Bacterial dormancy: A subpopulation of viable but non-culturable cells demonstrates better fitness for revival.

The viable but non culturable (VBNC) state is a condition in which bacterial cells are viable and metabolically active, but resistant to cultivation using a routine growth medium. We investigated the ability of V. parahaemolyticus to form VBNC cells, and to subsequently become resuscitated. The ability to control VBNC cell formation in the laboratory allowed us to selectively isolate VBNC cells using fluorescence activated cell sorting, and to differentiate subpopulations based on their metabolic activity, cell shape and the ability to cause disease in Galleria mellonella. Our results showed that two subpopulations (P1 and P2) of V. parahaemolyticus VBNC cells exist and can remain dormant in the VBNC state for long periods. VBNC subpopulation P2, had a better fitness for survival under stressful conditions and showed 100% revival under favourable conditions. Proteomic analysis of these subpopulations (at two different time points: 12 days (T12) and 50 days (T50) post VBNC) revealed that the proteome of P2 was more similar to that of the starting microcosm culture (T0) than the proteome of P1. Proteins that were significantly up or down-regulated between the different VBNC populations were identified and differentially regulated proteins were assigned into 23 functional groups, the majority being assigned to metabolism functional categories. A lactate dehydrogenase (lldD) protein, responsible for converting lactate to pyruvate, was significantly upregulated in all subpopulations of VBNC cells. Deletion of the lactate dehydrogenase (RIMD2210633:ΔlldD) gene caused cells to enter the VBNC state significantly more quickly compared to the wild-type, and adding lactate to VBNC cells aided their resuscitation and extended the resuscitation window. Addition of pyruvate to the RIMD2210633:ΔlldD strain restored the wild-type VBNC formation profile. This study suggests that lactate dehydrogenase may play a role in regulating the VBNC state.

Deductive automated pollen classification in environmental samples via exploratory deep learning and imaging flow cytometry.

Pollen and tracheophyte spores are ubiquitous environmental indicators at local and global scales. Palynology is typically performed manually by microscopic analysis; a specialised and time-consuming task limited in taxonomical precision and sampling frequency, therefore restricting data quality used to inform climate change and pollen forecasting models. We build on the growing work using AI (artificial intelligence) for automated pollen classification to design a flexible network that can deal with the uncertainty of broad-scale environmental applications. We combined imaging flow cytometry with Guided Deep Learning to identify and accurately categorise pollen in environmental samples; here, pollen grains captured within c. 5500 Cal yr BP old lake sediments. Our network discriminates not only pollen included in training libraries to the species level but, depending on the sample, can classify previously unseen pollen to the likely phylogenetic order, family and even genus. Our approach offers valuable insights into the development of a widely transferable, rapid and accurate exploratory tool for pollen classification in 'real-world' environmental samples with improved accuracy over pure deep learning techniques. This work has the potential to revolutionise many aspects of palynology, allowing a more detailed spatial and temporal understanding of pollen in the environment with improved taxonomical resolution.

Microbial pathways for advanced biofuel production.

Decarbonisation of the transport sector is essential to mitigate anthropogenic climate change. Microbial metabolisms are already integral to the production of renewable, sustainable fuels and, building on that foundation, are being re-engineered to generate the advanced biofuels that will maintain mobility of people and goods during the energy transition. This review surveys the range of natural and engineered microbial systems for advanced biofuels production and summarises some of the techno-economic challenges associated with their implementation at industrial scales.

Why is it so hard to enact responsible change?: Scientists need to work more closely with other social groups to implement sustainable innovation.

Science is key to developing sustainable products and solutions. But scientists also need to work more with governments, industry and society to help implement those solutions.

In Vivo Characterization of Endogenous Cardiovascular Extracellular Vesicles in Larval and Adult Zebrafish.

