Weed control and sesame (Sesamum indicum L.) response to preplant incorporated herbicides and method of incorporation

Field studies were conducted at two sesame-growing regions of Texas in 2004 and 2005 to determine weed control and sesame response to four dinitroaniline herbicides and their method of incorporation. Ethalfluralin, pendimethalin (formulated as Prowl EC), and trifluralin were applied at the X, 1X, and 2X of the suggested label dose for Gossypium hirsutum L. Pendimethalin (formulated as Prowl H₂O) was applied at the X, 1X, and 1X rate. Two methods of incorporation included rolling cultivator mixing wheels and spring tooth harrow. With rolling cultivator mixing wheels, all herbicides controlled Amaranthus tuberculatus (Moq.) J.D. Sauer at least 74% regardless of dose. The X dose of ethalfluralin and pendimethalin (formulated as Prowl EC), or the X and 1X dose of pendimethalin (formulated as Prowl H₂O) controlled Brachiaria platyphylla (Griseb.) Nash no better than 73% while all other doses of the herbicides controlled B. platyphylla at least 80%. The use of mixing wheels to incorporate the herbicides resulted in better sesame stands and less stunting than the use of the spring tooth harrow; however, sesame stands were reduced as herbicide rate increased when using mixing wheels. Ethalfluralin at the 1X dose, pendimethalin (formulated as Prowl H₂O) at the X dose, and trifluralin at the X dose produced the highest sesame yield while ethalfluralin at the 2X dose produced the lowest yield.     

GOAnnotator: linking protein GO annotations to evidence text

Background

Annotation of proteins with gene ontology (GO) terms is ongoing work and a complex task. Manual GO annotation is precise and precious, but it is time-consuming. Therefore, instead of curated annotations most of the proteins come with uncurated annotations, which have been generated automatically. Text-mining systems that use literature for automatic annotation have been proposed but they do not satisfy the high quality expectations of curators.

Results

In this paper we describe an approach that links uncurated annotations to text extracted from literature. The selection of the text is based on the similarity of the text to the term from the uncurated annotation. Besides substantiating the uncurated annotations, the extracted texts also lead to novel annotations. In addition, the approach uses the GO hierarchy to achieve high precision. Our approach is integrated into GOAnnotator, a tool that assists the curation process for GO annotation of UniProt proteins.

Conclusion

The GO curators assessed GOAnnotator with a set of 66 distinct UniProt/SwissProt proteins with uncurated annotations. GOAnnotator provided correct evidence text at 93% precision. This high precision results from using the GO hierarchy to only select GO terms similar to GO terms from uncurated annotations in GOA. Our approach is the first one to achieve high precision, which is crucial for the efficient support of GO curators. GOAnnotator was implemented as a web tool that is freely available at http://xldb.di.fc.ul.pt/rebil/tools/goa/.

     

Nipigon: A new high-yielding,early sizing table potato

Nipigon is a high-yielding, early sizing, table potato with good boiling and baking quality and is specifically adapted to northern Ontario. It has some resistance to late blight, rhizoctonia and viruses X and Y. The Nipigon potato was bred and initially selected within the Potato Breeding Project at the Fredericton Rcsearch Station of Agriculture Canada. This variety has been under test as seedling F61051 since 1965 throughout eastern Canada, but mostly in Ontario. Nipigon was selected from the progeny of a cross between two Fredericton seedlings; F53026 an early, scab-resistant seedling with very good tuber type and F51043, which has good processing quality and resistance to the common races of late blight,Phytophthora infestans (Mont.) de Bary. The pedigree is as follows:      

Jemseg: A new,early high-yielding potato variety with high resistance to virus Y and immune to virus X

Jemseg is an early sizing variety of early maturity. It has outyielded the variety Warba for total and marketable yield when dug at 80 days from planting. It has moderate resistance to common scab, is immune to virus X and has high resistance to virus Y, plus resistance to virus S. Jemseg was originated at Fredericton, New Brunswick, and is a product of the potato breeding program of Agriculture Canada. The variety has been under test in New Brunswick for 10 years as seedling F67072. It has also been tested extensively in the Maritime Provinces and throughout Canada through the facilities of regional and national evaluation trials. Jemseg was selected from a progeny of a cross between the variety Sable and a Fredericton seedling F55069. Sable is an early variety developed at Fredericton. F55069 is a Fredericton seedling bred for X immunity and scab resistance. Jemseg was first grown in the field in 1967. The pedigree follows:      

Antitumor and Antimicrobial Activity of Some Cyclic Tetrapeptides and Tripeptides Derived from Marine Bacteria

