Antibacterial Efficacy of Dihydroxylated Chalcones in Binary and Ternary Combinations with Nalidixic Acid and Nalidix Acid–Rutin Against Escherichia coli ATCC 25 922

In order to determine the existence of synergism, the bacteriostatic action of flavonoids against Escherichia coli ATCC 25 922 between dihydroxylated chalcones and a clinically interesting conventional antibiotic, binary combinations of 2′,3-dihydroxychalcone, 2′,4-dihydroxychalcone and 2′,4′-dihydroxychalcone with nalidixic acid and its ternary combinations with rutin (inactive flavonoid) were assayed against this Gram negative bacterium. Using a kinetic-turbidimetric method, growth kinetics were monitored in broths containing variable amounts of dihydroxychalcone alone, combinations of dihydroxychalcone variable concentration–nalidixic acid constant concentration and dihydroxychalcone variable concentration–nalidixic acid constant concentration–rutin constant concentration, respectively. The minimum inhibitory concentrations of dihydroxychalcones alone and its binary and ternary combinations were evaluated. All chalcones, and their binary and ternary combinations showed antibacterial activity, being rutin an excellent synergizing for the dihydroxychalcone–nalidixic acid binary combination against E. coli ATCC 25 922. Thus, this synergistic effect is an important way that could lead to the development of new combination antibiotics against infections caused by E. coli.     

An in vivo selection method to optimize trans-splicing ribozymes

Group I intron ribozymes can repair mutated mRNAs by replacing the 3′-terminal portion of the mRNA with their own 3′-exon. This trans-splicing reaction has the potential to treat genetic disorders and to selectively kill cancer cells or virus-infected cells. However, these ribozymes have not yet been used in therapy, partially due to a low in vivo trans-splicing efficiency. Previous strategies to improve the trans-splicing efficiencies focused on designing and testing individual ribozyme constructs. Here we describe a method that selects the most efficient ribozymes from millions of ribozyme variants. This method uses an in vivo rescue assay where the mRNA of an inactivated antibiotic resistance gene is repaired by trans-splicing group I intron ribozymes. Bacterial cells that express efficient trans-splicing ribozymes are able to grow on medium containing the antibiotic chloramphenicol. We randomized a 5′-terminal sequence of the Tetrahymena thermophila group I intron and screened a library with 9 × 10⁶ ribozyme variants for the best trans-splicing activity. The resulting ribozymes showed increased trans-splicing efficiency and help the design of efficient trans-splicing ribozymes for different sequence contexts. This in vivo selection method can now be used to optimize any sequence in trans-splicing ribozymes.     

Positive and negative tandem mass spectrometric fingerprints of lipids from the halophilic Archaea Haloarcula marismortui

Lipids from the extremely halophilic Archaea, Haloarcula marismortui, contain abundant phytanyl diether phospholipids, namely archaetidic acid (AA), archaetidylglycerol (AG), archaetidylglycerosulfate (AGS), with mainly archaetidylglycerophosphate methyl ester (AGP-Me). These were accompanied by a triglycosyl archaeol (TGA), lacking characteristic sulfate groups. Tandem-mass spectrometry was employed to provide fingerprints for identifying these known lipids, as well as small amounts of unsaturated phospholipids. These contained 3 and 6 double bonds in their archaeol moiety, suggested by negative tandem-MS of intact phospholipids, as indicated by differences between their pseudo-molecular ion and specific fragment ions designated as π₂. The core ether lipids were confirmed by electrospray ionization mass spectrometry (ESI-MS) as 2,3-di-O-phytanyl-sn-glycerol (C20, C20), which gave rise to a precursor-ion at m/z 660 [M+Li]⁺, and its fragment ion at m/z 379 [M+Li]⁺, consistent with mono-O-phytanyl-glycerol. Furthermore, lithiated ions at m/z 654 (MS¹), 379 (MS²) and m/z 648 (MS¹), 373 (MS²), combined with ¹H/¹³C NMR chemical shifts at δ 5.31-121.6 (C2/2′-H2/2′), 5.08-124.9 (C6/6′-H6/6′) and 5.10-126.0 (10/10′-H10/10′) confirmed the presence of unsaturated homologs of archaeol. We carried out a comprehensive study on the lipids present in cells of H. marismortui. We used positive and negative ESI-MS with tandem-MS, which served as a fingerprint analysis for identifying the majority of component lipids.     

