Potential antifouling strategies for marine finfish aquaculture: the effects of physical and chemical treatments on the settlement and survival of the hydroid Ectopleura larynx

The hydroid Ectopleura larynx is a common fouling organism on aquaculture nets. To contribute to the development of novel cleaning methods, laboratory and field studies determined the effects of heat (30, 40, 50 and 60°C for immersion times of 1 and 3 s) and acetic acid (0.2 and 2.0% for immersion times of 1, 3 and 10 s, 1 and 5 min) on the settlement of actinulae and the survival of juvenile and adult E. larynx. Laboratory studies showed that, regardless of immersion time, a temperature of 50°C was effective in preventing the settlement of actinulae and the survival of juveniles, while ≤12% of adult hydroids could survive. A temperature of 60°C killed all adult hydroids. For an acetic acid concentration of 0.2%, an immersion time of 1 min substantially reduced the settlement of actinulae and the survival of juvenile and adult hydroids, and none of the juvenile and adult hydroids survived after 5 min. For an acetic acid concentration of 2.0%, all immersion times were effective and reduced the mean settlement of actinulae and the survival of juvenile and adult hydroids to ≤10%. Field studies with fouled net panels exposed to selected heat or acetic acid treatments showed small reductions in mean wet weight and net aperture occlusion of the net panels 2 and 5 days after treatment. Visual inspections of the net panels showed that hydranths of the hydroids were shed, but the dead stolons of the hydroids remained on the treated net panels. Novel cleaning methods and devices may utilise these results to effectively kill E. larynx on aquaculture nets, while further studies are needed to determine the necessity of removing the dead hydroids before further biofouling accumulates on thenets.     

Characterization of the protein fraction of the temporary adhesive secreted by the tube feet of the sea star Asterias rubens

Sea stars are able to make firm but temporary attachments to various substrata by secretions released by their tube feet. After tube foot detachment, the adhesive secretions remain on the substratum as a footprint. Proteins presumably play a key role in sea star adhesion, as evidenced by the removal of footprints from surfaces after a treatment with trypsin. However, until now, characterisation was hampered by their high insolubility. In this study, a non-hydrolytic method was used to render most of the proteins constituting the adhesive footprints soluble. After analysis by SDS-PAGE, the proteins separated into about 25 bands, which ranged from 25 to 450 kDa in apparent molecular weight. Using mass spectrometry and a homology-database search, it was shown that several of the proteins are known intracellular proteins, presumably resulting from contamination of footprint material with tube foot epidermal cells. However, 11 protein bands, comprising the most abundant proteins, were not identified and might correspond to novel adhesive proteins. They were named ‘Sea star footprint proteins’ (Sfps). Tandem mass spectrometry analysis of the protein bands yielded 43 de novo-generated peptide sequences. Most of them were shared by several, if not all, Sfps. Polyclonal antibodies were raised against one of the peptides (HEASGEYYR from Sfp-115) and were used in immunoblotting. They specifically labelled Sfp-115 and other bands with lower apparent molecular weights. The different results suggest that all Sfps might belong to a single family of related proteins sharing similar motifs or, alternatively, they are the products of polymerization and/or degradation processes.     

Combined monitor for direct and indirect measurement of biofouling

Biofouling is one of the most important problems associated with heat exchangers, leading to a loss of thermal performance in their cycle. To maintain them in optimum working condition, biofouling must be kept under control and, to do so, instrumentation is required for its monitoring. The development of the biofouling layer can be qualitatively followed, but only during maintenance shutdown periods is it possible to attain a quantitative assessment. The CMDIMB [Combined Monitor for Direct and Indirect Measurement of Biofouling] was conceived as a means of discovering the evolution of the frictional resistance (f) and the heat transfer resistance (R _f) of a fluid because these are variables that indirectly define the biofouling deposited in the tubes of a seawater-cooled heat exchanger. They likewise serve to directly indicate its mass and thickness according to the total solid matter adhered over time. The results obtained allowed the values of the variables taken by the CMDIMB to be extrapolated to the heat exchanger that was set up in parallel. The CMDIMB is proposed as a highly useful tool for directly and indirectly monitoring biofouling growth in heat exchangers that do not possess the necessary instrumentation to monitor this phenomenon.     

A comparison of two fouling‐resistant heat exchangers

Fouling cannot always be prevented; it is important to consider the design of fouling‐resistant heat exchangers. To examine these exchangers, a test fluid whose fouling behaviour is understood should be used. Experiments have been conducted to examine the response of two model systems, a pulsatile flow and a fluid bed heat exchanger, to fouling from whey protein concentrates. Both systems are effective in certain cases, although the enhanced mass transfer possible in the pulsatile flow exchanger can increase fouling when mass transfer controls deposition. This demonstrates the possible danger in installing “antifouling”; systems. The possible mechanisms by which antifouling exchangers operate is discussed; they may work both by slowing the kinetics of fouling or enhancing the heat transfer coefficient. A simple model to demonstrate the design of antifouling exchangers is presented.     

The byssus of the zebra mussel (Dreissena polymorpha): spatial variations in protein composition

The notorious biofouling organism Dreissena polymorpha (the zebra mussel) attaches to a variety of surfaces using a byssus, a series of protein threads that connect the animal to adhesive plaques secreted onto hard substrata. Here, the use of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) to characterize the composition of different regions of the byssus is reported. All parts of the byssus show mass peaks corresponding to small proteins in the range of 3.7–7 kDa, with distinctive differences between different regions. Indeed, spectra from thread and plaques are almost completely non-overlapping. In addition, several peaks were identified that are unique to the interfacial region of the plaque, and therefore likely represent specialized adhesive proteins. These results indicate a high level of control over the distribution of proteins, presumably with different functions, in the byssus of this freshwater species.     

