Multiple omics revealed the growth-promoting mechanism of Bacillus velezensis strains on ramie.

Beneficial bacteria that promote plant growth can shield plants from negative effects. Yet, the specific biological processes that drive the relationships between soil microbes and plant metabolism are still not fully understood. To investigate this further, we utilized a combination of microbiology and non-targeted metabolomics techniques to analyze the impact of plant growth-promoting bacteria on both the soil microbial communities and the metabolic functions within ramie (Boehmeria nivea) tissues. The findings indicated that the yield and traits of ramie plants are enhanced after treatment with Bacillus velezensis (B. velezensis). These B. velezensis strains exhibit a range of plant growth-promoting properties, including phosphate solubilization and ammonia production. Furthermore, strain YS1 also demonstrates characteristics of IAA production. The presence of B. velezensis resulted in a decrease in soil bacteria diversity, resulting in significant changes in the overall structure and composition of soil bacteria communities. Metabolomics showed that B. velezensis significantly altered the ramie metabolite spectrum, and the differential metabolites were notably enriched (P < 0.05) in five main metabolic pathways: lipid metabolism, nucleotide metabolism, amino acid metabolism, plant secondary metabolites biosynthesis, and plant hormones biosynthesis. Seven common differential metabolites were identified. Correlation analysis showed that the microorganisms were closely related to metabolite accumulation and yield index. In the B. velezensis YS1 and B. velezensis Y4-6-1 treatment groups, the relative abundances of BIrii41 and Bauldia were significantly positively correlated with sphingosine, 9,10,13-TriHOME, fresh weight, and root weight, indicating that these microorganisms regulate the formation of various metabolites, promoting the growth and development of ramie. Conclusively, B. velezensis (particularly YS1) played an important role in regulating soil microbial structure and promoting plant metabolism, growth, and development. The application of the four types of bacteria in promoting ramie growth provides a good basis for future application of biological fertilizers and bio-accelerators.

Phytoremediation and environmental effects of three Amaranthaceae plants in contaminated soil under intercropping systems.

Intercropping is a widely used agricultural system; however, the effect of intercropping between accumulator plants on phytoextraction in heavy metal-contaminated soils remains unknown. Here, a field experiment was conducted to investigate the phytoextraction efficiency and related environmental effects of three Amaranthaceae plants (Amaranthus hypochondriacus, Celosia argentea, and Pfaffia glomerata) using mono- and intercropping models. In monocropping, the total biomass of A. hypochondriacus was only 51.2 % of that of C. argentea. Compared with monocropping, intercropping reduced the fresh weight per plant of A. hypochondriacus by 53.0 % (intercropping with C. argentea) and 40.5 % (intercropping with P. glomerata) but increased the biomass per plant of C. argentea and P. glomerata by 128.2 and 14.2 %, respectively. The Cd uptake of the three plants in the monocropping models showed the following trend: C. argentea > P. glomerata > A. hypochondriacus. Interplanting A. hypochondriacus and C. argentea further increased the phytoextraction efficiency by 361.2 % (compared with A. hypochondriacus monocropping) and 52.0 % (compared with C. argentea monocropping). Soil exchangeable Cd, Pb, Cu, Zn, K, and P, soil N-NO3- and N-NH4+, soil common bacteria and arbuscular mycorrhiza (AM) fungi, and soil total organic carbon (TOC) play key roles in Cd and Pb uptake by the three accumulator plants (p < 0.05). The biomass of common bacteria, Gm+, Gm- bacteria, fungi, AM fungi, and actinomycetes increased with the three accumulators planted in the mono- and intercropping models. Compared with C. argentea monocropping, the biomass of soil microbes in the rhizosphere soil was obviously increased in the intercropping A. hypochondriacus and C. argentea models. These results suggest that interplanting A. hypochondriacus and C. argentea can increase Cd removal efficiency from Cd-contaminated soils, and this model could be recommended to remediate Cd-contaminated soils on a field scale.

Diversity and Network Relationship Construction of Soil Fungal Communities in Lactarius hatsudake Tanaka Orchard during Harvest.

