Genetic diversity in adult and seedling populations of <Emphasis Type="Italic">Primula vulgaris</Emphasis> in a fragmented agricultural landscape

Habitat fragmentation is known to generally reduce the size of plant populations and increase their isolation, leading to genetic erosion and increased between-population genetic differentiation. In Flanders (northern Belgium) Primula vulgaris is very rare and declining. Populations have incurred strong fragmentation for the last decades and are now restricted to a few highly fragmented areas in an intensively used agricultural landscape. Previous studies showed that small populations of this long-lived perennial herb still maintained high levels of genetic variation and low genetic differentiation. This pattern can either indicate recent gene flow or represent historical variation. Therefore, we used polymorphic microsatellite loci to investigate genetic variation and structure in adult (which may still reflect historical variation) and seedling (recent generation, thus affected by current processes) life stages. The recent generation (seedlings) showed a significant loss of observed heterozygosity (H _o) together with lower expected heterozygosity (H _e), a trend for higher inbreeding levels (F _IS) and higher differentiation (F _ST) between populations compared to the adult generation. This might result from (1) a reduction in effective population size, (2) higher inbreeding levels in the seedlings, (3) a higher survival of heterozygotes over time due to a higher fitness of heterozygotes (heterosis) and/or a lower fitness of homozygotes (inbreeding depression), (4) overlapping generations in the adult life stage, or (5) a lack of establishment of new (inbred) adults from seedlings due to degraded habitat conditions. Combining restoration of both habitat quality and gene flow between populations may be indispensable to ensure a sustainable conservation of fragmented populations.     

Diversity,distribution and host-species associations of epiphytic orchids in Nepal

Associations between epiphytes and their hosts are among the main factors affecting the biodiversity and distribution of epiphytes. While several previous studies explored the association between epiphyte diversity and host characteristics, very little is known about the generality of such associations at larger spatial scales. We aim to explore the associations between diversity and distribution of epiphytic orchids and host characteristics in different localities in Nepal. Epiphytic orchids and their hosts were recorded along the transects in total of 23,539 host individuals. To describe the diversity of orchids in the different localities, a rarefaction function was used. Univariate and multivariate analyses were carried out to explore the associations with locality, host characteristics, and their interactions with locality. In total, we recorded 141 species of orchids growing on 192 host species. The five localities significantly differed in orchid diversity and abundance. The number of orchid individuals per host species significantly increased with increasing number of host individuals. Species richness, abundances, occupancy of orchid species on host species and composition of orchids varied across the localities. Species richness and abundance was significantly higher on hosts in the higher strata and differed between families of host species. Abundance was higher on evergreen hosts. Composition of orchid communities are also associated with host characteristics, such as habit (shrub/tree/climber), bark texture, nature (deciduous/evergreen) and the plant families of host species. This study revealed a high diversity of epiphytic orchids in the localities studied and strong associations between the orchids and their hosts. Future studies looking at the relationships between epiphyte communities and host characteristics need to identify relationships at a wider scale in order to determine whether they are really general rather than site-specific.     

Reformation process of the neuronal template for nestmate-recognition cues in the carpenter ant <Emphasis Type="Italic">Camponotus floridanus</Emphasis>

Ants use cuticular hydrocarbons (CHC-profiles) as multicomponent recognition cues to identify colony members (nestmates). Recognition cues (label) are thought to be perceived during ant–ant encounters and compared to a neuronal template that represents the colony label. Over time, the CHC-profile may change, and the template is adjusted accordingly. A phenotype mismatch between label and template, as happens with CHC-profiles of foreign workers (non-nestmates), frequently leads to aggressive behavior. We investigated the template reformation in workers of the carpenter ant Camponotus floridanus by masking their antennae with postpharyngeal gland (PPG) extracts from nestmates or non-nestmates. The behavioral response of manipulated workers encountering unmanipulated workers was measured independently after 2 and after 15 h. After 2 h of incubation, workers treated with either of the two PPG-extracts showed low aggression towards nestmates and high aggression towards non-nestmates. In contrast, after 15 h of incubation, workers treated with non-nestmate PPG-extract showed low aggression towards both nestmates and non-nestmates. The slow (>2 h) adjustment of the template indicates a reformation localized in the central nervous system rather than in chemosensory neurons. In addition, our data show that template adjustment to a new CHC-profile does not impair the assessment of the old CHC-profile as nestmate label.     

