Syntrophic Interactions Within a Butane-Oxidizing Bacterial Consortium Isolated from Puguang Gas Field in China.

Butane oxidation by the hydrocarbon degradation bacteria has long been described, but little is known about the microbial interaction in this process. To investigate this interaction, the efficiency of butane oxidation was estimated in monocultures and co-cultures of six strains of butane-oxidizing bacteria (BOB) and a butanol-oxidizing strain. Results showed that the butane degradation velocity was at least 26 times higher in the co-culture of the seven strains (228.50 nmol h(-1)) than in the six individual monocultures (8.71 nmol h(-1)). Gas chromatographic analysis of metabolites in the cultures revealed the accumulation of butanol in the monocultures of BOB strains but not in the co-culture with the butanol-oxidizing strain. These results evidenced a novel syntrophic association between BOB and butanol-oxidizing bacteria in the butane oxidation. The BOB strains oxidized butane into butanol, but this activity was inhibited by the accumulated butanol in monocultures, whereas the removal of butanol by the butanol-oxidizing strain in co-culture could eliminate the suppression and improve the butane degradation efficiency. In the co-culture, both BOB and butanol-oxidizing bacteria could grow and the time needed for butane complete removal was shortened from more than 192 h to less than 4 h. The unsuppressed effect of the co-culture was also consistent with the results of reverse transcription quantitative real-time PCR (RT-qPCR) of bmoX gene because increased expression of this gene was detected during the syntrophic growth compared with that in monoculture, pointing to the upregulation of bmoX in the syntrophic interaction.

Novosphingobium tardum sp. nov., isolated from sediment of a freshwater lake.

A Gram-negative, non-motive, aerobic and non-spore-forming strain 16-28-2(T) isolated from freshwater sediment of Taihu Lake was characterized by using a polyphasic approach. The optimum growth conditions were found to be as follows: 28 °C, pH 6.5 and 0-0.5 % NaCl in YG liquid medium. The major fatty acids were identified to be summed feature 3 (consisting of C16:1 ω7c and/or C16:1 ω6c), summed feature 8 (consisting of C18:1 ω7c and/or C18:1 ω6c), C14:0 2-OH, C17:1 ω6c, C16:0 and C18:1 ω7c 11-methyl (>5 %). Strain 16-28-2(T) was found to contain diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and sphingoglycolipid as the major polar lipids; and ubiquinone 10 (Q-10) as the major respiratory quinone. DNA G+C content of strain 16-28-2(T) was 63.5 mol % (Tm). A phylogenetic study of 16S rRNA gene indicated that strain 16-28-2(T) is a member of the genus Novosphingobium, with the highest 16S rRNA gene sequence similarity of 96.3 % with Novosphingobium lentum MT1(T) and below 96 % with the other Novosphingobium species. On the basis of the phylogenetic, phenotypic analyses and biochemical characterization, we suggest that strain 16-28-2(T) is a novel species in the genus Novosphingobium, for which the name Novosphingobium tardum sp. nov. is proposed. The type strain of N. tardum is 16-28-2(T) (=CGMCC 1.12989(T) =NBRC 110956(T)).

Sediment prokaryote communities in different sites of eutrophic Lake Taihu and their interactions with environmental factors.

To investigate the temporal variation of the sediment prokaryote communities and their relation with the rapid increase of algae population in Taihu, a shallow eutrophic freshwater Lake, water and surface sediments were sampled from seven sites in different stages of algal bloom. The physicochemical characterization revealed positive correlations among the nutrient (N, P) parameters in the water and sediments, as well as TN/TP ratio 30.79 in average in water and 0.13 in sediments, demonstrating that P content was the limit factor for bloom in Taihu and sediment was an important nutrient resource for the water body. T-RFLP analysis of 16S rRNA genes revealed a diversity decrease of sediment prokaryotic communities along the bloom. The bacterial communities in sediments were more sensitive and shaped by the temporal changes, while archaea were more sensitive to the trophic level. The pyrosequencing data showed clear spatial and temporal changes in diversity of sediment bacteria. Betaproteobacteria was the most abundant group in all the samples, following by Delta-, Gama- and Alpha-proteobacteria, Acidobacteria, Chlorobi, Chloroflexi etc. At the genus level, Thiobacillus and Sulfuricurvum were the most dominant groups in the sediments, and the increase of Thiobacillus abundance in February might be used as bioindicator for the subsequent bloom. In addition, NO3 (-)-N was evidenced to be the main factor to regulate the bacterial community structure in the sediments. These results offered some novel and important data for the evaluation and predict the algal bloom in Taihu and can be reference for other shallow fresh water lakes.

