Sulfobetaine-Phosphonate Block Copolymer Coated Iron Oxide Nanoparticles for Genomic Locus Targeting and Magnetic Micromanipulation in the Nucleus of Living Cells.

Exerting forces on biomolecules inside living cells would allow us to probe their dynamic interactions in their native environment. Magnetic iron oxide nanoparticles represent a unique tool capable of pulling on biomolecules with the application of an external magnetic field gradient; however, their use has been restricted to biomolecules accessible from the extracellular medium. Targeting intracellular biomolecules represents an additional challenge due to potential nonspecific interactions with cytoplasmic or nuclear components. We present the synthesis of sulfobetaine-phosphonate block copolymer ligands, which provide magnetic nanoparticles that are stealthy and targetable in living cells. We demonstrate, for the first time, their efficient targeting in the nucleus and their use for magnetic micromanipulation of a specific genomic locus in living cells. We believe that these stable and sensitive magnetic nanoprobes represent a promising tool to manipulate specific biomolecules in living cells and probe the mechanical properties of living matter at the molecular scale.

Network principal component analysis: a versatile tool for the investigation of multigroup and multiblock datasets.

MOTIVATION: Complex data structures composed of different groups of observations and blocks of variables are increasingly collected in many domains, including metabolomics. Analysing these high-dimensional data constitutes a challenge, and the objective of this article is to present an original multivariate method capable of explicitly taking into account links between data tables when they involve the same observations and/or variables. For that purpose, an extension of standard principal component analysis called NetPCA was developed. RESULTS: The proposed algorithm was illustrated as an efficient solution for addressing complex multigroup and multiblock datasets. A case study involving the analysis of metabolomic data with different annotation levels and originating from a chronic kidney disease (CKD) study was used to highlight the different aspects and the additional outputs of the method compared to standard PCA. On the one hand, the model parameters allowed an efficient evaluation of each group's influence to be performed. On the other hand, the relative relevance of each block of variables to the model provided decisive information for an objective interpretation of the different metabolic annotation levels. AVAILABILITY AND IMPLEMENTATION: NetPCA is available as a Python package with NumPy dependencies. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants.

Microsatellites, or simple sequence repeats (SSRs), are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development. Although 454 pyrosequencing datasets can be used for SSR development, this type of sequencing is no longer supported. This review aims to present an overview of the next generation sequencing, with a focus on the efficient use of de novo transcriptome sequencing (RNA-Seq) and related tools for mining and development of microsatellites in plants.

Genetic variation, heritability, divergence and biomass accumulation of rice genotypes resistant to bacterial blight revealed by quantitative traits and ISSR markers.

A field experiment was carried out in order to evaluate genetic diversity of 41 rice genotypes using physiological traits and molecular markers. All the genotypes unveiled variations for crop growth rate (CGR), relative growth rate (RGR), net assimilation rate (NAR), yield per hill (Yhill(-1)), total dry matter (TDM), harvest index (HI), photosynthetic rate (PR), leaf area index (LAI), chlorophyll-a and chlorophyll-b at maximum tillering stage. The CGR values varied from 0.23 to 0.76 gm cm(-2) day(-1). The Yhill(-1) ranged from 15.91 to 92.26 g, while TDM value was in the range of 7.49 to 20.45 g hill(-1). PR was found to vary from 9.40 to 22.34 µmol m(-2) s(-1). PR expressed positive relation with Yhill(-1). Significant positive relation was found between CGR and TDM (r = 0.61**), NAR and CGR (r = 0.62**) and between TDM and NAR (r = 0.31**). High heritability was found in RGR and Yhill(-1). Cluster analysis based on the traits grouped 41 rice genotypes into seven clusters. A total of 310 polymorphic loci were detected across the 20 inter-simple sequence repeats (ISSR) markers. The UPGMA dendrogram grouped 41 rice genotypes into 11 clusters including several sub-clusters. The Mantel test revealed positive correlation between quantitative traits and molecular markers (r = 0.41). On the basis of quantitative traits and molecular marker analyses parental genotypes, IRBB54 with MR84, IRBB60 with MR84, Purbachi with MR263, IRBB65 with BR29, IRBB65 with Pulut Siding and MRQ74 with Purbachi could be hybridized for future breeding program.

Glass-transition temperature gradient in nanocomposites: evidence from nuclear magnetic resonance and differential scanning calorimetry.