Lactarius hatsudake Tanaka is a mycorrhizal edible mushroom with rich economic and nutritional value. Although it is artificially planted, its yield is unstable. Soil fungi, including L. hatsudake, coexist with many other microorganisms and plants. Therefore, complex microbial communities have an influence on the fruiting body formation of L. hatsudake. L. hatsudake and its interactions with the rest of the fungal community over time are not completely understood. In this study, we performed high-throughput sequencing of microorganisms in the basal soil of the fruiting body (JT), mycorrhizosphere soil (JG), and non-mushroom-producing soil (CK) in a 6-year-old L. hatsudake plantation at harvest. The results showed that the soil of the L. hatsudake plantation was rich in fungal communities and a total of 10 phyla, 19 classes, 53 orders, 90 families, 139 genera, and 149 species of fungi were detected. At the phylum level, the major groups were Basidiomycota and Ascomycota. At the genus level, the dominant groups were Lactarius, Trichoderma, Suillus, and Penicillium. Among them, L. hatsudake had an absolute dominant position in the soil fungal community of the plantation, and was the only group of Lactarius in the plantation soil. Penicillium cryptum and Penicillium adametzii were unique to the JT soil sample. Chaetopsphaeria, Myxocephala, Devriesia, and Psathyrella were positively correlated with L. hatsudake. In the constructed fungal network, the total number of nodes were ranked in descending order as JG (441) > CK (405) > JT (399), while the total number of edges were ranked in descending order as CK (1360) > JG (647) > JT (586). Analysis of the fungal assembly process revealed that groups CK and JG have determinative processes that dominated community building, while the JT group exhibited a dominant random process with a 0.60 probability. The results indicated that L. hatsudake was successfully colonized in the plantation soil. During harvest, the CK group exhibited the largest network size and the most complex fungal interactions, while the fungal community structure in the mushroom cultivation zone (JT and JG) was stable and less susceptible to external environmental interference. L. hatsudake affects the fungal community in the soil surrounding its fruiting body.

The influence of residual pectin composition and content on nanocellulose films from ramie fibers: Micro-nano structure and physical properties.

In this study, cellulose nanofibril (CNF) films from ramie fibers were prepared with different pectin compositions and contents, and the influence of residual pectin on the overall performances of CNF films was evaluated. There was no significant effect of the residual pectin composition on the properties of obtained CNF films. However, when the content of residual pectin was increased from 0.45 % to 9.16 %, the surface area and water absorption of CNF films were increased from 0.2223 to 0.3300 m2/g, and from 93.51 % to 122.42 %, respectively. Pectin covers the CNF surface and act as a physical barrier between the cellulose fibrils; thus the nanocellulose films with high pectin content will have a loose and porous structure, resulting in a high surface area and a high water absorption. Besides, with the residual pectin content decreasing from 9.16 % to 0.45 %, the UVA light transmittance and tensile strength of CNF films were increased from 30.6 % to 59.9 %, and from 37.67 to 100.26 MPa, respectively. After removal of amorphous pectins in CNFs, the low pectin containing CNFs are able to pack more compactly to form a strong and thin film. This paper provides guidance for the preparation of CNF films with different performance requirements.

Two Bacillus spp. Strains Improve the Structure and Diversity of the Rhizosphere Soil Microbial Community of Lilium brownii var. viridulum.

Lily Fusarium wilt disease caused by Fusarium spp. spreads rapidly and is highly destructive, leading to a severe reduction in yield. In this study, lily (Lilium brownii var. viridulum) bulbs were irrigated after planting with suspensions of two Bacillus strains that effectively control lily Fusarium wilt disease to assess their effects on the rhizosphere soil properties and microbial community. A high-throughput sequencing of microorganisms in the rhizosphere soil was performed and the soil physicochemical properties were measured. The FunGuild and Tax4Fun tools were used for a functional profile prediction. The results showed that Bacillus amyloliquefaciens BF1 and B. subtilis Y37 controlled lily Fusarium wilt disease with control efficacies of 58.74% and 68.93%, respectively, and effectively colonized the rhizosphere soil. BF1 and Y37 increased the bacterial diversity and richness of the rhizosphere soil and improved the physicochemical properties of the soil, thereby favoring the proliferation of beneficial microbes. The relative abundance of beneficial bacteria was increased and that of pathogenic bacteria was decreased. Bacillus abundance in the rhizosphere was positively correlated with most soil physicochemical properties, whereas Fusarium abundance was negatively correlated with most physicochemical properties. Functional prediction revealed that irrigation with BF1 and Y37 significantly upregulated glycolysis/gluconeogenesis among metabolism and absorption pathways. This study provides insights into the mechanism by which two Bacillus strains with antifungal activity, BF1 and Y37, antagonize plant pathogenic fungi and lays the foundation for their effective application as biocontrol agents.