A Comparative Study on the Mechanical Properties of Open-Hole Carbon Fiber-Reinforced Thermoplastic and Thermosetting Composite Materials.

In this paper, the damage initiation/propagation mechanisms and failure modes of open-hole carbon fiber-reinforced thermoplastic composites and thermosetting composites with tension, compression, and bearing loads are investigated, respectively, by experiments and finite element simulations. The experimental evaluations are performed on the specimens using the Combined Loading Compression (CLC) test method, the tensile test method, and the single-shear test method. The differences in macroscopic damage initiation, evolution mode, and damage characteristics between thermoplastic composite materials and thermosetting composite material open-hole structures are obtained and analyzed under compressive load. Based on scanning electron microscope SEM images, a comparative analysis is conducted on the micro-failure modes of fibers, matrices, and fiber/matrix interfaces in the open-hole structures of thermoplastic and thermosetting composites under compressive load. The differences between thermoplastic and thermosetting composites were analyzed from the micro-failure mechanism. Finally, based on continuum damage mechanics (CDM), a damage model is also developed for predicting the initiation and propagation of damage in thermoplastic composites. The model, which can capture fiber breakage and matrix crack, as well as the nonlinear response, is used to conduct virtual compression tests, tensile test, and single-shear test, respectively. Numerical simulation results are compared with the extracted experimental results. The displacement-load curve and failure modes match the experimental result, which indicates that the finite element model has good reliability.

Genetic-basis analysis of heterotic loci in Dongxiang common wild rice (Oryza rufipogon Griff.).

Heterosis is widely used in genetic crop improvement; however, the genetic basis of heterosis is incompletely understood. The use of whole-genome segregating populations poses a problem for establishing the genetic basis of heterosis, in that interactions often mask the effects of individual loci. However, introgression line (IL) populations permit the partitioning of heterosis into defined genomic regions, eliminating a major part of the genome-wide epistasis. In our previous study, based on mid-parental heterosis (HMP) value with single-point analysis, 42 heterotic loci (HLs) associated with six yield-related traits were detected in wild and cultivated rice using a set of 265 ILs of Dongxiang common wild rice (Oryza rufipogon Griff.). In this study, the genetic effects of HLs were determined as the combined effects of both additive and dominant gene actions, estimated from the performance values of testcross F1s and the dominance effects estimated from the HMP values of testcross F1s. We characterized the gene action type at each HL. Thirty-eight of the 42 HLs were over-dominant, and in the absence of epistasis, four HLs were dominant. Therefore, we favour that over-dominance is a major genetic basis of 'wild-cultivar' crosses at the single functional Mendelian locus level.

Biodegradation of Leonardite by an alkali-producing bacterial community and characterization of the degraded products.

In this study, three bacterial communities were obtained from 12 Leonardite samples with the aim of identifying a clean, effective, and economic technique for the dissolution of Leonardite, a type of low-grade coal, in the production of humic acid (HA). The biodegradation ability and characteristics of the degraded products of the most effective bacterial community (MCSL-2), which degraded 50% of the Leonardite within 21 days, were further investigated. Analyses of elemental composition, (13)C NMR, and Fourier transform infrared revealed that the contents of C, O, and aliphatic carbon were similar in biodegraded humic acid (bHA) and chemically (alkali) extracted humic acid (cHA). However, the N and carboxyl carbon contents of bHA was higher than that of cHA. Furthermore, a positive correlation was identified between the degradation efficiency and the increasing pH of the culture medium, while increases of manganese peroxidase and esterase activities were also observed. These data demonstrated that both alkali production and enzyme reactions were involved in Leonardite solubilization by MCSL-2, although the former mechanism predominated. No fungus was observed by microscopy. Only four bacterial phylotypes were recognized, and Bacillus licheniformis-related bacteria were identified as the main group in MCSL-2 by analysis of amplified 16S rRNA genes, thus demonstrating that Leonardite degradation ability has a limited distribution in bacteria. Hormone-like bioactivities of bHA were also detected. In this study, a bacterial community capable of Leonardite degradation was identified and the products characterized. These data implicate the use of such bacteria for the exploitation of Leonardite as a biofertilizer.

