Atomic force microscopy in biology: technology and techniques

In this review, I describe the biological applications of the atomic force microscope (AFM). The historical background and the development of the microscope are described. The AFM can operate in many different modes relevant to biological systems including topography, chemical analysis, and forces relevant at the biological length scale (single cell to DNA dimensions and pico to nano Newton forces). A limited number of examples from the literature are described to illustrate some of the many capabilities of this microscope. The aim is to give an introduction of the technique to the inexperienced in this rapidly growing field.     

Predictive markers of safety and immunogenicity of adjuvanted vaccines

Vaccination represents one of the greatest public health triumphs; in part due to the effect of adjuvants that have been included in vaccine preparations to boost the immune responses through different mechanisms. Although a variety of novel adjuvants have been under development, only a limited number have been approved by regulatory authorities for human vaccines. This report reflects the conclusions of a group of scientists from academia, regulatory agencies and industry who attended a conference on the current state of the art in the adjuvant field. Held at the U.S. Pharmacopeial Convention (USP) in Rockville, Maryland, USA, from 18 to 19 April 2013 and organized by the International Association for Biologicals (IABS), the conference focused particularly on the future development of effective adjuvants and adjuvanted vaccines and on overcoming major hurdles, such as safety and immunogenicity assessment, as well as regulatory scrutiny. More information on the conference output can be found on the IABS website, http://www.iabs.org/.     

An Extracellullar Nuclease from Bacillus Firmus VKPACU-1: Specificity and Mode of Action

An extracellular nuclease from Bacillus firmus VKPACU-1 was multifunctional enzyme, this nuclease hydrolyzed poly U rapidly and more preferentially than the other homopolyribonucleotides. Hydrolysis of RNA this enzyme released mononucleotides in the order 5′UMP > 5′AMP > 5′GMP where as in hydrolysis of DNA the mononucleotides in the order of 5′dAMP > 5′dGMP > 5′dTMP and oligonucleotides. Uridylic linkages in RNA and adenylic linkages in DNA were preferentially cleaved by the nuclease. Nuclease produced oligonucleotides having only 3’ hydroxyl and 5’ phosphate termini. Present nuclease hydrolyzed RNA and DNA released oligonucleotides as major end products and mononucleotides, suggesting an endo mode of action.     

Synthesis,Characterization, and Evaluation of Five Coordinated Copper(II) Complexes as Antibacterial,Artificial Nuclease,and Sod Mimics

The copper(II) complexes with ciprofloxacin (CFLH), levofloxacin (LFLH), norfloxacin (NFLH), and neutral bidentate ligands have been synthesized and characterized. The complexes have been evaluated for their antibacterial activity against selective species. Complexes have been also checked for their interacting behavior with DNA, and were found to have two different modes of interaction, classical and partial intercalation. Tested complexes were found to be better antioxidants with their IC₅₀ values ranging from 0.51 to 0.97 μM.     

DNA-Binding and Photocleavage Properties of Ru(II) Polypyridyl Complexes with DNA and Their Toxicity Studies on Eukaryotic Microorganisms

Four Ru(II) polypyridyl complexes, [Ru(bpy)₂(7-NO₂-dppz)]²⁺, [Ru(bpy)₂(7-CH₃-dppz)]²⁺, [Ru(phen)₂(7-NO₂-dppz)]²⁺, and [Ru(phen)₂(7-CH₃-dppz)]²⁺ (bpy = 2,2′-bipyridine, phen = 1,10-phenanthroline), (7-Nitro-dppz = 7-Nitro dipyrido[3,2-a:2′-3′-c]phenazine, 7-CH₃-dppz = 7-Methyl dipyrido[3,2-a:2′-3′-c]phenazine), have been synthesized and characterized by IR, UV, elemental analysis, ¹H NMR, ¹³C-NMR, and mass spectroscopy. The DNA-binding properties of the four complexes were investigated by spectroscopic and viscosity measurements. The results suggest that all four complexes bind to DNA via an intercalative mode. Under irradiation at 365 nm, all four complexes were found to promote the photocleavage of plasmid pBR 322 DNA. Toxicological effects of the selected complexes were performed on industrially important yeasts (eukaryotic microorganisms).     

Characterization of bacteriocin bificin C6165: a novel bacteriocin

Aims

To purify and primarily characterize an anti‐Alicyclobacillus bacteriocin produced by Bifidobacterium animalis subsp. animalis CICC 6165, suggested to be named bificin C6165.

