Electron flow shift inClostridium acetobutylicum fermentation by electrochemically introduced reducing equivalent

Electrochemical energy as a source of reducing equivalent was applied to the cultures ofClostridum acetobutylicum to understand the effects of the pressure by reducing equivalent on anaerobic bacteria. The fermentation byC. acetobutylicum with methyl viologen and electrochemical energy produced more butanol (up to 26%) than the control culture, whilst less acetone (up to 25%) was produced. But no effect was observed on the growth of the culture. These results were indirectly supported byin vitro electrochemical reduction of NAD⁺ and artificial electron carriers.     

Energy distribution in the photochemical apparatus of Porphyridium cruentum: Picosecond fluorescence spectroscopy of cells in state 1 and state 2 at 77 K

Excitation energy distribution in Porphyridium cruentum in state 1 and state 2 was investigated by time resolved 77 K fluorescence emission spectroscopy. The fluorescence rise times of phycoerythrin, phycocyanin and allophycocyanin (in cells in state 1 and state 2) were very similar in contrast to the emission from chlorophyll a (Chl a) associated with the two photosystems. In state 2 photosystem II (PSII) Chl a fluorescence emission rose faster than the PSI Chl a emission and decayed more rapidly, and the converse was observed in state 1. These kinetic data support the concept of increased energy transfer from PSII Chl a to PSI Chl a in state 2 in P. cruentum.Abbreviations APC allophycocyanin - Chl a chlorophyll a - PSII photosystem II - PC phycocyanin - PE phycoerythrin     

The value of fat reserves and the tradeoff between starvation and predation

It is shown that in a range of models, the probability that a forager dies from starvation is, to a good approximation, an exponential function of energy reserves. Using a time and energy budget for a 19g passerine, we explore the consequences, in terms of starvation and predation, of various levels of energy reserves. It is shown that there exists an optimal level L of reserves at which total mortality (starvation plus predation) is minimized. L increases when the environment deteriorates as a result of a decrease in either temperature or mean gross gain or an increase in the mean search time. The effect of combined deteriorations is greater than the sum of their individual effects. At L, the probability of predation is much higher than the probability of starvation. A simple analytic model suggests that this result will be fairly general, but also indicates conditions under which the result might not hold.     

Radiationless transitions as a protection mechanism against photoinhibition in higher plants and a red alga

Exposure of the red alga Porphyra perforata or leaves of Phytolacca americana and Echinodorus sp. to white light equivalent to full sunlight for short periods induced large decreases of variable fluorescence measured at 695 nm at 77K. This change was not produced by photoinhibition but rather appeared to result from an inorease in the rate constant of radiationless transition in the reaction centers of photosystem II. It is proposed that this increase is related to the formation of the high energy state which serves as a photoprotective mechanism in plants.     

Conformations of cyclic 3',5'-nucleotides. Effect of the base on the synanti conformer distribution

The furanose and the phosphate rings of cyclic 3′,5′-nucleotides are locked in the ₄T³ and chair conformations respectively. The only variable which shows major conformational flexibility in these molecules is the rotation about the glycosyl bond which describes the orientation of the base relative to the sugar-phosphate bicyclic system. The glycosyl torsion angle has been analyzed for cyclic nucleotides with different purine and pyrimidine bases by use of conformational energy calculations. The results indicate that all the pyrimidine bases, U, T and C show a very strong energetic preference for the anti range of conformations. The calculations predict that among cyclic 3′,5′-purine nucleotides cyclic GMP and cyclic IMP favor the syn conformation to the anti by 95:5 and 70:30 respectively, while cyclic AMP shows a preference for the anti conformation to syn by 70:30. Thus the purines show a greater probability for the syn conformation than the pyrimidines in cyclic 3′,5′-nucleotides.     

