Global transcriptional analysis of stress-response strategies in Acidithiobacillus ferrooxidans ATCC 23270 exposed to organic extractant—Lix984n

Acidithiobacillus ferrooxidans (A. ferrooxidans) ATCC 23270 is a model bacteria for bioleaching research. Because of the use of extractant in metal extraction industry, A. ferrooxidans needs to cope with the water-organic two-phase system. To get insight into the molecular response of A. ferrooxidans to organic solvent, global gene expression pattern was examined in A. ferrooxidans ATCC 23270 cells subjected to Lix984n (an organic extractant) using the method of whole-genome DNA microarray. The data suggested that the global response of A. ferrooxidans to Lix984n stress was characterized by the up-regulation of genes involved in pentose phosphate pathway, fatty acid and glutamate biosynthesis. In further study, compared to heterotrophic bacteria in dealing with short-time stress, A. ferrooxidans has a special strategy of continuously enhancing the expression of genes encoding proteins involved in electron transport, such as petI, petII, cyo and cyd. Besides, acrAB-tolC operon encoding organic solvent efflux pump and its positive regulator gene ostR were addressed.     

An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for tetraploid groundnut (Arachis hypogaea L.)

Only a few genetic maps based on recombinant inbred line (RIL) and backcross (BC) populations have been developed for tetraploid groundnut. The marker density, however, is not very satisfactory especially in the context of large genome size (2800 Mb/1C) and 20 linkage groups (LGs). Therefore, using marker segregation data for 10 RILs and one BC population from the international groundnut community, with the help of common markers across different populations, a reference consensus genetic map has been developed. This map is comprised of 897 marker loci including 895 simple sequence repeat (SSR) and 2 cleaved amplified polymorphic sequence (CAPS) loci distributed on 20 LGs (a01-a10 and b01-b10) spanning a map distance of 3, 863.6 cM with an average map density of 4.4 cM. The highest numbers of markers (70) were integrated on a01 and the least number of markers (21) on b09. The marker density, however, was lowest (6.4 cM) on a08 and highest (2.5 cM) on a01. The reference consensus map has been divided into 20 cM long 203 BINs. These BINs carry 1 (a10_02, a10_08 and a10_09) to 20 (a10_04) loci with an average of 4 marker loci per BIN. Although the polymorphism information content (PIC) value was available for 526 markers in 190 BINs, 36 and 111 BINs have at least one marker with >0.70 and >0.50 PIC values, respectively. This information will be useful for selecting highly informative and uniformly distributed markers for developing new genetic maps, background selection and diversity analysis. Most importantly, this reference consensus map will serve as a reliable reference for aligning new genetic and physical maps, performing QTL analysis in a multi-populations design, evaluating the genetic background effect on QTL expression, and serving other genetic and molecular breeding activities in groundnut.     

JNK相互作用蛋白通过JNK途径影响鼻咽癌的增殖和凋亡

EB病毒编码的瘤蛋白潜伏膜蛋白（LMP1）所介导的活化蛋白（AP-1）信号转导途径在细胞增殖、分化、转化与凋亡方面发挥着重要作用.越来越多的证据表明,AP-1信号转导通路中上游激酶JNK在鼻咽癌的发生发展过程中起着重要作用.最近克隆出来的JNK相互作用蛋白(JIP-1)是一种能抑制JNK核移位的胞浆锚蛋白.为探讨JIP在LMP1调控AP-1信号通路中的作用机制,采用间接免疫荧光法和报告基因法,发现JIP通过有效地抑制磷酸化的JNK从胞浆移位入核,从而抑制LMP1上调的AP-1活性.同时,JIP导入鼻咽癌细胞中,MTT法发现JIP能够明显抑制鼻咽癌细胞的生长.进一步发现转染JIP后细胞的集落形成率与对照组相比大约降低了53.6%,也抑制了细胞. 提示JIP可明显抑制细胞的增殖作用.进一步采用流式细胞术分析,结果发现JIP引起细胞G1/S期细胞阻滞,说明JIP是抑制细胞增殖的重要调节子.进一步采用流式细胞术定量发现,转染JIP后细胞的24 h凋亡百分率由1.25%上升到8.25%,上升约6.6倍,48 h由1.04%上升到31.45%,上升约30倍. 采用激光共聚焦显微镜发现,转染JIP后细胞核发生显著变化,核质由均匀状态固缩成高凝集状态,形成了典型的胞膜体.提示JIP可有效地促进细胞凋亡.结果表明,JIP可通过抑制活化的JNK核移位,降低LMP1所介导的AP-1信号通路.并进一步发现JIP可有效地抑制细胞增殖和细胞凋亡,从而提示JIP可作为新的治疗肿瘤潜在靶分子.     

