Improved keratinase production for feather degradation by Bacillus licheniformis ZJUEL31410 in submerged cultivation

Optimal medium was used to improve the production of keratinase by Bacillus licheniformis ZJUEL31410, which has a promising application in the transformation of feather into soluble protein. The results of single factor design revealed that the concentration of feather at 20 g/l and the initial pH at value 8 was the best for the production of keratinase and the degradation of feather. Ammonia salt and nitrate salt strongly restricted the production of keratinase and the degradation of feather. Result of Box-Behnken design (BBD) experiment which was used to optimize concentrations of glucose, corn steep flour and K2HPO4 for further improvement of keratinase productivity showed that the optimal medium was composed of glucose (20 g/l), corn steep flour (7.5 g/l), K2HPO4 (1 g/l) and feather (20 g/l). The result of submerged batch cultivation of B. licheniformis ZJUEL31410 in the 5 L fermentor indicated that the optimal medium had the highest keratinase and the degree of feather degradation (DFD) at 54.9 U/ml and 72.4%; both were 5 times more than the basal medium. The degradation of feather was verified by the analysis of scanning electron microscopy (SEM). This study provides a foundation for the production of keratinase and the conversion of feather to soluble protein through submerged fermentation process by B. licheniformis ZJUEL31410.Key words: Bacillus licheniformis ZJUEL31410, keratinase, culture medium, optimization, Box-Behnken design, scanning electron microscopy, feather degradation

Effects of Reservoir Mainstream on Longitudinal Zonation in Reservoir Bays

Spatial longitudinal zonation in reservoir bays is poorly documented, and most published papers considered that longitudinal zonation in bays is similar to that in reservoirs. Our results from analyses of the benthic macroinvertebrate community in the bays of the Three-Gorges Reservoir, China, showed that a typical bay contains four distinct zones-one more zones than a reservoir. This newly distinguished zone lies along the mouth stretch of a reservoir bay, and we call it a mainstream zone because it is disturbed by the reservoir mainstream. The mainstream zone is characterized by a lower standing crop and a more unstable macroinvertebrate community than in the lacustrine zone. Longitudinal zonation of reservoir bays is related to their lengths, and lacustrine zones develop only where the bay is sufficiently long. Similar to reservoirs, longitudinal zonation in bays is also dynamic and is to some extent influenced by the ages of bays and seasons

Developing a Benthic Index of Biological Integrity and Some Relationships to Environmental Factors in the Subtropical Xiangxi River, China

The aim of this study is to develop a benthic index of biotic integrity (B-IBI) to help understand how the increasing anthropogenic pressure may impact the subtropical Xiangxi River in China. Benthic macroinvertebrate and environmental surveys were conducted at 77 sites in early summer 2004. Each collection site was categorized as reference or impaired based on physical, chemical, biological, and land-use information. Six non-redundant metrics from 35 metrics were used to differentiate between reference and impaired sites. We selected six metrics for the final IBI. The scoring criteria of each metric were normalized based on the quadrisection and 0-10 scaling systems. Both scaling methods were used to assess the aquatic health of each site in the Xiangxi River watershed. The results showed that most sites were in fairly poor condition. Furthermore, we identified the relationship between B-IBI metrics, water-quality, and land-use variables with a principal component analysis. A composite of nutrients and land-use intensity explained most variances. These results suggest that the B-IBI may be a suitable method for assessing river conditions within the subtropical Xiangxi River in central China

Seasonal dynamics of suspended solids in a giant subtropical reservoir (China) in relation to internal processes and hydrological features

To explore the factors regulating seasonal variation of total suspended solids (TSS) and its two fractions in a giant dendritic reservoir (the Three-Gorges Reservoir of China, TGR) in the subtropical monsoon region, suspended solids, chlorophyll a (a surrogate for lake internal processes) and water residence time (an index of hydrologic flushing) were examined monthly from August 2005 to July 2006. TSS ranged from 0.6 to 200.3 mg/L and from 0.6 to 78 mg/L respectively in the mainstream and in a typical reservoir-bay (the Xiangxi Bay) of the TGR,. TSS exhibited a typical seasonal pattern in the mainstream rather than in the Xiangxi Bay of the TGR. The fraction of non-volatile suspended solids (NVSS) was often more dominant in the mainstream than in the Xiangxi Bay, especially during the flood season. Regressions analysis showed that 87.6% and 89.8% of seasonal variation in TSS and NVSS of the mainstream, respectively, are explained by water residence time. In contrast, suspended solids (particularly volatile suspended solids, VSS) of the Xiangxi Bay displayed significant correlation with algal biomass, and no correlation with hydrological parameters. It implies that the Xiangxi Bay was a more autochthonous system than the mainstream of the TGR where exogenous influences were the more determinant factors. (C) 2009 Elsevier Ltd and INQUA. All rights reserved