Heat transfer simulation using energy conservative dissipative particle dynamics

Dissipative particle dynamics with energy conservation (eDPD) was used to investigate conduction heat transfer in two dimensions under steady-state condition. Various types of boundary condition were implemented to the conduction domain. Besides, 2D conduction with internal heat generation was studied and the heat generation term was used to measure the thermal conductivity and diffusivity of the eDPD system. The boundary conditions used include both the Neumann and Dirichlet boundary conditions. The Neumann boundary condition was applied via adiabatic surfaces and surfaces exposed to convection heat transfer. The DPD simulations were compared to analytical solutions and finite-difference techniques. It was found that DPD appropriately predicts the temperature distribution in the conduction regime. Details of boundary condition implementation and thermal diffusivity measurement are also described in this paper.     

The Genetic Algorithm and the Conformational Search of Polypeptides and Proteins

Abstract

The genetic algorithm is a technique of function optimization derived from the principles of evolutionary theory. We have adapted it to perform conformational search on polypeptides and proteins. The algorithm was first tested on several small polypeptides and the 46 amino acid protein crambin under the AMBER potential energy function. The probable global minimum conformations of the polypeptides were located 90% of the time and a non-native conformation of crambin was located that was 150kcal/mol lower in potential energy than the minimized crystal structure conformation. Next, we used a knowledge-based potential function to predict the structures of melittin, pancreatic polypeptide, and crambin. A 2.31 Å ΔRMS conformation of melittin and a 5.33 Å ΔRMS conformation of pancreatic polypeptide were located by genetic algorithm-based conformational search under the knowledge-based potential function. Although the ΔRMS of pancreatic polypeptide was somewhat high, most of the secondary structure was correct. The secondary structure of crambin was predicted correctly, but the potential failed to promote packing interactions. Finally, we tested the packing aspects of our potential function by attempting to predict the tertiary structure of cytochrome b ₅₆₂ given correct secondary structure as a constraint. The final predicted conformation of cytochrome b ₅₆₂ was an almost completely extended continuous helix which indicated that the knowledge-based potential was useless for tertiary structure prediction. This work serves as a warning against testing potential functions designed for tertiary structure prediction on small proteins.     

Density discriminates between thermophilic and mesophilic proteins

Despite an intense interest and a remarkable number of studies on the subject, the relationships between thermostability and (primary, secondary and tertiary) structure of proteins are still not fully understood. Here, comparing the protein density – defined by the ratio between the residue number and protein excluded volume – for a set of thermophilic/mesophilic pairs, we provide evidence that this property is connected to the optimal growth temperature. In particular, our results indicate that thermophilic proteins have – in general – a lower density with respect to the mesophilic counterparts, being such a correlation more pronounced for optimal growth temperature differences greater than 40°C. The effect of the protein thermostability changes on the molecular shape is also presented.     

Macromolecular Design,Nucleic Acid Junctions,and Crystal Formation

Abstract

The simplest form of macromolecular design involves the ligation of nucleic acids. Recent results on the concatenation of nucleic acid junctions show that these molecules can act as fairly rigid macromolecular valence clusters on the nanometer scale. These clusters can be joined to form closed stick figures in which each edge is double helical DNA or RNA and each vertex is a nucleic acid junction. The geometrical criteria for forming discrete-closed and periodic structures from these components are established. The helicity of each edge limits the possible structures that can be formed.

The formation of a periodic array from nucleic acid junction building blocks is compared with the crystallization of molecular systems. This comparison leads to a new interpretation of the nature of order in the solid state for molecular crystals. The suggestion is made that the structure of a solid molecular system described by the fewest unique orthogonal (Fourier) components is the one which will be entropically favored, since it contains the least information. This is the crystalline state, with a small number of molecules per asymmetric unit. The free energy from the proposed entropie driving force responsible for this behavior is available, in principle, to correct small deviations from ideality in forming covalent crystals from nucleic acid junction components, as well as in non-bonded molecular systems. Nucleic acid junction periodic arrays provide an appropriate vehicle with which to test this interpretation.     

Superhelical DNA as a preferential binding target of 14-3-3γ protein

The 14-3-3 protein family is a highly conserved and widely distributed group of proteins consisting of multiple isoforms in eukaryotes. Ubiquitously expressed, 14-3-3 proteins play key roles in DNA replication, cell cycle regulation, and apoptosis. The function of 14-3-3 proteins is mediated by interaction with a large number of other proteins and with DNA. It has been demonstrated that 14-3-3γ protein binds strongly to cruciform structures and is crucial for initiating replication. In this study, we analyzed DNA binding properties of the 14-3-3γ isoform to linear and supercoiled DNA. We demonstrate that 14-3-3γ protein binds strongly to long DNA targets, as evidenced by electrophoretic mobility shift assay on agarose gels. Binding of 14-3-3γ to DNA target results in the appearance of blurry, retarded DNA bands. Competition experiments with linear and supercoiled DNA on magnetic beads show very strong preference for supercoiled DNA. We also show by confocal microscopy that 14-3-3 protein in the HCT-116 cell line is co-localized with DNA cruciforms. This implies a role for the 14-3-3γ protein in its binding to local DNA structures which are stabilized by DNA supercoiling.