Uptake of fluoride by two paddy (Oryza sativa L.) varieties treated with fluoride-contaminated water

The use of fluoride enriched groundwater for irrigating the paddy crops is prevalent in many parts of the world. The fluoride in the irrigated water not only affects the growth and productivity of the crops, but is also accumulated in the plant tissues. We studied the accumulation of fluoride in roots, leaves and seeds two paddy varieties (i.e. Oryza sativa L. var. IR-36 and Oryza sativa L. var. Swarno) when treated with different concentrations of fluoridated water. The translocation pattern of fluoride was also observed. The water soluble fluoride ( $ {\text{F}}_{{{\text{H}}_{ 2} {\text{O}}}} $ ) in the soil and plant parts increased substantially with increasing fluoride concentration in treated water. The Swarno variety showed a slight but consistent higher uptake of fluoride than the IR-36 variety. Fluoride uptake by the germinated seedlings was many folds higher than the uptake by mature plants. At 30 mg l^?1 fluoride exposure, the mean $ {\text{F}}_{{{\text{H}}_{ 2} {\text{O}}}} $ accumulation (mg kg^?1 dry weight) in root, leaves, and seeds of Swarno was 54.1, 51.4 and 42.3, whereas the corresponding values in IR-36 were 50.9, 48.5 and 39.2. For the same exposure, the fluoride accumulation in root and shoot of Swarno and IR-36 seedlings were 3,480, 3,463 and 3,386, 3,360 mg kg^?1, respectively. Normally, the fluoride accumulation follows the order of soil > root > shoot > grain. However, at early stage of fluoride contamination (5 mg l^?1 NaF) roots tended to hyper accumulate fluoride from the soil.     

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/.

     

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.     

Prediction of potato yield using temperature and insolation data

A linear polynomial model is presented $$Y = \beta _0 + \beta _1 X_1 + \beta _2 X_2 + \beta _3 X_3 + \xi $$ where Y = plant yield of tubers > 1 cm diameter, X₁ = revised growing degree days $$\begin{gathered} RGDD = \frac{{max temp \left( { \leqslant 30^ \circ C} \right) + \min temp \left( { \geqslant 4.4^ \circ C} \right)}}{2} - 4.4^ \circ C \hfill \\ - \frac{{min temp \left( { > 4.4^ \circ C} \right) - 4.4^ \circ C}}{2} \hfill \\ \end{gathered} $$ X₂ = total insolation in cal cm^-2 at 350 to 1150 nm and X₃ = mean daily air temperature range in °C. The β₀ and ξ, (Y intercept and error term) and β₁, β₂ and β₃ coefficients are derived from fitting the experimental data. The model was developed by growing ‘Kennebec’ in large containers at sites ranging from 1533 m to 3198 m elevation under shaded (48% insolation reduction) and unshaded conditions at 39° to 41° N latitude. Mean maximum and minimum temperatures and insolation ranged from 29°C to 19°C, 14°C to 6°C, and 200 cal cm^?2 day^?1 to 530 cal cm² day^?1 respectively. Soil matric potential and soil fertility were not included as variables in the model since they were physically controlled. The model does not include the period from planting to emergence since environment was not permitted to vary differentially. A highly significant multiple linear model with a coefficient of determination of 0.93 was obtained. It is suggested that including the revision $$ - \frac{{min temp \left( { > 4.4^ \circ C} \right) - 4.4^ \circ C}}{2}$$ in the heat input estimation (GDD) as well as air temperature range, emphasizes the influence of respiration on productivity. The model should be tested further and adapted as a practical method for predicting potato yield under “grower” conditions.     

