Sorting out bacterial viability with optical tweezers

Selective Acoustic Trapping, Translating, Rotating, and Orienting of Organism From Heterogeneous Mixture

Selective contactless manipulation of organisms with intrinsic mobility from heterogeneous mixture is essential for biomedical engineering and microbiology. Acoustic manipulation, compared to its optical, magnetic, and electrostatic counterparts, provides superior bio-compatibility and additive-free properties. In this study, we present an acoustic manipulation system capable of selectively trapping, translating, rotating, and orienting individual organisms from in-Petri dish organism mixture using a phased transducer array and microscope, by dynamically steering the acoustic field. Specifically, using brine shrimp and zebrafish populations as example, the to-be-manipulated organisms with different sizes or morphologies can be manually designated by the user in microscopic image and interactively localized. Thereafter, the selected organisms can be automatically trapped from the heterogeneous mixture using a multiple focal point-based acoustic field steering method. Finally, the trapped organisms can be translated, rotated, and oriented in regard to the user's distinct manipulation objectives in instant response. In different tasks, closed-loop positioning and real-time motion planning control are performed, highlighting the innovation in terms of automation and accuracy of our manipulation technique. The results demonstrate that our acoustic manipulation system and acoustic field steering method enable selective, stable, precision, real-time, and in-Petri dish manipulation of organisms from heterogeneous mixture.

Deep learning-based method for analyzing the optically trapped sperm rotation

Optical tweezers exert a strong trapping force on cells, making it crucial to analyze the movement of trapped cells. The rotation of cells plays a significant role in their swimming patterns, such as in sperm cells. We proposed a fast deep-learning-based method that can automatically determine the projection orientation of ellipsoidal-like cells without additional optical design. This method was utilized for analyzing the planar rotation of trapped sperm cells using an optical tweezer, demonstrating its feasibility in extracting the rotation of the cell head. Furthermore, we employed this method to investigate sperm cell activity by examining variations in sperm rotation rates under different conditions, including temperature and laser output power. Our findings provide evidence for the effectiveness of this method and the rotation analysis method developed may have clinical potential for sperm quality evaluation.

Damage dynamics and the role of chance in the timing of E. coli cell death

Genetically identical cells in the same stressful condition die at different times. The origin of this stochasticity is unclear; it may arise from different initial conditions that affect the time of demise, or from a stochastic damage accumulation mechanism that erases the initial conditions and instead amplifies noise to generate different lifespans. To address this requires measuring damage dynamics in individual cells over the lifespan, but this has rarely been achieved. Here, we used a microfluidic device to measure membrane damage in 635 carbon-starved Escherichia coli cells at high temporal resolution. We find that initial conditions of damage, size or cell-cycle phase do not explain most of the lifespan variation. Instead, the data points to a stochastic mechanism in which noise is amplified by a rising production of damage that saturates its own removal. Surprisingly, the relative variation in damage drops with age: cells become more similar to each other in terms of relative damage, indicating increasing determinism with age. Thus, chance erases initial conditions and then gives way to increasingly deterministic dynamics that dominate the lifespan distribution.

Biochar enhanced high-solid mesophilic anaerobic digestion of food waste: Cell viability and methanogenic pathways

The underlying mechanisms of biochar enhance high-solid anaerobic digestion (HSAD) of food waste were investigated with a focus on the cell viability, microbial community, and methanogenic pathways. This study assessed the effects of different dosages of biochar in HSAD. Optimal biochar dosage was found to be 25 g/L, which produced accumulative methane yields of up to 251 mL CH₄/g VS significantly promote volatile fatty acid degradations, especially in butyric acid concentrations. Effects of biochar with a dosage of 25 g/L on the cell viability showed that viable cells based on cell membrane integrity increased from 2.9% to 6.4%. Meanwhile, intact and highly active cells with high DNA content were probably involved in direct interspecies electron transfer (DIET) via membrane-bound electron transport proteins. Further analysis demonstrated that Syntrophomonas and methanogens Methanosarcina &Methanocelleus were selectively enriched by biochar, which resulted in the methanogenic pathways shifting from acetoclastic/hydrogenotrophic methanogenic pathways to more metabolically diverse methanogenic pathways. Accordingly, biochar-mediated DIET was possibly established between Syntrophomonas and Methanosarcina species due to those viable cells. In conclusion, biochar is a feasible additive in enhancing HSAD methanogenic performance.

Effects of the straw inclusion in the diet of dairy calves on growth performance, rumen fermentation, and blood metabolites during pre- and post-weaning periods

