bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antibacterial Action of Visible 405-nm light for Bacterial Reduction in Blood Plasma
Authors: Stewart Caitlin Fiona , Ralston Heather , MacPherson Ruairidh , Wilson Mark , MacGregor Scott , Atreya Chintamani , Maclean Michelle 
Published: May 2022

The introduction of risk prevention measures, such as blood screening and donor deferrals have dramatically reduced the incidence of transfusion-transmitted viral infections. Nevertheless, bacterial contamination of blood transfusion products remains a concern to patient health, and a range of pathogen reduction technologies have been developed to reduce this risk. Visible violet-blue light, in the region of 405-nm, has recently demonstrated potential for in situ treatment of ex vivo stored plasma and platelet products, without the need for additional photosensitizers.
This study assessed the broad-spectrum efficacy of 405-nm light against a range of bacteria implicated in transfusion-transmitted infections: Staphylococcus aureus, Staphylococcus epidermidis, Bacillus cereus, Escherichia coli, Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella pneumoniaeandYersinia enterocolitica. Plasma was seeded with clinically-relevant low-level bacterial contamination (102-103CFUmL-1) and exposed to a 405-nm light dose of 360 Jcm-2 (1-hr at 100mWcm-2) using a small-scale exposure system. Broad spectrum antibacterial efficacy was observed, with 99.0 – 100% inactivation achieved for all bacterial species tested. Bacterial inactivation tests were then scaled-up to expose large volumes of prebagged plasma seeded with S. aureusat ~103 CFUmL-1, to 22mWcm-2 405-nm light, under agitation, (≤396 Jcm-2). Successful bacterial inactivation was observed using the large-scale exposure system, with a dose of 238 Jcm-2 (3-hr at ~22mWcm-2) achieving complete (3.5-log10) reductions in prebagged bacterial-seeded plasma (P=0.001). Results from this study support further development of visible 405-nm light technology as a bactericidal tool for application in transfusion medicine.
This abstract reflects the views of the author and should not be construed to represent FDA’s views or policies.
Synergistic biodegradation of a compostable film by a marine microbial community
Authors: Meyer-Cifuentes Ingrid E. , Öztürk Başak 
Published: May 2022

Background
The need for replacing conventional plastics has led to an increase of the use biodegradable plastics. Most biodegradable plastic materials are certified for compostability, and their degradation mechanisms by marine bacterial communities, are still largely unknown.

Methods
Bacterial communities that degrade a poly (butylene adipate-co-terephthalate)-based biodegradable film (PF) were enriched from marine samples. DNA, RNA and proteins were extracted simultaneously from the biofilm and free-living bacteria. Genes of hydrolases similar to the ones involved in polyethylene terephthalate (PET) and monoester mono-2-hydroxyethyl terephthalate (MHET) degradation (PETase and MHETases, respectively) were detected. A MHETase-like gene (Mle046) was then recombinantly expressed. The activity of Mle046 was tested against the end product of PET and PF degradation: MHET and 4-(4-hydroxybutoxycarbonyl) benzoic acid (Bte), respectively. The optimal incubation temperature and pH of Mle046 activity was determined.

Results
PETase-like (Ples) and MHETase-like (Mles) hydrolases and other enzymes needed for PF degradation were expressed within the microbial community. Within the biofilm, Ples were abundant and upregulated while Mles and terephthalate dioxygenases were abundant in the free-living fraction. Mle046 was the only Mle produced in this fraction and it was highly expressed. The purified Mle046 could degrade MHET and Bte. The optimum temperature of Mle046 activity was 20°C.