Mitochondrial K + transport: effect of N-ethyl maleimide on 42 K flux

The energy-linked flux of K⁺ into rat liver mitochondria is found to be stimulated by the sulfhydryl reagent, N-ethyl maleimide. The stimulation of K⁺ influx by N-ethyl maleimide is observed only at alkaline external pH. N-ethyl maleimide also stimulates efflux of K⁺ from the mitochondria. The stimulation by N-ethyl maleimide of K⁺ influx, but not K⁺ efflux, is dependent on the availability of metabolic energy. It is suggested that the effect of N-ethyl maleimide on K⁺ influx may be secondarily the result of an inhibition of phosphate-hydroxyl exchange. The dependence of energy-linked K⁺ influx on the external pH may be interpreted as evidence for a role of OH^? as a counterion accompanying K⁺ through the mitochondrial pump mechanism.     

Bioconversion of hydrogen sulfide by free and immobilized cells ofChlorobium thiosulfatophilum

Summary The transformation of hydrogen sulfide into elementary sulfur and sulfate was investigated in a photo-bioreactor using autotropic bacteriaChlorobium thiosulfatophilum. The accumulations of sulfur and sulfate in the reactor were found to be dependent on the light energy and the feed rate of H₂S. The optimum operation lines were established to limit sulfide or sulfate. Immobilization of the whole cells in strontium-alginate matrix enhanced the conversion more than with the free cells.     

Danggui Buxue Tang,a Chinese herbal decoction containing Astragali Radix and Angelicae Sinensis Radix,improves mitochrondial bioenergetics in osteoblast

Osteoporosis is the process of bone loss, particular after menopause, when the production of estrogen in women is decreaing. Bioenergetic function is one of the critical roles in bone remodeling. Danggui Buxue Tang (DBT) is an herbal mixture containing Astragali Radix (AR) and Angelicae Sinensis Radix (ASR), and which is consumed for “Qi-invigorating”, i.e., stimulating energy metabolism, as a traditional Chinese medicine (TCM). However, the role of DBT in metabolism of osteoblast has not been examined. Here, we employed a metabolic flux to examine the mitochondrial functions of cultured osteoblast in the presence of herbal extracts, including DBT, ASR, AR, AR + ASR (single mixing of two herbal extracts), as well as DBT_∆cal (a DBT extract depeleting calycosin), to examine their roles in osteoblastic metabolism, e.g. glycolysis and energy kinetics. By revealing the rates of oxygen consumption and extracellular acidification of mitochrondia, the DBT-treated osteoblasts were markedly strengthened with increases of maximal respiration, spare capacity, glycolysis capacity and glycolysis reserve, in comparing to other herbal extracts. In addition, the bioenergetic metabolism was modulated by DBT via the signaling of cellular Ca²⁺ and reactive oxgen species (ROS). Furthermore, DBT affected the morphology of mitochondria, as well as mitochondrial dynamic. Here, we propose that DBT can be regarded as benefit herbal extract in improving osteoblastic metabolism for bone disorders via central energy metabolism and mitochondrial bioenergetics.     

Extensive remodeling of the photosynthetic apparatus alters energy transfer among photosynthetic complexes when cyanobacteria acclimate to far-red light