Nitrogen Fertilizer Management Practices to Reduce N<Subscript>2</Subscript>O Emissions from Irrigated Processing Potato in Manitoba

Nitrogen fertilizer practices affect nitrous oxide (N₂O) emissions from agricultural soils. The “4R” nutrient stewardship framework of using N fertilizer at the right rate, right source, right placement and right time can reduce N₂O emissions while maintaining or improving yield of field crops, but understanding of how the various factors affect N₂O emissions from irrigated processing potato is lacking. We examined the effects of selected 4R practices on emissions, using results from two irrigated processing potato studies each conducted in 2011 and 2012 in Manitoba, Canada. Experiment 1 examined combinations of source (urea, ESN), placement (pre-plant incorporation [PPI], banding), and rate (100 and 200 kg N ha^-1) on a clay loam soil. Experiment 2 examined timing and source treatment combinations (urea PPI, ESN PPI, urea split, urea split/fertigation) on a loamy fine sandy soil. For Experiment 1, use of ESN at 200 kg ha^-1 did not reduce area-, yield- and applied fertilizer N- based N₂O emissions compared to urea at 200 kg ha^-1, irrespective of placement. Emissions from pre-plant banding ESN at 200 kg ha^?1, however, were 32% lower than from PPI ESN. For Experiment 2, compared to single pre-plant urea application, fertigation simulated by in-season application of urea ammonium nitrate (UAN) gave lower area-, yield- and applied fertilizer N- based emissions. Split urea ( \( \raisebox{1ex}{$2$}\!\left/ \!\raisebox{-1ex}{$3$}\right. \) pre-plant, \( \raisebox{1ex}{$1$}\!\left/ \!\raisebox{-1ex}{$3$}\right. \) hilling) also reduced area- and yield- based N₂O emissions compared to single pre-plant urea application. Emissions were generally lower at the site with loamy fine sandy soil than the site with clay loam soil. These results demonstrate that combinations of “4R” practices rather than source alone are best to achieve reductions in N₂O emissions from irrigated potato production.     

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.     

Structure of the Cell-Wall-Associated Polysaccharides from the Deep-Sea Marine Bacterium Devosia submarina KMM 9415T

Two cell-wall-associated polysaccharides were isolated and purified from the deep-sea marine bacterium Devosia submarina KMM 9415^T, purified by ultracentrifugation and enzymatic treatment, separated by chromatographic techniques, and studied by sugar analyses and NMR spectroscopy. The first polysaccharide with a molecular weight of about 20.7 kDa was found to contain d-arabinose, and the following structure of its disaccharide repeating unit was established: →2)-α-d-Araf-(1→5)-α-d-Araf-(1→. The second polysaccharide was shown to consist of d-galactose and a rare component of bacterial glycans-d-xylulose: →3)-α-d-Galp-(1→3)-β-d-Xluf-(1→.     

Fucoidan and Derived Oligo-Fucoses: Structural Features with Relevance in Competitive Inhibition of Gastrointestinal Norovirus Binding

Norovirus infections belong to the most common causes of human gastroenteritis worldwide and epidemic outbreaks are responsible for hundreds of thousands of deaths annually. In humans, noroviruses are known to bind to gastrointestinal epithelia via recognition of blood-group active mucin-type O-glycans. Considering the involvement of l-α-fucose residues in these glycans, their high valency on epithelial surfaces far surpasses the low affinity, though specific interactions of monovalent milk oligosaccharides. Based on these findings, we attempted to identify polyfucoses (fucans) with the capacity to block binding of the currently most prevalent norovirus strain GII.4 (Sydney, 2012, {"type":"entrez-nucleotide","attrs":{"text":"JX459908","term_id":"409032931"}}JX459908) to human and animal gastrointestinal mucins. We provide evidence that inhibitory effects on capsid binding are exerted in a competitive manner by α-fucosyl residues on Fucus vesiculosus fucoidan, but also on the galacto-fucan from Undaria pinnatifida and their oligo-fucose processing products. Insight into novel structural aspects of fucoidan and derived oligosaccharides from low-mass Undaria pinnatifida were revealed by GCMS and MALDI mass spectrometry. In targeting noroviral spread attenuation, this study provides first steps towards a prophylactic food additive that is produced from algal species.     