The aim of this study was to investigate the effects of the inclusion of chopped straw into a diet with pelleted starter feed on starter intake, growth performance, fermentation and blood metabolites of dairy calves during the pre- and post-weaning periods. Forty-four Holstein-Friesian female dairy calves were randomly assigned to four treatments: control (CON, starter without straw; n = 11), low straw (LS, starter feed containing 10% dry matter basis straw; n = 11), medium straw (MS, starter feed containing 15% dry matter basis straw; n = 11) and high straw (HS, starter feed containing 20% dry matter basis straw; n = 11). Starter intake and total dry matter intake were recorded daily, and bodyweight weekly until 84 days of age. The highest starter intake and total dry matter intake were noted in the LS and MS treatments during the post-weaning, and overall experiment periods. Also, the average daily gain was greater during the pre-weaning period for LS and MS than HS. Increasing chopped straw content in the starter feeds from 0% to 15% increased ruminal pH, especially at day 28, and molar concentration of acetate, and decreased concentrations of total volatile fatty acids and propionate throughout the trial. Concentrations of butyrate in the rumen were lower at day 28, and higher at day 56 and 84 in straw-supplemented calves compared to the CON treatment. Increasing chopped straw content in the starters feeds from 0% to 15% increased the total counts of bacteria and protozoa, but then this counts decreased with the content of 20% chopped straw. In conclusion, the inclusion of chopped triticale straw from 10% to 15% in the diet with pelleted starter feed can improve performance, and rumen fermentation in calves; however, increasing the dietary inclusion of straw to 20% can negatively affect growth performance.

Best practices on the differential expression analysis of multi-species RNA-seq

Advances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. Compared to single-species differential expression analysis, the design of multi-species differential expression experiments must account for the relative abundances of each organism of interest within the sample, often requiring enrichment methods and yielding differences in total read counts across samples. The analysis of multi-species transcriptomics datasets requires modifications to the alignment, quantification, and downstream analysis steps compared to the single-species analysis pipelines. We describe best practices for multi-species transcriptomics and differential gene expression.

Nontraditional systems in aging research: an update

Research on the evolutionary and mechanistic aspects of aging and longevity has a reductionist nature, as the majority of knowledge originates from experiments on a relatively small number of systems and species. Good examples are the studies on the cellular, molecular, and genetic attributes of aging (senescence) that are primarily based on a narrow group of somatic cells, especially fibroblasts. Research on aging and/or longevity at the organismal level is dominated, in turn, by experiments on Drosophila melanogaster, worms (Caenorhabditis elegans), yeast (Saccharomyces cerevisiae), and higher organisms such as mice and humans. Other systems of aging, though numerous, constitute the minority. In this review, we collected and discussed a plethora of up-to-date findings about studies of aging, longevity, and sometimes even immortality in several valuable but less frequently used systems, including bacteria (Caulobacter crescentus, Escherichia coli), invertebrates (Turritopsis dohrnii, Hydra sp., Arctica islandica), fishes (Nothobranchius sp., Greenland shark), reptiles (giant tortoise), mammals (blind mole rats, naked mole rats, bats, elephants, killer whale), and even 3D organoids, to prove that they offer biogerontologists as much as the more conventional tools. At the same time, the diversified knowledge gained owing to research on those species may help to reconsider aging from a broader perspective, which should translate into a better understanding of this tremendously complex and clearly system-specific phenomenon.

Massively Multiplexed Submicron Particle Patterning in Acoustically Driven Oscillating Nanocavities

Nanoacoustic fields are a promising method for particle actuation at the nanoscale, though THz frequencies are typically required to create nanoscale wavelengths. In this work, the generation of robust nanoscale force gradients is demonstrated using MHz driving frequencies via acoustic-structure interactions. A structured elastic layer at the interface between a microfluidic channel and a traveling surface acoustic wave (SAW) device results in submicron acoustic traps, each of which can trap individual submicron particles. The acoustically driven deformation of nanocavities gives rise to time-averaged acoustic fields which direct suspended particles toward, and trap them within, the nanocavities. The use of SAWs permits massively multiplexed particle manipulation with deterministic patterning at the single-particle level. In this work, 300 nm diameter particles are acoustically trapped in 500 nm diameter cavities using traveling SAWs with wavelengths in the range of 20-80 µm with one particle per cavity. On-demand generation of nanoscale acoustic force gradients has wide applications in nanoparticle manipulation, including bioparticle enrichment and enhanced catalytic reactions for industrial applications.

Digital Microfluidics for Single Bacteria Capture and Selective Retrieval Using Optical Tweezers

When screening microbial populations or consortia for interesting cells, their selective retrieval for further study can be of great interest. To this end, traditional fluorescence activated cell sorting (FACS) and optical tweezers (OT) enabled methods have typically been used. However, the former, although allowing cell sorting, fails to track dynamic cell behavior, while the latter has been limited to complex channel-based microfluidic platforms. In this study, digital microfluidics (DMF) was integrated with OT for selective trapping, relocation, and further proliferation of single bacterial cells, while offering continuous imaging of cells to evaluate dynamic cell behavior. To enable this, magnetic beads coated with Salmonella Typhimurium-targeting antibodies were seeded in the microwell array of the DMF platform, and used to capture single cells of a fluorescent S. Typhimurium population. Next, OT were used to select a bead with a bacterium of interest, based on its fluorescent expression, and to relocate this bead to a different microwell on the same or different array. Using an agar patch affixed on top, the relocated bacterium was subsequently allowed to proliferate. Our OT-integrated DMF platform thus successfully enabled selective trapping, retrieval, relocation, and proliferation of bacteria of interest at single-cell level, thereby enabling their downstream analysis.