Diel vertical migration of Peridiniopsis niei, Liu et al., a new species of dinoflagellates in an eutrophic bay of Three-Gorge Reservoir, China

In spring, a typical dinoflagellate (Peridiniopsis niei Liu et al.) constitutes most of the phytoplankton biomass in most of eutrophic bay of Three-Gorge Reservoir (TGR, China). There are few field observations on vertical migration of the members of the genus Peridiniopsis. We studied diel vertical migration of the new species (Peridiniopsis niei) at sampling stations A and B in an eutrophic bay (Xiangxi Bay) of TGR during both day and night in March 2007. The present study suggests that vertical migration by Peridiniopsis niei is similar in nature to the migration patterns observed for other dinoflagellates. Solar irradiance incident was an important factor regulating the ascent and descent of Peridiniopsis niei. The vertical descent of Peridiniopsis niei during nighttime was restricted when the thermocline (Temperature gradient > 1A degrees C m(-1)) was present in the station B

Suitable reference genes for real-time PCR in human HBV-related hepatocellular carcinoma with different clinical prognoses

<p>Abstract</p> <p>Background</p> <p>Housekeeping genes are routinely used as endogenous references to account for experimental differences in gene expression assays. However, recent reports show that they could be de-regulated in different diseases, model animals, or even under varied experimental conditions, which may lead to unreliable results and consequently misinterpretations. This study focused on the selection of suitable reference genes for quantitative PCR in human hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) with different clinical outcomes.</p> <p>Methods</p> <p>We evaluated 6 commonly used housekeeping genes' expression levels in 108 HBV-related HCCs' matched tumor and non-tomor tissue samples with different clinical outcomes and 26 normal liver specimens by real-time PCR. The expression stability of the 6 genes was compared using the software programs geNorm and NormFinder. To show the impact of reference genes on data analysis, we took PGK1 as a target gene normalized by each reference gene, and performed one-way ANOVA and the equivalence test.</p> <p>Results</p> <p>With the geNorm and NormFinder software programs, analysis of TBP and HPRT1 showed the best stability in all tissue samples, while 18s and ACTB were less stable. When 18s or ACTB was used for normalization, no significant difference of PGK1 expression (p > 0.05) was found among HCC tissues with and without metastasis, and normal liver specimens; however, dramatically differences (p < 0.001) were observed when either TBP or the combination of TBP and HPRT1 were selected as reference genes.</p> <p>Conclusion</p> <p>TBP and HPRT1 are the most reliable reference genes for q-PCR normalization in HBV-related HCC specimens. However, the well-used ACTB and 18S are not suitable, which actually lead to the misinterpretation of the results in gene expression analysis.</p

Suitable reference genes for real-time PCR in human HBV-related hepatocellular carcinoma with different clinical prognoses

<p>Abstract</p> <p>Background</p> <p>Housekeeping genes are routinely used as endogenous references to account for experimental differences in gene expression assays. However, recent reports show that they could be de-regulated in different diseases, model animals, or even under varied experimental conditions, which may lead to unreliable results and consequently misinterpretations. This study focused on the selection of suitable reference genes for quantitative PCR in human hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) with different clinical outcomes.</p> <p>Methods</p> <p>We evaluated 6 commonly used housekeeping genes' expression levels in 108 HBV-related HCCs' matched tumor and non-tomor tissue samples with different clinical outcomes and 26 normal liver specimens by real-time PCR. The expression stability of the 6 genes was compared using the software programs geNorm and NormFinder. To show the impact of reference genes on data analysis, we took PGK1 as a target gene normalized by each reference gene, and performed one-way ANOVA and the equivalence test.</p> <p>Results</p> <p>With the geNorm and NormFinder software programs, analysis of TBP and HPRT1 showed the best stability in all tissue samples, while 18s and ACTB were less stable. When 18s or ACTB was used for normalization, no significant difference of PGK1 expression (p > 0.05) was found among HCC tissues with and without metastasis, and normal liver specimens; however, dramatically differences (p < 0.001) were observed when either TBP or the combination of TBP and HPRT1 were selected as reference genes.</p> <p>Conclusion</p> <p>TBP and HPRT1 are the most reliable reference genes for q-PCR normalization in HBV-related HCC specimens. However, the well-used ACTB and 18S are not suitable, which actually lead to the misinterpretation of the results in gene expression analysis.</p

Electron beam-formed ferromagnetic defects on MoS2 surface along 1T phase transition

