The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

I read this book the same weekend that the Packers took on the Rams, and the experience of the latter event, obviously, colored my judgment. Although I abhor anything that smacks of being a handbook (like, \"How to Earn a Merit Badge in Neurosurgery\") because too many volumes in biomedical science already evince a boyscout-like approach, I must confess that parts of this volume are fast, scholarly, and significant, with certain reservations. I like parts of this well-illustrated book because Dr. Sj6strand, without so stating, develops certain subjects on technique in relation to the acquisition of judgment and sophistication. And this is important! So, given that the author (like all of us) is somewhat deficient in some areas, and biased in others, the book is still valuable if the uninitiated reader swallows it in a general fashion, realizing full well that what will be required from the reader is a modulation to fit his vision, propreception, adaptation and response, and the kind of problem he is undertaking. A major deficiency of this book is revealed by comparison of its use of physics and of chemistry to provide understanding and background for the application of high resolution electron microscopy to problems in biology. Since the volume is keyed to high resolution electron microscopy, which is a sophisticated form of structural analysis, but really morphology in a modern guise, the physical and mechanical background of The instrument and its ancillary tools are simply and well presented. The potential use of chemical or cytochemical information as it relates to biological fine structure , however, is quite deficient. I wonder when even sophisticated morphol-ogists will consider fixation a reaction and not a technique; only then will the fundamentals become self-evident and predictable and this sine qua flon will become less mystical. Staining reactions (the most inadequate chapter) ought to be something more than a technique to selectively enhance contrast of morphological elements; it ought to give the structural addresses of some of the chemical residents of cell components. Is it pertinent that auto-radiography gets singled out for more complete coverage than other significant aspects of cytochemistry by a high resolution microscopist, when it has a built-in minimal error of 1,000 A in standard practice? I don't mean to blind-side (in strict football terminology) Dr. Sj6strand's efforts for what is \"routinely used in our laboratory\"; what is done is usually well done. It's just that …

Methods in Enzymology.

The major strategies for designing surfaces that prevent fouling due to proteins, bacteria, and marine organisms are reviewed. Biofouling is of great concern in numerous applications ranging from biosensors to biomedical implants and devices, and from food packaging to industrial and marine equipment. The two major approaches to combat surface fouling are based on either preventing biofoulants from attaching or degrading them. One of the key strategies for imparting adhesion resistance involves the functionalization of surfaces with poly(ethylene glycol) (PEG) or oligo(ethylene glycol). Several alternatives to PEG-based coatings have also been designed over the past decade. While protein-resistant coatings may also resist bacterial attachment and subsequent biofilm formation, in order to overcome the fouling-mediated risk of bacterial infection it is highly desirable to design coatings that are bactericidal. Traditional techniques involve the design of coatings that release biocidal agents, including antibiotics, quaternary ammonium salts (QAS), and silver, into the surrounding aqueous environment. However, the emergence of antibiotic- and silver-resistant pathogenic strains has necessitated the development of alternative strategies. Therefore, other techniques based on the use of polycations, enzymes, nanomaterials, and photoactive agents are being investigated. With regard to marine antifouling coatings, restrictions on the use of biocide-releasing coatings have made the generation of nontoxic antifouling surfaces more important. While considerable progress has been made in the design of antifouling coatings, ongoing research in this area should result in the development of even better antifouling materials in the future.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/adma.201001215

Antifouling coatings: recent developments in the design of surfaces that prevent fouling by proteins, bacteria, and marine organisms.

Antibiotic resistance in Pseudomonas aeruginosa: mechanisms and alternative therapeutic strategies

This review aims to briefly discuss a short list of a broad variety of inflammatory cytokines. Numerous studies have implicated that inflammatory cytokines exert important effects with regard to various inflammatory diseases, yet the reports on their specific roles are not always consistent. They can be used as biomarkers to indicate or monitor disease or its progress, and also may serve as clinically applicable parameters for therapies. Yet, their precise role is not always clearly defined. Thus, in this review, we focus on the existing literature dealing with the biology of cytokines interleukin (IL)-6, IL-1, IL-33, tumor necrosis factor-alpha (TNF-α), IL-10, and IL-8. We will briefly focus on the correlations and role of these inflammatory mediators in the genesis of inflammatory impacts (e.g., shock, trauma, immune dysregulation, osteoporosis, and/or critical illness).

Cytokines in Inflammatory Disease.