Conclusion
PF degradation is achieved synergistically by labour division among film-attached and free-living bacteria. Understanding the biodegradability of these plastics will facilitate the development of more degradable materials. In addition, the discovery of new PETases- and MHETases-like enzymes will enable their future use in plastic recycling.
Examining Phosphate Physiology in Coccolithophore Life Cycle Stages
Authors: Sturm Daniela , Wheeler Glen , Brownlee Colin , Tyrell Toby 
Published: May 2022

Despite the significance of coccolithophores for biogeochemical cycling, much of their ecology remains poorly understood. In particular, their elusive haplo-diplontic life cyclehas been given little attention in the literature. Yet, it significantly impacts the extent of coccolithophore calcification, their vertical and horizontal distribution in the ocean, and potentially their global success.
The aim of this project is to establish physiological differences between the life cycle stages of the ecologically important coccolithophores Coccolithus braarudiiandCalcidiscus leptoporus in response to changes in the essential macronutrient phosphorus (P). Haploid coccolithophores are more commonly found in P-limited environments, raising the question which underlying mechanisms cause this variable distribution between life stages.
An initial investigation of growth, photophysiology, calcification, and storage of polyphosphate under P-limited conditions will determine which parts of coccolithophore physiology are heavily impacted by P-limitation. An in silicoanalysis of P acquisition and transport genes in coccolithophores and other closely related eukaryotes will highlight differences in P physiology among these groups. Comparing proteins expressed in haploid and diploid coccolithophores under P-limitation will then be used to reveal whether P acquisition strategies differ between the two life stages.
These results will further shed light on potential adaptations of haploid and diploid coccolithophores to different ecological niches. A profound understanding of coccolithophore physiology is vital to revealing their evolutionary success and their impact on ocean biogeochemistry and ecology.
Polyesterase activities in bacterial isolates from seaweed and sponges, with potential utility in polyethylene terephthalate plastic and nanoparticle hydrolysis
Authors: Carr Clodagh M. , Clarke David J. , Dobson Alan D. W. 
Published: May 2022

Many marine bacteria have evolved to produce a range of extracellular enzymes which facilitate their growth and survival in the harsh, oligotrophic conditions often present in marine environments. Marine sponge derived Streptomycesstrains have previously been reported to produce polyesterase enzymes, which are of interest for several biotechnological applications, including polyethylene terephthalate (PET) plastic hydrolysis.
Bacteria isolated from sponges and seaweed were screened for polyester hydrolysis activities using plate-clearing assays. Lipolytic and polyesterolytic activities were initially identified by employing tributyrin and polycaprolactone diol agar-based assay systems, respectively. Polyesterase activity was subsequently confirmed on both polycaprolactone and on PET-nanoparticle agar plates, resulting in the prioritisation of six isolates for Illumina next-generation genome sequencing.
These include three Bacillusspp., isolated from the brown seaweed Ascophyllum nodosum,and from marine lake sponges Stelligera stuposaand Eurypon major, together with a Maribacterstrain again isolated from S. stuposa, and Brachybacteriumsp. and Micrococcussp. isolates of deep-sea sponges Pheronemasp. and Inflatella pellicula, that were sampled at depths of 2129m and 2900m, respectively. Genome mining and comparative genomic analysis of these isolates is currently underway to identify genes encoding the observed activities and to assess homology with known PET hydrolases.
Microbes found living in association with filter-feeding sponges may have increased exposure to the plastics and microplastics that widely contaminate our marine ecosystems, thus representing a promising source of degradative activities towards synthetic polymers that could contribute to new plastic waste management strategies.
Beyond fluorescein: Use of fluorescent protein calibrants for direct and absolute quantification of protein production in synthetic biology
Authors: Csibra Eszter , Stan Guy-Bart 
Published: May 2022