Objective: Extracellular vesicles (EVs) facilitate molecular transport across extracellular space, allowing local and systemic signaling during homeostasis and in disease. Extensive studies have described functional roles for EV populations, including during cardiovascular disease, but the in vivo characterization of endogenously produced EVs is still in its infancy. Because of their genetic tractability and live imaging amenability, zebrafish represent an ideal but under-used model to investigate endogenous EVs. We aimed to establish a transgenic zebrafish model to allow the in vivo identification, tracking, and extraction of endogenous EVs produced by different cell types. Approach and Results: Using a membrane-tethered fluorophore reporter system, we show that EVs can be fluorescently labeled in larval and adult zebrafish and demonstrate that multiple cell types including endothelial cells and cardiomyocytes actively produce EVs in vivo. Cell-type specific EVs can be tracked by high spatiotemporal resolution light-sheet live imaging and modified flow cytometry methods allow these EVs to be further evaluated. Additionally, cryo electron microscopy reveals the full morphological diversity of larval and adult EVs. Importantly, we demonstrate the utility of this model by showing that different cell types exchange EVs in the adult heart and that ischemic injury models dynamically alter EV production. Conclusions: We describe a powerful in vivo zebrafish model for the investigation of endogenous EVs in all aspects of cardiovascular biology and pathology. A cell membrane fluorophore labeling approach allows cell-type specific tracing of EV origin without bias toward the expression of individual protein markers and will allow detailed future examination of their function.

Design of High-Affinity Metal-Controlled Protein Dimers.

The ability to precisely control protein complex formation has high utility in the expanding field of biomaterials. Driving protein-protein binding through metal-ligand bridging interactions is a promising method of achieving this goal. Furthermore, the capacity to precisely regulate both complex formation and dissociation enables additional control not available with constitutive protein complexes. Here we describe the design of three metal-controlled protein dimers that are completely monomeric in the absence of metal yet form high-affinity symmetric homodimers in the presence of zinc sulfate. The scaffold used for the designed dimers is the ß1 domain of streptococcal protein G. In addition to forming high-affinity dimers in the presence of metal, the complexes also dissociate upon addition of EDTA. Biophysical characterization revealed that the proteins maintain relatively high thermal stability, bind with high affinity, and are completely monodisperse in the monomeric and dimeric states. High-resolution crystal structures revealed that the dimers adopt the target structure and that the designed metal-binding histidine residues successfully bind zinc and function to drive dimer formation.

Higher levels of B-cell mutation in the early germinal centres of an inefficient secondary antibody response to a variant influenza haemagglutinin.

Designing improved vaccines against mutable viruses such as dengue and influenza would be helped by a better understanding of how the B-cell memory compartment responds to variant antigens. Towards this we have recently shown, after secondary immunization of mice with a widely variant dengue virus envelope protein with only 63% amino acid identity, that IgM+ memory B cells with few mutations supported an efficient secondary germinal centre (GC) and serum response, superior to a primary response to the same protein. Here, further investigation of memory responses to variant proteins, using more closely related influenza virus haemagglutinins (HA) that were 82% identical, produced a variant-induced boost response in the GC dominated by highly mutated B cells that failed, not efficiently improving serum avidity even in the presence of extra adjuvant, and that was worse than a primary response. This supports a hypothesis that over a certain level of antigenic differences, cross-reactive memory B-cell populations have reduced competency for affinity maturation. Combined with our previous observations, these findings also provide new parameters of success and failure in antibody memory responses.

Opportunities and challenges of real-time release testing in biopharmaceutical manufacturing.

Real-time release testing (RTRT) is defined as "the ability to evaluate and ensure the quality of in-process and/or final drug product based on process data, which typically includes a valid combination of measured material attributes and process controls" (ICH Q8[R2]). This article discusses sensors (process analytical technology, PAT) and control strategies that enable RTRT for the spectrum of critical quality attributes (CQAs) in biopharmaceutical manufacturing. Case studies from the small-molecule and biologic pharmaceutical industry are described to demonstrate how RTRT can be facilitated by integrated manufacturing and multivariable control strategies to ensure the quality of products. RTRT can enable increased assurance of product safety, efficacy, and quality-with improved productivity including faster release and potentially decreased costs-all of which improve the value to patients. To implement a complete RTRT solution, biologic drug manufacturers need to consider the special attributes of their industry, particularly sterility and the measurement of viral and microbial contamination. Continued advances in on-line and in-line sensor technologies are key for the biopharmaceutical manufacturing industry to achieve the potential of RTRT. Related article: http://onlinelibrary.wiley.com/doi/10.1002/bit.26378/full.

Human Papillomavirus Prevalence and Herd Immunity after Introduction of Vaccination Program, Scotland, 2009-2013.