iTRAQ-based proteomics analysis of autophagy-mediated immune responses against the vascular fungal pathogen Verticillium dahliae in Arabidopsis

The mechanisms underlying the functional link between autophagy and plant innate immunity remain largely unknown. In this study, we investigated the autophagy-mediated plant defense responses against Verticillium dahliae (V. dahliae) infection by comparative proteomics and cellular analyses. An assessment of the autophagy activity and disease development showed that autophagic processes were tightly related to the tolerance of Arabidopsis plant to Verticillium wilt. An isobaric tags for relative and absolute quantification (iTRAQ)-based proteomics analysis was performed, and we identified a total of 780 differentially accumulated proteins (DAPs) between wild-type and mutant atg10-1 Arabidopsis plants upon V. dahliae infection, of which, 193 ATG8-family-interacting proteins were identified in silico and their associations with autophagy were verified for several selected proteins. Three important aspects of autophagy-mediated defense against V. dahliae infection were revealed: 1) autophagy is required for the activation of upstream defense responses; 2) autophagy-mediated mitochondrial degradation (mitophagy) occurs and is an important player in the defense process; and 3) autophagy promotes the transdifferentiation of perivascular cells and the formation of xylem hyperplasia, which are crucial for protection against this vascular disease. Together, our results provide several novel insights for understanding the functional association between autophagy and plant immune responses.     

Contrasting hypoxia tolerance and adaptation in Malus species is linked to differences in stomatal behavior and photosynthesis

We examined the potential differences in tolerance to hypoxia by two species of apple rootstocks. Stomatal behavior and photosynthesis were compared between Malus sieversii and Malus hupehensis. Plants were hydroponically grown for 15 days in normoxic or hypoxic nutrient solutions. Those of M. sieversii showed much greater sensitivity, with exposure to hypoxia resulting in higher leaf concentrations of abscisic acid (ABA) that prompted stomatal closure. Compared with the control plants of that species, stomatal density was greater in both new and mature leaves under stress conditions. In contrast, stomatal density was significantly decreased in leaves from M. hupehensis, while stomatal length was unaffected. Under stress, the net photosynthetic rate, stomatal conductance and chlorophyll contents were markedly reduced in M. sieversii. The relatively hypoxia‐tolerant genotype M. hupehensis, however, showed only minor changes in net photosynthesis or chlorophyll content, and only a slight decrease in stomatal conductance due to such treatment. Therefore, we conclude that the more tolerant M. hupehensis utilizes a better protective mechanism for retaining higher photosynthetic capacity than does the hypoxia‐sensitive M. sieversii. Moreover, this contrast in tolerance and adaptation to stress is linked to differences in their stomatal behavior, photosynthetic capacity and possibly their patterns of native distribution.     

Genomewide association study for economic traits in the large yellow croaker with different numbers of extreme phenotypes