Synergistic effect of BAP and GA3 on in vitro flowering of Guizotia abyssinica Cass.-A multipurpose oil crop

Apical and axillary buds of Guizotia abyssinica Cass., isolated from seedlings raised in vitro, were cultured. High frequency of shoot regeneration was achieved on MS medium with BAP (1 mgl⁻¹). Effect of BAP, Kn and GA₃ applied successively in culture on shoot regeneration and flower bud formation has been studied. The shoots differentiated in cultures elongated on this medium. These rooted subsequently on half strength MS medium. The shoots flowered in vitro on MS medium with a combination of BAP (0.1mgl⁻¹) + GA₃ (0.1 mgl⁻¹). The plantlets thus formed were successfully hardened with 90 % survival.     

Preparation of selective and segmentally labeled single-stranded DNA for NMR by self-primed PCR and asymmetrical endonuclease double digestion

We demonstrate a new, efficient and easy-to-use method for enzymatic synthesis of (stereo-)specific and segmental ¹³C/¹⁵N/²H isotope-labeled single-stranded DNA in amounts sufficient for NMR, based on the highly efficient self-primed PCR. To achieve this, new approaches are introduced and combined. (i) Asymmetric endonuclease double digestion of tandem-repeated PCR product. (ii) T4 DNA ligase mediated ligation of two ssDNA segments. (iii) In vitro dNTP synthesis, consisting of in vitro rNTP synthesis followed by enzymatic stereo-selective reduction of the C2′ of the rNTP, and a one-pot add-up synthesis of dTTP from dUTP. The method is demonstrated on two ssDNAs: (i) a 36-nt three-way junction, selectively ¹³C₉/¹⁵N₃/²H_{(1′,2″,3′,4′,5′,5″)}-dC labeled and (ii) a 39-nt triple-repeat three-way junction, selectively ¹³C₉/¹⁵N₃/²H_{(1′,2″,3′,4′,5′,5″)}-dC and ¹³C₉/¹⁵N₂/²H_{(1′,2″,3′,4′,5′,5″)}-dT labeled in segment C20-C39. Their NMR spectra show the spectral simplification, while the stereo-selective ²H-labeling in the deoxyribose of the dC-residues, straightforwardly provided assignment of their C1′–H2′ and C2′–H2′ resonances. The labeling protocols can be extended to larger ssDNA molecules and to more than two segments.     

Improved replication of the baculovirus Anticarsia gemmatalis nucleopolyhedrovirus (AgMNPV) in vitro using proteins from Lonomia obliqua hemolymph

The baculovirus Anticarsia gemmatalis nucleopolyhedrovirus (AgMNPV), a member of the family Baculoviridae, has been widely applied as a biopesticide for the control of the velvetbean caterpillar, a pest of soybean crop field. Baculoviruses are considered safe and efficient agents for this purpose, because they do not infect vertebrates, being safe for the health of humans and animals, as well as to the environment. The objective of this work was to identify proteins obtained from Lonomia obliqua hemolymph with potential application in the optimization of baculovirus AgMNPV replication in Sf9 insect cell culture. In this work the improvement of the cell culture and viral replication of the AgMNPV baculovirus was observed when Grace medium was supplemented with 10 % (v/v) Fetal Bovine Serum (FBS), 1 % (v/v) hemolymph extract, or 3 % (v/v) of hemolymph fractions or hemolymph sub-fractions obtained by purifying hemolymph through High Performance Liquid Chromatography. Hemolymph presented a positive effect on the synthesis of polyhedra and enhanced baculovirus replication in Spodoptera frugiperda (Sf9) cells (TCID₅₀/mL), and led to Sf9 cell culture improvement. Grace medium supplemented with 10 % (v/v) FBS and 1 % (v/v) hemolymph provided an increase of baculovirus replication, when the cells were infected with multiplicity of infection of 1. In this case, the baculovirus replication was 6,443.91 times greater than that obtained with the control: Grace medium supplemented with 10 % (v/v) FBS. In addition, this work suggests that hemolymph from L. obliqua could have an interesting application in biotechnology, due to an increase in the viability of the cells and virus replication.     