While inter-lab calibration standards are approaching mainstream usage in synthetic biology, such calibrations are not in fact sufficient for absolute protein quantification required for modelling synthetic circuits. Fluorescein-based calibration of plate reader and flow cytometry instruments allows the measurement of green fluorescent protein (GFP) in synthetic cells to graduate from arbitrary units to calibrated units, but retains important caveats. Fluorescein is only a good calibrant for green FPs, leaving other FPs uncalibrated, and only provides conversions to units of brightness, not to molecule numbers.
Ideal assay calibrants in molecular biology consist of the same molecule as the one to be measured – in this case, a purified preparation of the appropriate fluorescent protein. Here we show that by using purified FP calibrants, all protein species in a synthetic circuit can be quantified in absolute terms using no advanced instrumentation. We develop a SEVA (Standardised European Vector Architecture)-based expression vector that allows the high-level production of soluble protein and describe a straightforward 2-day protocol for the purification of micrograms of FP, followed by a calibration that relates fluorescence activity to protein mass.
We validate this protocol by calculating conversion factors for a panel of commonly-used FPs including superfolder GFP, mCherry, mScarlet-I and mTagBFP2 on multiple laboratory instruments, and use these calibrations to debug synthetic circuits. We also demonstrate that the suspected bias of the presence of mCherry on OD600 measurements is real, but in practice requires extreme overexpression (~100,000 proteins per cell) to have a meaningful impact on cell density estimates.
Insights into Otitis Media: Dissecting the interaction of C-Reactive Protein with Non-Typeable Haemophilus influenzae
Authors: Bharj Gurpreet , Vikhe Pratik , Brown Steve , Hood Derek 
Published: May 2022

Otitis Media (OM) is the inflammation of the middle ear (ME). Non-typeable Haemophilus influenzae (NTHi) is one of the leading otopathogens in causing OM. Phosphocholine (PCho) on the NTHi lipopolysaccharide influences host-pathogen interaction. C-Reactive Protein (CRP), an acute phase protein recognizes PCho, and can mediate bacterial killing. However, some strains of NTHi survive even in the presence of CRP. We aim to study the interaction of CRP with NTHi to understand its role in bacterial survival and OM.
NTHi can efficiently infect the Junbo mouse, a characterised model of chronic and acute OM. CRP levels were highest 1 day post-intranasal inoculation in the ME fluid (MEF) and nasal passage (NP) washes. We show CRP is a localized response to NTHi as serum CRP levels were unaffected in NTHi inoculated and non-inoculated mice at 1, 3 and 7-day post intranasal inoculation. Further, we confirm the presence of NTHi influences CRP levels in the MEF and NP washes. We show CRP binding is influenced by the position and expression of PCho on the NTHi surface. Serum bactericidal assays indicate that the expression and position of PCho affects NTHi survival. The removal of CRP from the serum restores NTHi survival. The expression of PCho also influences opsonophagocytosis activity in macrophages, thereby confirming the importance of PCho in NTHi survival.
The CRP-NTHi interaction is currently under investigation to advance our understanding of its role in the complex biological processes that influence bacterial killing and the onset, progression and resolution of OM caused by NTHi.
A potential new paradigm of denitrification in Neisseria gonorrhoeae
Authors: Bolton Jack , Djoko Karrera 
Published: May 2022

Metals are bacterial nutrients. Upon infection by microorganisms, the animal host innate immune system typically reduces the availability of metals. In response, bacterial pathogens can activate pathways for metal uptake to avoid metal starvation. This competition for metals at the host-pathogen interface is termed “nutritional immunity”.
We are interested in how the obligate human pathogen Neisseria gonorrhoeae acquires nutrient copper (Cu). This Gram-negative bacterium expresses several respiratory cuproenzymes that are required for growth and metabolism in both aerobic and anaerobic conditions. These cuproenzymes include the putative nitrous oxide reductase (NosZ). NosZ contains 12 Cu atoms per functional dimer and it catalyses the reduction of nitrous oxide (N2O) to dinitrogen (N2). This reduction is an intermediate step in the denitrification pathway, in which nitrite (NO2-) is used as the terminal electron acceptor for respiration instead of O2. In this project, we will determine whether NosZ is expressed as a functional enzyme in N. gonorrhoeae. We will then examine how this enzyme acquires nutrient Cu and subsequently assembles its active site.
Given the rise in antibiotic resistance and the worldwide recognition of multidrug-resistant N. gonorrhoeae as a major threat to public health, we hope that a fundamental understanding of the physiology and metabolism of this organism will yield new strategies for anti-infectives, for instance by manipulating Cu availability at the site of infection.
Cell-to-cell ATP differences can modulate cellular decision-making
Authors: Kerr Ryan , Jabbari Sara , Johnston Iain 
Published: May 2022

