself. Instead, reading might capitalize on evolutionary older mechanisms that originally supported other tasks. Accordingly, animals such as baboons can be trained to perform visual word recognition. This suggests that the visual mechanisms supporting reading might be phylogenetically old and domain-general. Here we propose that if the human reading system relies on domain-general visual mechanisms, effects that are typically found within the domain of reading should also be observable with non-orthographic visual stimuli. To test this hypothesis, we systematically tested different types of visual material with the same experimental design. Subjects were passively familiarized with a set of composite visual items, and then tested in an oddball paradigm for their ability to detect novel stimuli. Some of these novel stimuli shared their statistical structure with the familiar items, and were found to be hard to detect in two experiments using strings of letter-like symbols; this replicates the well-known, and supposedly reading-specific, bigram effect. Crucially, in two further experiments we show that the same effect emerges with made-up, 3D objects and sinusoidal gratings. The effect size was equivalent across experiments, despite the use of radically different stimuli. These data suggest that a fundamental mechanism behind visual word learning also supports the learning of other visual stimuli, implying that such mechanism is general-purpose. This mechanism would enable the statistical learning of regularities in the visual environment.