Some cyanobacteria remodel their photosynthetic apparatus by a process known as Far-Red Light Photoacclimation (FaRLiP). Specific subunits of the phycobilisome (PBS), photosystem I (PSI), and photosystem II (PSII) complexes produced in visible light are replaced by paralogous subunits encoded within a conserved FaRLiP gene cluster when cells are grown in far-red light (FRL; λ = 700–800 nm). FRL-PSII complexes from the FaRLiP cyanobacterium, Synechococcus sp. PCC 7335, were purified and shown to contain Chl a, Chl d, Chl f, and pheophytin a, while FRL-PSI complexes contained only Chl a and Chl f. The spectroscopic properties of purified photosynthetic complexes from Synechococcus sp. PCC 7335 were determined individually, and energy transfer kinetics among PBS, PSII, and PSI were analyzed by time-resolved fluorescence (TRF) spectroscopy. Direct energy transfer from PSII to PSI was observed in cells (and thylakoids) grown in red light (RL), and possible routes of energy transfer in both RL- and FRL-grown cells were inferred. Three structural arrangements for RL-PSI were observed by atomic force microscopy of thylakoid membranes, but only arrays of trimeric FRL-PSI were observed in thylakoids from FRL-grown cells. Cells grown in FRL synthesized the FRL-specific complexes but also continued to synthesize some PBS and PSII complexes identical to those produced in RL. Although the light-harvesting efficiency of photosynthetic complexes produced in FRL might be lower in white light than the complexes produced in cells acclimated to white light, the FRL-complexes provide cells with the flexibility to utilize both visible and FRL to support oxygenic photosynthesis.This article is part of a Special Issue entitled Light harvesting, edited by Dr. Roberta Croce.     

Selective substrate uptake: The role of ATP-binding cassette (ABC) importers in pathogenesis

The uptake of nutrients, including metals, amino acids and peptides are required for many biological processes. Pathogenic bacteria scavenge these essential nutrients from microenvironments to survive within the host. Pathogens must utilize a myriad of mechanisms to acquire these essential nutrients from the host while mediating the effects of toxicity. Bacteria utilize several transport proteins, including ATP-binding cassette (ABC) transporters to import and expel substrates. ABC transporters, conserved across all organisms, are powered by the energy from ATP to move substrates across cellular membranes. In this review, we will focus on nutrient uptake, the role of ABC importers at the host–pathogen interface, and explore emerging therapies to combat pathogenesis. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain.     

Some characteristics of the cellulase of Aspergillus candidus

Summary The effects of pH, temperature and substrate concentration on the cellulase (B-1,4-endoglucanase) activity ofA. candidus were studied. Maximum enzyme activities were obtained when the concentration of the substrate (CMC) was 6 mg per ml, at pH 4, and temperature 50 C. The enzyme retained 85% of its original activity under optimal conditions of pH and temperature after 36 hours of incubation. The Km constant of the reaction was calculated as 2.3 mg of CMC per ml and the energy of activation of the enzyme as 7.92 k cal per mole.     

Phosphorus-31 NMR of rat brain in vivo with bloodless perfluorocarbon perfused rat

Rat brain in vivo has been examined by ³¹p NMR under conditions of normal blood perfusion (hematocrit 38%) and under conditions in which a perfluorocarbon blood substitute, devoid of any phosphorus containing compounds, largely replaced the animal's normal blood supply (hematocrit 7%). These studies demonstate that 2,3-diphosphoglycerate does not — as has been suggested — contribute to, and thus does not interfere with, the ³¹p NMR analysis of rat brain in vivo. However, low intensity ³¹P resonances assigned to choline phosphate, glycerol 3-phosphorylethanolamine, and glycerol 3-phosphorylcholine are observed. “High energy phosphorus” metabolite levels show no marked change over two hours with perfluorocarbon blood substitution from those of the normal blood perfused animal. This supports use of perfluorocarbon media for tissue perfusion in vitro and for ¹⁹F NMR vascular imaging in vivo.     

Isolation and characterization of a symbiotic cellulolytic mixed bacterial culture

Summary By using batch-culture enrichment techniques a mixed culture of two bacterial spe cies identified as Cellulomonas flavigena and Xanthomonas sp was isolated. The capacity of both bacteria to grow as pure cultures in a min eral medium with alkaline pretreated sugar cane bagasse or cellobiose was tested. C. flavigena as pure culture was able to grow on both substrates only when yeast extract or biotin and thiamine were added to the culture medium, while Xanthomonas sp. could not grow on sugar cane ba gasse, but assimilated cellobiose if yeast extract was supplied. However, both bacteria in mixed culture grew very well on both substrates and did not require any growth factor. It was concluded that the interaction was favourable to both species. The mixed culture had the capacity to degrade a number of different agricul tural wastes and to use them as the sole carbon and energy source for the production mainly of biomass. More than 80% of pineapple bagasse, without chemical pretreatment, was used up by the microbial system.     

