Characterization of extracellular cellulose-degrading enzymes from Bacillus thuringiensis strains

The gram-positive spore-forming bacteria, Bacillus thuringiensis (Bt) strains produced novel cellulases which could liberate glucose from soluble cellulose, carboxymethyl cellulose (CMC), and insoluble crystalline cellulose. The maximal cellulase activities were obtained after 60 hrs incubation at 28\ubaC in a LB broth medium with 1% CMC. Maximum CMCase activities were got at 40\ubaC and pH 4.0, respectively, and more than 50% of its maximal activity was retained at 40-60\ubaC for 1 hr, while approximately 40% of its maximal activity was also retained after incubating at 70\ubaC for 1 hr. Most metal ions and reagents such as Ca2+, Mg2+, Cd2+, Pb2+, Zn2+, Cu2+, EDTA, and SDS inhibited the enzyme activities, but K+ and Mn2+ activated the activities. The enzymes from Bacillus thuringiensis strains could be applied in bioconversion of lignocellulosic biomass into fermentable sugars

Public involvement in setting a national research agenda

<p>(A) Graphical map of the BLAST results showing nucleotide identity between <i>A</i>. <i>fasciata</i> mitogenome and 15 related species listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0136297#pone.0136297.t001" target="_blank">Table 1</a>, as generated by the CGView comparison tool (CCT). CCT arranges BLAST result in an order where sequence that is most similar to the reference (<i>A</i>. <i>fasciata</i>) is placed closer to the outer edge of the map. The rings labelled 1 to17 indicate BLAST results of <i>A</i>. <i>fasciata</i> mitogenome against <i>A</i>. <i>chrysaetos</i>, <i>N</i>. <i>nipalensis</i>, <i>N</i>. <i>alboniger</i>, <i>S</i>. <i>cheela</i>, <i>A</i>. <i>monachus</i>, <i>B</i>. <i>lagopus</i>, <i>B</i>. <i>buteo</i>, <i>B</i>. <i>buteo burmanicus</i>, <i>A</i>. <i>soloensis</i>, <i>A</i>. <i>virgatus</i>, <i>A</i>. <i>gentilis</i>, <i>A</i>. <i>nisus</i>, <i>P</i>. <i>haliaetus</i>, <i>S</i>. <i>serpentarius</i>, <i>C</i>. <i>aura</i>, <i>P</i>. <i>badius</i>, and <i>S</i>. <i>leptogrammica</i>, respectively. (B) Nucleotide-based phylogenetic tree of 16 Accipitriformes species, with two Strigiformes birds as outgroups. This analysis is based on 13PCGs. Both ML and Bayesian analyses produced identical tree topologies. The ML bootstrap and Bayesian posterior probability values for each node are indicated.</p

budgerigar_mirnaomes_rawdata

Budgerigar mirnaomes rawdat

Evolution of plant Ash1 SET genes: structural divergence and functional differentiation

Plant Ash1 SET proteins are involved in H3K36 methylation, and play a key role in plant reproductive development. Genes encoding Ash1 SET proteins constitute a multigene family in which the copy number varies among plant species and functional divergence appears to have occurred repeatedly. To investigate the evolutionary history and functional differentiation of the Ash1 SET gene family, we made a comprehensive evolutionary analysis of this gene family from eleven major representatives of green plants. A novel deep sister relationship grouping previously resolved II-1 and II-2 orthologous groups was identified. The absence of AWS domain in the group II-2 suggests that the independent losses of AWS domain have occurred during evolution. A diversity of gene structures in plant Ash1 SET gene family have been presented since the divergence of Physcomitrella patens (moss) from the other land plants. A small proportion of codons in SET domain regions were detected to be under positive selection along the branches ancestral to land plant and angiosperms, which may have allowed changes of substrate specificity among different evolutionary groups while maintaining the primary function of SET domains. Our predictive subcellular localization and comparative anatomical meta-expression analyses can assort with the structural divergences of Ash1 SET proteins

Plastomes of <i>Bletilla</i> (Orchidaceae) and Phylogenetic Implications

The genus Bletilla is a small genus of only five species distributed across Asia, including B. chartacea, B. foliosa, B. formosana, B. ochracea and B. striata, which is of great medicinal importance. Furthermore, this genus is a member of the key tribe Arethuseae (Orchidaceae), harboring an extremely complicated taxonomic history. Recently, the monophyletic status of Bletilla has been challenged, and the phylogenetic relationships within this genus are still unclear. The plastome, which is rich in both sequence and structural variation, has emerged as a powerful tool for understanding plant evolution. Along with four new plastomes, this work is committed to exploring plastomic markers to elucidate the phylogeny of Bletilla. Our results reveal considerable plastomic differences between B. sinensis and the other three taxa in many aspects. Most importantly, the specific features of the IR junction patterns, novel pttRNA structures and codon aversion motifs can serve as useful molecular markers for Bletilla phylogeny. Moreover, based on maximum likelihood and Bayesian inference methods, our phylogenetic analyses based on two datasets of Arethuseae strongly imply that Bletilla is non-monophyletic. Accordingly, our findings from this study provide novel potential markers for species identification, and shed light on the evolution of Bletilla and Arethuseae

Immunomodulatory activity of a novel polysaccharide from Lonicera japonica in immunosuppressed mice induced by cyclophosphamide.

