Comparison of identity by descent and identity by state for detecting genetic regions under selection in a sorghum pedigree breeding program

Seventy sorghum inbred lines which formed part of the Queensland Department of Primary Industries (QDPI) sorghum breeding program were screened with 104 previously mapped RFLP markers. The lines were related by pedigree and consisted of ancestral source lines, intermediate lines and recent releases from the program. We compared the effect of defining marker alleles using either identity by state (IBS) or identity by descent (IBD) on our capacity to trace markers through the pedigree and detect evidence of selection for particular alleles. Allelic identities defined using IBD were much more sensitive for detecting non-Mendelian segregation in this pedigree. Only one marker allele showed significant evidence of selection when IBS was used compared with ten regions with particular allelic identities when IBD was used. Regions under selection were compared with the location of QTLs for agronomic traits known to be under selection in the breeding program. Only two of the ten regions were associated with known QTLs that matched with knowledge of the agronomic characteristics of the ancestral lines. Some of the other regions were hypothesised to be associated with genes for particular traits based on the properties of the ancestral source lines.     

Whole-Genome Shotgun Optical Mapping of Rhodospirillum rubrum

Rhodospirillum rubrum is a phototrophic purple nonsulfur bacterium known for its unique and well-studied nitrogen fixation and carbon monoxide oxidation systems and as a source of hydrogen and biodegradable plastic production. To better understand this organism and to facilitate assembly of its sequence, three whole-genome restriction endonuclease maps (XbaI, NheI, and HindIII) of R. rubrum strain ATCC 11170 were created by optical mapping. Optical mapping is a system for creating whole-genome ordered restriction endonuclease maps from randomly sheared genomic DNA molecules extracted from cells. During the sequence finishing process, all three optical maps confirmed a putative error in sequence assembly, while the HindIII map acted as a scaffold for high-resolution alignment with sequence contigs spanning the whole genome. In addition to highlighting optical mapping's role in the assembly and confirmation of genome sequence, this work underscores the unique niche in resolution occupied by the optical mapping system. With a resolution ranging from 6.5 kb (previously published) to 45 kb (reported here), optical mapping advances a “molecular cytogenetics” approach to solving problems in genomic analysis.     

Ectopic overexpression of tomato JERF3 in tobacco activates downstream gene expression and enhances salt tolerance

Plant Molecular Biology - The ethylene, jasmonic acid and osmotic signaling pathways respond to environmental stimuli and in order to understand how plants adapt to biotic and abiotic stresses it...     

Do effects of ultraviolet radiation on microbial films have indirect effects on larval attachment of the barnacle Balanus amphitrite?

We have examined the indirect effects of UV-A and UV-B on cypris attachment of the barnacle Balanus amphitrite Darwin through their effects on microbial films. Specifically, we tested the hypothesis that both UV-A and UV-B radiation can indirectly affect the larval attachment of barnacles by altering the microbial film bioactivity. Microbial films were developed from mid-intertidal region (∼1 m above Mean Low Water Level) for 6 days and subjected to ambient levels of ultraviolet radiation. Response of cyprids to untreated and UV-treated microbial films was investigated using double-dish still water choice bioassay. Results showed that both UV-A and UV-B caused a decrease in the percentage of respiring bacterial cells in microbial films and this effect increased with UV energy. With the same UV energy, UV-B caused a greater decrease in respiring bacterial cells than UV-A. However, despite strong UV radiation, the bioactivities of microbial films (i.e., stimulation of cypris attachment) remain unchanged. Results of this study suggest that increased UV radiation, which might occur due to ozone depletion, may not significantly affect the barnacle recruitment by means of affecting the inductive larval attachment cues of microbial films.     

Vertical Distribution of Bacterivorous Nematodes under Different Land Uses

The vertical distribution of dominant genera of bacterivorous nematodes to 150-cm depth in an aquic brown soil was compared after 14 years of four contrasting land uses, i.e., cropland-rice (CR), cropland-maize (CM), abandoned cropland (AC), and woodland (WL). The study was conducted at the Shenyang Experimental Station of Ecology, a Chinese Ecosystem Research Network (CERN) site in Northeast China. Data were analyzed using two-way analysis of variance with land use and depth as independent variables. More than 70% of Chiloplacus, Eucephalobus, and Monhystera spp. were present in the uppermost soil layer (0 to 5 cm) in the CR treatment. In contrast, Chiloplacus and Prismatolaimus spp. were distributed down to 100-cm depth in the AC and CM treatments, respectively. Differences in numbers of Acrobeles, Acrobeloides, Cephalobus, Chiloplacus, Eucephalobus, Monhystera, Plectus, and Prismatolaimus were found among land uses and at various depths. Soil C and N were correlated positively with numbers of Monhystera and Plectus in the CR treatment, Acrobeloides in the CM treatment, and Acrobeles and Acrobeloides in the AC treatment. Soil pH was correlated negatively with Monhystera, Plectus (CR), and Acrobeloides (CM, AC). The relationship of pH with Acrobeles depended on land use: positive in the WL treatment and negative in the AC treatment. Our results suggested that Cephalobus and Prismatolaimus in the CR treatment, and Chiloplacus and Prismatolaimus in the WL treatment, were insensitive to soil properties measured. Differences in vertical distribution should be considered when studying dominant bacterivorous nematode genera among land uses.     