Optical Tweezers in Studies of Red Blood Cells

Optical tweezers (OTs) are innovative instruments utilized for the manipulation of microscopic biological objects of interest. Rapid improvements in precision and degree of freedom of multichannel and multifunctional OTs have ushered in a new era of studies in basic physical and chemical properties of living tissues and unknown biomechanics in biological processes. Nowadays, OTs are used extensively for studying living cells and have initiated far-reaching influence in various fundamental studies in life sciences. There is also a high potential for using OTs in haemorheology, investigations of blood microcirculation and the mutual interplay of blood cells. In fact, in spite of their great promise in the application of OTs-based approaches for the study of blood, cell formation and maturation in erythropoiesis have not been fully explored. In this review, the background of OTs, their state-of-the-art applications in exploring single-cell level characteristics and bio-rheological properties of mature red blood cells (RBCs) as well as the OTs-assisted studies on erythropoiesis are summarized and presented. The advance developments and future perspectives of the OTs' application in haemorheology both for fundamental and practical in-depth studies of RBCs formation, functional diagnostics and therapeutic needs are highlighted.

Stability of the Salmonella Typhimurium rcsC11 mutant under different stress conditions

The virulence genes of Salmonella are modulated during infection by several regulatory systems, and the RcsCDB system is one of the most important of these. The S. Typhimurium EG14873 (rcsC11) strain harbours the rcsC11 point mutation, displaying a constitutive activation of this system, which is characterized by mucoid colonies and attenuated virulence phenotypes. In this work, the stability of the rcsC11 mutation was analysed under stress conditions. Under acid and anaerobic stresses, we observed the appearance of small and non-mucoid colonies of the rcsC11 strain. The sequencing of the rcsC gene from these colonies showed that the mutation is conserved. Moreover, we found that small colonies were also generated when the wild-type strain grew in acid and anaerobic conditions. It is worth noting that the transition from normal to atypical colonies of both strains only took place after several days of incubation and was not observed during eukaryotic cell infection. Therefore, the appearance of these atypical colonies is a characteristic feature of S. Typhimurium strains under stressful situations and does not involve a reversion of the rcsC11 allele and nor does it imply any risk to mammalian cells. Therefore, we propose that the S. Typhimurium rcsC11 strain is a good candidate for the development of attenuated vaccines.

Temporal scaling of aging as an adaptive strategy of Escherichia coli

Natural selection is thought to shape the evolution of aging patterns, although how life-history trajectories orchestrate the inherently stochastic processes associated with aging is unclear. Tracking clonal growth-arrested Escherichia coli cohorts in an homogeneous environment at single-cell resolution, we demonstrate that the Gompertz law of exponential mortality characterizes bacterial lifespan distributions. By disentangling the rate of aging from age-independent components of longevity, we find that increasing cellular maintenance through the general stress pathway reduces the aging rate and rescales the lifespan distribution at the expense of growth. This trade-off between aging and growth underpins the evolutionary tuning of the general stress response pathway in adaptation to the organism's feast-or-famine lifestyle. It is thus necessary to involve both natural selection and stochastic physiology to explain aging patterns.

Acoustic tweezers for the life sciences

Acoustic tweezers are a versatile set of tools that use sound waves to manipulate bioparticles ranging from nanometer-sized extracellular vesicles to millimeter-sized multicellular organisms. Over the past several decades, the capabilities of acoustic tweezers have expanded from simplistic particle trapping to precise rotation and translation of cells and organisms in three dimensions. Recent advances have led to reconfigured acoustic tweezers that are capable of separating, enriching, and patterning bioparticles in complex solutions. Here, we review the history and fundamentals of acoustic-tweezer technology and summarize recent breakthroughs.

The Development of an Effective Bacterial Single-Cell Lysis Method Suitable for Whole Genome Amplification in Microfluidic Platforms

Single-cell sequencing is a powerful technology that provides the capability of analyzing a single cell within a population. This technology is mostly coupled with microfluidic systems for controlled cell manipulation and precise fluid handling to shed light on the genomes of a wide range of cells. So far, single-cell sequencing has been focused mostly on human cells due to the ease of lysing the cells for genome amplification. The major challenges that bacterial species pose to genome amplification from single cells include the rigid bacterial cell walls and the need for an effective lysis protocol compatible with microfluidic platforms. In this work, we present a lysis protocol that can be used to extract genomic DNA from both gram-positive and gram-negative species without interfering with the amplification chemistry. Corynebacterium glutamicum was chosen as a typical gram-positive model and Nostoc sp. as a gram-negative model due to major challenges reported in previous studies. Our protocol is based on thermal and chemical lysis. We consider 80% of single-cell replicates that lead to >5 ng DNA after amplification as successful attempts. The protocol was directly applied to Gloeocapsa sp. and the single cells of the eukaryotic Sphaerocystis sp. and achieved a 100% success rate.

Investigation of albumin-derived perfluorocarbon-based capsules by holographic optical trapping

Albumin-derived perfluorocarbon-based capsules are promising as artificial oxygen carriers with high solubility. However, these capsules have to be studied further to allow initial human clinical tests. The aim of this paper is to provide and characterize a holographic optical tweezer to enable contactless trapping and moving of individual capsules in an environment that mimics physiological (in vivo) conditions most effectively in order to learn more about the artificial oxygen carrier behavior in blood plasma without recourse to animal experiments. Therefore, the motion behavior of capsules in a ring shaped or vortex beam is analyzed and optimized on account of determination of the optical forces in radial and axial direction. In addition, due to the customization and generation of dynamic phase holograms, the optical tweezer is used for first investigations on the aggregation behavior of the capsules and a statistical evaluation of the bonding in dependency of different capsule sizes is performed. The results show that the optical tweezer is sufficient for studying individual perfluorocarbon-based capsules and provide information about the interaction of these capsules for future use as artificial oxygen carriers.