A traditional genomewide association study (GWAS) detects genotype–phenotype associations by the vast number of genotyped individuals. This method requires large-scale samples and considerable sequencing costs. Extreme phenotypic sampling proposes make GWAS more cost-efficient and are applied more widely. With extreme phenotypic sampling, we performed a GWAS for n-3 highly unsaturated fatty acids (HUFA) and eviscerated weight (EW) traits in the large yellow croaker population. Of the 32,249 and 29,748 detected SNPs for the two traits, three candidate regions were found in each trait. Three candidate regions associated with HUFA were known near genes on chromosomes 4 and 11, and three candidate regions were on chromosome 6, and 15 for the EW trait. By combing through our GWAS results and the biological functional analysis of the genes, we suggest that the FABP, DGAT, ATP8B1, FAF2 and CERS2 genes,  as well as the IGF2, BORA, CYP1A1, GRTP1 and HOX genes are promising candidate genes for n-3 HUFA and EW, respectively, in the large yellow croaker. Moreover, compared with the different numbers of the extreme phenotypic sampling, we conclude that 60% of the extreme phenotypic subsample can obtain a similar result as GWAS with whole phenotypes. Thus, extreme phenotypic sampling could save 40% of the cost for genotyping and DNA extraction without loss of the candidate regions and functional genes. Our study may provide a basis for further genomic breeding and a reference for others who want to perform GWAS with extreme phenotypes.     

Adsorption of Ni2+ and Cu2+ using Bio-Mineral: Adsorption Isotherms and Mechanisms

Heavy metal pollution has become one of the most serious environmental pollution problems. This study aimed to determine the adsorption and desorption characteristics of Ni²⁺ and Cu²⁺ by bio-mineral which was induced by Bacillus subtilis, and to explore the effect of pH on adsorption characteristics. The results showed that the Langmuir model gave a better fit to the experimental data than the Freundlich model, which demonstrated the adsorption was of a single-molecule layer form. The maximum adsorption capacities of the bio-mineral for Ni²⁺ and Cu²⁺ were determined as 67.114 mg/g and 69.930 mg/g, respectively. The desorption rates of Ni²⁺ and Cu²⁺ were very low, especially for Ni²⁺ which was almost 0. Besides, the bio-mineral maintained high adsorption capability for metals ions within a wide pH range (pH ≥ 3). It did not show any new phases after adsorption of Ni²⁺ and Cu²⁺ tested by FTIR, indicating that the bio-mineral and heavy metal ions might mainly physically be adsorbed. The bio-mineral has a larger internal and external specific surface area, pore volume and colloidal properties which are beneficial for the adsorption of metals ions, but shows limits in desorption. This study provides a theoretical basis for the utilization of bio-mineral and opens a new perspective for the remediation of heavy metals pollution.     

Protective Effect of Betaine on Respiratory Enzymes

Effects of betaine and NaC1 in various concentrations on the activities of enzymes in tricarboxylic acid cycle (isocitric dehydrogenase, malic dehydrogenase, succinic dehydrogenase and fumarase), terminal oxidation (cytochrome oxidase) and photorespiratory pathway (glycolate oxidase and hydroxypyruvate reductase) have been studied. Betaine, in contrast to electolyte NaC1 was non-inhibitory to these enzymes up to 500 mmol/L. Partial protection against NaC1 inhibition to the activities of these enzymes were afforded by betaine. These results were consistent with the postulated role of betaine in cytoplasmic osmoregulation. These results showed that betaine was a superior compatible solute.     

Isolation and identification of a non-specific tandemly repeated DNA sequence in Oryza species

A tandemly repeated DNA sequence (RRS7) was isolated from Oryza alta (CCDD). RRS7-related sequences were also found tandemly arrayed in genomes AA, BB, BBCC, CC, and EE, and a small amount of RRS7-related sequences were detected in genome FF and the Oryza species with unknown genomes. DNA sequence analysis of the 1844-bp insert of RRS7 revealed that it contained six tandemly repeated units, of which five were 155 bp in length and one was 194 bp in length and contained an imperfect internal 39-bp duplication. Southern blot analysis showed that the boundary sequence contained in RRS7 is a single-copy sequence. A 155-bp consensus sequence derived from the six monomeric repeats contained no internal repeat and showed no significant homology to other currently known sequences. The results of Southern blot and sequence analysis revealed that there are at least two subfamilies present in the RRS7 family; these are represented by the DraI site and the MspI site, respectively. Restriction digestion with two pairs of isoschizomers MboI/Sau3A and MspI/HpaII demonstrated that most of the C residues in the GATC sites and the internal C in the CCGG sites of the RRS7 family in O. Alta were methylated. The usefulness of the RRS7 family in determining the evolutionary relationship of the genome DD and other Oryza genomes is discussed.