The slowing-down of the dynamics of a polymer chain near a surface has been observed for many years now. Here we show that the behavior of model nanocomposites can be quantitatively described with a gradient of glass-transition temperature. We describe with a single parameter-the range of this gradient-the temperature and solvent effect on the spin relaxation dynamics. Moreover, this parameter allows a quantitative description of the nanocomposite calorimetric response from the one of the bulk polymer.

Highly enhanced affinity of multidentate versus bidentate zwitterionic ligands for long-term quantum dot bioimaging.

High colloidal stability in aqueous conditions is a prerequisite for fluorescent nanocrystals, otherwise known as "quantum dots", intended to be used in any long-term bioimaging experiment. This essential property implies a strong affinity between the nanoparticles themselves and the ligands they are coated with. To further improve the properties of the bidentate monozwitterionic ligand previously developed in our team, we synthesized a multidentate polyzwitterionic ligand, issued from the copolymerization of a bidentate monomer and a monozwitterionic one. The nanocrystals passivated by this polymeric ligand showed an exceptional colloidal stability, regardless of the medium conditions (pH, salinity, dilution, and biological environment), and we demonstrated the affinity of the polymer exceeded by 3 orders of magnitude that of the bidentate ligand (desorption rates assessed by a competition experiment). The synthesis of the multidentate polyzwitterionic ligand proved also to be easily tunable and allowed facile functionalization of the corresponding quantum dots, which led to successful specific biomolecules targeting.

Gaining Insights Into Metabolic Networks Using Chemometrics and Bioinformatics: Chronic Kidney Disease as a Clinical Model.

Because of its ability to generate biological hypotheses, metabolomics offers an innovative and promising approach in many fields, including clinical research. However, collecting specimens in this setting can be difficult to standardize, especially when groups of patients with different degrees of disease severity are considered. In addition, despite major technological advances, it remains challenging to measure all the compounds defining the metabolic network of a biological system. In this context, the characterization of samples based on several analytical setups is now recognized as an efficient strategy to improve the coverage of metabolic complexity. For this purpose, chemometrics proposes efficient methods to reduce the dimensionality of these complex datasets spread over several matrices, allowing the integration of different sources or structures of metabolic information. Bioinformatics databases and query tools designed to describe and explore metabolic network models offer extremely useful solutions for the contextualization of potential biomarker subsets, enabling mechanistic hypotheses to be considered rather than simple associations. In this study, network principal component analysis was used to investigate samples collected from three cohorts of patients including multiple stages of chronic kidney disease. Metabolic profiles were measured using a combination of four analytical setups involving different separation modes in liquid chromatography coupled to high resolution mass spectrometry. Based on the chemometric model, specific patterns of metabolites, such as N-acetyl amino acids, could be associated with the different subgroups of patients. Further investigation of the metabolic signatures carried out using genome-scale network modeling confirmed both tryptophan metabolism and nucleotide interconversion as relevant pathways potentially associated with disease severity. Metabolic modules composed of chemically adjacent or close compounds of biological relevance were further investigated using carbon transfer reaction paths. Overall, the proposed integrative data analysis strategy allowed deeper insights into the metabolic routes associated with different groups of patients to be gained. Because of their complementary role in the knowledge discovery process, the association of chemometrics and bioinformatics in a common workflow is therefore shown as an efficient methodology to gain meaningful insights in a clinical context.

Valorization of rare earth processing byproducts for agriculture usage.

Sandy texture soil, a major problem for agriculture requires structure and capacity improvements. However, utilization of soil conditioner may arrest this problem. This research was carried out to investigate the accumulated levels of metal ions and radionuclides in water, soil and plants following phosphogypsum organic (PG organic) added to a sandy soil for 23-month in 3 cropping seasons. The condition in the field was simulated in the laboratory using an open leaching column for 30-day under constant but different pH of leachant. More ions were released at pH < 4.6 and decreases greatly at pH > 5.6. The metal ions measured in the surface and borehole water, and soils were below the target values for respective standard raw drinking water. The metal ions did not accumulate in soil, plant and grain, and water as indicated by biological accumulation coefficients, contamination factors, I-geo index and pollution load index in a sandy soil that received the PG organic. Naturally occurring radionuclide concentrations, such as 226Ra, 228Ra, and 40K, in soil and plant tissue were found to be lower than the average value reported by several earlier studies. Under field condition the pH of water (i.e., rainfall) was greater than pH 5.6, thus renders PG organic became less soluble. There was no leaching of natural occurring radionuclides to the groundwater. Therefore, the application of PG organic to the studied soil had no impact on the soil, plants, and water and suitable as a soil conditioner in sandy texture soils.