Cells generate phenotypic diversity both during development and in response to stressful and changing environments, aiding survival. Functionally vital cell fate decisions from a range of phenotypic choices are made by regulatory networks, the dynamics of which rely on gene expression and hence depend on the cellular energy budget (and particularly ATP levels). However, despite pronounced cell-to-cell ATP differences observed across biological systems, the influence of energy availability on regulatory network dynamics is often overlooked as a cellular decision-making modulator, limiting our knowledge of how energy budgets affect cell behaviour. Here, we consider a mathematical model of a highly generalisable, ATP-dependent, decision-making regulatory network, and show that cell-to-cell ATP variability changes the sets of decisions a cell can make. Our model shows that increasing intracellular energy levels can increase the number of supported stable phenotypes, corresponding to increased decision-making capacity. Model cells with sub-threshold intracellular energy are limited to a singular phenotype, forcing the adoption of a specific cell fate. We suggest that energetic differences between cells may be an important consideration to help explain observed variability in cellular decision-making across a broad range of biological systems, including bacteria and the blood stem cell system.
*NOTE: Our work is highly interdisciplinary and if you believe it would be better suited to another topic area, then I would be delighted to discuss that further.
Regulatory mutants of Serratia with modulated antibiotic production due to intergenic transposon insertions
Authors: Plaza Daniel , Salmond George 
Published: May 2022

Antibiotic resistance is an increasing problem, exacerbated by global dissemination of drug resistance genes under selection pressure. Moreover, the rate of new antibiotic discovery declined over previous decades and so there is a growing need for new antibiotic discovery and a deeper appreciation of the various genetic and physiological factors that influence antibiotic biosynthesis.
The enterobacterium Serratia sp. ATCC 39006 (Serratia) is a useful model for studies on the biosynthesis and regulation of bioactive secondary metabolites, including two antibiotics - a carbapenem and prodigiosin. Both compounds are tightly regulated in response to various physiological and environmental signals, including quorum sensing.
We have identified novel regulators of antibiotic production after random transposon mutagenesis. Multiple regulatory mutations mapped to a small locus defining an intergenic region (IGR). These IGR insertion mutants display elevated production of both the carbapenem and prodigiosin antibiotics and they also exhibit reduced motility, confirming pleiotropic impacts. Exploiting phage transduction, we constructed double mutants with 15 known Serratia regulators and showed that the IGR mutant phenotype was epistatic over several of these. Further analysis suggested the presence of a putative gene encoded within the IGR locus, which may play an impactful role in the intricate regulatory network. Functional characterisation of the IGR region and its physiological impacts in both the modulation of antibiotic production and in wider pleiotropy were dissected. Mechanistic understanding of the regulatory mechanisms involved may prove exploitable in enhancing controlled antibiotic hyperproduction.
Back to soil: Awakening the production of cryptic antibiotics in Streptomyces
Authors: Schniete Jana Katharina , Paros Joseph , Fernández-Martínez Lorena 
Published: May 2022

