Genome-wide identification and characterization of novel microRNAs in seed development of soybean

MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in eukaryotes. However, the information about miRNAs population and their regulatory functions involving in soybean seed development remains incomplete. Base on the Dicer-like1-mediated cleavage signals during miRNA processing could be employed for novel miRNA discovery, a genome-wide search for miRNA candidates involved in seed development was carried out. As a result, 17 novel miRNAs, 14 isoforms of miRNA (isomiRs) and 31 previously validated miRNAs were discovered. These novel miRNAs and isomiRs represented tissue-specific expression and the isomiRs showed significantly higher abundance than that of their miRNA counterparts in different tissues. After target prediction and degradome sequencing data-based validation, 13 novel miRNA–target pairs were further identified. Besides, five targets of 22-nt iso-gma-miR393h were found to be triggered to produce secondary trans-acting siRNA (ta-siRNAs). Summarily, our results could expand the repertoire of miRNAs with potentially important functions in soybean.     

Expression of polyhydroxybutyric acid as a model for metabolic engineering of soybean seed coats

The feasibility of genetically engineering soybean seed coats to divert metabolism towards the production of novel biochemicals was tested. The genes phbA, phbB, phbC from Ralstonia eutropha each under the control of the seed coat peroxidase promoter were introduced into soybean and the production of polyhydroxybutyrate (PHB) was assayed. The analysis of seed coats arising from 4 independent transformation events demonstrated that PHB was produced at a mean of 0.12% seed coat dried weight with individual values up to 0.36%. These values demonstrate that it is possible to metabolically engineer soybean seed coats.     

Preparation of soybean seed samples for FT-IR microspectroscopy

Typical preparation of seed samples for infrared (IR) microspectroscopy involves imbibition of the seed for varying time periods followed by cryosectioning. Imbibition, however, may initiate germination even at 4° C with associated changes in the chemistry of the sample. We have found that it is possible to section seeds that are sufficiently hard, such as soybeans, on a standard laboratory microtome without imbibition. The use of dry sectioning of unimbibed seeds is reported here, as well as a comparison of different mounting media and modes of analysis. Glycerol, Tissue-Tek, and ethanol were used as mounting media, and the quality of the resulting spectra was assessed. Ethanol was the preferred mountant, because it dried quickly with no residue and thus did not interfere with the spectrum of interest. Analysis in transmission mode using barium fluoride windows to hold the samples was compared with transmission-reflection analysis with sections mounted on special infrared-reflecting slides. The two modes of analysis performed well in different regions of the spectrum. The mode of analysis (transmission vs. transmission-reflection) should be based on the components of greatest interest in the sample.     

Yield and composition of soybean seed as a function of potassium supply

Summary A reduction in K supply to soybean plants to deficiency levels during both vegetative and reproductive development resulted in reductions not only in yield, but also in oil and K concentrations in the seed and a concomittant increase in seed protein concentration. Correlations between mean fruit yield and oil, protein and K concentrations, over a wide range of K regimes, were 0.97, −0.94 and 0.98, respectively. When K supply was increased well above the level necessary to produce maximum yields,i.e. luxury consumption, there was no significant change in K concentration in the seed, indicating a high degree of control in the movement of K to the developing seed under high K regimes. When the K supply to the plant was limiting, the rate of accumulation of oil and carbohydrate fractions, but not of seed protein, declined during the latter part of podfilling. This resulted in a fall in the C/N ratio in the non-structural seed components during this part of seed development. Depriving plants of K only during seed development had no effect on seed composition or yield, whereas resupplying K to deficient plants after anthesis resulted in almost the same seed composition and yield as that which occurred with control plants. Possible mechanisms whereby K deficiency influences soybean seed composition and yield are discussed in terms of movement of carbohydrate and nitrogen to the seed. We suggest that potassium-deficient soils are likely to produce crops with low yields and low seed oil levels; the crop may respond to K fertilizers as late as anthesis.     