Marine derived cyclo(Gly-l-Ser-l-Pro-l-Glu) was selected as a lead to evaluate antitumor-antibiotic activity. Histidine was chosen to replace the serine residue to form cyclo(Gly-l-His-l-Pro-l-Glu). Cyclic tetrapeptides (CtetPs) were then synthesized using a solution phase method, and subjected to antitumor and antibiotic assays. The benzyl group protected CtetPs derivatives, showed better activity against antibiotic-resistant Staphylococcus aureus in the range of 60–120 μM. Benzyl group protected CtetPs 3 and 4, exhibited antitumor activity against several cell lines at a concentration of 80–108 μM. However, shortening the size of the ring to the cyclic tripeptide (CtriP) scaffold, cyclo(Gly-l-Ser-l-Pro), cyclo(Ser-l-Pro-l-Glu) and their analogues showed no antibiotic or antitumor activity. This phenomenon can be explained from their backbone structures.     

Structural Characteristics and Anticancer Activity of Fucoidan from the Brown Alga Sargassum mcclurei

Three different fucoidan fractions were isolated and purified from the brown alga, Sargassum mcclurei. The SmF1 and SmF2 fucoidans are sulfated heteropolysaccharides that contain fucose, galactose, mannose, xylose and glucose. The SmF3 fucoidan is highly sulfated (35%) galactofucan, and the main chain of the polysaccharide contains a →3)-α-l-Fucp(2,4SO₃⁻)-(1→3)-α-l-Fucp(2,4SO₃⁻)-(1→ motif with 1,4-linked 3-sulfated α-l-Fucp inserts and 6-linked galactose on reducing end. Possible branching points include the 1,2,6- or 1,3,6-linked galactose and/or 1,3,4-linked fucose residues that could be glycosylated with terminal β-d-Galp residues or chains of alternating sulfated 1,3-linked α-l-Fucp and 1,4-linked β-d-Galp residues, which have been identified in galactofucans for the first time. Both α-l-Fucp and β-d-Galp residues are sulfated at C-2 and/or C-4 (and some C-6 of β-d-Galp) and potentially the C-3 of terminal β-d-Galp, 1,4-linked β-d-Galp and 1,4-linked α-l-Fucp residues. All fucoidans fractions were less cytotoxic and displayed colony formation inhibition in colon cancer DLD-1 cells. Therefore, these fucoidan fractions are potential antitumor agents.     

Petiole nitrate content of Maine-grown Russet Burbank and Shepody potatoes in response to varying nitrogen rate

Russet Burbank and Shepody potatoes were grown with at-planting nitrogen fertilizer rates varying from 0 to 270 kg ha^?1 following small grains and red clover. Petiole samples were collected from the 4th and 5th leaflets at four to six dates each during the 1986 to 1989 growing seasons. The samples were dried and analyzed for NO ₃ ^? N content. Petiole NO ₃ ^? N levels were strongly related to nitrogen rate regardless of cultivar, growing season, and cropping system. Differences among treatments and NO ₃ ^? N content varied substantially as the growing season progressed with petiole NO ₃ ^? N levels declining rapidly in underfertilized plots as the plants aged. Petiole NO ₃ ^? N levels were higher at midseason following red clover than following small grains. Sampling 50 to 60 days after planting (DAP) is most appropriate as a tool for scheduling supplemental nitrogen applications. At 50 DAP, critical petiole NO ₃ ^? N levels were 1.6 and 1.7% for Russet Burbank and Shepody, respectively. Petiole NO ₃ ^? N levels above 2.2% at 50 DAP resulted in lower yields of Russet Burbank than when petiole NO ₃ ^? N levels were in the 1.6 to 2.2% range. Petiole NO ₃ ^? N testing should be particularly useful as a diagnostic tool in management strategies which make maximum use of previous crop residues, organic amendments, and soil reserves as nitrogen sources.     

Structural and Immunological Activity Characterization of a Polysaccharide Isolated from Meretrix meretrix Linnaeus

Polysaccharides from marine clams perform various biological activities, whereas information on structure is scarce. Here, a water-soluble polysaccharide MMPX-B2 was isolated from Meretrix meretrix Linnaeus. The proposed structure was deduced through characterization and its immunological activity was investigated. MMPX-B2 consisted of d-glucose and d-galctose residues at a molar ratio of 3.51:1.00. The average molecular weight of MMPX-B2 was 510 kDa. This polysaccharide possessed a main chain of (1→4)-linked-α-d-glucopyranosyl residues, partially substituted at the C-6 position by a few terminal β-d-galactose residues or branched chains consisting of (1→3)-linked β-d-galactose residues. Preliminary immunological tests in vitro showed that MMPX-B2 could stimulate the murine macrophages to release various cytokines, and the structure-activity relationship was then established. The present study demonstrated the potential immunological activity of MMPX-B2, and provided references for studying the active ingredients in M. meretrix.     

