Direct visualization of the EcoRII-DNA triple synaptic complex by atomic force microscopy

Interactions between distantly separated DNA regions mediated by specialized proteins lead to the formation of synaptic protein-DNA complexes. This is a ubiquitous phenomenon which is critical in various genetic processes. Although such interactions typically occur between two sites, interactions among three specific DNA regions have been identified, and a corresponding model has been proposed. Atomic force microscopy was used to test this model for the EcoRII restriction enzyme and provide direct visualization and characterization of synaptic protein-DNA complexes involving three DNA binding sites. The complex appeared in the images as a two-loop structure, and the length measurements proved the site specificity of the protein in the complex. The protein volume measurements showed that an EcoRII dimer is the core of the three-site synaptosome. Other complexes were identified and analyzed. The protein volume data showed that the dimeric form of the protein is responsible for the formation of other types of synaptic complexes as well. The applications of these results to the mechanisms of the protein-DNA interactions are discussed.     

Determination of human platelet membrane permeability coefficients using the Kedem-Katchalsky formalism: estimates from two- vs three-parameter fits.

Attempts to cryopreserve human blood platelets have resulted in poor postthaw survival rates and have been inadequate for routine clinical application. As a result, most blood banks maintain platelets in nonfrozen solutions. Using this approach, platelets can be stored for only about 5 days and are then discarded. This situation greatly limits the use of platelet transfusion in clinical practice. Information regarding fundamental cryobiological characteristics can be applied to predict platelet response to cryoprotective agent (CPA) addition/removal and to cooling/warming. Methods can then be engineered to optimize cryopreservation procedures, thereby minimizing platelet damage and maximizing postthaw recovery. It was therefore the purpose of this study to determine some of the necessary biophysical parameters required for this process: (i) plasma membrane hydraulic conductivity (Lp), (ii) cryoprotectant solute permeability coefficient (Ps), (iii) the associated reflection coefficient (sigma), and (iv) their activation energies. The CPAs studied included dimethyl sulfoxide (Me2SO) and propylene glycol at 1.5 M concentration. Permeability was measured at 22, 10, and 4 degrees C using a modified Coulter counter in conjunction with a water-jacketed beaker system for temperature regulation. The Kedem-Katchalsky formalism was used to estimate the parameters using: (1) a three-parameter fit and (2) a two-parameter fit in which a noninteracting value of sigma was calculated. Two-parameter estimates were in closer agreement with previously published values, and these were used in a model to simulate addition and removal of 0.64 M (5%) and 1.0 M (7.8%) Me2SO, the most common CPA currently used in empirically determined platelet cryopreservation protocols.     

Identification of Aerobically and Anaerobically Induced Genes in Enterococcus faecalis by Random Arbitrarily Primed PCR

Enterococci have emerged among the leading causes of nosocomial infection. With the goal of analyzing enterococcal genes differentially expressed in environments related to commensal or environmental colonization and infection sites, we adapted and optimized a method more commonly used in the study of eukaryotic gene expression, random arbitrarily primed PCR (RAP-PCR). The RAP-PCR method was systematically optimized, allowing the technique to be used in a highly reproducible manner with gram-positive bacterial RNA. In the present study, aerobiosis was chosen as a variable for the induction of changes in gene expression by Enterococcus faecalis. Aerobically and anaerobically induced genes were detected and identified to the sequence level, and differential gene expression was confirmed by quantitative, specifically primed RT-PCR. Differentially expressed genes included several sharing identity with those of other organisms related to oxygen metabolism, as well as hypothetical genes lacking identity to known genes.     