Ethanol production byZymomonas mobilis in continuous culture at high glucose concentrations

Summary Ethanol production byZ.mobilis has been studied in continuous culture with 10, 15 and 20% glucose media. At 10% glucose, steady state conditions were achieved under glucose-limited conditions. At 15 and 20% glucose, the glucose was not fully metabolized even at low dilution rates and oscillatory behavior was evident. It is proposed that ethanol inhibition of growth is responsible for these phenomena. Comparison of kinetic parameters with those from previously published batch data revealed similar values. The maintenance energy coefficient (m) forZ.mobilis was relatively high and was calculated as 1.6 g/g/h for 10% glucose and 3.1 g/g/h for 15% glucose.     

Isolation and characterization of a novel bacterium, <Emphasis Type="Italic">Sphingomonas bisphenolicum</Emphasis> strain AO1, that degrades bisphenol A

Bisphenol A (2,2-bis(4-hydroxyphenyl) propane, BPA), which is used as a synthetic resin material or a plasticizer, is a pollutant that␣possesses endocrine-disrupting activity. Bioremediation of BPA is used to decrease its polluting effects, and here we report a novel bacterial strain AO1, which is able to degrade BPA. This strain was isolated using enrichment cultivation from a soil sample from a vegetable-growing field; the sample was one of 500 soil samples collected across Japan. Strain AO1 degraded 100 mg/l BPA to an undetectable level within 6 h in MYPG medium (containing malt extract, yeast extract, peptone, and glucose) and within 48 h in minimum medium containing 1% glucose at 30°C. Strain AO1 can utilize BPA as a sole source of carbon and as an energy source under aerobic conditions. The estrogenic activity of BPA in MYPG medium was ultimately reduced by strain AO1, although the activity initially increased. Taxonomical analysis showed that strain␣AO1 is closely related to Sphingomonas chlorophenolicum and S. herbicidovorans, neither of which have a capacity for BPA degradation. DNA–DNA hybridization showed that strain AO1 is a novel species of the Sphingomonas genus, and we designated AO1 as S. bisphenolicum.     

Validation of inhibitors of an ABC transporter required to transport lipopolysaccharide to the cell surface in Escherichia coli

The presence of lipopolysaccharide (LPS) in the outer leaflet of the outer membrane (OM) of Gram-negative bacteria creates a permeability barrier that prevents the entry of most currently available antibiotics. The seven lipopolysaccharide transport (Lpt) proteins involved in transporting and assembling this glycolipid are essential for growth and division in Escherichia coli; therefore, inhibiting their functions leads to cell death. LptB, the ATPase that provides energy for LPS transport and assembly, forms a complex with three other inner membrane (IM) components, LptC, F, and G. We demonstrate that inhibitors of pure LptB can also inhibit the full IM complex, LptBFGC, purified in detergent. We also compare inhibition of LptB and the LptBFGC complex with the antibiotic activity of these compounds. Our long-term goal is to develop tools to study inhibitors of LPS biogenesis that could serve as potentiators by disrupting the OM permeability barrier, facilitating entry of clinically used antibiotics not normally used to treat Gram-negative infections, or that can serve as antibiotics themselves.     