Subacute ruminal acidosis affects fermentation and endotoxin concentration in the rumen and relative expression of the CD14/TLR4/MD2 genes involved in lipopolysaccharide systemic immune response in dairy cows

The first objective of this study was to investigate the effects of subacute ruminal acidosis (SARA) on fermentation, ruminal free lipopolysaccharides (LPS), and expression of the cluster of differentiation 14 (CD14), toll-like receptor 4 (TLR4), and myeloid differentiation protein 2 (MD2) complex in white blood cells involved in the systemic immune response in dairy cows. The second objective was a study of whether increased expression of the LPS receptor complex led to increases in the concentrations of plasma high-density lipoprotein (HDL) and serum Ca. Three hundred five dairy cows located in 13 Polish high-yielding dairy commercial farms were selected according to their days in milk (40-150 d; average = 75), 305-d milk yield (10,070-12,041 kg; average = 10,940), and number of lactations (primiparous, n = 139 and multiparous, n = 166). Next, the herds were segregated into 3 groups based on the percentages of cows with an assigned value of ruminal fluid pH: SARA-positive, SARA-risk, and SARA-negative herds. Moreover, 305 selected dairy cows were divided according to the classification based on ruminal fluid pH into 3 groups as healthy (pH >5.81), risk (pH 5.8-5.6) and acidotic cows (pH <5.6). Rumen fluid samples were collected via rumenocentesis. In the AC group, we recorded higher concentrations of ruminal free LPS [4.57 Log₁₀ endotoxin units (EU)/mL; 42,206 EU/mL] compared with the healthy group (4.48 Log₁₀ EU/mL; 34,179 EU/mL). Similarly, the concentration of ruminal free LPS was higher in SARA-positive herds (4.60 Log₁₀ EU/mL; 43,000 EU/mL) compared with SARA-negative herds (4.47 Log₁₀ EU/mL; 32,225 EU/mL). The relative mRNA abundance of genes associated with the function of LPS receptors, such as CD14, TLR4, and MD2, in white blood cells differed between all experimental groups on both cow and herd levels. In the acidotic group, we recorded higher concentrations of HDL (78.16 vs. 68.32 mg/dL) and serum amyloid A (10.80 vs. 9.16 µg/mL) and lower concentrations of Ca (8.26 vs. 10.16 mg/dL) and haptoglobin (470.19 vs. 516.85 ng/mL) compared with the healthy group. Similar results were obtained in the SARA herd status analysis, but the concentration of lipopolysaccharide-binding protein differed statistically. Moreover, the pH of ruminal fluid was negatively correlated with relative mRNA abundance of genes such as CD14, TLR4, MD2, and concentrations of serum HDL and serum amyloid A, although positively correlated with serum Ca. The results indicated that decreases in ruminal fluid pH increased the release of free LPS into the rumen and stimulated the expression of the LPS receptor complex and immune response. Moreover, an increase in the expression of the LPS receptor led to higher concentrations of plasma HDL and lower serum Ca, which may be a protective mechanism against endotoxemia. However, the biological significance of these results needs to be investigated further in larger field trials.

Tools for Genomic and Transcriptomic Analysis of Microbes at Single-Cell Level

Microbiologists traditionally study population rather than individual cells, as it is generally assumed that the status of individual cells will be similar to that observed in the population. However, the recent studies have shown that the individual behavior of each single cell could be quite different from that of the whole population, suggesting the importance of extending traditional microbiology studies to single-cell level. With recent technological advances, such as flow cytometry, next-generation sequencing (NGS), and microspectroscopy, single-cell microbiology has greatly enhanced the understanding of individuality and heterogeneity of microbes in many biological systems. Notably, the application of multiple ‘omics’ in single-cell analysis has shed light on how individual cells perceive, respond, and adapt to the environment, how heterogeneity arises under external stress and finally determines the fate of the whole population, and how microbes survive under natural conditions. As single-cell analysis involves no axenic cultivation of target microorganism, it has also been demonstrated as a valuable tool for dissecting the microbial ‘dark matter.’ In this review, current state-of-the-art tools and methods for genomic and transcriptomic analysis of microbes at single-cell level were critically summarized, including single-cell isolation methods and experimental strategies of single-cell analysis with NGS. In addition, perspectives on the future trends of technology development in the field of single-cell analysis was also presented.

Nano-engineering the Antimicrobial Spectrum of Lantibiotics: Activity of Nisin against Gram Negative Bacteria

Lantibiotics, bacteria-sourced antimicrobial peptides, are very good candidates for effective and safe food additives. Among them, nisin is already approved by the EU and FDA, and has been used in food preservation for the past 40 years. Now, there is a possibility and strong interest to extend its applicability to biomedicine for designing innovative alternatives to antibiotics. The main obstacle is, however, its naturally narrow spectrum of antimicrobial activity, focused on Gram positive bacteria. Here we demonstrate broadening nisin's spectrum to Gram negative bacteria using a nano-engineering approach. After binding nisin molecules to the surface of gold nano-features, uniformly deposited on spherical carbon templates, we created a nanocomposite with a high density of positively charged groups. Before assembly, none of the components of the nanocomposite showed any activity against bacterial growth, which was changed after assembly in the form of the nanocomposite. For the first time we showed that this type of structure enables interactions capable of disintegrating the wall of Gram negative bacteria. As confirmed by the nisin model, the developed approach opens up new horizons for the use of lantibiotics in designing post-antibiotic drugs.