Absorption and mobility of foliar-applied boron in soybean as affected by plant boron status and application as a polyol complex

In the present study (i) the impact of plant Boron (B) status on foliar B absorption and (ii) the effect of B complexation with polyols (sorbitol or mannitol) on B absorption and translocation was investigated. Soybean (Glycine max (L.) Meer.) plants grown in nutrient solution containing 0 ??M, 10 ??M, 30 ??M or 100 ??M ¹¹B labelled boric acid (BA) were treated with 50 mM ¹⁰B labelled BA applied to the basal parts of two leaflets of one leaf, either pure or in combination with 500 mM sorbitol or mannitol. After one week, ¹⁰B concentrations in different plant parts were determined. In B deficient leaves (0 ??M ¹¹B), ¹⁰B absorption was significantly lower than in all other treatments (9.7% of the applied dose vs. 26%?C32%). The application of BA in combination with polyols increased absorption by 18?C25% as compared to pure BA. The absolute amount of applied ¹⁰B moving out of the application zone was lowest in plants with 0 ??M ¹¹B supply (1.1% of the applied dose) and highest in those grown in 100 ??M ¹¹B (2.8%). The presence of sorbitol significantly decreased the share of mobile ¹⁰B in relation to the amount absorbed. The results suggest that ¹¹B deficiency reduces the permeability of the leaf surface for BA. The addition of polyols may increase ¹⁰B absorption, but did not improve ¹⁰B distribution within the plant, which was even hindered when applied a sorbitol complex.     

循环血中microRNAs作为疾病标志物的研究进展

新近研究发现成熟的microRNA能够游离于细胞之外,稳定存在于循环血中,具备疾病分子生物标志物的某些优点,已在多种肿瘤和非肿瘤疾病的早期诊断和预后中显示了独特的价值,同时循环血中microRNA的功能研究也已开始。该文针对近两年循环血中microRNA标志物及功能研究的成果,对microRNA研究中的这一热点问题进行综述。     

Preparation of soybean seed samples for FT-IR microspectroscopy.

Typical preparation of seed samples for infrared (IR) microspectroscopy involves imbibition of the seed for varying time periods followed by cryosectioning. Imbibition, however, may initiate germination even at 4 degrees C with associated changes in the chemistry of the sample. We have found that it is possible to section seeds that are sufficiently hard, such as soybeans, on a standard laboratory microtome without imbibition. The use of dry sectioning of unimbibed seeds is reported here, as well as a comparison of different mounting media and modes of analysis. Glycerol, Tissue-Tek, and ethanol were used as mounting media, and the quality of the resulting spectra was assessed. Ethanol was the preferred mountant, because it dried quickly with no residue and thus did not interfere with the spectrum of interest. Analysis in transmission mode using barium fluoride windows to hold the samples was compared with transmission-reflection analysis with sections mounted on special infrared-reflecting slides. The two modes of analysis performed well in different regions of the spectrum. The mode of analysis (transmission vs. transmission-reflection) should be based on the components of greatest interest in the sample.     

SoyProDB: A database for the identification of soybean seed proteins

Soybean continues to serve as a rich and inexpensive source of protein for humans and animals. A substantial amount of information has been reported on the genotypic variation and beneficial genetic manipulation of soybeans. For better understanding of the consequences of genetic manipulation, elucidation of soybean protein composition is necessary, because of its direct relationship to phenotype. We have conducted studies to determine the composition of storage, allergen and anti-nutritional proteins in cultivated soybean using a combined proteomics approach. Two-dimensional polyacrylamide gel electrophoresis (2DPAGE) was implemented for the separation of proteins along with matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) and liquid chromatography mass spectrometry (LC-MS/MS) for the identification of proteins. Our analysis resulted in the identification of several proteins, and a web based database named soybean protein database (SoyProDB) was subsequently built to house and allow scientists to search the data. This database will be useful to scientists who wish to genetically alter soybean with higher quality storage proteins, and also helpful for consumers to get a greater understanding about proteins that compose soy products available in the market. The database is freely accessible.

Availability

http://bioinformatics.towson.edu/Soybean_Seed_Proteins_2D_Gel_DB/Home.aspx     

Retargeted clostridial neurotoxins as novel agents for treating chronic diseases

Botulinum neurotoxin (BoNT) A and B are used to treat neuropathic disorders; if retargeted, these agents could be used to treat medical conditions that involve secretion from nonneuronal cells. Here, we report novel strategies for successfully retargeting BoNTs, and also tetanus neurotoxin (TeNT), to primary human blood monocyte-derived macrophages where BoNT/B inhibited the release of tumor necrosis factor-α, a cytokine that plays a key role in inflammation. Furthermore, mice treated with retargeted BoNT/B exhibited a significant reduction in macrophage (MΦ) recruitment, indicating that these toxins can be used to treat chronic inflammation.     