Most of the antibiotic biosynthetic gene clusters (BGCs) in Streptomyces are not expressed under laboratory conditions, however these clusters are maintained in the genomes, therefore indicating that they must play important roles in adaptation and survival within their ecological niches.
Understanding the global regulation patterns that affect transcription of antibiotic BGCs in soil conditions versus laboratory conditions allows us to identify novel routes for up- or down- regulation in order to trigger expression of these BGCs and therefore production of these antibiotics under controlled laboratory and fermentation conditions. Cryptic pathways represent an untapped resource in terms of new metabolites that could be very useful in the clinic if we can awaken their expression and production.
We are using RNA sequencing to analyse global transcriptional patterns of S. venezuelae and S. rimosus grown in sterile soil, non-sterile soil and standard laboratory solid medium, as well as using an unbiased metabolomics approach to identify compounds produced in soils. These results will enable the identification of global regulatory pathways that activate cryptic clusters in nature and lead to the production of these compounds in soil.
This will enable us to generate genetically modified strains engineered to increase the yield of both well characterised and cryptic clusters which encode potentially novel compounds under industrial fermentation conditions. It is worth noting that the transcriptional data may also help shed light on the complex regulation of the life cycle of these Streptomyces strains in an ecologically relevant environment.
How do Streptomyces coordinate DNA repair and cell division following DNA damage?
Authors: Stratton Kathryn , Bush Matthew , Chandra Govind , Findlay Kim , Schlimpert Susan 
Published: May 2022

DNA damage often results in a pause of cell division until damage is repaired. In bacteria, a widely conserved response to DNA damage is the SOS response which relies on two proteins: the multifunctional recombinase RecA and the transcriptional repressor LexA. Under DNA-damaging conditions, this response activates proteins involved in DNA repair and the inhibition of cell division which in most unicellular bacteria results in temporarily filamentous growth. However, it is unknown how naturally filamentous growing bacteria like Streptomyces cope with DNA damage and how DNA damage repair is coordinated with cell division.
To identify novel regulators of cell division in Streptomyces that specifically function during DNA damaging growth conditions, we investigated the global response of Streptomyces venezuelae to several genotoxic agents, including mitomycin C, ciprofloxacin and methane methylsulfonate. To this end we have performed ChIP-seq experiments to identify the LexA regulon in Streptomycesandconducted RNA-seq experiments to determine the global response to DNA damaging agents in the wildtype and a recA mutant. The combined analysis of the available data sets has allowed us to obtain a comprehensive overview about the genes involved in the SOS response in Streptomycesand further analysis will enable us to understand how damage repair and cell division are coordinated in these bacteria.
Global diversity and potential functioning of prophages in plant pathogenic Ralstonia solanacearum bacterium
Authors: Greenrod Samuel , Stoycheva Martina , Friman Ville-Petri 
Published: May 2022

Ralstonia solanacearum is a destructive plant pathogenic bacterium which harbours a wide variety of virulence genes allowing it to infect over 200 plant species worldwide. Its virulence is also affected by the presence of integrated bacteriophages, termed prophages. While several such prophages have been identified, the global distribution and diversity of R. solanacearum prophages is unknown.
To study this, we first identified prophages present in a diverse collection of 192 assembled R. solanacearum genomes. Prophage diversity was explored by calculating prophage genetic distances and clustering with characterised prophages in a neighbour-joining tree. Prophage clusters were further verified by assessing gene content, GC content, and prophage length. Prophage identities were determined using the NCBI Virus database, and prophage-encoded virulence genes identified by analysing pangenome content.
343 intact prophages were identified, forming ten prophage clusters with distinct gene content, GC content, and length profiles. Five prophage clusters, containing 159 prophages, belonged to the Inoviridae, Myoviridae, and Siphoviridae phage families. The remaining 184 prophages were uncharacterised and may therefore represent novel prophages. Transcriptional regulators with potential virulence effects were identified in three prophage clusters, including one uncharacterised cluster. These prophage clusters were unequally distributed throughout the R. solanacearum population being host genotype specific.
This research demonstrates that R. solanacearum contains a high level of uncharacterised prophage diversity and highlights novel prophages that could contribute to pathogen virulence. Given their potential host-genotype-specific virulence effects, R. solanacearumprophages could be co-evolving with their hosts, and may contribute to global variation in R. solanacearum virulence.