In 2008, a national human papillomavirus (HPV) immunization program using a bivalent vaccine against HPV types 16 and 18 was implemented in Scotland along with a national surveillance program designed to determine the longitudinal effects of vaccination on HPV infection at the population level. Each year during 2009-2013, the surveillance program conducted HPV testing on a proportion of liquid-based cytology samples from women undergoing their first cervical screening test for precancerous cervical disease. By linking vaccination, cervical screening, and HPV testing data, over the study period we found a decline in HPV types 16 and 18, significant decreases in HPV types 31, 33, and 45 (suggesting cross-protection), and a nonsignificant increase in HPV 51. In addition, among nonvaccinated women, HPV types 16 and 18 infections were significantly lower in 2013 than in 2009. Our results preliminarily indicate herd immunity and sustained effectiveness of the bivalent vaccine on virologic outcomes at the population level.

Synthetic promoter design for new microbial chassis.

The judicious choice of promoter to drive gene expression remains one of the most important considerations for synthetic biology applications. Constitutive promoter sequences isolated from nature are often used in laboratory settings or small-scale commercial production streams, but unconventional microbial chassis for new synthetic biology applications require well-characterized, robust and orthogonal promoters. This review provides an overview of the opportunities and challenges for synthetic promoter discovery and design, including molecular methodologies, such as saturation mutagenesis of flanking regions and mutagenesis by error-prone PCR, as well as the less familiar use of computational and statistical analyses for de novo promoter design.

In vivo chemical and structural analysis of plant cuticular waxes using stimulated Raman scattering microscopy.

The cuticle is a ubiquitous, predominantly waxy layer on the aerial parts of higher plants that fulfils a number of essential physiological roles, including regulating evapotranspiration, light reflection, and heat tolerance, control of development, and providing an essential barrier between the organism and environmental agents such as chemicals or some pathogens. The structure and composition of the cuticle are closely associated but are typically investigated separately using a combination of structural imaging and biochemical analysis of extracted waxes. Recently, techniques that combine stain-free imaging and biochemical analysis, including Fourier transform infrared spectroscopy microscopy and coherent anti-Stokes Raman spectroscopy microscopy, have been used to investigate the cuticle, but the detection sensitivity is severely limited by the background signals from plant pigments. We present a new method for label-free, in vivo structural and biochemical analysis of plant cuticles based on stimulated Raman scattering (SRS) microscopy. As a proof of principle, we used SRS microscopy to analyze the cuticles from a variety of plants at different times in development. We demonstrate that the SRS virtually eliminates the background interference compared with coherent anti-Stokes Raman spectroscopy imaging and results in label-free, chemically specific confocal images of cuticle architecture with simultaneous characterization of cuticle composition. This innovative use of the SRS spectroscopy may find applications in agrochemical research and development or in studies of wax deposition during leaf development and, as such, represents an important step in the study of higher plant cuticles.

The effect of intermolecular interaction on excited states in p-DTS(FBTTH2)2.

Using optical spectroscopy in solution and thin film, and supported by quantum chemical calculations, we investigated the aggregation process of the donor-acceptor type molecule p-DTS(FBTTH2)2. We demonstrate that cooling a solution induces a disorder-order phase transition that proceeds in three stages analogous to the steps observed in semi-rigid conjugated polymers. By analyzing the spectra, we are able to identify the spectral signature of monomer and aggregate in absorption and emission. From this we find that in films, the fraction of aggregates is near 100% which is in contrast to films made from semi-rigid conjugated polymers.

Synthesis of customized petroleum-replica fuel molecules by targeted modification of free fatty acid pools in Escherichia coli.

Biofuels are the most immediate, practical solution for mitigating dependence on fossil hydrocarbons, but current biofuels (alcohols and biodiesels) require significant downstream processing and are not fully compatible with modern, mass-market internal combustion engines. Rather, the ideal biofuels are structurally and chemically identical to the fossil fuels they seek to replace (i.e., aliphatic n- and iso-alkanes and -alkenes of various chain lengths). Here we report on production of such petroleum-replica hydrocarbons in Escherichia coli. The activity of the fatty acid (FA) reductase complex from Photorhabdus luminescens was coupled with aldehyde decarbonylase from Nostoc punctiforme to use free FAs as substrates for alkane biosynthesis. This combination of genes enabled rational alterations to hydrocarbon chain length (Cn) and the production of branched alkanes through upstream genetic and exogenous manipulations of the FA pool. Genetic components for targeted manipulation of the FA pool included expression of a thioesterase from Cinnamomum camphora (camphor) to alter alkane Cn and expression of the branched-chain α-keto acid dehydrogenase complex and ß-keto acyl-acyl carrier protein synthase III from Bacillus subtilis to synthesize branched (iso-) alkanes. Rather than simply reconstituting existing metabolic routes to alkane production found in nature, these results demonstrate the ability to design and implement artificial molecular pathways for the production of renewable, industrially relevant fuel molecules.