Characterization of growth and Oryctes rhinoceros nudivirus production in attached cultures of the DSIR-HA-1179 coleopteran insect cell line

The DSIR-HA-1179 coleopteran cell line is a susceptible and permissive host to the Oryctesrhinoceros nudivirus (OrNV), which has been used as a biocontrol agent against the coconut rhinoceros beetle (Oryctes rhinoceros); a pest of palms in the Asia-Pacific region. However, little is known about growth and metabolism of this cell line, knowledge of which is necessary to develop an in vitro large-scale OrNV production process. The strong anchorage-dependent characteristics of the cell line, its particular fragility and its tendency to form dense clumps when manipulated, are the most likely reasons that have precluded further development of the cell line. In order to characterize DSIR-HA-1179 cells, there was first a need for a reliable technique to count the cells. A homogenous cell suspension suitable for enumeration could be produced by treatment with TrypLE Express™ with optimum mean time for cell release calculated as 30 min. The cell line was adapted to grow in four serum-supplemented culture media namely TC-100, IPL-41, Sf-900 II and Sf-900 III and cell growth, glucose consumption, lactate and ammonia production were assessed from static-batch cultures. The maximum viable cell density was reached in Sf-900 II (17.9 × 10⁵ cells/ml), with the maximum specific growth rate observed in this culture medium as well (0.0074 h⁻¹). Higher production of OrNV was observed in IPL-41 and TC-100 (4.1 × 10⁷ TCID₅₀/ml) than in cultures infected in Sf-900 III (2.0 × 10⁷ TCID₅₀/ml) and Sf-900 II (1.4 × 10⁷ TCID₅₀/ml). At the end of the growth period, glucose was completely consumed in cultures grown in TC-100, while remained in excess in the other three culture media. The cell line produced lactate and ammonia to very low levels in the TC-100 culture medium which is a promising aspect for its cultivation at large-scale.     

Cloning of a Family 11 Xylanase Gene from Bacillus amyloliquefaciens CH51 Isolated from Cheonggukjang

Bacillus amyloliquefaciens CH51, an isolate from cheonggukjang, Korean fermented soyfood, secretes several enzymes into culture medium. A gene encoding 19 kDa xylanase was cloned by PCR. Sequencing showed that the gene encoded a glycohydrolase family 11 xylanase and named xynA. xynAHis, xynA with additional codons for his-tag, was overexpressed in Escherichia coli BL21(DE3) using pET-26b(+). XynAHis was purified using HisTrap affinity column. K_m and V_max of XynAHis were 0.363 mg/ml and 701.1 μmol/min/mg, respectively with birchwood xylan as a substrate. The optimum pH and temperature were pH 4 and 25 °C, respectively. When xynA was introduced into Bacillus subtilis WB600, active XynA was secreted into culture medium.     

A temporary immersion system improves in vitro regeneration of peach palm through secondary somatic embryogenesis

Background and Aims

Secondary somatic embryogenesis has been postulated to occur during induction of peach palm somatic embryogenesis. In the present study this morphogenetic pathway is described and a protocol for the establishment of cycling cultures using a temporary immersion system (TIS) is presented.

Methods

Zygotic embryos were used as explants, and induction of somatic embryogenesis and plantlet growth were compared in TIS and solid culture medium. Light microscopy, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were used to describe in vitro morphogenesis and accompany morpho-histological alterations during culture.

Key Results

The development of secondary somatic embryos occurs early during the induction of primary somatic embryos. Secondary somatic embryos were observed to develop continually in culture, resulting in non-synchronized development of these somatic embryos. Using these somatic embryos as explants allowed development of cycling cultures. Somatic embryos had high embryogenic potential (65·8 ± 3·0 to 86·2 ± 5·0 %) over the period tested. The use of a TIS greatly improved the number of somatic embryos obtained, as well as subsequent plantlet growth. Histological analyses showed that starch accumulation precedes the development of somatic embryos, and that these cells presented high nucleus/cytoplasm ratios and high mitotic indices, as evidenced by DAPI staining. Morphological and SEM observations revealed clusters of somatic embryos on one part of the explants, while other parts grew further, resulting in callus tissue. A multicellular origin of the secondary somatic embryos is hypothesized. Cells in the vicinity of callus accumulated large amounts of phenolic substances in their vacuoles. TEM revealed that these cells are metabolically very active, with the presence of numerous mitochondria and Golgi apparatuses. Light microscopy and TEM of the embryogenic sector revealed cells with numerous amyloplasts, large nuclei and nucleoli, and numerous plasmodesmata. Plantlets were obtained and after 3 months in culture their growth was significantly better in TIS than on solid culture medium. However, during acclimatization the survival rate of TIS-grown plantlets was lower.

