Growth of Bacillus amyloliquefaciens as influence by Si nutrition.

The aim of study was to determine the influence of soluble and solid forms of Si on the growth of B. amyloliquefaciens. The experiment was conducted at two regimes: under sterile conditions (without B. amyloliquefaciens) and infected conditions (with B. amyloliquefaciens). New formed silica gel, diatomite and monosilicic acid at 1 mM Si and 2 mM Si were used as source of Si. The concentration of monosilicic acid in the solution was measured on second and tenth days of experiment. The total carbon in the solution before and after centrifugation was determined on day 10 of the experiment. The experiment has demonstrated a significant positive effect (by 4.7-41.2%) on B. amyloliquefaciens growth in water system. The presence of B. amyloliquefaciens in Si-rich solution reduced the concentration of monosilicic acid in the solution up to 16.2%. About 13.5-30.7% of B. amyloliquefaciens can be attached to the Si-rich surface without formation of cell clusters. Si can be classified as a beneficial nutrient for B. amyloliquefaciens. The tested strain of Bacillus can form channels in silica gel. The presence of monosilicic acid resulted in the formation of an aligned positioning of cells in water-based solution. This study is the first to demonstrate the direct influence of active Si forms on bacteria growth. The research showed that monosilicic acid or Si-rich solid substances with high solubility on Si can be recommended to increase B. amyloliquefaciens growth in soil, water or reactors.

Recessive Host Range Mutants and Unsusceptible Cells That Inactivate Virions without Genome Penetration: Ecological and Technical Implications.

Although microviruses do not possess a visible tail structure, one vertex rearranges after interacting with host lipopolysaccharides. Most examinations of host range, eclipse, and penetration were conducted before this "host-induced" unique vertex was discovered and before DNA sequencing became routine. Consequently, structure-function relationships dictating host range remain undefined. Biochemical and genetic analyses were conducted with two closely related microviruses, α3 and ST-1. Despite ∼90% amino acid identity, the natural host of α3 is Escherichia coli C, whereas ST-1 is a K-12-specific phage. Virions attached and eclipsed to both native and unsusceptible hosts; however, they breached only the native host's cell wall. This suggests that unsusceptible host-phage interactions promote off-pathway reactions that can inactivate viruses without penetration. This phenomenon may have broader ecological implications. To determine which structural proteins conferred host range specificity, chimeric virions were generated by individually interchanging the coat, spike, or DNA pilot proteins. Interchanging the coat protein switched host range. However, host range expansion could be conferred by single point mutations in the coat protein. The expansion phenotype was recessive: genetically mutant progeny from coinfected cells did not display the phenotype. Thus, mutant isolation required populations generated in environments with low multiplicities of infection (MOI), a phenomenon that may have impacted past host range studies in both prokaryotic and eukaryotic systems. The resulting genetic and structural data were consistent enough that host range expansion could be predicted, broadening the classical definition of antireceptors to include interfaces between protein complexes within the capsid.IMPORTANCE To expand host range, viruses must interact with unsusceptible host cell surfaces, which could be detrimental. As observed in this study, virions were inactivated without genome penetration. This may be advantageous to potential new hosts, culling the viral population from which an expanded host range mutant could emerge. When identified, altered host range mutations were recessive. Accordingly, isolation required populations generated in low-MOI environments. However, in laboratory settings, viral propagation includes high-MOI conditions. Typically, infected cultures incubate until all cells produce progeny. Thus, coinfections dominate later replication cycles, masking recessive host range expansion phenotypes. This may have impacted similar studies with other viruses. Last, structural and genetic data could be used to predict site-directed mutant phenotypes, which may broaden the classic antireceptor definition to include interfaces between capsid complexes.

Optimization of triacetate cellulose hollow fiber vitrification (HFV) method for cryopreservation of in vitro matured bovine oocytes.

The aim of the current work was to evaluate applicability of triacetate cellulose hollow fiber vitrification (HFV) method for cryopreservation of groups of in vitro matured bovine oocytes (12-17 oocytes per device). We also attempted to optimize HFV protocol by altering concentration of non-permeating cryoprotectant (sucrose) in vitrification solution and concentration of extracellular Ca2+ by using a calcium-free base medium for preparation of vitrification/rewarming solutions with ethylene glycol (EG) as a single permeating cryoprotectant. Neither of modifications of HFV protocol significantly affected survival or fertilization rates of the vitrified bovine oocytes. Embryo development rates in the vitrification groups were lower than those in the control (31.2% of blastocysts at Day 8 post IVF). Use of vitrification/rewarming solutions with lower Ca2+ concentration and EG did not significantly improve embryo development rates. An increase of sucrose concentration in vitrification solution from 0.5 to 1.0 M significantly improved blastocyst yield on Day 8 post IVF (21.1-23.4% vs 3.1-3.5%; p < 0.05). Obtained results indicated that sufficient dehydration of the oocytes and/or the solution surrounding them in hollow fiber before immersion into liquid nitrogen is an important factor for successful vitrification. Use of HFV method allowed simplification and standardization of vitrification/rewarming procedures. Triacetate cellulose hollow fibers can be used successfully for cryopeservation of groups of in vitro matured bovine oocytes.

Salting out in organic solvents: a new route to carbon nanotube bundle engineering.