Marine macroalgae and their associated microbiomes as a source of antimicrobial chemical diversity

ABSTRACT

This article reviews the role of microbial biofilms in infection, and the antimicrobial chemical diversity of marine macroalgae and their associated microbiomes. Antimicrobial resistance (AMR) represents one of the major health threats faced by humanity over the next few years. To prevent a global epidemic of antimicrobial-resistant infections, the discovery of new antimicrobials and antibiotics, better anti-infection strategies and diagnostics, and changes to our current use of antibiotics have all become of paramount importance. Numerous studies investigating the bioactivities of seaweed extracts as well as their secondary and primary metabolites highlight the vast biochemical diversity of seaweeds, with new modes of action making them ideal sources for the discovery of novel antimicrobial bioactive compounds of pharmaceutical interest. In recent years, researchers have focused on characterizing the endophytic and epiphytic microbiomes of various algal species in an attempt to elucidate host-microbe interactions as well as to understand the function of microbial communities. Although environmental and host-associated factors crucially shape microbial composition, microbial mutualistic and obligate symbionts are often found to play a fundamental role in regulating many aspects of host fitness involving ecophysiology and metabolism. In particular, algal ‘core’ epiphytic bacterial communities play an important role in the protection of surfaces from biofouling, pathogens and grazers through the production of bioactive metabolites. Together, marine macroalgae and their associated microbiomes represent unique biological systems offering great potential for the isolation and identification of novel compounds and strategies to counteract the rise and dissemination of AMR.     

Therapeutic Targeting of MLL Degradation Pathways in MLL-Rearranged Leukemia

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Mitochondrial apoptosis is amplified through gap junctions

The death of one cell can precipitate the death of nearby cells in a process referred to as the bystander effect. We investigated whether mitochondrial apoptosis generated a bystander effect and, if so, by which pathway. Microinjection with cytochrome c mimicked function of the mitochondrial apoptosis-induced channel MAC and caused apoptosis of both target and nearby osteoblasts. This effect was suppressed by inhibiting gap junction intercellular communication. A bystander effect was also observed after exogenous expression of tBid, which facilitates MAC formation and cytochrome c release. Interestingly, in connexin-43 deficient osteoblasts, microinjection of cytochrome c induced apoptosis only in the target cell. These findings indicate that a death signal was generated downstream of MAC function and was transmitted through gap junctions to amplify apoptosis in neighboring cells. This concept may have implications in development of new therapeutic approaches.     

Microbiological interactions with cold plasma

There is a diverse range of microbiological challenges facing the food, healthcare and clinical sectors. The increasing and pervasive resistance to broad‐spectrum antibiotics and health‐related concerns with many biocidal agents drives research for novel and complementary antimicrobial approaches. Biofilms display increased mechanical and antimicrobial stability and are the subject of extensive research. Cold plasmas (CP) have rapidly evolved as a technology for microbial decontamination, wound healing and cancer treatment, owing to the chemical and bio‐active radicals generated known collectively as reactive oxygen and nitrogen species. This review outlines the basics of CP technology and discusses the interactions with a range of microbiological targets. Advances in mechanistic insights are presented and applications to food and clinical issues are discussed. The possibility of tailoring CP to control specific microbiological challenges is apparent. This review focuses on microbiological issues in relation to food‐ and healthcare‐associated human infections, the role of CP in their elimination and the current status of plasma mechanisms of action.     

Comprehensive inhibitor profiling of the Proteus mirabilis metalloprotease virulence factor ZapA (mirabilysin)

In this study we report for the first time the comprehensive inhibitor profiling of the Proteus mirabilis metalloprotease virulence factor ZapA (mirabilysin) using a 160 compound focused library of N-alpha mercaptoamide dipeptides, in order to map the and binding site preferences of this important enzyme. This study has revealed a preference for the aromatic residues tyrosine and tryptophan in and aliphatic residues in . From this library, six compounds were identified which exhibited sub- to low-micromolar K_i values. The most potent inactivator, SH–CO₂–Y–V–NH₂ was capable of preventing ZapA-mediated hydrolysis of heat-denatured IgA, indicating that these inhibitors may be capable of protecting host proteins against ZapA during colonisation and infection.