Flow cytometric and 16S sequencing methodologies for monitoring the physiological status of the microbiome in powdered infant formula production

The aim of this study was to develop appropriate protocols for flow cytometric (FCM) and 16S rDNA sequencing investigation of the microbiome in a powdered infant formula (PIF) production facility. Twenty swabs were collected from each of the three care zones of a PIF production facility and used for preparing composite samples. For FCM studies, the swabs were washed in 200 mL phosphate buffer saline (PBS). The cells were harvested by three-step centrifugation followed by a single stage filtration. Cells were dispersed in fresh PBS and analyzed with a flow cytometer for membrane integrity, metabolic activity, respiratory activity and Gram characteristics of the microbiome using various fluorophores. The samples were also plated on agar plates to determine the number of culturable cells. For 16S rDNA sequencing studies, the cells were harvested by centrifugation only. Genomic DNA was extracted using a chloroform-based method and used for 16S rDNA sequencing studies. Compared to the dry low and high care zones, the wet medium care zone contained a greater number of viable, culturable, and metabolically active cells. Viable but non-culturable cells were also detected in dry-care zones. In total, 243 genera were detected in the facility of which 42 were found in all three care zones. The greatest diversity in the microbiome was observed in low care. The genera present in low, medium and high care were mostly associated with soil, water, and humans, respectively. The most prevalent genera in low, medium and high care were Pseudomonas, Acinetobacter, and Streptococcus, respectively. The integration of FCM and metagenomic data provided further information on the density of different species in the facility

A study of the scattering of fast neutrons in large samples

In the present work, the elastic scattering of fast neutrons from iron and concrete samples were studied at incident neutron energies of 14.0 and 14.4 Mev, using a neutron spectrometer based on the associated particle time-of-flight technique. These samples were chosen because of their importance in the design of fusion reactor shielding and construction. Using the S.A.M.E.S. accelerator and the 3 M v Dynamitron accelerator at the Radiation Centre, 14.0 and 14.4 Mev neutrons were produced by the T(d, n)4He reaction at incident deuteron energies of 140 keV and 900 keV mass III ions respectively. The time of origin of the neutron was determined by detecting the associated alpha particles. The samples used were extended flat plates of thicknesses up to 1.73 mean free paths for iron and 2.3 mean free paths for concrete. The associated alpha particles and fast neutrons were detected by means of a plastic scintillator mounted on a fast focused photomultiplier tube. The differential neutron elastic scattering cross-sections were measured for 14 Mev neutrons in various thicknesses of iron and concrete in the angular range from zero to 90°. In addition, the angular distributions of 14.4 Mev neutrons after passing through extended samples of iron were measured at several scattering angles in the same angular range. The measurements obtained for the thin sample of iron were compared with the results of Coon et al. The differential cross-sections for the thin iron sample were also analyzed on the optical model using the computer code RAROMP. For the concrete sample, the angular distribution of the thin sample was compared with the cross-sections calculated from the major constituent elements of concrete, and with the predicted values of the optical model for those elements. No published data could be found to compare with the results of the concrete differential cross-sections. In the case of thick samples of iron and concrete, the number of scattered neutrons were compared with a phenomological calculation based on the continuous slowing down model. The variation of measured cross-sections with sample thickness were found to follow the empirical relation σ = σ0 eαx. By using the universal constant "K", good fits were obtained to the experimental data. In parallel with the work at 14.0 and 14.4 Mev, an associated particle time-of-flight spectrometer was investigated which used the 2H(d,n)3He reaction for 3.02 Mev neutron energy at the incident deuteron energy of 1 Mev

Physiology of escherichia coli in orange juice: applications of flow cytometry

Flow cytometry (FCM) was utilized for monitoring the physiology of $E.$ $coli$ cells in orange juice (OJ) as well as a model orange juice (MOJ). Compared to FCM, plate counts highly underestimated the true number of viable cells in OJ. As a part of this study, the effects of the change in major components of OJ on viability of the cells in OJ and MOJ was investigated using FCM. Increase in ascorbic acid and amino acid concentrations of MOJ improved both the culturability and FCM viability of the cells. FCM was also employed for studying the effects of OJ clarification on viability of $E.$ $coli$ in OJ. Although, reduction in cloud content of OJ increased the number of healthy cells, however, the removal of cloud particles of larger than 0.7 μm appeared to increase the antimicrobial efficacy of particles of smaller than 0.7 μm. The effects of washing E. coli cells with available chlorine, H$_2$O$_2$ and organic acids on their subsequent viability in OJ was also investigated. While increase in concentration of sanitizers resulted in a significant reduction in healthy populations, the total number of viable cells either remained constant or increased particularly in case of H$_2$O$_2$-washed cells

Transient accumulation and bidirectional movement of KIF13B in primary cilia.