1 T phase incorporation into 2H-MoS2 via an optimal electron irradiation leads to induce a weak ferromagnetic state at room temperature, together with the improved transport property. In addition to the 1T-like defects, the electron irradiation on the cleaved MoS2 surface forms the concentric circletype defects that are caused by the 2 H/1 T phase transition and the vacancies of the nearby S atoms of the Mo atoms. The electron irradiation-reduced bandgap is promising in vanishing the Schottky barrier to attaining spintronics device. The simple method to control and improve the magnetic and electrical properties on the MoS2 surface provides suitable ways for the low-dimensional device applications.ope

QTL meta-analysis of root traits in Brassica napus under contrasting phosphorus supply in two growth systems

A high-density SNP-based genetic linkage map was constructed and integrated with a previous map in the Tapidor x Ningyou7 (TNDH) Brassica napus population, giving a new map with a total of 2041 molecular markers and an average marker density which increased from 0.39 to 0.97 (0.82 SNP bin) per cM. Root and shoot traits were screened under low and ‘normal’ phosphate (Pi) supply using a ‘pouch and wick’ system, and had been screened previously in an agar based system. The P-efficient parent Ningyou7 had a shorter primary root length (PRL), greater lateral root density (LRD) and a greater shoot biomass than the P-inefficient parent Tapidor under both treatments and growth systems. Quantitative trait loci (QTL) analysis identified a total of 131 QTL, and QTL meta-analysis found four integrated QTL across the growth systems. Integration reduced the confidence interval by ~41%. QTL for root and shoot biomass were co-located on chromosome A3 and for lateral root emergence were co-located on chromosomes A4/C4 and C8/C9. There was a major QTL for LRD on chromosome C9 explaining ~18% of the phenotypic variation. QTL underlying an increased LRD may be a useful breeding target for P uptake efficiency in Brassica

Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana

<p>Abstract</p> <p>Background</p> <p>All sequenced genomes contain a proportion of lineage-specific genes, which exhibit no sequence similarity to any genes outside the lineage. Despite their prevalence, the origins and functions of most lineage-specific genes remain largely unknown. As more genomes are sequenced opportunities for understanding evolutionary origins and functions of lineage-specific genes are increasing.</p> <p>Results</p> <p>This study provides a comprehensive analysis of the origins of lineage-specific genes (LSGs) in <it>Arabidopsis thaliana </it>that are restricted to the Brassicaceae family. In this study, lineage-specific genes within the nuclear (1761 genes) and mitochondrial (28 genes) genomes are identified. The evolutionary origins of two thirds of the lineage-specific genes within the <it>Arabidopsis thaliana </it>genome are also identified. Almost a quarter of lineage-specific genes originate from non-lineage-specific paralogs, while the origins of ~10% of lineage-specific genes are partly derived from DNA exapted from transposable elements (twice the proportion observed for non-lineage-specific genes). Lineage-specific genes are also enriched in genes that have overlapping CDS, which is consistent with such novel genes arising from overprinting. Over half of the subset of the 958 lineage-specific genes found only in <it>Arabidopsis thaliana </it>have alignments to intergenic regions in <it>Arabidopsis lyrata</it>, consistent with either <it>de novo </it>origination or differential gene loss and retention, with both evolutionary scenarios explaining the lineage-specific status of these genes. A smaller number of lineage-specific genes with an incomplete open reading frame across different <it>Arabidopsis thaliana </it>accessions are further identified as accession-specific genes, most likely of recent origin in <it>Arabidopsis thaliana</it>. Putative <it>de novo </it>origination for two of the <it>Arabidopsis thaliana</it>-only genes is identified via additional sequencing across accessions of <it>Arabidopsis thaliana </it>and closely related sister species lineages. We demonstrate that lineage-specific genes have high tissue specificity and low expression levels across multiple tissues and developmental stages. Finally, stress responsiveness is identified as a distinct feature of Brassicaceae-specific genes; where these LSGs are enriched for genes responsive to a wide range of abiotic stresses.</p> <p>Conclusion</p> <p>Improving our understanding of the origins of lineage-specific genes is key to gaining insights regarding how novel genes can arise and acquire functionality in different lineages. This study comprehensively identifies all of the Brassicaceae-specific genes in <it>Arabidopsis thaliana </it>and identifies how the majority of such lineage-specific genes have arisen. The analysis allows the relative importance (and prevalence) of different evolutionary routes to the genesis of novel ORFs within lineages to be assessed. Insights regarding the functional roles of lineage-specific genes are further advanced through identification of enrichment for stress responsiveness in lineage-specific genes, highlighting their likely importance for environmental adaptation strategies.</p