Metabolomics and transcriptomics reveal the effect of hetero-chitooligosaccharides in promoting growth of Brassica napus.

The hetero-chitooligosaccharide (HTCOS) is a naturally occurring biopolymer in the exoskeleton of crustaceans and insects. Although some studies have been carried out on HTCOS in inducing plant resistance and promoting growth, the molecular mechanism of HTCOS in plants is not clear. In this study, an integrated analysis of metabolomics and transcriptomics was performed to analyze the response of Brassica napus to hetero-chitooligosaccharides treatment. The levels of 26 metabolites in B. napus were significantly changed under the HTCOS treatment. Amongst these metabolites, 9 metabolites were significantly up-regulated, including pentonic acid, indole-3-acetate, and γ-aminobutyric acid. Transcriptome data showed that there were 817 significantly up-regulated genes and 1064 significantly down-regulated genes in B. napus under the HTCOS treatment. Interestingly, the indole-3-acetate (IAA) content under the HTCOS treatment was about five times higher than that under the control condition. Moreover, four genes related to plant hormone signal transduction, three AUX/IAA genes, and one ARF gene, were significantly up-regulated under the HTCOS treatment. Furthermore, the plant height, branching number, and biomass of B. napus under the HTCOS treatment were significantly increased compared to that in the control condition. This evidence indicated that the HTCOS treatment contributed to accumulating the content of plant hormone IAA in the B. napus, up-regulating the expression of key genes in the signaling pathway of plant growth and improving the agronomic traits of B. napus.

Effects of residual pectin composition and content on the properties of cellulose nanofibrils from ramie fibers.

In this study, a series of pretreatment methods (pectin extraction) were employed to prepare cellulose nanofibrils (CNFs) with different pectin composition and contents from ramie fibers. The comprehensive effects of residual pectin on the final properties of CNFs were investigated. The residual pectin did not have a significant effect on the size distribution of the obtained CNFs. While the presence of pectin led to higher zeta potential value, improved dispersion stability and enhanced storage modulus of the CNF dispersion, with the sodium carbonate extraction method showing the greatest impact. The possible mechanism for enhanced dispersion stability of CNFs is the formation of self-assembled hierarchical pectin-hemicellulose/lignin-cellulose nanostructures, offering abundant electrostatic repulsion and steric hindrance between the nanoparticles. This work provides guidelines for the tailored production of CNFs to meet the requirements for different applications.

A high-quality genome assembly of Lactarius hatsudake strain JH5.

Lactarius hatsudake is a species of Lactarius commonly found in pine forests, is edible with a delicious and nutritious fruiting body, and exhibits medicinal properties. It is an ideal natural multifunctional food with bioactive components including fungal polysaccharides, crude fiber, unsaturated fatty acids, nucleic acid derivatives, various amino acids, and vitamins. However, biological and genomic analyses of this mycorrhizal mushroom are sparse, thereby hindering large-scale cultivation. Previously, we isolated and screened L. hatsudake JH5 strains and have applied our garnered knowledge to the large-scale cultivation of mycorrhizal seedlings. In this study, we produced a high-quality genome assembly of L. hatsudake JH5 by combining Illumina paired-end and PacBio single molecule real-time sequencing, resulting in PacBio single molecule real-time reads of 7.67 Gb and Illumina Pair-End reads of 1,560 Mb. Based on the distribution of k-mer frequencies, the genome size of this strain was estimated to be 63.84 Mb (1.14% heterozygosity). Based on de novo genome assembly, the final genome size was determined to be 76.7 Mb, with scaffold N50 of 223.2 kb and N90 of 54.5 kb, and a GC content of 54.38%. BUSCO assessment showed that genome completeness was 89.0%. The N50 length of the JH5 genome was 43.6% longer than that of the previously published L. hatsudake MG20 genome. This high-quality L. hatsudake genome assembly will facilitate research on the functional genome, molecular breeding, yield enhancement, and sustainability of L. hatsudake cultivation.