Three New Asperentin Derivatives from the Algicolous Fungus Aspergillus sp. F00785

Three new asperentin-type compounds, 6-O-α-d-ribosylasperentin (1) and 6-O-α-d-ribosyl-8-O-methylasperentin (2) and 5-hydroxyl-6-O-methylasperentin (3), along with asperentin (4) and its known analogues (5–9), were isolated from a halotolerant Aspergillus sp. strain {"type":"entrez-nucleotide","attrs":{"text":"F00785","term_id":"707638","term_text":"F00785"}}F00785, an endotrophic fungus from marine alga. Their structures were determined using extensive NMR and HRESIMS spectroscopic analysis, including the X-ray crystallographic data for the assignment of the absolute configurations of compound 9. Compound 4 exhibited highly potent inhibitory activity against crop pathogens, Colletotrichum gleosporioides Penz. and Colletotrichum gleosporioides (Penz.) Sacc.     

Activation of Dormant Secondary Metabolite Production by Introducing Neomycin Resistance into the Deep-Sea Fungus,Aspergillus versicolor ZBY-3

A new ultrasound-mediated approach has been developed to introduce neomycin-resistance to activate silent pathways for secondary metabolite production in a bio-inactive, deep-sea fungus, Aspergillus versicolor ZBY-3. Upon treatment of the ZBY-3 spores with a high concentration of neomycin by proper ultrasound irradiation, a total of 30 mutants were obtained by single colony isolation. The acquired resistance of the mutants to neomycin was confirmed by a resistance test. In contrast to the ZBY-3 strain, the EtOAc extracts of 22 of the 30 mutants inhibited the human cancer K562 cells, indicating that these mutants acquired a capability to produce antitumor metabolites. HPLC-photodiode array detector (PDAD)-UV and HPLC-electron spray ionization (ESI)-MS analyses of the EtOAc extracts of seven bioactive mutants and the ZBY-3 strain indicated that diverse secondary metabolites have been newly produced in the mutant extracts in contrast to the ZBY-3 extract. The followed isolation and characterization demonstrated that six metabolites, cyclo(d-Pro-d-Phe) (1), cyclo(d-Tyr-d-Pro) (2), phenethyl 5-oxo-l-prolinate (3), cyclo(l-Ile-l-Pro) (4), cyclo(l-Leu-l-Pro) (5) and 3β,5α,9α-trihydroxy-(22E,24R)-ergosta-7,22-dien-6-one (6), were newly produced by the mutant u2n2h3-3 compared to the parent ZBY-3 strain. Compound 3 was a new compound; 2 was isolated from a natural source for the first time, and all of these compounds were also not yet found in the metabolites of other A. versicolor strains. Compounds 1–6 inhibited the K562 cells, with inhibition rates of 54.6% (1), 72.9% (2), 23.5% (3), 29.6% (4), 30.9% (5) and 51.1% (6) at 100 μg/mL, and inhibited also other human cancer HL-60, BGC-823 and HeLa cells, to some extent. The present study demonstrated the effectiveness of the ultrasound-mediated approach to activate silent metabolite production in fungi by introducing acquired resistance to aminoglycosides and its potential for discovering new compounds from silent fungal metabolic pathways. This approach could be applied to elicit the metabolic potentials of other fungal isolates to discover new compounds from cryptic secondary metabolites.     

Estimating soil hydraulic conductivity using different data-driven models of ANN,GMDH and GMDH-HS

The saturated hydraulic conductivity (\(K_{\text{s}}\)) is one of the important soil hydraulic properties which plays a significant role in developing flow transport models and irrigation and drainage practices. In this research, artificial neural networks approaches, group method of data handling (GMDH) model and a hybrid intelligent model based on combination of GMDH and harmony search (HS) model (GMDH-HS) were developed to estimate \(K_{\text{s}}\) based on 151 field samples collected from the northeast of Iran. Eleven topsoil properties were used as input parameters to estimate \(K_{\text{s}}\). The five quantitative standard statistical performance evaluation measures, i.e., coefficient of efficiency, root-mean-square error, mean square relative error, mean absolute percentage error and relative bias, were employed to evaluate the performance of various developed models. Statistical results indicated that the best performance can be obtained by GMDH-HS in terms of different evaluated criteria during the training and testing datasets for \(K_{\text{s}}\) estimation.     