TiO2-containing and ZnO-containing borosilicate glass-a novel thin glass with exceptional antibiofilm performances to prevent microfouling

Biofilm formation, also known as microfouling, on indwelling medical devices such as catheters or prosthetic joints causes difficult to treat and recurrent infections. It is also the initial step for biocorrosion of surfaces in aquatic environment. An efficient prevention of microfouling is preferable but the development of antibiofilm surfaces is enormously challenging. Therefore, soda-lime, aluminosilicate, and three borosilicate glasses with different TiO₂ and ZnO compositions were investigated on their feasibility to prevent biofilm formation by standardized in vitro biofilm assays using different pathogenic bacteria. Furthermore, the biocompatibility of these glasses was evaluated using eukaryotic cell lines end erythrocytes. Only two borosilicate glasses, containing TiO₂ and ZnO, showed an increased antibiofilm performance inhibiting biofilm adhesion and formation. The biofilm thickness and area were significantly reduced by over 90 % and characterized by diffuse structures. All tested glass types showed neither cytotoxicity nor hemotoxicity. Therefore, the antibiofilm borosilicate-thin glasses are qualified for surface coatings where biofilms are not desirable such as on medical devices.

Reevaluating multicolor flow cytometry to assess microbial viability

Flow cytometry is a rapid and quantitative method to determine bacterial viability. Although different stains can be used to establish viability, staining protocols are inconsistent and lack a general optimization approach. Very few "true" multicolor protocols, where dyes are combined in one sample, have been developed for microbiological applications. In this mini-review, the discrepancy between protocols for cell-permeant nucleic acid and functional stains are discussed as well as their use as viability dyes. Furthermore, optimization of staining protocols for a specific setup are described. Original data using the red-excitable SYTO dyes SYTO 59 to 64 and SYTO 17, combined with functional stains, for double and triple staining applications is also included. As each dye and dye combination behaves differently within a certain combination of medium matrix, microorganism, and instrument, protocols need to be tuned to obtain reproducible results. Therefore, single, double, and triple stains are reviewed, including the different parameters that influence staining such as stain kinetics, optimal stain concentration, and the effect of the chelator EDTA as membrane permeabilizer. In the last section, we highlight the need to investigate the stability of multicolor assays to ensure correct results as multiwell autoloaders are now commonly used.

Detecting Bacterial Surface Organelles on Single Cells Using Optical Tweezers

Bacterial cells display a diverse array of surface organelles that are important for a range of processes such as intercellular communication, motility and adhesion leading to biofilm formation, infections, and bacterial spread. More specifically, attachment to host cells by Gram-negative bacteria are mediated by adhesion pili, which are nanometers wide and micrometers long fibrous organelles. Since these pili are significantly thinner than the wavelength of visible light, they cannot be detected using standard light microscopy techniques. At present, there is no fast and simple method available to investigate if a single cell expresses pili while keeping the cell alive for further studies. In this study, we present a method to determine the presence of pili on a single bacterium. The protocol involves imaging the bacterium to measure its size, followed by predicting the fluid drag based on its size using an analytical model, and thereafter oscillating the sample while a single bacterium is trapped by an optical tweezer to measure its effective fluid drag. Comparison between the predicted and the measured fluid drag thereby indicate the presence of pili. Herein, we verify the method using polymer coated silica microspheres and Escherichia coli bacteria expressing adhesion pili. Our protocol can in real time and within seconds assist single cell studies by distinguishing between piliated and nonpiliated bacteria.

Tissue repair in myxobacteria: A cooperative strategy to heal cellular damage

Damage repair is a fundamental requirement of all life as organisms find themselves in challenging and fluctuating environments. In particular, damage to the barrier between an organism and its environment (e.g. skin, plasma membrane, bacterial cell envelope) is frequent because these organs/organelles directly interact with the external world. Here, we discuss the general strategies that bacteria use to cope with damage to their cell envelope and their repair limits. We then describe a novel damage-coping mechanism used by multicellular myxobacteria. We propose that cell-cell transfer of membrane material within a population serves as a wound-healing strategy and provide evidence for its utility. We suggest that--similar to how tissues in eukaryotes have evolved cooperative methods of damage repair--so too have some bacteria that live a multicellular lifestyle.

Photonic Crystal Optical Tweezers with High Efficiency for Live Biological Samples and Viability Characterization

We propose and demonstrate a new optical trapping method for single cells that utilizes modulated light fields to trap a wide array of cell types, including mammalian, yeast, and Escherichia coli cells, on the surface of a two-dimensional photonic crystal. This method is capable of reducing the required light intensity, and thus minimizing the photothermal damage to living cells, thereby extending cell viability in optical trapping and cell manipulation applications. To this end, a thorough characterization of cell viability in optical trapping environments was performed. This study also demonstrates the technique using spatial light modulation in patterned manipulation of live cell arrays over a broad area.