Conclusions

The present study confirms the occurrence of secondary somatic embryos in peach palm and describes a feasible protocol for regeneration of peach palm in vitro. Further optimizations include the use of explants obtained from adult palms and improvement of somatic embryo conversion rates.     

Non-synonymous polymorphisms in the P2RX 4 are related to bone mineral density and osteoporosis risk in a cohort of Dutch fracture patients

In the present study we investigated whether single nucleotide polymorphisms (SNPs) in the P2RX₄, which alter the P2X₄R function, are associated with the development of osteoporosis and whether an interaction between the P2X₄R and P2X₇R confer a synergistic effect of these two receptors on osteoporosis risk. Patients with fracture (690 females and 231 males, aged ≥50 years) were genotyped for three non-synonymous P2X₄R SNPs. Bone mineral density (BMD) was measured at the total hip, lumbar spine, and femoral neck. Subject carrying the variant allele of the Tyr315Cys polymorphism showed a 2.68-fold (95 % CI, 1.20–6.02) higher risk of osteoporosis compared with wild-type subject. Furthermore, significant lower lumbar spine BMD values were observed in subjects carrying the Cys315 allele as compared with wild-type (0.85 ± 0.17 and 0.93 ± 0.17 g/cm², respectively; p < 0.001). Assuming a recessive model, carriers of the variant allele of the Ser242Gly polymorphism showed increased BMD values at the lumbar spine compare to wild-type subject (1.11 ± 0.35 and 0.92 ± 0.17 g/cm², respectively; p = 0.0045). This is the first study demonstrating an association of non-synonymous polymorphisms in the P2RX₄ and the risk of osteoporosis, suggesting a role of the P2X₄R in the regulation of bone mass.

Electronic supplementary material

The online version of this article (doi:10.1007/s11302-012-9337-0) contains supplementary material, which is available to authorized users.     

A Nematode Growth Factor from Baker's Yeast

An extract prepared from commercially available yeast supported maturation of the free-living nematode Caenorhabditis briggsae. The extract can be used to supplement a chemically defined medium or, after a limited dialysis, as a complete medium. Several biologically active fractions were prepared; those containing larger amounts of ribonucleic acid (RNA) had greater biological activity, the most active being a pellet resuspended after centrifugation at 30,000 × g for 30 min. This fraction could be substituted for serum in a medium which supports the maturation of the animal parasites Trichinella spiralis and Hymenolepis nana. Addition of protamine sulfate decreased the RNA content, leaving inactive protein fractions which could be reactivated by specific treatments that caused protein precipitation. It is postulated that biological activity is associated with protein sedimented with ribosomes.     

Kinetic and Thermodynamic Characterization of Glucoamylase from Colletotrichum sp. KCP1

Extracellular glucoamylase of Colletotrichum sp. KCP1 produced through solid state fermentation was purified by two steps purification process comprising ammonium sulphate precipitation followed by gel permeation chromatography (GPC). The Recovery of glucoamylase after GPC was 50.40 % with 19.3-fold increase in specific activity. The molecular weight of enzyme was found to be 162.18 kDa by native-PAGE and was dimeric protein of two sub-units with molecular weight of 94.62 and 67.60 kDa as determined by SDS-PAGE. Activation energy for starch hydrolysis was 26.45 kJ mol⁻¹ while temperature quotient (Q₁₀) was found to be 1.9. The enzyme was found to be stable over wide pH range and thermally stable at 40–50 °C up to 120 min while exhibited maximum activity at 50 °C with pH 5.0. The pKa₁ and pKa₂ of ionisable groups of active site controlling V_max were 3.5 and 6.8, respectively. V_max, K_m and K_cat for starch hydrolysis were found to be 58.82 U ml⁻¹, 1.17 mg (starch) ml⁻¹ and 449 s⁻¹, respectively. Activation energy for irreversible inactivation (E_a(d)) of glucoamylase was 74.85 kJ mol⁻¹. Thermodynamic parameters of irreversible inactivation of glucoamylase and starch hydrolysis were also determined.     

