辅色剂对紫淮山花色苷稳定性的影响及其热降解动力学研究

为探究谷胱甘肽和没食子酸对紫淮山花色苷的辅色作用,本文研究了谷胱甘肽和没食子酸对紫淮山花色苷降解率、热稳定性及色差的影响。试验表明,谷胱甘肽和没食子酸能有效抑制花色苷的降解,且最佳添加量分别为0.03%和0.2%。在此添加量条件下,紫淮山花色苷在50、70、90℃水浴中的热降解均符合一级降解反应动力学规律。添加谷胱甘肽和没食子酸的紫淮山花色苷降解速率常数(k)小于对照组,半衰期(t 1/2)和活化能(Ea)高于对照组,说明谷胱甘肽和没食子酸能够增强花色苷的热稳定性。色差测定结果表明,经谷胱甘肽和没食子酸辅色后的紫淮山花色苷,其明度指数(L*)和色品指数(a*、b*)较对照组变化缓慢,颜色的稳定性增强。     

A comparative study of <Emphasis Type="Italic">k</Emphasis>-spectrum-based error correction methods for next-generation sequencing data analysis

Background

Innumerable opportunities for new genomic research have been stimulated by advancement in high-throughput next-generation sequencing (NGS). However, the pitfall of NGS data abundance is the complication of distinction between true biological variants and sequence error alterations during downstream analysis. Many error correction methods have been developed to correct erroneous NGS reads before further analysis, but independent evaluation of the impact of such dataset features as read length, genome size, and coverage depth on their performance is lacking. This comparative study aims to investigate the strength and weakness as well as limitations of some newest k-spectrum-based methods and to provide recommendations for users in selecting suitable methods with respect to specific NGS datasets.

Methods

Six k-spectrum-based methods, i.e., Reptile, Musket, Bless, Bloocoo, Lighter, and Trowel, were compared using six simulated sets of paired-end Illumina sequencing data. These NGS datasets varied in coverage depth (10× to 120×), read length (36 to 100 bp), and genome size (4.6 to 143 MB). Error Correction Evaluation Toolkit (ECET) was employed to derive a suite of metrics (i.e., true positives, false positive, false negative, recall, precision, gain, and F-score) for assessing the correction quality of each method.

Results

Results from computational experiments indicate that Musket had the best overall performance across the spectra of examined variants reflected in the six datasets. The lowest accuracy of Musket (F-score?=?0.81) occurred to a dataset with a medium read length (56 bp), a medium coverage (50×), and a small-sized genome (5.4 MB). The other five methods underperformed (F-score?<?0.80) and/or failed to process one or more datasets.

Conclusions

This study demonstrates that various factors such as coverage depth, read length, and genome size may influence performance of individual k-spectrum-based error correction methods. Thus, efforts have to be paid in choosing appropriate methods for error correction of specific NGS datasets. Based on our comparative study, we recommend Musket as the top choice because of its consistently superior performance across all six testing datasets. Further extensive studies are warranted to assess these methods using experimental datasets generated by NGS platforms (e.g., 454, SOLiD, and Ion Torrent) under more diversified parameter settings (k-mer values and edit distances) and to compare them against other non-k-spectrum-based classes of error correction methods.

     

Satellite detection of cumulative and lagged effects of drought on autumn leaf senescence over the Northern Hemisphere

Climate change has substantial influences on autumn leaf senescence, that is, the end of the growing season (EOS). Relative to the impacts of temperature and precipitation on EOS, the influence of drought is not well understood, especially considering that there are apparent cumulative and lagged effects of drought on plant growth. Here, we investigated the cumulative and lagged effects of drought (in terms of the Standardized Precipitation–Evapotranspiration Index, SPEI) on EOS derived from the normalized difference vegetation index (NDVI3g) data over the Northern Hemisphere extra‐tropical ecosystems (>30°N) during 1982–2015. The cumulative effect was determined by the number of antecedent months at which SPEI showed the maximum correlation with EOS (i.e., R_max‐cml) while the lag effect was determined by a month during which the maximum correlation between 1‐month SPEI and EOS occurred (i.e., R_max‐lag). We found cumulative effect of drought on EOS for 27.2% and lagged effect for 46.2% of the vegetated land area. For the dominant time scales where the R_max‐cml and R_max‐lag occurred, we observed 1–4 accumulated months for the cumulative effect and 2–6 lagged months for the lagged effect. At the biome level, drought had stronger impacts on EOS in grasslands, savannas, and shrubs than in forests, which may be related to the different root functional traits among vegetation types. Considering hydrological conditions, the mean values of both R_max‐cml and R_max‐lag decreased along the gradients of annual SPEI and its slope, suggesting stronger cumulative and lagged effects in drier regions as well as in areas with decreasing water availability. Furthermore, the average accumulated and lagged months tended to decline along the annual SPEI gradient but increase with increasing annual SPEI. Our results revealed that drought has strong cumulative and lagged effects on autumn phenology, and considering these effects could provide valuable information on the vegetation response to a changing climate.     