Characterisation of the Poly-(Vinylpyrrolidone)-Poly-(Vinylacetate-Co-Crotonic Acid) (PVP:PVAc-CA) Interpolymer Complex Matrix Microparticles Encapsulating a Bifidobacterium lactis Bb12 Probiotic Strain

The method of producing poly-(vinylpyrrolidone)-poly-(vinylacetate-co-crotonic acid) (PVP:PVAc-CA) interpolymer complex matrix microparticles in supercritical carbon dioxide (scCO2), encapsulating bacteria, has recently been developed. This study was aimed at probing the external and internal structure of these microparticles, which can be used in food. The encapsulation efficiency and distribution of encapsulated Bifidobacterium lactis Bb12 within these microparticles were also investigated. Scanning electron microscopy (SEM) revealed irregular, mostly small, smooth microparticles with no visible bacterial cells on the surface. However, some of the microparticles appeared to have porous surfaces. The results of a Microtrac S3500 particle size analyzer showed that the PVP:PVAc-CA interpolymer complex matrix microparticles encapsulating B. lactis Bb12 had an average particle size of 166.1 μm (<350 μm designated standard size for microparticles). The D 10, D 50 and D 90 values for these microparticles were 48.16, 166.06 and 382.55 μm, respectively. Both SEM and confocal laser scanning microscopy showed a high density of bacterial cells within the microparticles. An average encapsulation efficiency of 96% was achieved. Consequently, the microparticles have the potential to be evenly distributed in foods, deliver adequate amounts of probiotics and produce minimal adverse effects on the texture and mouth feel of the foods into which they are incorporated.

Short communication: A nanoemulsified form of oil blends positively affects the fatty acid proportion in ruminal batch cultures

Two consecutive rumen batch cultures were used to study the effect of nanoemulsified oils as a new type of supplement, on the in vitro fatty acid proportion and vaccenic acid formation. Three levels (3, 5, and 7%) of 2 different oil blends [soybean:fish oil (SF) or rapeseed-fish oil (RF)] were used. Both oil blends were used either in the raw form (SF or RF, respectively) or in the nanoemulsified form (NSF or NRF, respectively). The diets were the control (0%), which consisted of a dry total mixed ration without any supplements, the control plus 3, 5, or 7% of the SF or RF oil blend in appropriate form (raw or nanoemulsified). For each treatment, 6 incubation vessels were used. Each batch culture was incubated for 24h and conducted twice in 2 consecutive days. All supplements were calculated as a percentage of the substrate dry matter (400mg). Nanoemulsified supplements were recalculated to make sure the oil amount was equal to the raw oil supplementation levels. The results from both experiments indicated that the proportions of vaccenic acid and cis-9,trans-11 C18:2 increased when a raw oil blend was supplemented; on the other hand, no influence of nanoemulsified form of oil blend was observed on the proportion cis-9,trans-11 C18:2. Generally, supplementation with the nanoemulsified oil blends had less effect on biohydrogenation intermediates than the raw form of oil blends. However, the nanoemulsified form had a greater effect on the increase of n-3 and n-6 fatty acids. Nanoemulsified oil blends had a positive effect on decreasing the transformation rate of polyunsaturated fatty acids to saturated fatty acids in the biohydrogenation environment. Supplements of nanoemulsified oil blends tended to be more effective than supplements of raw oils in preserving a greater proportion of polyunsaturated fatty acids in the fermentation culture.

Identification of individual biofilm-forming bacterial cells using Raman tweezers

A method for in vitro identification of individual bacterial cells is presented. The method is based on a combination of optical tweezers for spatial trapping of individual bacterial cells and Raman microspectroscopy for acquisition of spectral “Raman fingerprints” obtained from the trapped cell. Here, Raman spectra were taken from the biofilm-forming cells without the influence of an extracellular matrix and were compared with biofilm-negative cells. Results of principal component analyses of Raman spectra enabled us to distinguish between the two strains of Staphylococcus epidermidis. Thus, we propose that Raman tweezers can become the technique of choice for a clearer understanding of the processes involved in bacterial biofilms which constitute a highly privileged way of life for bacteria, protected from the external environment.

Evaluating the toxic effect of an antimicrobial agent on single bacterial cells with optical tweezers

We implement an optical tweezers technique to assess the effects of chemical agents on single bacterial cells. As a proof of principle, the viability of a trapped Escherichia coli bacterium is determined by monitoring its flagellar motility in the presence of varying concentrations of ethyl alcohol. We show that the "killing time" of the bacterium can be effectively identified from the correlation statistics of the positional time series recorded from the trap, while direct quantification from the time series or associated power spectra is intractable. Our results, which minimize the lethal effects of bacterial photodamage, are consistent with previous reports of ethanol toxicity that used conventional culture-based methods. This approach can be adapted to study other pairwise combinations of drugs and motile bacteria, especially to measure the response times of single cells with better precision.

