Rumen microbial degradation of bromoform from red seaweed(Asparagopsis taxiformis)and the impact on rumen fermentation and methanogenic archaea

Background The red macroalgae Asparagopsis is an effective methanogenesis inhibitor due to the presence of halogenated methane(CH_(4))analogues,primarily bromoform(CHBr_(3)).This study aimed to investigate the degradation process of CHBr3 from A taxiformis in the rumen and whether this process is diet-dependent.An in vitro batch culture system was used according to a 2×2 factorial design,assessing two A taxiformis inclusion rates[0(CTL)and 2%DM diet(AT)]and two diets[high-concentrate(HC)and high-forage diet(HF)].Incubations lasted for 72 h and samples of headspace and fermentation liquid were taken at 0,0.5,1,3,6,8,12,16,24,48 and 72 h to assess the pattern of degradation of CHBr_(3) into dibromomethane(CH_(2)Br_(2))and fermentation parameters.Additionally,an in vitro experiment with pure cultures of seven methanogens strains(Methanobrevibacter smithii,Methanobrevibacter ruminantium,Methanosphaera stadtmanae,Methanosarcina barkeri,Methanobrevibacter millerae,Methanorhermobacter wolfei and Methanobacterium mobile)was conducted to test the effects of increasing concentrations of CHBr3(0.4,2,10and 50μmol/L).Results The addition of AT significantly decreased CH_(4) production(P=0.002)and the acetate:propionate ratio(P=0.003)during a 72-h incubation.The concentrations of CHBr_(3) showed a rapid decrease with nearly 90%degraded within the first 3 h of incubation.On the contrary,CH_(2)Br_(2) concentration quickly increased during the first 6 h and then gradually decreased towards the end of the incubation.Neither CHBr_(3) degradation nor CH_(2)Br_(2) synthesis were affected by the type of diet used as substrate,suggesting that the fermentation rate is not a driving factor involved in CHBr_(3)degradation.The in vitro culture of methanogens showed a dose-response effect of CHBr3 by inhibiting the growth of M.smithii,M.ruminantium,M.stadtmanae,M.barkeri,M.millerae,M.wolfei,and M.mobile.Conclusions The present work demonstrated that CHBr_(3) from A.taxiformis is quickly degraded to CH_(2)Br_(2)in the rumen and that the fermentation rate promoted by different diets is not a driving factor involved in CHBr_(3)degradation.

Protein Bodies in Cotyledon Cells Exhibit Differential Patterns of Legumin-Like Proteins Mobilization during Seedling Germinating States

Olive (Olea europaea L.) tree is one of the most extensive and important agricultural crop in Mediterranean countries due to its beneficial health and nutritional properties and its high economic value. Currently, olive tree constitutes the sixth most important cultivated plant in the world, spreading from the Mediterranean region of origin to new production areas such as Australia, South and North America and South Africa. However, the mobilization processes of storage materials i.e. reserve proteins during seed germination, which are largely involved in essential physiological process including plant growth and development, remain poorly understood. Morphometric and immunohistochemistry analyses of protein bodies contained in olive seed storage tissues, cotyledon and endosperm, were performed by using different microscopy techniques, including light (bright-field and fluorescence) microscopy and transmission electron microscopy. Furthermore, we used legumin-like proteins (11S-type globulins) as a molecular marker to study the mobilization of reserve proteins from PBs of cotyledons at germinating seedling stages by using immunofluorescence assays. Results demonstrated that cotyledon and endosperm are characterized by distinct PBs populations containing legumin-like proteins, distinctly discriminated by the number of PBs per cell and tissue, size, immunofluorescence and histochemical staining. These features reflect differential PBs biogenesis during development and maturation processes in olive seed tissues endosperm and cotyledon, in relation to proteins (polypeptides) final composition, SSPs processing and/or packaging during seed maturation. Three different mobilization patterns of legumin-like proteins were identified for the first time in cotyledon PBs during seedling germinating process. Mature proteins composition and/or processing, cell types and enzyme composition and/or differential activation have been discussed as key features determining how proteins mobilize from PBs for further degradation in the cotyledon.