Dynamics and diversity of a microbial community during the fermentation of industrialized <Emphasis Type="Italic">Qingcai</Emphasis> paocai,a traditional Chinese fermented vegetable food,as assessed by Illumina MiSeq sequencing,DGGE and qPCR assay

Paocai is a traditional Chinese fermented food and typically produced via spontaneous fermentation. We have investigated the microbial community utilized for the fermentation of industrialized Qingcai paocai using the combination of Illumina MiSeq sequencing, PCR-mediated denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative PCR (qPCR) assay. Three main phyla, namely Firmicutes, Proteobacteria and Bacteroidetes, were identified by both MiSeq sequencing and PCR-DGGE. The dominant genera observed in the fermentation were Lactobacillus, Pseudomonas, Vibrio and Halomonas. Most genera affiliated with Proteobacteria or Bacteroidetes were detected more often during the earlier part of the fermentation, while Lactobacillus (affiliated with Firmicutes) was dominant during the later fermentation stages. Fungal community analysis revealed that Debaryomyces, Pichia and Kazachstania were the main fungal genera present in industrialized Qingcai paocai, with Debaryomyces being the most dominant during the fermentation process. The quantities of dominant genera Lactobacillus and Debaryomyces were monitored using qPCR and shown to be 10⁹–10¹² and 10⁶–10¹⁰ copies/mL, respectively. During the later fermentation process of industrialized Qingcai paocai, Lactobacillus and Debaryomyces were present at 10¹¹ and 10⁸ copies/mL, respectively. These results facilitate further understanding of the unique microbial ecosystem during the fermentation of industrialized Qingcai paocai and guide future improvement of the fermentation process.     

RNA Interference-Based Transgenic Maize Resistant to Maize Dwarf Mosaic Virus

Maize dwarf mosaic virus (MDMV) is a widespread pathogenic virus that causes serious loss of yield in maize (Zea mays). RNA interference (RNAi) triggered by hairpin RNA (hpRNA) transcribed from a transgenic inverted-repeat sequence is an effective way to defend against viruses in plants. In this study, an hpRNA expression vector containing a sense arm and an antisense arm of 150 bp separated by an intron of the maize actin gene was constructed to target the P1 protein (protease) gene of MDMV and used to transform Agrobacterium tumefaciens strain EHA105. The transformed Agrobacterium strain was used to transform maize embryonic calli isolated from immature embryos by an improved culture technique. In all, 46 plants were regenerated after stringent hygromycin B selection, and 18 of them were certified to be positive by PCR amplification. Of these positive plants, 13 were grown to produce offspring, and nine were identified by Southern blotting to have the transgene integrated with one or two copies. The resistance of three T₂ lines was evaluated in a field trial of dual MDMV inoculation in two environments and was found to be improved compared with the non-transformed control. The disease indexes of the transgenic plant lines h2, 13, and h1 were not significantly different from the highly resistant control line H9-21. The viral titers of the inoculated plants were detected by double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA), and the result was in accord with the resistance evaluated in the field trial. The addition of uniconazole S3307 (0.25 mg l⁻¹) and ABT root-promoting powder (0.5 mg l⁻¹) showed a significant improvement of hardening in regenerated plantlets, which were stronger and generated a better fibrous root system than the control. This improvement could facilitate the transgenic operation of maize.     

Enantiomeric Polyketides from the Starfish‐Derived Symbiotic Fungus Penicillium sp. GGF16‐1‐2

One new racemic mixture, penicilliode A ( 1 ) and four pairs of enantiomeric polyketides, penicilliode B and C ( 2 and 3 ) and coniochaetone B and C ( 4 and 5 ), were obtained from the starfish‐derived symbiotic fungus Penicillium sp. GGF16‐1‐2. Interestingly, the strain GGF16‐1‐2 can produce enantiomers. The absolute configuration of 1 was determined by X‐ray diffraction (XRD) analysis, and the absolute configurations of 2 – 4 were determined by the optical rotation (OR) values and electronic circular dichroism (ECD) calculations. Compounds 1 – 5 were firstly isolated from the marine‐derived fungus Penicillium as racemates, and 2 – 5 were separated by HPLC with a chiral stationary phase. All the compounds were evaluated for their antibacterial, cytotoxic and inhibitory activities against PDE4D2.     

Genome-scale metabolic reconstruction and <Emphasis Type="Italic">in silico</Emphasis> analysis of methylotrophic yeast <Emphasis Type="Italic">Pichia pastoris</Emphasis> for strain improvement

Background  

Pichia pastoris has been recognized as an effective host for recombinant protein production. A number of studies have been reported for improving this expression system. However, its physiology and cellular metabolism still remained largely uncharacterized. Thus, it is highly desirable to establish a systems biotechnological framework, in which a comprehensive in silico model of P. pastoris can be employed together with high throughput experimental data analysis, for better understanding of the methylotrophic yeast's metabolism.     