The sugarcane defense protein SUGARWIN2 causes cell death in Colletotrichum falcatum but not in non-pathogenic fungi

Plants respond to pathogens and insect attacks by inducing and accumulating a large set of defense-related proteins. Two homologues of a barley wound-inducible protein (BARWIN) have been characterized in sugarcane, SUGARWIN1 and SUGARWIN2 (sugarcane wound-inducible proteins). Induction of SUGARWINs occurs in response to Diatraea saccharalis damage but not to pathogen infection. In addition, the protein itself does not show any effect on insect development; instead, it has antimicrobial activities toward Fusarium verticillioides, an opportunistic fungus that usually occurs after D. saccharalis borer attacks on sugarcane. In this study, we sought to evaluate the specificity of SUGARWIN2 to better understand its mechanism of action against phytopathogens and the associations between fungi and insects that affect plants. We used Colletotrichum falcatum, a fungus that causes red rot disease in sugarcane fields infested by D. saccharalis, and Ceratocystis paradoxa, which causes pineapple disease in sugarcane. We also tested whether SUGARWIN2 is able to cause cell death in Aspergillus nidulans, a fungus that does not infect sugarcane, and in the model yeast Saccharomyces cerevisiae, which is used for bioethanol production. Recombinant SUGARWIN2 altered C. falcatum morphology by increasing vacuolization, points of fractures and a leak of intracellular material, leading to germling apoptosis. In C. paradoxa, SUGARWIN2 showed increased vacuolization in hyphae but did not kill the fungi. Neither the non-pathogenic fungus A. nidulans nor the yeast S. cerevisiae was affected by recombinant SUGARWIN2, suggesting that the protein is specific to sugarcane opportunistic fungal pathogens.

Hydroxyapatite/gold/arginine: designing the structure to create antibacterial activity

Structural analogy with antibacterial peptides provides antibacterial property in newly developed HAp/Au/arginine nanocomposite. The material possesses: (i) high antibacterial activity, (ii) high cytocompatibility and (iii) good stability in physiological environment.

Green fluorescent protein as an indicator of cryoinjury in tissues

The fluorescence intensity of Green Fluorescent Protein (GFP) has previously been demonstrated to be an accurate indicator of cellular viability following cryoinsult in individual GFP-transfected cells. In an attempt to ascertain whether GFP fluorescence intensity may also be used as a viability indicator following cryogenic insults in whole tissues, this study examines the transient fluorescence intensity of GFP-transfected mouse hepatic tissue ex vivo following cryoinsult. The observed trends are compared with diffusion-based models. It was observed that the fluorescence intensity of the exposed tissues exhibited slow exponential decay, while the solution in which the tissues were placed inversely gained fluorescence. This slow decay (~3 h) is in contrast to the rapidly diminished fluorescence intensity (seconds) seen in GFP-cell cultures following cryoinsult. These trends suggest that mass diffusion of GFP in the interstitial space, and ultimately into the surrounding medium, is the primary mechanism which determines the fluorescence loss in cryoinjured tissues. These results suggest GFP-transfected tissues may be effectively used as indicators of cryoinjury, and hence viability, following hypothermal insult provided that a sufficiently long incubation is held before observation. It was found that a meaningful observation (15% reduction in fluorescence) could be made three hours subsequent to cryoinjury for the tissues used in this study.

The future is now: single-cell genomics of bacteria and archaea

Interest in the expanding catalog of uncultivated microorganisms, increasing recognition of heterogeneity among seemingly similar cells, and technological advances in whole-genome amplification and single-cell manipulation are driving considerable progress in single-cell genomics. Here, the spectrum of applications for single-cell genomics, key advances in the development of the field, and emerging methodology for single-cell genome sequencing are reviewed by example with attention to the diversity of approaches and their unique characteristics. Experimental strategies transcending specific methodologies are identified and organized as a road map for future studies in single-cell genomics of environmental microorganisms. Over the next decade, increasingly powerful tools for single-cell genome sequencing and analysis will play key roles in accessing the genomes of uncultivated organisms, determining the basis of microbial community functions, and fundamental aspects of microbial population biology.

Optical trapping of microalgae at 735-1064 nm: photodamage assessment

Living microalgal cells differ from other cells that are used as objects for optical micromanipulation, in that they have strong light absorption in the visible range, and by the fact that their reaction centers are susceptible to photodamage. We trapped cells of the microalga Trachydiscus minutus using optical tweezers with laser wavelengths in the range from 735 nm to 1064 nm. The exposure to high photon flux density caused photodamage that was strongly wavelength dependent. The photochemical activity before and after exposure was assessed using a pulse amplitude modulation (PAM) technique. The photochemical activity was significantly and irreversibly suppressed by a 30s exposure to incident radiation at 735, 785, and 835 nm at a power of 25 mW. Irradiance at 885, 935 and 1064 nm had negligible effect at the same power. At a wavelength 1064 nm, a trapping power up to 218 mW caused no observable photodamage.

Self-sorting of deformable particles in an asynchronous logic microfluidic circuit

A microfluidic circuit can automatically sort deformable particles based on the hydrodynamic resistance that the particles induce in a constrained microfluidic channel while flowing through it.