Lonicera japonica is a typical Chinese herbal medicine. We previously reported a method to isolate polysaccharides from Lonicera japonica (LJP). In this study, we first performed a qualitative analysis of LJP using the Fourier Transform Infrared Spectrometer (FT-IR) and explored the monosaccharide composition of LJP using the pre-column derivatization high performance liquid chromatography (HPLC) method. We then investigated the immunomodulatory function of LJP in cyclophosphamide (CTX)-induced immunosuppressed mouse models. The results showed that LJP had the characteristic absorption of typical polysaccharides consisting of 6 types of monosaccharides. In addition, LJP can increase significantly the organ index, splenic lymphocyte proliferation, macrophage phagocytosis, and natural killer (NK) cell activity in CTX-treated mice. LJP could also restore the levels of serum cytokines interleukin (IL-2), tumor necrosis factor (TNF-α) and Interferon-γ (IFN-γ) in the CTX-treated mice. Finally, the results on measuring the T-lymphocytes subsets of spleen also confirmed LJP-induced immunomodulatory activity in immunosuppressed mice from another perspective. Therefore, LJP could be used as a potential immunomodulatory agent

Genome-Wide Characterization of Sedum plumbizincicola&nbsp;HMA Gene Family Provides Functional Implications in Cadmium Response

Heavy-metal ATPase (HMA), an ancient family of transition metal pumps, plays important roles in the transmembrane transport of transition metals such as Cu, Zn, Cd, and Co. Although characterization of HMAs has been conducted in several plants, scarcely knowledge was revealed in Sedum plumbizincicola, a type of cadmium (Cd) hyperaccumulator found in Zhejiang, China. In this study, we first carried out research on genome-wide analysis of the HMA gene family in S. plumbizincicola and finally identified 8 SpHMA genes and divided them into two subfamilies according to sequence alignment and phylogenetic analysis. In addition, a structural analysis showed that SpHMAs were relatively conserved during evolution. All of the SpHMAs contained the HMA domain and the highly conserved motifs, such as DKTGT, GDGxNDxP, PxxK S/TGE, HP, and CPx/SPC. A promoter analysis showed that the majority of the SpHMA genes had cis-acting elements related to the abiotic stress response. The expression profiles showed that most SpHMAs exhibited tissue expression specificity and their expression can be regulated by different heavy metal stress. The members of Zn/Co/Cd/Pb subgroup (SpHMA1-3) were verified to be upregulated in various tissues when exposed to CdCl2. Here we also found that the expression of SpHMA7, which belonged to the Cu/Ag subgroup, had an upregulated trend in Cd stress. Overexpression of SpHMA7 in transgenic yeast indicated an improved sensitivity to Cd. These results provide insights into the evolutionary processes and potential functions of the HMA gene family in S. plumbizincicola, laying a theoretical basis for further studies on figuring out their roles in regulating plant responses to biotic/abiotic stresses

miRNAome expression profiles in the gonads of adult Melopsittacus undulatus

The budgerigar (Melopsittacus undulatus) is one of the most widely studied parrot species, serving as an excellent animal model for behavior and neuroscience research. Until recently, it was unknown how sexual differences in the behavior, physiology, and development of organisms are regulated by differential gene expression. MicroRNAs (miRNAs) are endogenous short non-coding RNA molecules that can post-transcriptionally regulate gene expression and play a critical role in gonadal differentiation as well as early development of animals. However, very little is known about the role gonadal miRNAs play in the early development of birds. Research on the sex-biased expression of miRNAs in avian gonads are limited, and little is known about M. undulatus. In the current study, we sequenced two small non-coding RNA libraries made from the gonads of adult male and female budgerigars using Illumina paired-end sequencing technology. We obtained 254 known and 141 novel miRNAs, and randomly validated five miRNAs. Of these, three miRNAs were differentially expressed miRNAs and 18 miRNAs involved in sexual differentiation as determined by functional analysis with GO annotation and KEGG pathway analysis. In conclusion, this work is the first report of sex-biased miRNAs expression in the budgerigar, and provides additional sequences to the avian miRNAome database which will foster further functional genomic research

Mitogenomic Codon Usage Patterns of Superfamily Certhioidea (Aves, Passeriformes): Insights into Asymmetrical Bias and Phylogenetic Implications

The superfamily Certhioidea currently comprises five families. Due to the rapid diversification, the phylogeny of Certhioidea is still controversial. The advent of next generation sequencing provides a unique opportunity for a mitogenome-wide study. Here, we first provided six new complete mitogenomes of Certhioidea (Certhia americana, C. familiaris, Salpornis spilonota, Cantorchilus leucotis, Pheugopedius coraya, and Pheugopedius genibarbis). We further paid attention to the genomic characteristics, codon usages, evolutionary rates, and phylogeny of the Certhioidea mitogenomes. All mitogenomes we analyzed displayed typical ancestral avian gene order with 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and one control region (CR). Our study indicated the strand-biased compositional asymmetry might shape codon usage preferences in mitochondrial genes. In addition, natural selection might be the main factor in shaping the codon usages of genes. Additionally, evolutionary rate analyses indicated all mitochondrial genes were under purifying selection. Moreover, MT-ATP8 and MT-CO1 were the most rapidly evolving gene and conserved genes, respectively. According to our mitophylogenetic analyses, the monophylies of Troglodytidae and Sittidae were strongly supported. Importantly, we suggest that Salpornis should be separated from Certhiidae and put into Salpornithidae to maintain the monophyly of Certhiidae. Our findings are useful for further evolutionary studies within Certhioidea