Stability study on the nitrile hydratase of Nocardia sp. 108: From resting cells to crude enzyme preparation

In recent years nitrile hydratases (NHases) have drawn increasing attention due to their critical roles in organic synthesis. In the present paper an extensive investigation on the stability and activity of NHase from Nocardia sp. 108, which has succeeded in industrial application in China, was conducted by bioconversion of acrylonitrile to acrylamide in a batch manner. A study of cultivation demonstrated that biosynthesis of NHase changed significantly with the time of the culture, and the optimal NHase biosynthesis phase was 45 h after inoculation with NHase activity of a biomass of 1209.8 U/g. A stability study indicated that both crude enzyme preparations exhibited a good stability when exposed to a pH 7.2 tris-HCl buffer at 4°C for 4 h. The text was submitted by the authors in English.     

One-step enzymatic synthesis of blue pigments from geniposide for fabric dyeing

In this study, we describe a one-step chemoenzymatic reaction for the production of natural blue pigments, in which the geniposide from Gardenia extracts is transformed by glycosidases to genipin. Genipin is then allowed to react with amino acids, thereby generating a natural blue pigment. The β-glycosidases, most notably isolase (a variant of β-glucanase), recombinant β-glucosidase, Cellulase T, and amylases, were shown to hydrolyze geniposide to produce the desired pigments, whereas the α-glycosidases did not. Among the 20 tested amino acids, glycine and tyrosine were associated with the highest dye production yields. The optimal molar ratio of geniposide to glycine, two reactants relevant to pigment production, was unity. The natural blue pigments produced in this study were used to dye cotton, silk, and wool. The color yields of the pigments were determined to be significantly higher than those of other natural dyes. Furthermore, the color fastness properties of these dyes were fairly good, even in the absence of mordant.     

New and reassessed species of Strobilanthes (Acanthaceae) in the flora of China

Several problems in Strobilanthes Blume (Acanthaceae: Ruelliae) are clarified as a result of collaboration between Chinese and western botanists. Examination of pollen has permitted clear delimitation of four morphologically similar species, Strobilanthes szechuanica (Batalin) J. R. I. Wood & Y. F. Deng, S. labordei H. Lév., S. wakasana Wakasugi & Naruhashi and S. wilsonii J. R. I. Wood & Y. F. Deng, the latter described for the first time in this paper, although first collected more than a hundred years ago. A key is provided to help distinguish these species. The globose, echinulate pollen found in several species from China and Japan and assigned to the genus Championella by Bremekamp is shown by SEM photography to be distinct from other pollen hitherto regarded as the same. Three new species, S. abbreviata Y. F. Deng & J. R. I. Wood, S. lihengiae Y. F. Deng & J. R. I. Wood and S. vallicola Y. F. Deng & J. R. I. Wood are described. S. austinii C. B. Clarke ex W. W. Sm. is lectotypified to show that it is conspecific with S. lamiifolia (Nees) T. Anderson, a species demonstrating trans-Himalayan links. New combinations are made for four species as the authors recognize only a single genus, Strobilanthes within the Strobilanthinae as defined by Bremekamp. S. gongshanensis Tsui and S. aenobarba W. W. Sm. are shown to be only varieties of S. inflata T. Anderson. Illustrations are provided for all new species.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 150 , 369–390.     

A characteristic pharmacological action of ‘Yang-invigorating’ Chinese tonifying herbs: Enhancement of myocardial ATP-generation capacity

In order to investigate the pharmacological basis of ‘Yang-invigorating’ action, the effect of oral treatment with the methanolic extract of ‘Yang-invigorating’ herbs on ATP-generation capacity was examined, using heart homogenates prepared from herb-pretreated mice. Tonifying (i.e., health-promoting) herbs of other functional categories were also included for comparison. The results indicated that ‘Yang-invigorating’ Chinese tonifying herbs could invariably enhance myocardial ATP-generation capacity, with the extent of stimulation varying among the herbs. In contrast, ‘Yin-nourishing’ herbs either did not stimulate or even decreased myocardial ATP-generation capacity. While ‘Qi-invigorating’ herbs produced variable effects on myocardial ATP-generation capacity, most of the ‘blood-enriching’ herbs did not cause any significant changes. The results obtained from studies using myocardial mitochondrial fractions isolated from herb-pretreated mice suggest that ‘Yang-invigorating’ herbs might speed up ATP generation by increasing mitochondrial electron transport. The ensemble of results has provided evidence for the first time to support the pharmacological basis of ‘Yang invigoration’ in Chinese medicine.