Primary cilia are microtubule-based sensory organelles whose assembly and function rely on the conserved bidirectional intraflagellar transport (IFT) system, which is powered by anterograde kinesin-2 and retrograde cytoplasmic dynein-2 motors. Nematodes additionally employ a cell-type-specific kinesin-3 motor, KLP-6, which moves within cilia independently of IFT and regulates ciliary content and function. Here, we provide evidence that a KLP-6 homolog, KIF13B, undergoes bursts of bidirectional movement within primary cilia of cultured immortalized human retinal pigment epithelial (hTERT-RPE1) cells. Anterograde and retrograde intraciliary velocities of KIF13B were similar to those of IFT (as assayed using IFT172–eGFP), but intraciliary movement of KIF13B required its own motor domain and appeared to be cell-type specific. Our work provides the first demonstration of motor-driven, intraciliary movement by a vertebrate kinesin other than kinesin-2 motors.post-print449 K

Approaches for improvement in digestive survival of probiotics, a comparative study

The aim of this study was to compare approaches commonly recommended in the literature for the improvement of the survival of probiotics in the human digestive tract. The survival of two probiotics, L. casei W56 and B. lactis W52, in the presence or absence of prebiotics, maize starch, fermented milk and upon encapsulation in calcium alginate-chitosan were evaluated. While B. lactis W52 was resistant to stomach juice, but sensitive to duodenal juice, L. casei W56 showed an exactly opposite behaviour. Overall the digestive survivability of probiotics was not improved by prebiotics, maize starch or encapsulation. A significant improvement of the overall survivability of B. lactis W52 (but not L. casei W56) during in vitro digestion was noted in milk and fermented milk, possibly due to reduction of the activity of bile against this probiotic. Overall no one method could be recommended universally for the improvement of probiotic survivability. Nevertheless, this research indicated that certain probiotic characteristics, such as susceptibility to bile or acid or ability to utilise matrix components as an energy source could perhaps be used in further research to select the most effective approaches to deliver viable cells into lower parts of the digestive tract

A targeted multi-proteomics approach generates a blueprint of the ciliary ubiquitinome

Establishment and maintenance of the primary cilium as a signaling-competent organelle requires a high degree of fine tuning, which is at least in part achieved by a variety of post-translational modifications. One such modification is ubiquitination. The small and highly conserved ubiquitin protein possesses a unique versatility in regulating protein function via its ability to build mono and polyubiquitin chains onto target proteins. We aimed to take an unbiased approach to generate a comprehensive blueprint of the ciliary ubiquitinome by deploying a multi-proteomics approach using both ciliary-targeted ubiquitin affinity proteomics, as well as ubiquitin-binding domain-based proximity labelling in two different mammalian cell lines. This resulted in the identification of several key proteins involved in signaling, cytoskeletal remodeling and membrane and protein trafficking. Interestingly, using two different approaches in IMCD3 and RPE1 cells, respectively, we uncovered several novel mechanisms that regulate cilia function. In our IMCD3 proximity labeling cell line model, we found a highly enriched group of ESCRT-dependent clathrin-mediated endocytosis-related proteins, suggesting an important and novel role for this pathway in the regulation of ciliary homeostasis and function. In contrast, in RPE1 cells we found that several structural components of caveolae (CAV1, CAVIN1, and EHD2) were highly enriched in our cilia affinity proteomics screen. Consistently, the presence of caveolae at the ciliary pocket and ubiquitination of CAV1 specifically, were found likely to play a role in the regulation of ciliary length in these cells. Cilia length measurements demonstrated increased ciliary length in RPE1 cells stably expressing a ubiquitination impaired CAV1 mutant protein. Furthermore, live cell imaging in the same cells revealed decreased CAV1 protein turnover at the cilium as the possible cause for this phenotype. In conclusion, we have generated a comprehensive list of cilia-specific proteins that are subject to regulation via ubiquitination which can serve to further our understanding of cilia biology in health and disease

Use of flow cytometry and total viable count to determine the effects of orange juice composition on the physiology of Escherichia coli

Orange juice (OJ) contains numerous compounds some of which are known to play key roles in growth and survival of bacteria. This study aimed to investigate the effects of natural or processing‐induced variations in OJ composition on the physiology of Escherichia coli. OJ and model OJ (MOJ) samples containing various sugars, organic acids, amino acids, or ascorbic acid were inoculated with E. coli K‐12 MG1655 in different growth phases. The culturability, viability, and physiology of the cells were investigated during storage using plate counting and flow cytometry. Generally, stationary‐phase cells displayed the greatest survival in both MOJ and OJ. Increase in incubation temperature from 4 to 22.5ºC caused a significant decrease in both healthy and culturable cell populations. Supplementation of MOJ with ascorbic acid and amino acids increased both the viability and culturability of the cells. Similar trends were observed in amino acid‐supplemented OJ, albeit at a slower rate. In contrast, variations in sugar or organic acid composition had negligible effects on the physiological status of the cells. In summary, natural variation in ascorbic acid or amino acid concentrations could potentially have an adverse effect on the microbiological safety of orange juice

Time, space, and disorder in the expanding proteome universe

Proteins are highly dynamic entities. Their myriad functions require specific structures, but proteins’ dynamic nature ranges all the way from the local mobility of their amino acid constituents to mobility within and well beyond single cells. A truly comprehensive view of the dynamic structural proteome includes: (i) alternative sequences, (ii) alternative conformations, (iii) alternative interactions with a range of biomolecules, (iv) cellular localizations, (v) alternative behaviors in different cell types. While these aspects have traditionally been explored one protein at a time, we highlight recently emerging global approaches that accelerate comprehensive insights into these facets of the dynamic nature of protein structure. Computational tools that integrate and expand on multiple orthogonal data types promise to enable the transition from a disjointed list of static snapshots to a structurally explicit understanding of the dynamics of cellular mechanisms.D.P.M. is funded by BBSRC grant BB/N010493/1

A study of the scatetring of fast neutrons in large samples

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