Evaluation of seed dressing and soil application formulations of Trichoderma species for integrated management of dry root rot of chickpea

The efficacy of the newly developed seed dressing and soil application formulations of Trichoderma viride, T. virens and T. harzianum were evaluated individually and in combinations under pot and field experiments for the management of dry root rot (Rhizoctonia bataticola) of chickpea (Cicer arientinum). In pot experiments, T. harzianum based seed dressing formulation, Pusa 5SD, and soil application formulations, Pusa Biogranule 5 (PBG 5) and Pusa Biopellet 10G (PBP 10G), were found to be effective in reducing dry root rot incidence in chickpea and increasing the seed germination, shoot and root lengths of the crop. Under field experiments, a combination of soil application of T. harzianum based PBP 10G and seed treatment with Pusa 5SD+carboxin was found to be the best by providing the highest seed germination, shoot and root lengths and grain yield and the lowest dry root rot incidence in chickpea.     

氯苯胁迫对大豆种子萌发的伤害

在实验室人工控制条件下 ,研究了不同浓度 1,2 ,4 三氯苯胁迫对大豆种子萌发和幼苗生长的影响 .结果表明 ,5 0～ 2 0 0 μg·g-1的 1,2 ,4 三氯苯胁迫对大豆种子的发芽率影响甚小 ,但延迟大豆种子的出苗速率 ;30 0 μg·g-1的 1,2 ,3 三氯苯胁迫使种子停止发芽 .在正常条件下 ,大豆种子播种后第 4天其下胚轴超氧化物歧化酶 (SOD)活性达到高峰 ,之后趋于稳定 .不同浓度 1,2 ,4 三氯苯处理使大豆下胚轴SOD活性下降 ,丙二醛 (MDA)、蛋白质含量及下胚轴直径增加 ;幼苗的生长受抑制 ,干重、鲜重有一定程度的下降 ;而鲜重 /干重的比值变化不大 .受害程度随着 1,2 ,4 三氯苯浓度的增加而加重 .初生根比下胚轴对 1,2 ,4 三氯苯胁迫较为敏感 .     

Molecular cloning and characterization of two soybean protein disulfide isomerases as molecular chaperones for seed storage proteins

Protein disulfide isomerase family proteins play important roles in the folding of nascent polypeptides and the formation of disulfide bonds in the endoplasmic reticulum. In this study, we cloned two similar protein disulfide isomerase family genes from soybean leaf (Glycine max L. Merrill. cv Jack). The cDNAs encode proteins of 525 and 551 amino acids, named GmPDIL-1 and GmPDIL-2, respectively. Recombinant versions of GmPDIL-1 and GmPDIL-2 expressed in Escherichia coli exhibited oxidative refolding activity for denatured RNaseA. Genomic sequences of both GmPDIL-1 and GmPDIL-2 were cloned and sequenced. The comparison of soybean genomic sequences with those of Arabidopsis, rice and wheat showed impressive conservation of exon-intron structure across plant species. The promoter sequences of GmPDIL-1 apparently contain a cis-acting regulatory element functionally linked to unfolded protein response. GmPDIL-1, but not GmPDIL-2, expression was induced under endoplasmic reticulum-stress conditions. GmPDIL-1 and GmPDIL-2 promoters contain some predicted regulatory motifs for seed-specific expression. Both proteins were ubiquitously expressed in soybean tissues, including cotyledon, and localized to the endoplasmic reticulum. Data from coimmunoprecipitation experiments suggested that GmPDIL-1 and GmPDIL-2 associate with proglycinin, a precursor of the seed storage protein glycinin, and the alpha'-subunit of beta-conglycinin, a seed storage protein found in cotyledon cells under conditions that disrupt the folding of glycinin or beta-conglycinin, suggesting that GmPDIL-1 and GmPDIL-2 are involved in the proper folding or quality control of such storage proteins as molecular chaperones.     

Impact of neonicotinoid seed treatments on thrips (Thysanoptera: Thripidae) and soybean yield in Virginia and North Carolina

Currently there are several neonicotinoid insecticide seed treatments registered for use on soybean (Glycine max L.), with disparity in adoption rates in the eastern United States. A complex of seedling insect pests is found in mid-south soybean, but thrips are the primary early season pest of soybean in Virginia and North Carolina. Published knowledge regarding their impact on soybean yield is minimal, as is the impact of thrips on soybean yield; thrips species composition is also understudied. In 2008 through 2010, nine field experiments in Virginia and North Carolina were conducted to evaluate the impact on thrips population dynamics; the influence on yield of neonicotinoid seed treatments, imidacloprid and thiamethoxam, was reported from nine of these experiments. Moreover, thrips species abundance was recorded in three of these experiments. Both imidacloprid and thiamethoxam reduced thrips densities compared with untreated soybean. Thiamethoxam was more effective than imidacloprid in reducing adult thrips densities at 5 wk after planting. Adult densities peaked at 3 wk after planting, followed by larval densities, which peaked at 4 wk after planting. The most abundant thrips species was Frankliniella fusca (Hinds), followed by Neohydatothrips variabilis (Beach). Other common species included F. occidentalis (Pergande) and F. tritici (Fitch). In general, F. fusca was more common earlier in the season, while N. variabilis was more common later in the season. There were no significant differences in yield among any of the treatments or in the untreated controls. Although neonicotinoid insecticides reduced thrips abundance, data collected in these studies demonstrated that there was no positive yield response.     