The influence of cone age on the relative longevity of Banksia seeds

Background and Aims

Serotiny is common in the genus Banksia, so any seed collection is likely to be comprised of seeds that were produced in many different years. This study aimed to determine the impact of cone age and degree of serotiny on longevity in ex situ storage.

Methods

Cones of identifiable age classes were collected from three species of Banksia. Seeds were extracted from cones and the degree of serotiny calculated. An estimate of initial viability (K_i), the time for viability to fall by one probit (σ) and the relative longevity of seeds (p₅₀) for each species and cone age class was determined using a comparative longevity test (50 °C, 63 % relative humidity).

Key Results

The degree of serotiny ranged from moderate (7·9) for Banksia attenuata to strong (40·4) for B. hookeriana. Survival curves for all seed age classes within each species could be described by regressions with a common slope (1/σ), but with different values for K_i. The time taken for viability to fall by one probit (σ) could be described by a common value (29·1 d) for all three species.

Conclusions

Differences in seed longevity between cone age classes and species was related to variation in initial viability (K_i) rather than to differences in σ. While targeting the youngest mature seed cohort on a plant will maximize the viability of seeds collected, a wide range of age classes should be collected (but stored as separate cohorts if possible) for quality conservation/restoration seed collections where genetic diversity is important.     

Root morphology, hydraulic conductivity and plant water relations of high-yielding rice grown under aerobic conditions

Background and Aims

Increasing physical water scarcity is a major constraint for irrigated rice (Oryza sativa) production. ‘Aerobic rice culture’ aims to maximize yield per unit water input by growing plants in aerobic soil without flooding or puddling. The objective was to determine (a) the effect of water management on root morphology and hydraulic conductance, and (b) their roles in plant–water relationships and stomatal conductance in aerobic culture.

Methods

Root system development, stomatal conductance (g_s) and leaf water potential (Ψ_leaf) were monitored in a high-yielding rice cultivar (‘Takanari’) under flooded and aerobic conditions at two soil moisture levels [nearly saturated (> –10 kPa) and mildly dry (> –30 kPa)] over 2 years. In an ancillary pot experiment, whole-plant hydraulic conductivity (soil-leaf hydraulic conductance; K_pa) was measured under flooded and aerobic conditions.

Key Results

Adventitious root emergence and lateral root proliferation were restricted even under nearly saturated conditions, resulting in a 72–85 % reduction in total root length under aerobic culture conditions. Because of their reduced rooting size, plants grown under aerobic conditions tended to have lower K_pa than plants grown under flooded conditions. Ψ_leaf was always significantly lower in aerobic culture than in flooded culture, while g_s was unchanged when the soil moisture was at around field capacity. g_s was inevitably reduced when the soil water potential at 20-cm depth reached –20 kPa.

Conclusions

Unstable performance of rice in water-saving cultivations is often associated with reduction in Ψ_leaf. Ψ_leaf may reduce even if K_pa is not significantly changed, but the lower Ψ_leaf would certainly occur in case K_pa reduces as a result of lower water-uptake capacity under aerobic conditions. Rice performance in aerobic culture might be improved through genetic manipulation that promotes lateral root branching and rhizogenesis as well as deep rooting.     

Optimization of Antimicrobial Production by a Marine Actinomycete Streptomyces afghaniensis VPTS3-1 Isolated from Palk Strait, East Coast of India

Totally 25 marine soil samples were collected from the region of Palk Strait of Bay of Bengal, Tamil Nadu, and were subjected to the isolation of actinomycetes. Sixty-eight morphologically distinct isolates were obtained and 37% (25) of them had antimicrobial activity. The potential producer was named as Streptomyces sp. VPTS3-1 and the phylogenetic evaluation on the basis of 16S rDNA sequence further categorized the organism as Streptomyces afghaniensis VPTS3-1. Further, the antimicrobial compound was extracted from the isolate using various solvents and the antimicrobial efficacies were tested against bacterial and fungal pathogens. In addition, in vitro optimization of parameters for the antimicrobial compound production revealed that the suitable pH as 7–8, the period of incubation as 9 days, temperature (30°C), salinity (2%), and starch and KNO₃ as the suitable carbon and nitrogen sources respectively in starch–casein medium.