Construction of second generation protease-deficient hosts of Bacillus subtilis for secretion of foreign proteins

Although one of the major factors limiting the application of Bacillus subtilis as an expression host has been its production of at least eight extracellular proteases, researchers have also noticed that some proteases benefited the secretion of foreign proteins at times. Therefore, to maximize the yield of a foreign protein, the proteases should be selectively inactivated. This raises a new question that how to identify the favorable and unfavorable proteases for a target protein. Here, an evaluation system containing nine mutant strains of B. subtilis 168 was developed to address this question. The mutant strain PD8 has all the eight proteases inactivated whereas each of the other eight mutant strains expresses only one kind of these eight proteases. The target protein is secreted in these nine mutant strains; if the production of target protein in a mutant strain is higher than that in strain PD8, the corresponding protease is regarded as favorable. Accordingly, the optimal protease-deficient host is constructed through inactivating the unfavorable proteases. The effectiveness of this system was confirmed by expressing three foreign proteins. This study provides a strategy for improving the secretion of a foreign protein in B. subtilis through tailoring a personalized protease-deficient host.     

Enhancing fractalkine/CX3CR1 signalling pathway can reduce neuroinflammation by attenuating microglia activation in experimental diabetic retinopathy

The concept of diabetic retinopathy (DR) has been extended from microvascular disease to neurovascular disease in which microglia activation plays a remarkable role. Fractalkine (FKN)/CX3CR1 is reported to regulate microglia activation in central nervous system diseases. To characterize the effect of FKN on microglia activation in DR, we employed streptozotocin‐induced diabetic rats, glyoxal‐treated R28 cells and hypoxia‐treated BV2 cells to mimic diabetic conditions and explored retinal neuronal apoptosis, reactive oxygen species (ROS), as well as the expressions of FKN, Iba‐1, TSPO, NF‐κB, Nrf2 and inflammation‐related cytokines. The results showed that FKN expression declined with diabetes progression and in glyoxal‐treated R28 cells. Compared with normal control, retinal microglia activation and inflammatory factors surged in both diabetic rat retinas and hypoxia‐treated microglia, which was largely dampened by FKN. The NF‐κB and Nrf2 expressions and intracellular ROS were up‐regulated in hypoxia‐treated microglia compared with that in normoxia control, and FKN significantly inhibited NF‐κB activation, activated Nrf2 pathway and decreased intracellular ROS. In conclusion, the results demonstrated that FKN deactivated microglia via inhibiting NF‐κB pathway and activating Nrf2 pathway, thus to reduce the production of inflammation‐related cytokines and ROS, and protect the retina from diabetes insult.     

A mitogen-activated protein kinase gene (MGV1) in Fusarium graminearum is required for female fertility,heterokaryon formation,and plant infection

Fusarium graminearum is an important pathogen of small grains and maize in many areas of the world. Infected grains are often contaminated with mycotoxins harmful to humans and animals. During the past decade, F. graminearum has caused several severe epidemics of head scab in wheat and barley. In order to understand molecular mechanisms regulating fungal development and pathogenicity in this pathogen, we isolated and characterized a MAP kinase gene, MGV1, which is highly homologous to the MPS1 gene in Magnaporthe grisea. The MGV1 gene was dispensable for conidiation in F. graminearum but essential for female fertility during sexual reproduction. Vegetative growth of mgv1 deletion mutants was normal in liquid media but reduced on solid media. Mycelia of the mgv1 mutants had weak cell walls and were hypersensitive to cell wall degrading enzymes. Interestingly, the mgv1 mutants were self-incompatible when tested for heterokaryon formation, and their virulence was substantially reduced. The ability of the mutants to accumulate trichothecene mycotoxins on inoculated wheat was also greatly reduced. Our data suggest that MGV1 in F. graminearum is involved in multiple developmental processes related to sexual reproduction, plant infection, and cell wall integrity.     

Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs

The wild rice species Oryza rufipogon with wide intraspecific variation is thought to be the progenitor of the cultivated rice species Oryza sativa with two ecotypes, japonica and indica. To determine the origin of cultivated rice, subfamily members of the rice retroposon p-SINE1, which show insertion polymorphism in the O. sativa -O. rufipogon population, were identified and used to "bar code" each of 101 cultivated and wild rice strains based on the presence or absence of the p-SINE1 members at the respective loci. A phylogenetic tree constructed based on the bar codes given to the rice strains showed that O. sativa strains were classified into two groups corresponding to japonica and indica, whereas O. rufipogon strains were in four groups, in which annual O. rufipogon strains formed a single group, differing from the perennial O. rufipogon strains of the other three groups. Japonica strains were closely related to the O. rufipogon perennial strains of one group, and the indica strains were closely related to the O. rufipogon annual strains, indicating that O. sativa has been derived polyphyletically from O. rufipogon. The subfamily members of p-SINE1 constitute a powerful tool for studying the classification and relationship of rice strains, even when one has limited knowledge of morphology, taxonomy, physiology, and biochemistry of rice strains.     

Novel TNF-α converting enzyme (TACE) inhibitors as potential treatment for inflammatory diseases

Our research on hydantoin based TNF-α converting enzyme (TACE) inhibitors has led to an acetylene containing series that demonstrates sub-nanomolar potency (K(i)) as well as excellent activity in human whole blood. These studies led to the discovery of highly potent TACE inhibitors with good DMPK profiles.