Metalloprotease ADAMTS-1 decreases cell migration and invasion modulating the spatiotemporal dynamics of Cdc42 activity

ADAMTSs (A Disintegrin And Metalloproteinase with ThromboSpondin motifs) are secreted proteases dependent on Zn²⁺/Ca²⁺, involved in physiological and pathological processes and are part of the extracellular matrix (ECM). Here, we investigated if ADAMTS-1 is required for invasion and migration of cells and the possible mechanism involved. In order to test ADAMTS-1's role in ovarian cancer cells (CHO, NIH-OVCAR-3 and ES2) and NIH-3 T3 fibroblasts, we modified the levels of ADAMTS-1 and compared those to parental. Cells exposed to ADAMTS-1-enriched medium exhibited a decline in cell migration and invasion when compared to controls with or without a functional metalloproteinase domain. The opposite was observed in cells when ADAMTS-1 was deleted via the CRISPR/Cas9 approach. The decline in ADAMTS-1 levels enhanced the phosphorylated form of Src and FAK. We also evaluated the activities of cellular Rho GTPases from cell lysates using the GLISA® kit. The Cdc42-GTP signal was significantly increased in the CRISPR ADAMTS-1 ES-2 cells. By a Förster resonance energy transfer (FRET) biosensor for Cdc42 activity in ES-2 cells we demonstrated that Cdc42 activity was strongly polarized at the leading edge of migrating cells with ADAMTS-1 deletion, compared to the wild type cells. As conclusion, ADAMTS-1 inhibits proliferation, polarization and migration.     

Dynamic docking of small molecules targeting RNA CUG repeats causing myotonic dystrophy type 1

Expansion of RNA CUG repeats causes myotonic dystrophy type 1 (DM1). Once transcribed, the expanded CUG repeats strongly attract muscleblind-like 1 (MBNL1) proteins and disturb their functions in cells. Because of its unique structural form, expanded RNA CUG repeats are prospective drug targets, where small molecules can be utilized to target RNA CUG repeats to inhibit MBNL1 binding and ameliorate DM1-associated defects. In this contribution, we developed two physics-based dynamic docking approaches (DynaD and DynaD/Auto) and applied them to nine small molecules known to specifically target RNA CUG repeats. While DynaD uses a distance-based reaction coordinate to study the binding phenomenon, DynaD/Auto combines results of umbrella sampling calculations performed on 1 × 1 UU internal loops and AutoDock calculations to efficiently sample the energy landscape of binding. Predictions are compared with experimental data, displaying a positive correlation with correlation coefficient (R) values of 0.70 and 0.81 for DynaD and DynaD/Auto, respectively. Furthermore, we found that the best correlation was achieved with MM/3D-RISM calculations, highlighting the importance of solvation in binding calculations. Moreover, we detected that DynaD/Auto performed better than DynaD because of the use of prior knowledge about the binding site arising from umbrella sampling calculations. Finally, we developed dendrograms to present how bound states are connected to each other in a binding process. Results are exciting, as DynaD and DynaD/Auto will allow researchers to utilize two novel physics-based and computer-aided drug-design methodologies to perform in silico calculations on drug-like molecules aiming to target complex RNA loops.     

Function of Y in codon-anticodon interaction of tRNA Phe

Molar association constants of binding oligonucleotides to the anticodon loops of (yeast) tRNA^Phe, (yeast) tRNA_HCl^Phe and (E. coli) tRNA_F^Met have been determined by equilibrium dialysis. From the temperature dependence of the molar association constants, ΔF, ΔH and ΔS of oligomer-anticodon loop interaction have been determined. The data indicate that the free energy change of codon-anticodon interaction is highly influenced by the presence of a modified purine (tRNA^Phe), of an unmodified purine (tRNA_F^Met) or its absence (tRNA_HCl^Phe). Excision of the modified purine Y in the anticodon loop of tRNA^Phe results in a conformational change of the anticodon loop, which is discussed on the basis of the corresponding changes in ΔF, ΔH and ΔS.     

Gelatin-entrapped whole-cell invertase

Summary The investigated biocatalyst consists of gelatin-entrapped cells of Saccharomyces cerevisiae retaining invertase activity. Comparative examination of pH profile, apparent K_m, saturation velocity and activation energy indicates that the entrapment procedure did not influence invertase affinity with sucrose but lead to some loss of activity probably due to either enzyme inactivation or cell-wall impairment as well as to substrate diffusion limitation in the gel matrix.