Anaerobic digestion of secondary residuals from an anaerobic bioreactor at a brewery to enhance bioenergy generation

Many beer breweries use high-rate anaerobic digestion (AD) systems to treat their soluble high-strength wastewater. Biogas from these AD systems is used to offset nonrenewable energy utilization in the brewery. With increasing nonrenewable energy costs, interest has mounted to also digest secondary residuals from the high-rate digester effluent, which consists of yeast cells, bacteria, methanogens, and small (hemi)cellulosic particles. Mesophilic (37 °C) and thermophilic (55 °C) lab-scale, low-rate continuously-stirred anaerobic digestion (CSAD) bioreactors were operated for 258 days by feeding secondary residuals at a volatile solids (VS) concentration of ∼40 g l⁻¹. At a hydraulic retention time (HRT) of 15 days and a VS loading rate of 2.7 g VS l⁻¹ day⁻¹, the mesophilic bioreactor showed an average specific volumetric biogas production rate of 0.88 l CH₄ l⁻¹ day⁻¹ and an effluent VS concentration of 22.2 g VS l⁻¹ (43.0% VS removal efficiency) while the thermophilic bioreactor displayed similar performances. The overall methane yield for both systems was 0.21 l CH₄ g⁻¹ VS fed and 0.47–0.48 l CH₄ g⁻¹ VS removed. A primary limitation of thermophilic digestion of this protein-rich waste is the inhibition of methanogens due to higher nondissociated (free) ammonia (NH₃) concentrations under similar total ammonium (NH₄ ⁺) concentrations at equilibrium. Since thermophilic AD did not result in advantageous methane production rates or yields, mesophilic AD was, therefore, superior in treating secondary residuals from high-rate AD effluent. An additional digester to convert secondary residuals to methane may increase the total biogas generation at the brewery by 8% compared to just conventional high-rate digestion of brewery wastewater alone. JIMB-2008: BioEnergy—Special issue.     

Magnesium Supplementation did not Affect the Increasing Bone Zinc Concentration in Rats Given Excess Calcium as Carbonate

We investigated the effect of magnesium supplementation on zinc distribution in rats given excess calcium as carbonate. Rats were given a control diet (5 g/kg calcium and 0.5 g/kg magnesium), a high calcium diet (HC, 25 g/kg calcium and 0.5 g/kg magnesium) or the high calcium diet supplied with magnesium (HCM, 25 g/kg calcium and 2.5 g/kg magnesium) for 4 weeks. Calcium carbonate and magnesium oxide were used for increasing these mineral concentrations in diets. Although feed intake did not differ among the groups, the excess calcium suppressed feed efficiency, irrespective of dietary magnesium concentration. Femoral magnesium concentration was lower in the HC group than in the control and the HCM groups. Femoral zinc concentration was higher in the HC group and the HCM group than in the control group. The zinc concentration in the kidney was lower in the HC group and the HCM group than in the control group. The excess calcium did not affect zinc concentration in plasma and other tissues such as the liver, testis, and spleen, irrespective of dietary magnesium. These results suggest that the increasing bone zinc and the decreasing renal zinc do not result from magnesium insufficiency in rats given excess calcium as carbonate.     

Effect of acidic pH on the invasion efficiency and the type III secretion system of <Emphasis Type="Italic">Burkholderia thailandensis</Emphasis>

Burkholderia thailandensis is a close relative of Burkholderia pseudomallei. These organisms are very similar, but B. thailandensis is far less virulent than B. pseudomallei. Nucleotide sequencing and analysis of 14 B. thailandensis isolates revealed variation in the regions coding for the type III secreted BipD protein. The degree of B. thailandensis BipD sequence variation was greater than that found in B. pseudomallei. Western blot analysis indicated that, unlike B. pseudomallei, B. thailandensis type III secreted proteins including BipD and BopE could not be detected in the supernatant of culture medium unless induced by acidic conditions. In addition, culturing B. thailandensis under acidic growth conditions (pH 4.5) can induce the ability of this bacterium to invade human respiratory epithelial cells A549. The identification of an environmental stimulus that increases the invasion capability of B. thailandensis invasion is of value for those who would like to use this bacterium as a model to study B. pseudomallei virulence.