OBJECTIVES To evaluate the effect of microblepharon exfoliation on the number of eyelid bacteria and their lipase activity and the relationship of these to contact lens discomfort. METHODS Thirty experienced contact lens wearers had their eyelid margin physiology, tear properties, and comfort scores assessed. The number, type, and frequency of lower eyelid margin bacteria, and their lipase activity, were measured. Eyelids were treated with a foam cleanser or microblepharon exfoliation. Clinical and microbiological tests were repeated at each visit. Changes and correlations were examined. RESULTS Symptomatic lens wearers had a higher ratio for the number and frequency of gram-positive rods and cocci. Microblepharon exfoliation reduced the number and ratio of gram-positive rods to cocci from baseline for symptomatic wearers that lasted 7 to 10 days after treatment (P<0.05). Numbers of bacteria, the ratio of rods to cocci, and lipase activity correlated with lash contamination (r≥0.385; P≤0.046) and anterior blepharitis (r≥0.359; P≤0.048). Bacterial lipase correlated with meibomian gland secretions (r=0.422; P=0.038) and the tear evaporation rate (r=0.479; P=0.022). Microblepharon exfoliation produced a significant reduction in CLDEQ-8 scores and converted 10 symptomatic into asymptomatic lens wearers. CONCLUSIONS There was dysbiosis in the lid microbiome of symptomatic lens wearers. Microblepharon exfoliation reduced the number, frequency of isolation, and ratio of gram-positive rods and cocci. Bacterial numbers and their lipase production correlated with changes to clinical signs and symptoms. Symptomatic lens wearers could be converted to asymptomatic lens wearers after microblepharon exfoliation.

Effect of Eyelid Treatments on Bacterial Load and Lipase Activity in Relation to Contact Lens Discomfort

Objective To assess the incidence of adverse events during the use of a povidone-iodine disinfecting solution (cleadew) and the microbial contamination in contact lens cases. Methods A prospective, single-center, open-label, controlled study evaluating the use of cleadew cleaning and disinfecting system in existing daily wear soft contact lens wearers over a 3-month period was conducted. Ocular signs and symptoms during lens wear were assessed at baseline and after 1 and 3 months of using cleadew. Contact lens cases were assessed for the frequency of microbial contamination and the types of microbes, using traditional microbial culture, followed by identification of bacteria using 16S rRNA sequencing. Results Use of cleadew was well tolerated. There was reduction in corneal staining (0.5±0.5 at 3 months of use) compared with the participant's habitual multipurpose disinfecting system (1.1±1.0); all other clinical signs were not significantly different. There were no cases of solution-induced corneal staining. There was a low adverse event rate of 0.8% per 100 participant-months. Contact lens case contamination was low, with 30% of cases having no culturable microbes. Comparison with previously published data showed that use of cleadew resulted in low frequencies of Gram-positive (49%) and fungal (8%) contamination and a low, but higher than some other disinfecting solutions, level of Gram-negative bacteria. Conclusions Cleadew cleaning and disinfecting system was associated with low levels of adverse events during use. Contact lens cases were significantly less frequently contaminated than for some other types of disinfecting solutions.

Clinical Outcomes and Contact Lens Case Contamination Using a Povidone-Iodine Disinfection System

PurposeTo evaluate the amoebicidal efficacy of protamine with polyhexamethylene biguanide (PHMB) and ethylenediamine tetraacetic acid (EDTA).MethodsThe International Organization for Standardization 14729:2001 procedure was modified to test amoebicidal activity. Acanthamoeba cells were inocu

Protamine as a potential amoebicidal agent for contact lens disinfection.

PURPOSE Contact lens cases become contaminated with microbes during use. We wished to compare the adhesion of uncommon bacterial contaminants isolated from lens cases to contact lenses with and without organic soil. METHODS Strains of Delftia acidovorans (001), Stenotrophomonas maltophilia (002 and 006), and Achromobacter xylosoxidans (001) isolated from contact lens cases (test strains) and Pseudomonas aeruginosa (Paer1) isolated from eyes at the time of infiltrative response (control strain) were used. Bacteria were grown and resuspended in phosphate-buffered saline (PBS) or 10% organic soil (heat-killed Saccharomyces cerevisiae resuspended in complement inactivated bovine serum). Two silicone hydrogel (senofilcon A and comfilcon A) and one hydrogel lens (etafilcon A) lens materials were used. Bacteria (1.0×10 and 1.0×10 colony-forming units/mL; CFU/mL) adhered to lenses for 24 hr and the numbers of bacteria adherent to each lens type (with and without organic soil) were estimated by culture. RESULTS All the four test strains adhered in significantly greater numbers to contact lenses after incubation in inoculum prepared with organic soil compared with PBS-D. acidovorans 001 (0.7 log10 CFU; P 0.05). Achromobacter xylosoxidans 001 (P<0.01), D. acidovorans 001 (P<0.01), and S. maltophilia 002 (P<0.01) significantly differed in their adhesion to the three contact lens materials. CONCLUSION Bacteria that are commonly found in contact lens cases adhered to contact lenses in relatively high numbers in the presence of organic soil. This might indicate that a similar phenomenon occurs in the presence of tears. This may facilitate their transfer from the lens to the cornea and the production of corneal infiltrates.

Ajay Kumar Vijay

Papers

Effect of Eyelid Treatments on Bacterial Load and Lipase Activity in Relation to Contact Lens Discomfort

Clinical Outcomes and Contact Lens Case Contamination Using a Povidone-Iodine Disinfection System

Protamine as a potential amoebicidal agent for contact lens disinfection.

Adhesion of Stenotrophomonas maltophilia, Delftia acidovorans and Achromobacter xylosoxidans to contact lenses

Adhesion of Stenotrophomonas maltophilia, Delftia acidovorans, and Achromobacter xylosoxidans to Contact Lenses.