Isolation and characterization of antagonistic Paenibacillus polymyxa HX-140 and its biocontrol potential against Fusarium wilt of cucumber seedlings.

OBJECTIVE: The aim of this study is to evaluate the efficacy of the strain Paenibacillus polymyxa HX-140, isolated from the rhizosphere soil of rape, to control Fusarium wilt of cucumber seedlings caused by Fusarium oxysporum f. sp. cucumerinum. RESULTS: Strain HX-140 was able to produce protease, cellulase, ß-1,3-glucanase and antifungal volatile organic compounds. An in vitro dual culture test showed that strain HX-140 exhibited broad spectrum antifungal activity against soil-borne plant pathogenic fungi. Strain HX-140 also reduced the infection of Fusarium wilt of cucumber seedlings by 55.6% in a greenhouse pot experiment. A field plot experiment confirmed the biocontrol effects and further revealed that antifungal activity was positively correlated with inoculum size by the root-irrigation method. Here, inoculums at 106 107 and 108 cfu/mL of HX-140 bacterial suspension reduced the incidence of Fusarium wilt of cucumber seedling by 19.5, 41.1, and 50.9%, respectively. CONCLUSIONS: Taken together, our results suggest that P. polymyxa HX-140 has significant potential in the control of Fusarium wilt and possibly other fungal diseases of cucumber.

Two birds with one stone: Porous poly(ionic liquids) membrane with high efficiency for the separation of amino acids mixture and its antibacterial properties.

Poly(ionic liquid) membranes (PILMs) can be potentially applied as polyelectrolyte materials in the separation of ampholytes such as amino acids. Therefore, poly(amino acid ionic liquid) membranes (PAAILMs) were prepared by blending poly(amino acid ionic liquids) (PAAILs) and polyvinylidene fluoride (PVDF) in this study. These PAAILMs were characterized by Fourier transform infrared (FT-IR) spectroscopy, scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS), and thermal gravimetric analysis (TGA). Moreover, their mechanical properties, antibacterial and antifouling properties were evaluated. The zeta potential, pore size distribution, porosity, and specific surface area of these membranes were also measured. The membranes were used to separate the amino acid mixture of l-phenylalanine and l-aspartic acid, which are essential for the synthesis of aspartame. The PAAILMs can be used for the selective separation of l-phenylalanine and l-aspartic acid through the Donnan effect. A maximum selectivity of 65% was obtained for the mixed amino acids via one-step separation. These PAAILMs have the advantages of low operating pressure, high water flux, good antibacterial and antifouling properties, and excellent reusability, thereby indicating their potential for industrial application in the separation of l-phenylalanine and l-aspartic acid.

Comparison of Deep Eutectic Solvents on Pretreatment of Raw Ramie Fibers for Cellulose Nanofibril Production.

Deep eutectic solvents (DESs), featured as promising green solvents, were applied to examine their effectiveness in pretreating raw ramie fibers (RFs) for cellulose nanofibril (CNF) production. The pretreatment performance of three DESs, i.e., choline chloride-urea (CU), choline chloride-oxalic acid dihydrate (CO), and choline chloride-glycerol (CG), was evaluated based on chemical composition analysis and structural and morphological changes. CO attained the most dramatic morphological changes of RFs, followed by CG and CU. Its high structural disruption of RFs during the pretreatment process, shown in the results from scanning electron microscopy and atomic force microscopy, could be due to an outstanding ability to remove amorphous cellulose and noncellulosic components from raw RFs, confirmed by the results of chemical composition analysis, Fourier transform infrared spectroscopy, and X-ray diffractometry. Overall, this study provided an innovative and effective pretreatment process for fractionating raw cellulosic fibers, so as to promote the subsequent preparation of CNFs.

Selection of Reference Genes for qPCR Analyses of Gene Expression in Ramie Leaves and Roots across Eleven Abiotic/Biotic Treatments.