In this study we investigate salt effects on bundle formation of carbon nanotubes (CNTs) dispersed in an organic solvent, N-methyl-2-pyrrolidone (NMP). Addition of NaI salt leads to self-assembly of CNTs into well-recognizable bundles. It is possible to control the size of the CNT bundles by varying the salt concentration.

Predicting Functions of Uncharacterized Human Proteins: From Canonical to Proteoforms.

Despite tremendous efforts in genomics, transcriptomics, and proteomics communities, there is still no comprehensive data about the exact number of protein-coding genes, translated proteoforms, and their function. In addition, by now, we lack functional annotation for 1193 genes, where expression was confirmed at the proteomic level (uPE1 proteins). We re-analyzed results of AP-MS experiments from the BioPlex 2.0 database to predict functions of uPE1 proteins and their splice forms. By building a protein-protein interaction network for 12 ths. identified proteins encoded by 11 ths. genes, we were able to predict Gene Ontology categories for a total of 387 uPE1 genes. We predicted different functions for canonical and alternatively spliced forms for four uPE1 genes. In total, functional differences were revealed for 62 proteoforms encoded by 31 genes. Based on these results, it can be carefully concluded that the dynamics and versatility of the interactome is ensured by changing the dominant splice form. Overall, we propose that analysis of large-scale AP-MS experiments performed for various cell lines and under various conditions is a key to understanding the full potential of genes role in cellular processes.

α-Cyclodextrin/aminobenzoic acid binding in salt solutions at different pH: dependence on guest structure.

Influence of Na(+) and K(+) cations on α-cyclodextrin guest-host complex formation with isomeric aminobenzoic acids was examined at different pH and temperature of 298.15 K by (1)H NMR and calorimetry methods. More pronounced influence of Na(+) on inclusion complex formation of α-CD with aminobenzoic acid anions compare to the effects of Na(+) on α-CD complex formation with zwitterionic aminobenzoic acid molecules was revealed. For the first time, the dependence of salt effects on the structure, ionization and the hydration state of the guest molecule was demonstrated and analysed on the basis of the obtained thermodynamic parameters of complex formation and calculated free energy of hydration of different ionized forms of aminobenzoic acids.

Molecular sinkers: X-ray photoemission and atomistic simulations of benzoic acid and benzoate at the aqueous solution/vapor interface.

In this work, we provide a detailed microscopic picture of the behavior of benzoic acid at the aqueous solution/vapor interface in its neutral as well as in its dissociated form (benzoate). This is achieved through a combination of highly surface-sensitive X-ray photoelectron spectroscopy experiments and fully atomistic molecular simulations. We show that significant changes occur in the interface behavior of the neutral acid upon release of the proton. The benzoic acid molecules are found to be strongly adsorbed at the interface layer with the planes of the aromatic rings oriented almost parallel to the water surface. In contrast, in the benzoate form, the carboxylate group shows a sinker-like behavior while the aromatic ring acts as a buoy, oriented nearly perpendicular to the surface. Furthermore, a significant fraction of the molecular ions move from the interface layer into the bulk of the solution. We rationalize these findings in terms of the very different hydration properties of the carboxylic group in the two charge states. The molecule has an amphiphilic nature, and the deprotonation thus changes the hydrophobic/hydrophilic balance between the nonpolar aromatic and the polar carboxylic parts of the molecule. That, consequently, leads to a pronounced reorientation and depletion of the molecules at the interface.

Selective Na(+)/K(+) effects on the formation of α-cyclodextrin complexes with aromatic carboxylic acids: competition for the guest.

We investigated the effects of K(+) and Na(+) ions on the formation of α-cyclodextrin complexes with ionized aromatic carboxylic acids. Using solution calorimetry and (1)H NMR, we performed the thermodynamic and structural investigation of α-cyclodextrin complex formation with benzoic and nicotinic acids in different aqueous solutions containing K(+) and Na(+) ions as well as in pure water. The experiments show that the addition of sodium ions to solution leads to a decrease in the binding constants of the carboxylic acids with α-cyclodextrin as compared to pure water and solutions containing potassium ions. From another side, the effect of potassium ions on the binding constants is insignificant as compared to pure water solution. We suggest that the selectivity of cation pairing with carboxylates is the origin of the difference between the effects of sodium and potassium ions on complex formation. The strong counterion pairing between the sodium cation and the carboxylate group shifts the equilibrium toward dissociation of the binding complexes. In turn, the weak counterion pairing between the potassium cation and the carboxylate group has no effect on the complex formation. We complemented the experiments with molecular modeling, which shows the molecular scale details of the formation of cation pairs with the carboxylate groups of the carboxylic acids. The fully atomistic molecular simulations show that sodium ions mainly form direct contact pairs with the carboxylate group. At the same time, potassium ions practically do not form direct contact pairs with the carboxylate groups and usually stay in the second solvation shell of carboxylate groups. That confirms our hypotheses that the selective formation of ion pairs is the main cause of the difference in the observed effects of sodium and potassium salts on the guest-host complex formation of α-cyclodextrin with aromatic carboxylic acids. We propose a molecular mechanism explaining the effects of salts, based on competition between the cations and α-cyclodextrin for binding with the ionized carboxylic acids.