Advances in Modelling the Potato Crop: Sufficiency and Accuracy Considering Uses and Users, Data, and Errors

When we consider complex, multi-step processes such as crop growth or the progress of a disease then simple mathematical functions are inadequate to describe them and we generally use some kind of mathematical model. The commonest form in use is one that we call a simulation model although there are other forms of model such as Rule-based, (e.g. Gu et al. AI Appl 10:13–24, 1996), Bayesian (Gold, Plant Disease Epidemiol 4:84–122, 1989) and ‘fuzzy’ (Burrough, J Soil Sci 40:477–492, 1989), depending upon the application. Models may sometimes be combined into packages that we call decision support systems. This paper will consider simulation modelling and also the combination of complementary models. Mathematical models of the potato crop have been devised, in a range of sophistication, over a long period of years and a quite proper question is: “Where next? What are the developments that are sought or, more importantly, that are needed?”     

Assessment of antioxidant activity and rheological properties of wheat and buckwheat milling fractions

This study examined the antioxidant properties of the ethanolic extracts of wheat milling fractions (wheat flour type 500 and type 850, and bran) and their polyphenol and tocopherol content, and rheological characteristics of wheat dough supplemented with buckwheat flours (light and wholegrain). The results obtained in this study were correlated with our previously published data on wheat flour type 400, wholegrain wheat flour and buckwheat flours.Buckwheat flours exhibited significantly higher (P < 0.05) antiradical activity on hydroxyl (OH), superoxide anion (O₂⁻) and (1,1-diphenyl-2-picrylhydrazyl) DPPH radicals, antioxidant activity and reducing power than all investigated wheat milling fractions when their corresponding IC₅₀ values were compared.The rheological parameters of wheat dough supplemented with light and wholegrain buckwheat flour (0-50%) were obtained by using Mixolab. Results indicated changes in protein and starch properties of dough.The obtained results indicate the benefit of using buckwheat flours in wheat-based food products, i.e. their contribution in functional and tailor-made-food production.     

Synthesis and Bioactivity of Ancorinoside B,a Marine Diglycosyl Tetramic Acid

The sponge metabolite ancorinoside B was prepared for the first time in 16 steps and 4% yield. It features a β-d-galactopyranosyl-(1→4)-β-d-glucuronic acid tethered to a d-aspartic acid-derived tetramic acid. Key steps were the synthesis of a fully protected d-lactose derived thioglycoside, its attachment to a C₂₀-aldehyde spacer, functionalization of the latter with a terminal N-(β-ketoacyl)-d-aspartate, and a basic Dieckmann cyclization to close the pyrrolidin-2,4-dione ring with concomitant global deprotection. Ancorinoside B exhibited multiple biological effects of medicinal interest. It inhibited the secretion of the cancer metastasis-relevant matrix metalloproteinases MMP-2 and MMP-9, and also the growth of Staphylococcus aureus biofilms by ca 87% when applied at concentrations as low as 0.5 µg/mL. This concentration is far below its MIC of ca 67 µg/mL and thus unlikely to induce bacterial resistance. It also led to a 67% dispersion of preformed S. aureus biofilms when applied at a concentration of ca 2 µg/mL. Ancorinoside B might thus be an interesting candidate for the control of the general hospital, catheter, or joint protheses infections.     

Synthesis of the Oligosaccharides Related to Branching Sites of Fucosylated Chondroitin Sulfates from Sea Cucumbers

Natural anionic polysaccharides fucosylated chondroitin sulfates (FCS) from sea cucumbers attract great attention nowadays due to their ability to influence various biological processes, such as blood coagulation, thrombosis, angiogenesis, inflammation, bacterial and viral adhesion. To determine pharmacophore fragments in FCS we have started systematic synthesis of oligosaccharides with well-defined structure related to various fragments of these polysaccharides. In this communication, the synthesis of non-sulfated and selectively O-sulfated di- and trisaccharides structurally related to branching sites of FCS is described. The target compounds are built up of propyl β-d-glucuronic acid residue bearing at O-3 α-l-fucosyl or α-l-fucosyl-(1→3)-α-l-fucosyl substituents. O-Sulfation pattern in the fucose units of the synthetic targets was selected according to the known to date holothurian FCS structures. Stereospecific α-glycoside bond formation was achieved using 2-O-benzyl-3,4-di-O-chloroacetyl-α-l-fucosyl trichloroacetimidate as a donor. Stereochemical outcome of the glycosylation was explained by the remote participation of the chloroacetyl groups with the formation of the stabilized glycosyl cations, which could be attacked by the glycosyl acceptor only from the α-side. The experimental results were in good agreement with the SCF/MP2 calculated energies of such participation. The synthesized oligosaccharides are regarded as model compounds for the determination of a structure-activity relationship in FCS.