Colonization of the developing rhizosphere of sugar beet seedlings by potential biocontrol agents applied as seed treatments

AIMS: Poor colonization of the rhizosphere is a major constraint of seed treatment biological control. The objectives of this study were to; examine the colonization of the rhizosphere of sugar beet seedlings by selected rhizobacteria; determine the influence of the host rhizosphere and percolating water on the distribution of the bacteria; and deliver two biological control agents (BCAs) by co-inoculation. METHODS AND RESULTS: Rifampicin-resistant bacterial strains (Rif +) applied as single treatments to seed sown in columns of field soil produced persistent populations of 5-9 log10 cfu g-1 in the infection court of the damping-off pathogen Aphanomyces cochlioides in a controlled environment. However, isolates varied in their ability to colonize the lower rhizosphere. Percolating water significantly increased the colonization of the upper rhizosphere. Bacterial populations in the soil profiles of "non-rhizosphere" controls declined markedly with time. There was no interaction between the two selected BCAs applied as a seed treatment mixture. CONCLUSIONS: The distribution of the bacteria resulted primarily from root colonization although percolating water may modify the colonization profiles. Co-inoculation of the sugar-beet rhizosphere is a viable proposition. SIGNIFICANCE AND IMAPCT OF THE STUDY: Potential BCAs were successfully delivered to the known infection court of A. cochloides and persisted for the infection period. This bioassay can be used as a tool for the selection of BCAs for field trials.     

Antigenic relationship of legume seed proteins to the 7S seed storage protein of soybean

Extracts enriched for globulin proteins were prepared from the seeds of a large number of legume species and were tested for homology to antisera prepared against the glycosylated 7S seed storage protein of the soybean (Glycine max). Electrophoretic identification and subsequent analysis of proteins precipitated with 7S antisera was useful at relatively short taxonomic distances, particularly within the tribe Phaseoleae, to which G. max belongs. Glycine and most other members of the subtribe Glycininae are unusual within the Phaseoleae in having high molecular weight ($\text{> 70 000}$ dalton) subunit polypeptides. Seeds from other plants representing other subtribes of the Phaseoleae also contained proteins that cross-reacted with the G. max antisera; the molecular weights of these proteins varied from 30 000 to nearly 90 000 daltons. Homology was detected across a wider range of legume tribes within the subfamily Papilionoideae by enzyme-linked immunosorbent assay (ELISA). The results of these experiments suggest both that the 7S proteins of these tribes are evolutionarily related and that at least some features of these apparently rapidly-evolving proteins are under relatively strong selectional constraint.     

Hot-water treatment of seed as a method for decreasing the incidence of certain cotton and flax seedling diseases

Improved pathogen-free seed germination and better seedling growth were obtained by hot-water treatments at 60 °C for 10 min of seed of the cotton varieties Karnak and Ashmouni, and at 45 °C for 5 min of seed of the flax varieties Giza 4 and Baladi. These treatments also reduced pre- and post-emergence losses due to Rhizoctonia solani and Fusarium oxysporum f.sp. vasinfectum in cotton, and to F. oxysporum f.sp. lini in flax, and resulted in better growth of the surviving plants.     

Endogenous lectin as a possible regulator of the hydrolysis of physiological substrates by soybean seed acid phosphatase

The effects of two lectins concanavalin A (conA) and soybean agglutinin, on soybean seed acid phosphatase activity were investigated using p-nitrophenylphosphate (pNPP), pyrophosphate (PPi) and phosphoenolpyruvate (PEP) as substrates. Of the four acid phosphatase isoforms (AP1, AP2, AP3A and AP3B) purified from soybean seeds, only AP1 was activated 40 and 60% by conA and soybean agglutinin, respectively. Both lectins affected some of the kinetic parameters of AP1. The activation by lectins was not affected by 1 mM Ca2+ or Mn2+ but glucose and methylmannopyranoside (100 mM) prevented activation by conA. Under the same conditions, galactose had no effect. These results suggest that plant acid phosphatases may be regulated by lectins, the effects vary according to the substrate used.