Genetic analysis and fine mapping of LH1 and LH2, a set of complementary genes controlling late heading in rice (Oryza sativa L.).

Heading date in rice (Oryza sativa L.) is a critical agronomic trait with a complex inheritance. To investigate the genetic basis and mechanism of gene interaction in heading date, we conducted genetic analysis on segregation populations derived from crosses among the indica cultivars Bo B, Yuefeng B and Baoxuan 2. A set of dominant complementary genes controlling late heading, designated LH1 and LH2, were detected by molecular marker mapping. Genetic analysis revealed that Baoxuan 2 contains both dominant genes, while Bo B and Yuefeng B each possess either LH1 or LH2. Using larger populations with segregant ratios of 3 : 1, we fine-mapped LH1 to a 63-kb region near the centromere of chromosome 7 flanked by markers RM5436 and RM8034, and LH2 to a 177-kb region on the short arm of chromosome 8 between flanking markers Indel22468-3 and RM25. Some candidate genes were identified through sequencing of Bo B and Yuefeng B in these target regions. Our work provides a solid foundation for further study on gene interaction in heading date and has application in marker-assisted breeding of photosensitive hybrid rice in China.

Endovascular treatment vs drug therapy alone in patients with mild ischemic stroke and large infarct cores.

BACKGROUND: Treatment decision making is strictly associated with the outcomes in patients with ischemic stroke who show a large core infarct. Medical care alone may result in suboptimal treatment efficacy, and endovascular treatment may be accompanied by safety issues. Whether endovascular treatment is superior to medical care is not well investigated in the clinical studies. AIM: To investigate the efficacy of endovascular treatment and drug therapy alone in mild ischemic stroke patients with large infarct cores. METHODS: Fifty patients with mild ischemic stroke and 50 patients with acute ischemic stroke caused by anterior large vessel occlusion were selected at the First Affiliated Hospital of Hebei North University between January 2021 and December 2021. Patients were divided into an endovascular therapy group and a drug therapy group according to different treatment methods. In the endovascular therapy group, there were 28 patients with minor stroke and 22 patients with large infarct cores. The drug therapy group had 22 patients with minor stroke and 28 patients with large infarct cores. The National Institutes of Health Stroke Scale (NIHSS) scores were collected and compared between the two groups immediately after the operation and 24 h and 7 d after the operation. The modified Rankin scale (mRS) and/or activity of daily living were assessed at hospital discharge. RESULTS: There was no significant difference in NIHSS scores between the two groups before the operation (P > 0.05). NIHSS scores were lower in the endovascular therapy group than in the drug therapy group at 24 h and 7 d after the operation and at hospital discharge (all P < 0.05). The incidence of early neurologic deterioration was significantly lower in the endovascular therapy group than in the drug therapy group (P < 0.05). At hospital discharge, the mRS score was lower in the endovascular treatment group than in the drug therapy group, and the activity of daily living score was better in the endovascular treatment group than in the drug therapy group (all P < 0.05). During a follow-up of 3 mo, 17 patients (34.0%) had good prognosis (mRS ≤ 2), 33 patients (66.0%) had poor prognosis (mRS > 2), and 11 patients (22.0%) died. In the medical treatment group, 16 patients (mRS ≤ 2) had good prognosis (32.0%), 34 patients (mRS > 2) had poor prognosis (68.0%), and 14 patients (28.0%) died. There was no significant difference in prognosis and mortality between the two groups (P > 0.05). CONCLUSION: Endovascular therapy can improve NIHSS score and mRS score in patients with mild ischemic stroke and large infarct cores. It is suitable for clinical application.

Genetic analysis of heterotic loci detected in a cross between indica and japonica rice (Oryza sativa L.).