Quantitative real-time PCR (qPCR) is commonly used for deciphering gene functions. For effective qPCR analyses, suitable reference genes are needed for normalization. The objective of this study is to identify the appropriate reference gene(s) for qPCR analyses of the leaves and roots of ramie (Boehmeria nivea L.), an important natural fiber crop. To accomplish this goal, we investigated the expression patterns of eight common plant qPCR reference genes in ramie leaves and roots under five abiotic stresses, five hormonal treatments, and one biotic stress. The relative expression stabilities of the eight genes were evaluated using four common but different approaches: geNorm, NormFinder, BestKeeper, and RefFinder. Across the 11 tested conditions, ACT1 was the most stably expressed among the eight genes while GAPDH displayed the biggest variation. Overall, while variations in the suggested reference genes were found for different tissue x treatment combinations, our analyses revealed that together, genes ACT1, CYP2, and UBQ can provide robust references for gene expression studies of ramie leaves under most conditions, while genes EF-1α, TUB, and ACT1 can be used for similar studies of ramie roots. Our results should help future functional studies of the genes in ramie genome across tissues and environmental conditions.

Assessment of the toxicity and biodegradation of amino acid-based ionic liquids.

Amino acid-based ionic liquids (AAILs) are generally thought of as green solvents and widely used in many regions without systematic assessment of their effect on the environment or human health. In this work, a series of AAILs with different cations and amino acid anions were prepared and characterized, after which their microbial toxicity, phytotoxicity, and biodegradability were evaluated. The results showed that not all AAILs had low toxicity against microorganisms and that some AAILs were highly toxic towards the targeted microorganisms. The phytotoxic effect of the AAILs on rice (Oryza sativa L.) further demonstrated that AAILs should not be presumed to be non-toxic to plants. Moreover, the biodegradability tests showed that majority of AAILs were not satisfactorily biodegradable. In summary, not all AAILs are non-toxic or biodegradable, and their effect on the environment and human health must be assessed before their mass preparation and application.

Deletion of the sex-determining gene SXI1α enhances the spread of mitochondrial introns in Cryptococcus neoformans.

BACKGROUND: Homing endonuclease genes (HEGs) are widely distributed genetic elements in the mitochondrial genomes of a diversity of eukaryotes. Due to their ability to self-propagate within and between genomes, these elements can spread rapidly in populations. Whether and how such elements are controlled in genomes remains largely unknown. RESULTS: Here we report that the HEG-containing introns in the mitochondrial COX1 gene in Cryptococcus neoformans are mobile and that their spread in sexual crosses is influenced by mating type (MAT) α-specific homeodomain gene SXI1α. C. neoformans has two mating types, MATa and MATα . In typical crosses between strains of the two mating types, only a small portion (< 7%) of diploid fusants inherited the HEGs from the MATα parent. However, disruption of the SXI1α gene resulted in the majority (> 95%) of the diploid fusants inheriting the HEG-containing introns from the MATα parent, a frequency significantly higher than those of intronless mitochondrial genes. CONCLUSIONS: Our results suggest that SXI1α not only determines uniparental mitochondrial inheritance but also inhibits the spread of HEG-containing introns in the mitochondrial genome in C. neoformans.

Assessment of the cytotoxicity of ionic liquids on Spodoptera frugiperda 9 (Sf-9) cell lines via in vitro assays.

Cytotoxicity studies are important tools for the assessment of the toxicity of ionic liquids (ILs). In the present study, the cytotoxicity of eleven ILs against Spodoptera frugiperda 9 (Sf-9) cell lines were evaluated via 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assays. The effect on cellular morphology, ultrastructural morphology, and nuclear morphology induced by 1-ethyl-3-methylimidazolium bromide ([C2mim][Br]) was studied via inverted light microscopy observation, acridine orange staining, and transmission electron microscope (TEM) analysis, respectively. The effect on cell DNA fragmentation, cell apoptosis and cell cycle induced by [C2mim][Br] was also investigated via DNA agarose gel electrophoresis and flow cytometry analysis, respectively. The results showed that the cytotoxic effect of ILs on Sf-9 cells was related to the IL structures, concentrations, and length of exposure. The morphological features of apoptosis induced by [C2mim][Br] such as cell shrinkage and convolution, apoptotic bodies, pyknosis, and karyorrhesis were observed. All these phenomena confirmed that Sf-9 cells exposed to [C2mim][Br] died via apoptosis. This study complements the current knowledge about the cytotoxic properties of ILs on insect cells and highlights the mechanism by which ILs kill these cells. Furthermore, it provides a basis for further studies on the future applications of ILs as insecticides.