Genome sequencing and next-generation sequence data analysis: A comprehensive compilation of bioinformatics tools and databases

Genomics has become a ground-breaking field in all areas of the life sciences. The advanced genomics and the development of high-throughput techniques have lately provided insight into whole-genome characterization of a wide range of organisms. In the post-genomic era, new technologies have revealed an outbreak of prerequisite genomic sequences and supporting data to understand genome wide functional regulation of gene expression and metabolic pathways reconstruction. However, the availability of this plethora of genomic data presents a significant challenge for storage, analyses and data management. Analysis of this mega-data requires the development and application of novel bioinformatics tools that must include unified functional annotation, structural search, and comprehensive analysis and identification of new genes in a wide range of species with fully sequenced genomes. In addition, generation of systematically and syntactically unambiguous nomenclature systems for genomic data across species is a crucial task. Such systems are necessary for adequate handling genetic information in the context of comparative functional genomics. In this paper, we provide an overview of major advances in bioinformatics and computational biology in genome sequencing and next-generation sequence data analysis. We focus on their potential applications for efficient collection, storage, and analysis of genetic data/information from a wide range of gene banks. We also discuss the importance of establishing a unified nomenclature system through a functional and structural genomics approach.

Heavy metal phytoextraction by Sedum alfredii is affected by continual clipping and phosphorus fertilization amendment

Improving the efficacy of phytoextraction is critical for its successful application in metal contaminated soils. Mineral nutrition affects plant growth and metal absorption and subsequently the accumulation of heavy metal through hyper-accumulator plants. This study assessed the effects of di-hydrogen phosphates (KH2PO4, Ca(H2PO4)2, NaH2PO4 and NH4H2PO4) application at three levels (22, 88 and 352 mg P/kg soil) on Sedum alfredii growth and metal uptake by three consecutive harvests on aged and Zn/Cd combined contaminated paddy soil. The addition of phosphates (P) significantly increased the amount of Zn taken up by S. alfredii due to increased shoot Zn concentration and dry matter yield (DMY) (P < 0.05). The highest phytoextraction of Zn and Cd was observed in KH2PO4 and NH4H2PO4 treatment at 352 mg P/kg soil. The amount of Zn removed by phytoextraction increased in the order of 1st clipping < 2nd clipping < 3rd clipping, and for Cd extraction the order was 2nd clipping < 1st clipping < 3rd clipping. These results indicate that the application of P fertilizers coupled with multiple cuttings can enhance the removal of Zn and Cd from contaminated soils by S. alfredii, thus shortening the time needed for accomplishing remediation goals.

The Quaternary Structure of NADPH Thioredoxin Reductase C Is Redox-Sensitive

NADPH thioredoxin reductase C (NTRC ) 是能结合 NADPH thioredoxin reductase (NTR ) 和 thioredoxin (TRX ) 的叶绿体酶为 2-Cys peroxiredoxin (2-Cys PRX ) 的有效减小的活动。因为 NADPH 能在黑暗期间在叶绿体被生产， NTRC 在夜里期间为植物过氧化物 detoxification 起一个关键作用。这里， NTRC 的第四级的结构高度依赖于它的氧化还原作用地位，这被显示出。在 vitro，大多数酶采用了一个 oligomeric 状态在在 NADPH， NADH，或 DTT 的增加之上的 dimers 的那 disaggregated。胶化过滤和从 Arabidopsis 叶绿体基质的蛋白质摘录的西方的污点分析证明本国的 NTRC 形成总数，它对 NADPH 和 DTT 敏感，建议聚集状态可能是在 vivo 的 NTRC 活动的一个重要方面。而且，酶在在 Arabidopsis 叶绿体的簇是局部性的。NTRC 三倍、双的异种， A164G-V182E-R183F 和 A164G-R183F，代替 NADPH 有约束力的地点的关键残余，显示出减少的活动，但是仍然能随中间人形式的增加不过使聚合成二聚物。把结果基于这些，我们建议 NTRC 的催化地活跃的形式更暗淡，形成它被 NADPH 导致。