The study on the genetic basis of heterosis has received significant attention in recent years. In this study, using a set of introgression lines (ILs) and corresponding testcross F(1) populations, we investigated heterotic loci (HL) associated with six yield-related traits in both Oryza sativa L. subsp. indica and japonica. A total of 41 HL were detected on the basis of mid-parent heterosis values with single-point analysis. The F(1) test-cross population showed superiority in most yield-related traits and was characterized by a high frequency of overdominant HL. Thirty-eight of the 41 HL were overdominant, and in the absence of epistasis, three HL were dominant, suggesting that heterotic effects at the single-locus level mainly appeared to be overdominant in rice. Twenty-four HL had a real positive effect, suggesting that they are viable candidates for the improvement of rice yield potential. Compared with the quantitative trait loci (QTLs) detected in the ILs, only six out of the 41 (14.6%) HL were detected in QTL analysis under the same statistical threshold, indicating that heterosis and trait performance may be conditioned by different sets of loci.

[Progress in the study of producing reversible male sterile line by genetic engineering].

Plant male sterility is a kind of resource of heterosis, which has important value in production. It may be derived from natural mutations, artificial mutations, distant hybridizations, and now through cell engineering and genetic engineering. This paper reviews the progress of strategies in production of plant male sterile lines and their corresponding fertile lines via genetic engineering approach. All strategies can be grouped into "single component strategy" and "two-component strategy". "Single component strategy" produces conditional (reversible) male sterile line, whose fertility can be switched under given condition. Conditional male sterile line has two roles, which are CMS and maintainer line for breeding in practice; "two-component strategy" takes advantage of gene interaction and parental hybridization to generate male sterile line. Otherwise, it develops sterile line and restorer line respectively for three-line hybrid system for seed production through gene interaction. This paper discusses the advantages and disadvantages of gene engineering approaches of "single component strategy" and "two-component strategy" for developing male sterile line and corresponding restorer line, as well as the current status and perspective of these approaches in practice.

[Over-expression of OsPSK3 increases chlorophyll content of leaves in rice].

Phytosulfokine (PSK) is a newly discovered plant hormone, which can promote cell division and induce cell differentiation. It has 7 members in rice genome. So far, how the OsPSK functions and regulates in vivo is remaining unclear. In this study, we first did structural comparison and phylogenetic analysis of the 7-OsPSK-gene family via bioinformatics. Based on the phylogenetic analysis of the PSK genes in rice and Arabidopsis, we draw the conclusion that the formation of two paralogous PSK genes from the ancestral one was earlier than the monocotyledon-dicotyledon divergence; in addition, OsPSK1 and the rest OsPSK2-OsPSK7 stemmed from two different ancestors. Interrogating expression profiles of each OsPSK family member in different tissues showed different genes with different expression patterns. By means of the method of particle bombardment, we developed an OsPSK3 transgenic line, and further put much effort on studying rice growth under OsPSK3 overexpression background. It showed that the OsPSK3 overexpression line, OsPSK3ox increased OsPSK3 expression about 40% over the wild type, and presented obvious growth vigor with more fibrous roots and more root hairs at seedling stage. Plant height of OsPSK3ox-1 was higher from seedling to the full ripe stage. Notably in chlorophyll content of leaves, OsPSK3ox plants increased 2.3 times over that of the wild type.

Full dose, half dose, or discontinuation of etanercept biosimilar in early axial spondyloarthritis patients: a real-world study in China.

INTRODUCTION: To investigate the effect of dose maintenance, reduction, or discontinuation of the etanercept biosimilar Yisaipu (YSP) on early axial spondyloarthritis (axSpA) patients in remission with YSP 50 mg once weekly (QW). MATERIAL AND METHODS: Patients were enrolled in three groups: full dose (YSP50), half dose (YSP25), and discontinuation (YSP0). Patients were assessed by the same rheumatologist every 8 weeks for 48 weeks. The primary endpoint was the proportion of non-failure patients in each group. If a flare occurred during the study period, the patient resumed YSP 50 mg QW or was switched to another tumor necrosis factor inhibitor. RESULTS: A total of 144 patients were included and each group included 48 patients. The proportion of non-failure patients was significantly greater in the YSP50 group than in the YSP0 group at 48 weeks (91.7% vs. 72.9%, p = 0.032). The difference in the other two comparisons was not statistically significant (YSP50 vs. YSP25 group, p = 0.522; YSP25 vs. YSP0 group, p = 0.132). The median time to flare did not differ significantly between the three groups (p > 0.05). Most patients who flared regained remission rapidly after resuming YSP 50 mg QW or starting adalimumab 40 mg every other week. CONCLUSIONS: For patients with early axSpA in remission on YSP for more than 12 weeks, continuation of YSP at full dose was superior to discontinuation of YSP, but not superior to halving the dose.