Optofluidic cell selection from complex microbial communities for single-genome analysis

Genetic analysis of single cells is emerging as a powerful approach for studies of heterogeneous cell populations. Indeed, the notion of homogeneous cell populations is receding as approaches to resolve genetic and phenotypic variation between single cells are applied throughout the life sciences. A key step in single-cell genomic analysis today is the physical isolation of individual cells from heterogeneous populations, particularly microbial populations, which often exhibit high diversity. Here, we detail the construction and use of instrumentation for optical trapping inside microfluidic devices to select individual cells for analysis by methods including nucleic acid sequencing. This approach has unique advantages for analyses of rare community members, cells with irregular morphologies, small quantity samples, and studies that employ advanced optical microscopy.

A single-cell perspective on non-growing but metabolically active (NGMA) bacteria

A long-standing and fundamental problem in microbiology is the non-trivial discrimination between live and dead cells. The existence of physically intact and possibly viable bacterial cells that fail to replicate during a more or less protracted period of observation, despite environmental conditions that are ostensibly propitious for growth, has been extensively documented in many different organisms. In clinical settings, non-culturable cells may contribute to non-apparent infections capable of reactivating after months or years of clinical latency, a phenomenon that has been well documented in the specific case of Mycobacterium tuberculosis. The prevalence of these silent but potentially problematic bacterial reservoirs has been highlighted by classical approaches such as limiting culture dilution till extinction of growing cells, followed by resuscitation of apparently "viable but non-culturable" (VBNC) subpopulations. Although these assays are useful to demonstrate the presence of VBNC cells in a population, they are effectively retrospective and are not well suited to the analysis of non-replicating cells per se. Here, we argue that research on a closely related problem, which we shall refer to as the "non-growing but metabolically active" state, is poised to advance rapidly thanks to the recent development of novel technologies and methods for real-time single-cell analysis. In particular, the combination of fluorescent reporter dyes and strains, microfluidic and microelectromechanical systems, and time-lapse fluorescence microscopy offers tremendous and largely untapped potential for future exploration of the physiology of non-replicating cells.

Assessing chronological aging in bacteria

Bacteria, which are often considered as avid reproductive organisms under constant selective pressure to utilize available nutrients to proliferate, might seem an inappropriate model to study aging. However, environmental conditions are rarely supporting the exponential growth that is most often studied in laboratories. In the wild, Escherichia coli inhabits environments of relative nutritional paucity. Not surprisingly, under such circumstances, members of an E. coli population age and progressively lose the ability to reproduce, even when environmental conditions provide such an opportunity. Here, we review the methods to study chronological aging in bacteria and some of the mechanisms that may contribute to their age-dependent loss of viability.

Electron spin resonance of nitrogen-vacancy centers in optically trapped nanodiamonds

Using an optical tweezers apparatus, we demonstrate three-dimensional control of nanodiamonds in solution with simultaneous readout of ground-state electron-spin resonance (ESR) transitions in an ensemble of diamond nitrogen-vacancy color centers. Despite the motion and random orientation of nitrogen-vacancy centers suspended in the optical trap, we observe distinct peaks in the measured ESR spectra qualitatively similar to the same measurement in bulk. Accounting for the random dynamics, we model the ESR spectra observed in an externally applied magnetic field to enable dc magnetometry in solution. We estimate the dc magnetic field sensitivity based on variations in ESR line shapes to be approximately 50 μT/√Hz. This technique may provide a pathway for spin-based magnetic, electric, and thermal sensing in fluidic environments and biophysical systems inaccessible to existing scanning probe techniques.

Effects on groundwater microbial communities of an engineered 30-day in situ exposure to the antibiotic sulfamethoxazole

Effects upon microbial communities from environmental exposure to concentrations of antibiotics in the μg L(-1) range remain poorly understood. Microbial communities from an oligotrophic aquifer (estimated doubling rates of only once per week) that were previously acclimated (AC) or unacclimated (UAC) to historical sulfamethoxazole (SMX) contamination, and a laboratory-grown Pseudomonas stutzeri strain, were exposed to 240-520 μg L(-1) SMX for 30 days in situ using filter chambers allowing exposure to ambient groundwater, but not to ambient microorganisms. SMX-exposed UAC bacterial communities displayed the greatest mortality and impairment (viable stain assays), the greatest change in sensitivity to SMX (dose-response assays), and the greatest change in community composition (Terminal Restriction Fragment Length Polymorphism; T-RFLP). The sul1 gene, encoding resistance to SMX at clinically relevant levels, and an element of Class I integrons, was not detected in any community. Changes in microbial community structure and SMX resistance over a short experimental period in previously nonexposed, slow-growing aquifer communities suggest concentrations of antibiotics 2-3 orders of magnitude less than those used in clinical applications may influence ecological function through changes in community composition, and could promote antibiotic resistance through selection of naturally resistant bacteria.

Can dead bacterial cells be defined and are genes expressed after cell death?

There is a paucity of knowledge on gene expression in dead bacterial cells. Why would this knowledge be useful? The cells are dead. However, the time duration of gene expression following cell death is often unknown, and possibly in the order of minutes. In addition, it is a challenge to determine if bacterial cells are dead, or viable but non-culturable (VBNC), and what is an agreed upon correct definition of dead bacteria. Cells in the bacterial population or community may die at different rates or times and this complicates both the viability and gene expression analysis. In this article, the definition of dead bacterial cells is discussed and its significance in continued gene expression in cells following death. The definition of living and dead has implications for possible, completely, synthetic bacterial cells that may be capable of growth and division.