Draft genome analysis provides insights into the fiber yield, crude protein biosynthesis, and vegetative growth of domesticated ramie (Boehmeria nivea L. Gaud).

Plentiful bast fiber, a high crude protein content, and vigorous vegetative growth make ramie a popular fiber and forage crop. Here, we report the draft genome of ramie, along with a genomic comparison and evolutionary analysis. The draft genome contained a sequence of approximately 335.6 Mb with 42,463 predicted genes. A high-density genetic map with 4,338 single nucleotide polymorphisms (SNPs) was developed and used to anchor the genome sequence, thus, creating an integrated genetic and physical map containing a 58.2-Mb genome sequence and 4,304 molecular markers. A genomic comparison identified 1,075 unique gene families in ramie, containing 4,082 genes. Among these unique genes, five were cellulose synthase genes that were specifically expressed in stem bark, and 3 encoded a WAT1-related protein, suggesting that they are probably related to high bast fiber yield. An evolutionary analysis detected 106 positively selected genes, 22 of which were related to nitrogen metabolism, indicating that they are probably responsible for the crude protein content and vegetative growth of domesticated varieties. This study is the first to characterize the genome and develop a high-density genetic map of ramie and provides a basis for the genetic and molecular study of this crop.

Molecular Cloning, Recombinant Expression and Antifungal Activity of BnCPI, a Cystatin in Ramie (Boehmeria nivea L.).

Phytocystatins play multiple roles in plant growth, development and resistance to pests and other environmental stresses. A ramie (Boehmeria nivea L.) phytocystatin gene, designated as BnCPI, was isolated from a ramie cDNA library and its full-length cDNA was obtained by rapid amplification of cDNA ends (RACE). The full-length cDNA sequence (691 bp) consisted of a 303 bp open reading frame (ORF) encoding a protein of 100 amino acids with deduced molecular mass of 11.06 kDa and a theoretical isoelectric point (pI) of 6.0. The alignment of genome DNA (accession no. MF153097) and cDNA sequences of BnCPI showed that an intron (~104 bp) exists in the coding region. The BnCPI protein contains most of the highly conserved blocks including Gly5-Gly6 at the N-terminal, the reactive site motif QxVxG (Q49V50V51S52G53), the L79-W80 block and the [LVI]-[AGT]-[RKE]-[FY]-[AS]-[VI]-x-[EDQV]-[HYFQ]-N (L22G23R24 F25A26V27 D28D29H30 N31) block that is common among plant cystatins. BLAST analysis indicated that BnCPI is similar to cystatins from Glycine max (77%), Glycine soja (76%), Hevea brasiliensis (75%) and Ricinus communis (75%). The BnCPI was subcloned into expression vector pSmart-I and then overexpressed in Escherichia coli BL21 (DE3) as a His-tagged recombinant protein. The purified reBnCPI has a molecular mass of 11.4 kDa determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Purified reBnCPI can efficiently inhibit the protease activity of papain and ficin toward BANA (Nα-benzoyl-L-arginine-2-naphthyamide), as well as the mycelium growth of some important plant pathogenic fungi. The data further contribute to our understanding of the molecular functions of BnCPI.

Transcriptome Analysis of Ramie (Boehmeria nivea L. Gaud.) in Response to Ramie Moth (Cocytodes coerulea Guenée) Infestation.