Effects of solvent additive on "s-shaped" curves in solution-processed small molecule solar cells.

A novel molecular chromophore, p-SIDT(FBTThCA8)2, is introduced as an electron-donor material for bulk heterojunction (BHJ) solar cells with broad absorption and near ideal energy levels for the use in combination with common acceptor materials. It is found that films cast from chlorobenzene yield devices with strongly s-shaped current-voltage curves, drastically limiting performance. We find that addition of the common solvent additive diiodooctane, in addition to facilitating crystallization, leads to improved vertical phase separation. This yields much better performing devices, with improved curve shape, demonstrating the importance of morphology control in BHJ devices and improving the understanding of the role of solvent additives.

Holey fiber mode-selective couplers.

Directional mode coupling in an asymmetric holey fiber coupler is demonstrated both numerically and experimentally for the first time. The holey fiber mode couplers have interesting spectral characteristics and are also found to exhibit increased dimensional tolerances. Following a design based on numerical investigations, a dual-core polymer holey fiber coupler for LP(01) and LP(11) mode multiplexing was fabricated via a drilling and drawing technique. The measurements are compared with the simulation results.

Characterizing substrate selectivity of ubiquitin C-terminal hydrolase-L3 using engineered α-linked ubiquitin substrates.

The ubiquitin-proteasome system (UPS) is highly complex and entails the concerted actions of many enzymes that function to ubiquitinate proteins targeted to the proteasome as well as enzymes that remove and recycle ubiquitin for additional rounds of proteolysis. Ubiquitin C-terminal hydrolase-L3 (UCH-L3) is a human cytosolic deubiquitinase whose precise biological function is not known. It is believed to hydrolyze small peptides or chemical adducts from the C-terminus of ubiquitin that may be remnant from proteasomal processing. In addition, UCH-L3 is a highly effective biotechnological tool that is used to produce small or unstable peptides/proteins recalcitrant to production in Escherichia coli expression systems. Previous research, which explored the substrate selectivity of UCH-L3, demonstrated a substrate size limitation for proteins/peptides expressed as α-linked C-terminal fusions to ubiquitin and also suggested that an additional substrate property may affect UCH-L3 hydrolysis [ Larsen , C. N. et al. (1998) Biochemistry 37 , 3358 - 3368 ]. Using a series of engineered protein substrates, which are similar in size yet differ in secondary structure, we demonstrate that thermal stability is a key factor that significantly affects UCH-L3 hydrolysis. In addition, we show that the thermal stabilities of the engineered substrates are not altered by fusion to ubiquitin and offer a possible mechanism as to how ubiquitin affects the structural and unfolding properties of natural in vivo targets.

Topological considerations for the design of molecular donors with multiple absorbing units.

The molecule AT1, with two weakly conjugated chromophores, was designed, synthesized, and examined within the context of its film forming tendencies. While the addition of the second chromophore to the central core enables broadening of the absorption spectrum, this change is mostly apparent in films that are grown slowly. Grazing incidence X-ray scattering (GIWAXS) analysis indicates that these spectral characteristics correspond to an increase in solid state ordering. This information, in combination with differential scanning calorimetry, suggests that the overall molecular shape provides a kinetic barrier to crystallization. As a result, one finds the absence of molecular order when AT1 is combined with PC71BM in solution-cast blends. These findings highlight the importance of molecular topology when designing molecular components for solar cell devices.

Silaindacenodithiophene-based molecular donor: morphological features and use in the fabrication of compositionally tolerant, high-efficiency bulk heterojunction solar cells.