Different Morphologies of Leishmania major Amastigotes with No Molecular Diversity in a Neglected Endemic Area of Zoonotic Cutaneous Leishmaniasis in Iran

Background:

Molecular diversity of Leishmania major and its morphological changes have become a controversial issue among researchers. Some aspects of polymorphic shapes of amastigotes in clinical manifestations along with molecular variation were evaluated among suspected patients of some exceptional zoonotic cutaneous leishmaniasis locations in Northern Khuzestan, Southwestern Iran.

Methods:

Suspected patients (n = 165) were sampled in zoonotic cutaneous leishmaniasis foci over two consecutive years during 2012-2014. Prepared smears were stained, scaled and measured by ocular micrometer. DNA was extracted from smears; ITS-rDNA and Cytochrome b (Cyt b) markers were amplified, and PCR products were digested by BsuR1 restriction enzyme. Then the RFLP and sequencing were employed.

Results:

Only L. major was identified in patients containing regular amastigotes'' shapes (oval or round) with a size of 2-4 µm in each of classical wet, dry, mixed lesions. Meanwhile, irregular shapes (spindle, pear, or cigarette) were observed separately in non-classical wet lesions with more than 4 µm. Interestingly, a few amastigotes with an external flagellum were observed in some lesions. All sequenced ITS-rDNA and Cyt b genes of L. major did not show any molecular variation (χ ² P > 0.05), including only one common haplotype (GenBank access no. {"type":"entrez-nucleotide","attrs":{"text":"EF413075","term_id":"151936076","term_text":"EF413075"}}EF413075).

Conclusion:

Findings proved that unlike other endemic foci, there is not a meaningful correlation between phenotypic and genotypic features of L. major isolates. This study is considered as the first comprehensive report to incriminate morphometric shapes of L. major amastigotes, which enhances our knowledge concerning their relevance with various clinical appearances and genotypic traits. Key Words: Leishmania major, Nuclear gene, Mitochondrial gene, Amastigote shapes, Iran     

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.     

Assessment of bioflocculant production by Bacillus sp. Gilbert, a marine bacterium isolated from the bottom sediment of Algoa Bay

The bioflocculant-producing potentials of a marine bacteria isolated from the bottom sediment of Algoa Bay was investigated using standard methods. The 16S rDNA sequence analysis revealed 98% similarity to that of Bacillus sp. HXG-C1 and the nucleotide sequence was deposited in GenBank as Bacillus sp. Gilbert with accession number {"type":"entrez-nucleotide","attrs":{"text":"HQ537128","term_id":"312064208","term_text":"HQ537128"}}HQ537128. Bioflocculant was optimally produced when sucrose (72% flocculating activity) and ammonium chloride (91% flocculating activity) were used as sole sources of carbon and nitrogen, respectively; an initial pH 6.2 of the production medium; and Mg²⁺ as cation. Chemical analysis of the purified bioflocculant revealed the compound to be a polysaccharide.     

An open-source framework for large-scale,flexible evaluation of biomedical text mining systems

Background

Improved evaluation methodologies have been identified as a necessary prerequisite to the improvement of text mining theory and practice. This paper presents a publicly available framework that facilitates thorough, structured, and large-scale evaluations of text mining technologies. The extensibility of this framework and its ability to uncover system-wide characteristics by analyzing component parts as well as its usefulness for facilitating third-party application integration are demonstrated through examples in the biomedical domain.

Results

Our evaluation framework was assembled using the Unstructured Information Management Architecture. It was used to analyze a set of gene mention identification systems involving 225 combinations of system, evaluation corpus, and correctness measure. Interactions between all three were found to affect the relative rankings of the systems. A second experiment evaluated gene normalization system performance using as input 4,097 combinations of gene mention systems and gene mention system-combining strategies. Gene mention system recall is shown to affect gene normalization system performance much more than does gene mention system precision, and high gene normalization performance is shown to be achievable with remarkably low levels of gene mention system precision.