The ramie moth Cocytodes coerulea Guenée (RM) is an economically important pest that seriously impairs the yield of ramie, an important natural fiber crop. The molecular mechanisms that underlie the ramie-pest interactions are unclear up to date. Therefore, a transcriptome profiling analysis would aid in understanding the ramie defense mechanisms against RM. In this study, we first constructed two cDNA libraries derived from RM-challenged (CH) and unchallenged (CK) ramie leaves. The subsequent sequencing of the CH and CK libraries yielded 40.2 and 62.8 million reads, respectively. Furthermore, de novo assembling of these reads generated 26,759 and 29,988 unigenes, respectively. An integrated assembly of data from these two libraries resulted in 46,533 unigenes, with an average length of 845 bp per unigene. Among these genes, 24,327 (52.28%) were functionally annotated by predicted protein function. A comparative analysis of the CK and CH transcriptome profiles revealed 1,980 differentially expressed genes (DEGs), of which 750 were upregulated and 1,230 were downregulated. A quantitative real-time PCR (qRT-PCR) analysis of 13 random selected genes confirmed the gene expression patterns that were determined by Illumina sequencing. Among the DEGs, the expression patterns of transcription factors, protease inhibitors, and antioxidant enzymes were studied. Overall, these results provide useful insights into the defense mechanism of ramie against RM.

Identification of Ramie Genes in Response to Pratylenchus coffeae Infection Challenge by Digital Gene Expression Analysis.

Root lesion disease, caused by Pratylenchus coffeae, seriously impairs the growth and yield of ramie, an important natural fiber crop. The ramie defense mechanism against P. coffeae infection is poorly understood, which hinders efforts to improve resistance via breeding programs. In this study, the transcriptome of the resistant ramie cultivar Qingdaye was characterized using Illumina sequence technology. About 46.3 million clean pair end (PE) reads were generated and assembled into 40,826 unigenes with a mean length of 830 bp. Digital gene expression (DGE) analysis was performed on both the control roots (CK) and P. coffeae-challenged roots (CH), and the differentially expressed genes (DEGs) were identified. Approximately 10.16 and 8.07 million cDNA reads in the CK and CH cDNA libraries were sequenced, respectively. A total of 137 genes exhibited different transcript abundances between the two libraries. Among them, the expressions of 117 and 20 DEGs were up- and down-regulated in P. coffeae-challenged ramie, respectively. The expression patterns of 15 candidate genes determined by qRT-PCR confirmed the results of DGE analysis. Time-course expression profiles of eight defense-related genes in susceptible and resistant ramie cultivars were different after P. coffeae inoculation. The differential expression of protease inhibitors, pathogenesis-related proteins (PRs), and transcription factors in resistant and susceptible ramie during P. coffeae infection indicated that cystatin likely plays an important role in nematode resistance.

[Variations of pulmonary venous drainage and venous ostium index detection in atrial fibrillation patients prior to radiofrequency catheter ablation by MDCT pulmonary venography].

OBJECTIVE: To evaluate variations of pulmonary venous drainage and venous ostium index (VOI) in patients with atrial fibrillation (AF) prior to radio-frequency catheter ablation (RFCA) by MDCT pulmonary venography. METHODS: 16-detector row CT pulmonary venography was performed in 64 AF patients referred to RFCA from June, 2005 to May, 2006. Variations in pulmonary venous drainage were observed in volume render imagines. Anterior-posterior and superior-inferior diameters of pulmonary venous ostium were measured on maximum intensity projection images. VOI derived from left superior, left inferior, right superior, right inferior pulmonary veins and variations in pulmonary venous drainage were calculated. RESULTS: Classic pulmonary veins anatomy was found in 11 patients (17.18%), early branching veins in 45 patients (70.31%), left common ostium in 5 patients (7.81%), right common ostia in 1 patient, right accessory (middle) pulmonary vein in 5 patients (7.81%) and left accessory (middle) pulmonary vein in 1 patient (1.56%). VOI of homolateral pulmonary veins and bilateral superior pulmonary veins were similar (P > 0.05) while there was a significant difference on VOIs derived from left superior and right inferior; two inferior, left inferior versus right superior veins (P < 0.05). Right inferior pulmonary venous ostium was most rounded and had the highest index (0.88) and left inferior pulmonary venous ostium was most oval and had the lowest index (0.72). CONCLUSION: Multidetector row CT pulmonary venography (MDCT-PV) could provide valuable informations on pulmonary venous anatomy in AF patients referred to RFCA and should be used as a routine examination prior to the operation.