A novel solution-processable small molecule, namely, benzo[1,2-b:4,5-b]bis(4,4'-dihexyl-4H-silolo[3,2-b]thiophene-2,2'-diyl)bis(6-fluoro-4-(5'-hexyl-[2,2'-bithiophene]-5-yl)benzo[c][1,2,5]thiadiazole (p-SIDT(FBTTh2)2), was designed and synthesized by utilizing the silaindacenodithiophene (SIDT) framework as the central D(2) donor unit within the D(1)AD(2)AD(1) chromophore configuration. Relative to the widely studied 7,7'-[4,4-bis(2-ethylhexyl)-4H-silolo[3,2-b:4,5-b']dithiophene-2,6-diyl]bis[6-fluoro-4-(5'-hexyl-[2,2'-bithiophene]-5-yl)benzo[c][1,2,5]thiadiazole] (p-DTS(FBTTh2)2), which contains the stronger donor fragment dithienosilole (DTS) as D(2), one finds that p-SIDT(FBTTh2)2 exhibits a wider band gap and can be used to fabricate bulk heterojunction solar cells with higher open circuit voltage (0.91 V). Most remarkably, thin films comprising p-SIDT(FBTTh2)2 can achieve exceptional levels of self-organization directly via solution deposition. For example, high-resolution transmission electron microscopy analysis shows that p-SIDT(FBTTh2)2 spin-cast from chlorobenzene organizes into crystalline domains with lattice planes that extend over length scales on the order of hundreds of nanometers. Such features suggest liquid crystalline properties during the evolution of the film. Moreover, grazing incidence wide-angle X-ray scattering analysis shows a strong tendency for the molecules to exist with a strong "face-on" orientation relative to the substrate plane. Similar structural features, albeit of more restricted dimensions, can be observed within p-SIDT(FBTTh2)2:PC71BM bulk heterojunction thin films when the films are processed with 0.4% diiodooctane (DIO) solvent additive. DIO use also increases the solar cell power conversion efficiencies (PCEs) from 1.7% to 6.4%. Of significance from a practical device fabrication perspective is that, for p-SIDT(FBTTh2)2:PC71BM blends, there is a wide range of compositions (from 20:80 to 70:30 p-SIDT(FBTTh2)2:PC71BM) that provide good photovoltaic response, i.e., PCE = 4-6%, indicating a robust tendency to form the necessary continuous phases for charge carrier collection. Light intensity photocurrent measurements, charge selective diode fabrication, and internal quantum efficiency determinations were carried out to obtain insight into the mechanism of device operation. Inclusion of DIO in the casting solution results in films that exhibit much lower photocurrent dependence on voltage and a concomitant increase in fill factor. At the optimum blend ratio, devices show high charge carrier mobilities, while mismatched hole and electron mobilities in blends with high or low donor content result in reduced fill factors and device performance.

Femtosecond direct-written integrated mode couplers.

We report the design and fabrication of three-dimensional integrated mode couplers operating in the C-band. These mode-selective couplers were inscribed into a boro-aluminosilicate photonic chip using the femtosecond laser direct-write technique. Horizontally and vertically written two-core couplers are shown to allow for the multiplexing of the LP11a and LP11b spatial modes of an optical fiber, respectively, with excellent mode extinction ratios (25-37 + dB) and low loss (~1 dB) between 1500 and 1580 nm. Furthermore, optimized fabrication parameters enable coupling ratios close to 100%. When written in sequence, the couplers allow for the multiplexing of all LP01, LP11a and LP11b modes. This is also shown to be possible using a single 3-dimensional three-core coupler. These integrated mode couplers have considerable potential to be used in mode-division multiplexing for increasing optical fiber capacity. The three-dimensional capability of the femtosecond direct-write technique provides the versatility to write linear cascades of such two- and three-core couplers into a single compact glass chip, with arbitrary routing of waveguides to ensure a small footprint. This technology could be used for high-performance, compact and cost-effective multiplexing of large numbers of modes of an optical fiber.

A bacterial process for selenium nanosphere assembly.

During selenate respiration by Thauera selenatis, the reduction of selenate results in the formation of intracellular selenium (Se) deposits that are ultimately secreted as Se nanospheres of approximately 150 nm in diameter. We report that the Se nanospheres are associated with a protein of approximately 95 kDa. Subsequent experiments to investigate the expression and secretion profile of this protein have demonstrated that it is up-regulated and secreted in response to increasing selenite concentrations. The protein was purified from Se nanospheres, and peptide fragments from a tryptic digest were used to identify the gene in the draft T. selenatis genome. A matched open reading frame was located, encoding a protein with a calculated mass of 94.5 kDa. N-terminal sequence analysis of the mature protein revealed no cleavable signal peptide, suggesting that the protein is exported directly from the cytoplasm. The protein has been called Se factor A (SefA), and homologues of known function have not been reported previously. The sefA gene was cloned and expressed in Escherichia coli, and the recombinant His-tagged SefA purified. In vivo experiments demonstrate that SefA forms larger (approximately 300 nm) Se nanospheres in E. coli when treated with selenite, and these are retained within the cell. In vitro assays demonstrate that the formation of Se nanospheres upon the reduction of selenite by glutathione are stabilized by the presence of SefA. The role of SefA in selenium nanosphere assembly has potential for exploitation in bionanomaterial fabrication.