Conclusion

The software presented in this paper demonstrates the potential for novel discovery resulting from the structured evaluation of biomedical language processing systems, as well as the usefulness of such an evaluation framework for promoting collaboration between developers of biomedical language processing technologies. The code base is available as part of the BioNLP UIMA Component Repository on SourceForge.net.

     

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.     

Anne O'Tate: A tool to support user-driven summarization,drill-down and browsing of PubMed search results

Background

PubMed is designed to provide rapid, comprehensive retrieval of papers that discuss a given topic. However, because PubMed does not organize the search output further, it is difficult for users to grasp an overview of the retrieved literature according to non-topical dimensions, to drill-down to find individual articles relevant to a particular individual's need, or to browse the collection.

Results

In this paper, we present Anne O'Tate, a web-based tool that processes articles retrieved from PubMed and displays multiple aspects of the articles to the user, according to pre-defined categories such as the "most important" words found in titles or abstracts; topics; journals; authors; publication years; and affiliations. Clicking on a given item opens a new window that displays all papers that contain that item. One can navigate by drilling down through the categories progressively, e.g., one can first restrict the articles according to author name and then restrict that subset by affiliation. Alternatively, one can expand small sets of articles to display the most closely related articles. We also implemented a novel cluster-by-topic method that generates a concise set of topics covering most of the retrieved articles.

Conclusion

Anne O'Tate is an integrated, generic tool for summarization, drill-down and browsing of PubMed search results that accommodates a wide range of biomedical users and needs. It can be accessed at [4]. Peer review and editorial matters for this article were handled by Aaron Cohen.

     

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.     

Collaborative development of the Arrowsmith two node search interface designed for laboratory investigators

Arrowsmith is a unique computer-assisted strategy designed to assist investigators in detecting biologically-relevant connections between two disparate sets of articles in Medline. This paper describes how an inter-institutional consortium of neuroscientists used the UIC Arrowsmith web interface http://arrowsmith.psych.uic.edu in their daily work and guided the development, refinement and expansion of the system into a suite of tools intended for use by the wider scientific community.     

Are figure legends sufficient? Evaluating the contribution of associated text to biomedical figure comprehension

Background

Biomedical scientists need to access figures to validate research facts and to formulate or to test novel research hypotheses. However, figures are difficult to comprehend without associated text (e.g., figure legend and other reference text). We are developing automated systems to extract the relevant explanatory information along with figures extracted from full text articles. Such systems could be very useful in improving figure retrieval and in reducing the workload of biomedical scientists, who otherwise have to retrieve and read the entire full-text journal article to determine which figures are relevant to their research. As a crucial step, we studied the importance of associated text in biomedical figure comprehension.

Methods

Twenty subjects evaluated three figure-text combinations: figure+legend, figure+legend+title+abstract, and figure+full-text. Using a Likert scale, each subject scored each figure+text according to the extent to which the subject thought he/she understood the meaning of the figure and the confidence in providing the assigned score. Additionally, each subject entered a free text summary for each figure-text. We identified missing information using indicator words present within the text summaries. Both the Likert scores and the missing information were statistically analyzed for differences among the figure-text types. We also evaluated the quality of text summaries with the text-summarization evaluation method the ROUGE score.

Results

Our results showed statistically significant differences in figure comprehension when varying levels of text were provided. When the full-text article is not available, presenting just the figure+legend left biomedical researchers lacking 39–68% of the information about a figure as compared to having complete figure comprehension; adding the title and abstract improved the situation, but still left biomedical researchers missing 30% of the information. When the full-text article is available, figure comprehension increased to 86–97%; this indicates that researchers felt that only 3–14% of the necessary information for full figure comprehension was missing when full text was available to them. Clearly there is information in the abstract and in the full text that biomedical scientists deem important for understanding the figures that appear in full-text biomedical articles.

Conclusion

We conclude that the texts that appear in full-text biomedical articles are useful for understanding the meaning of a figure, and an effective figure-mining system needs to unlock the information beyond figure legend. Our work provides important guidance to the figure mining systems that extract information only from figure and figure legend.