Methods and Results

During purification of the bificin C6165, optimal recovery was achieved with ammonium sulfate precipitation followed by two chromatographic steps. Mass spectrometry analyses revealed a distinctive peak corresponding to a molecular mass of 3395·1 Da. This bacteriocin was heat stable, effective after refrigerated storage and freeze–thaw cycles. The primary mode of action of bificin C6165 is most probably due to pore formation, as indicated by the efflux of K⁺ from metabolically active cells of Alicyclobacillus acidoterrestris. In the presence of 10 mmol l^?1 gadolinium, bificin C6165 did not affect cells of Alicyclobacillus acidoterrestris. This suggests that the mode of action of bificin C6165 relies on a net negatively charged cell surface.

Conclusions

Bificin C6165 is indeed a novel bacteriocin and it exhibited remarkable potency for Alicyclobacillus control.

Significance and Impact of the Study

Application of bacteriocins in preservation of fruit juices has seldom been studied. Bificin C6165 may be an alternative method to control juice spoilage by this Alicyclobacillus acidoterrestris and meet increasing consumer demand for nature and artificial chemical additive‐free food products.     

Reproductive biology of Bagrus docmak in the Victoria Nile,Uganda

Aspects of the reproductive biology of Bagrus docmak in the Victoria Nile were investigated between November 2005 and October 2006. Macroscopic and histological analysis of the gonads confirmed it as an asynchronous batch spawner which spawns throughout the year with bimodal spawning peaks coinciding with rainfall seasons. The first spawning peak occurred from March to May, the second from September to November. The sex ratio did not significantly deviate from 1:1. Length at sexual maturity was 33.6 cm and 31.6 cm fork length (FL) for females and males, respectively. Batch fecundity ranged from 1 000 eggs in 34 cm FL fish to 43 000 eggs in 79 cm FL fish, and correlated linearly with FL (r = 0.72) and body weight (r = 0.79). Mean relative batch fecundity was 6 eggs g^?1 (SE 2). These results could guide research into the possibility of artificially inducing the fish to spawn, and its subsequent culture.     

Genetic monitoring of progeny derived from natural spawning of Acipenser ruthenus Linnaeus, 1758 and Acipenser stellatus Pallas, 1771 as well as their hybrids in the Lower Volga river during the period 2017 to 2019

The state of natural spawning of sturgeons in the Lower Volga River was investigated through genetic monitoring of juveniles (larvae, fingerlings, subadults) captured at seven traditionally used monitoring locations. Sampling was performed during the period 2017–2019. In total, 460 individuals were caught and genotyped using a set of six microsatellite loci (Afug41, Afug51, Afug135, An20, AoxD161, AoxD165) and mtDNA control region sequencing. The observed species-specific microsatellite alleles revealed the presence of juvenile sturgeons originating from natural spawning also included some hybrids between Acipenser stellatus and A. ruthenus. Thus, the majority of sterlet breeding takes place in natural spawning grounds but also sterlet hybridizes with a small number of stellate sturgeons. Juveniles of other sturgeon species were not identified, and it is concluded that natural spawning activities of Russian sturgeon, beluga and ship sturgeon were insignificant or even absent in the Lower Volga during the observation period.     

Trait-dependency of trophic interactions in zooplankton food webs

Anthropogenic change in the abundance or identity of dominant top predators may induce reorganizations in whole food webs. Predicting these reorganizations requires identifying the biological rules that govern trophic niches. However, we still lack a detailed understanding of the respective contributions of body size, behaviour (e.g. match between predator hunting mode and prey antipredator strategy), phylogeny and/or ontogeny in determining both the presence and strength of trophic interactions. Here, we address this question by measuring zooplankton numerical response to fish predators in lake enclosures. We compared the fit to zooplankton count data of models grouping zooplankters based either on 1) body sizes, 2) antipredator behaviour, 3) body size combined with antipredator behaviour or on 4) phylogeny combined with ontogeny (i.e. different life stages of copepods). Body size was a better predictor of zooplankton numerical response to fish than antipredator behaviour, but combining body size and behaviour provided even better predictions. Models based on phylogeny combined with ontogeny clearly outperformed those based on other zooplankton grouping rules, except when phylogeny was poorly resolved. Removing ontogenetic information plagued the predictive power of the highly-resolved (genus-level) phylogenetic grouping but not of medium-resolved or poorly-resolved phylogenetic grouping. Our results support the recent use of phylogeny as a superior surrogate for traits controlling trophic niches, and further highlight the added value of combining phylogeny with ontogenetic traits. Further improvements in our mechanistic understanding of how trophic networks are shaped are bound to uncovering the trophic traits captured by phylogeny and ontogeny, but that currently remain hidden to us.