Water-Soluble Humic Materials Regulate Quorum Sensing in Sinorhizobium meliloti Through a Novel Repressor of expR.

Quorum sensing (QS) plays an important role in the growth, nodulation, and nitrogen fixation of rhizobia. In this study, we show that water-soluble humic materials (WSHM) repress the expression of the QS related genes sinI, sinR, and expR in Sinorhizobium meliloti. This decreased the production of N-acetyl homoserine lactones (AHL) and exopolysaccharides (EPS), and ultimately increased S. meliloti cell density. We also identified a novel regulator, SMc03890 (renamed QsrR), which binds directly to the expR promoter. Deletion of qsrR increased expR expression. WSHM repressed the expression of expR by augmenting the interaction between QsrR and the expR promoter; this was determined by a bacterial-one-hybrid assay. These effects of WSHM on the QS system in S. meliloti may be the underlying mechanism by which WSHM increase the symbiotic nitrogen fixation of Medicago sativa inoculated with S. meliloti. This study provides the first evidence that humic acids regulate the QS of rhizobia and suggests that WSHM could be used as fertilizers to improve the efficiency of symbiotic nitrogen fixation.

[Isolation and analysis of a novel MYC gene from rice].

A MYC (Myelocytomatosis) transcription factor gene, OsMYC, was cloned in rice (Oryza sativa L.). The putative protein of the OsMYC gene has a typical DNA binding domain: basic/helix-loop-helix (bHLH) motif at the C-terminus. Its nucleocide sequnce has 78%, 48%, 46% identity with that of the AtMYC2, MYC7E and PG1 genes, respectively. The identity of deduced amino acid between OsMYC and AtMYC2, MYG7E and PG1 is 95%, 84%, and 77% in the bHLH domain, and that is 81%, 54% and 52% in the N-terminus conserved region. The identity is 100% in the nuclear localization signal between them. Phylogenetic comparisons revealed that the OsMYC protein was related to the Arabidopsis AtMYC2, Zea MYC7E and Phaseolus vulgaris PG1. OsMYC gene was expressed at high level in stem, but low level in leaf and root and can be induced by ABA and Fe3+, which is similar to the expression pattern of MYC7E and RAP1 genes. Thus, this gene is a new member of the rice MYC family.

Molecular cloning of a novel LOS2 gene from Capsella bursa-pastoris.

A new LOS2 gene was cloned from C. bursa-pastoris by rapid amplification of cDNA ends (RACE). The full-length cDNA of C. bursa-pastoris LOS2 gene (designated as Cblos2) was 1694 bp containing a 1332 bp open reading frame (ORF) encoding a 444 amino acid protein. The predicted CbLOS2 protein contained enolase-N domain, enolase domain, conserved putative DNA-binding and repression domains like LOS2 from A. thaliana. Bioinformatic analysis indicated that CbLOS2 had similarity with other enolase proteins. Cold acclimation assay revealed that Cblos2 expressed constitutively in C. bursa-pastoris and was involved in the cold acclimation process, implying CbLOS2 was a bi-functional enolase.

Cloning and prokaryotic expression of a cDNA encoding a putative mitochondrial malate dehydrogenase in Oryza sativa.

Malate dehydrogenase (MDH) has been characterized as a key player in oxaloacetate (OAA) biosynthesis mechanism in citrate acid cycle that generates reducing powers for further assimilation in the whole cell. Here we present the cloning, characterization and prokaryotic expression of a putative Mdh (OsmMDH) in Oryza sativa. Sequence alignment shows that there is a high homology between the deduced amino acid sequence of OsmMDH and MDH portein in Eucalyptus gunnii (80%), as well as between the deduced amino acid sequence of OsmMDH and other MDHs. Moreover, pI and the mitochondrial location of OsmMDH are predicted. The tissue-specific expression pattern of OsmMDH reveals that it is abundant in young panicle and immature seed, while its expression level is mush lower in leaf and root. Its expression in E. coli BL21 as a fusion gene is studied further.

cDNA cloning and expression analysis of the rice (Oryza sativa L.) RNase L inhibitor.

A subtractive cDNA library was constructed using rice (Oryza sativa L.) callus cDNA as driver and differentiating callus cDNA as tester. A novel cDNA fragment encoding RNase L inhibitor (RLI) was isolated by screening the subtractive library, which had a higher expression level in differentiating callus than in callus. The full-length cDNA of rice-RLI was obtained by the method of rapid amplification of cDNA ends, which contained a 1812-bp open reading frame encoding a 604 amino acid polypeptide. Homologous analysis showed that rice-RLI contained the conserved motifs (two repeated P-loops, two ATP-binding boxes and an iron-sulfur binding motif). The fluorescence quantitative PCR analysis showed that it was a constitutive expressed gene but up-regulated in abiotic stress (low temperature and NaCl treatment) and down-regulated under the treatments of NAA and IAA.

Isolation, characterization and expression analysis of a leaf-specific phosphoenolpyruvate carboxylase gene in Oryza sativa.

Suppression subtractive hybridization was carried out to enrich gene fragments over-expressed in rice leaves by subtraction to rice roots, from which two identical cDNA fragments were identified to encode putative phosphoenolpyruvate carboxylase. Then the corresponding full-length cDNA (Osppc) is isolated by RT-PCR and sequenced, which indicates an open reading frame of 2895bp is contained. Its deduced protein is encoded in 10 exons and shows high similarity to many other plant PEPCs. Comparing with maize and bacterial PEPCs, it is revealed that OSPPC shares many conserved domains and active sites that responsible for the structure, activity and regulation of this enzyme. Phylogenetic analysis demonstrates that OSPPC is grouped with C3 form PEPCs of wheat, maize and sorghum, which is consistent with the classification of rice. And a putative promoter element is predicted with DOF binding box, CAAT box and TATA box in the 5'-flanking sequence of Osppc gene. Moreover, Quantitative RT-PCR analyses are performed in hybrid rice and its parents, which show that Osppc is specifically expressed in leaf including leaf vein and sheath.

Cloning, characterization and prokaryotic expression of cytosolic malate dehydrogenase from Oryza sativa.

cDNA sequences of malate dehydrogenase (MDH) were cloned from various species, and MDH was identified to play an important role in cell energy metabolism. Here, we present the isolation and characterization of its homologue (OscMDH) in Oryza sativa. Comparison of the results to the genome details indicated that OscMDH consisted of seven exons. Sequence alignment showed that the deduced amino acid sequence of OscMDH shared a significant similarity with cMDH protein in Zea mays, as well as with other cMDH gene products. The different expression patterns of OscMDH in different tissues revealed that OscMDH mRNA was highly transcribed in either young panicle or immature seed, while its abundance was much low in green leaf and root. A nearly 56-kDa fusion protein generated by adding a Trx-His-tag at the N-terminal of OscMDH was induced by IPTG in Escherichia coli BL21 and an obvious MDH activity was detected in the protein by native PAGE analysis. All these results suggest that OscMDH encodes a cytosolic MDH in rice.

Cloning and characterization of a novel Hsp100/Clp gene (osClpD) from Oryza sativa.

A novel osClpD gene, encoding a highly conservative ClpD subfamily member, was first isolated and characterized from Oryza sativa. The full-length cDNA of osClpD gene was 3140 bp and contained a 2884 bp open reading frame encoding a 938 amino acid protein. The phylogenetic tree and blast search showed that OSClpD belonged to the ClpD subfamily of the Hsp100/Clp family, and contained all protein motifs characteristic for the ClpD subfamily of Hsp100/Clp proteins. The real-time quantitative PCR analysis proved that it was inducible by water deficit and temperature stress in vegetative tissues.