Phosphorus leaching in an acid tropical soil "recapitalized" with phosphate rock and triple superphosphate.

With high rates of phosphorus applied to increase "capital P" as a stock for plant uptake over several years, the question of P leaching is inevitable. We conducted an intact soil column experiment in the field to evaluate P leached from soils treated with triple superphosphate (TSP) and Gafsa phosphate rock (GPR) at 300, 600, and 900 kg P ha-1 with and without integration of cattle manure. The lysimeters, made from PVC tubes of 30-cm length, were inserted into the soil up to the 25-cm depth. The tubes were fitted with a resin bag containing a mixture of cation and anion exchange resin (50:50) at the lower end of the tube inserted into the soil. The tubes, arranged in a completely randomized design, were sampled randomly at 10-week intervals for 12 months. Phosphorus extractable from the top- and subsoil at the end of experiment and leached P were determined. More P was leached out from TSP (threefold) compared to GPR, and the amount of P leached increased with increasing rates of P fertilizer applied. Application of manure intensified the amounts of P leached from TSP, particularly at the 6-month sampling time. There was hardly any substantial P leached from the soil treated with GPR. Thus, for effective and efficient long-term P fertilizer management strategies, choosing the right P fertilizer source and monitoring P losses through leaching has to be done for enhanced fertilizer use efficiency and thus reducing P pollution of ground waters.

Comparison of soil phosphorus tests for assessing plant availability of phosphorus in an ultisol amended with water-soluble and phosphate rock sources.

The effectiveness of different soil tests in assessing soil phosphorus (P) in soils amended with phosphate rocks (PRs) is uncertain. We evaluated the effects of triple superphosphate (TSP) and PRs on extractable P by conventional soil tests (Mehlich 3 [Meh3] and Bray-1 [B1]) and a nonconventional test (iron oxide-impregnated paper, strip). Extracted amounts of P were in the order: Meh3 >B1 > strip. All the tests were significantly correlated (p = 0.001). Acidic reagents extracted more P from TSP than PRs, while the strip removed equal amounts from the two sources. The P removed by the three tests was related significantly to dry matter yield (DMY), but only in the first harvest, except for B1. Established critical P levels (CPLs) differed for TSP and PRs. In PR-fertilized soils, CPLs were 27, 17, and 12 mg P kg(-1) soil for Meh3, B1, and strip, respectively, and 42, 31, and 12 mg P kg(-1) soil, respectively, in TSP-fertilized soils. Thus, the strip resulted in a common CPL for TSP and PRs (12 mg P kg(-1) soil). This method can be used effectively in soils where integrated nutrient sources have been used, but there is need to establish CPLs for different crops. For cost-effective fertilizer P recommendations based on conventional soil tests, there is a need to conduct separate calibrations for TSP- and PR-fertilized soils.

A promising "metastable" liquid crystal stationary phase for gas chromatography.

The liquid crystal state is an ordered physical state between a solid and a liquid. Previous research, in gas chromatography, proved that it provides a geometric selectivity, which allows the separation of geometric position isomers and cis-trans isomers that are difficult to separate on conventional gas chromatography stationary phases (polydimethyl siloxane derived and polyethylene glycol stationary phases). However, their use was generally very limited by the rather high temperature at which they must be operated, normally above the solid-liquid crystal transition temperature. In the present study we are interested in a new synthesized material, 1,4- bis (4-bromohexyloxy benzoate) phenyl (BHOBP). The first characterizations of BHOBP were carried out by thermogravimetric analysis, hot-stage optical microscopy and differential scanning calorimetry to control the thermal stability of the BHOBP as well as the nematic texture of the mesophase highlighted in a well-defined temperature range (120 °C-200 °C). When heated, the solid compound led to a stable liquid crystal state. Its cooling has revealed "a new metastable physical state, which is the supercooled liquid crystal phase". After these first characterizations, the new material was used as a stationary phase for gas chromatography. The BHOBP was deposited in a capillary column by the dynamic method. The inverse gas chromatography study of the column revealed a solid-stable nematic phase transition temperature, in agreement with the first characterization methods. The stable liquid crystal phase showed good resolutions in the analysis of some geometric isomers of low volatility as PAHs. The presence of the supercooled liquid crystal state in the chromatographic column has also been confirmed. This new metastable state is particularly interesting because it enlarged the scope of this material by improving the resolution of several mixtures. Thus, the separation of highly volatile mixtures of geometric isomers (e.g. cis and trans-decalin) was achieved only through this metastable mesophase confirming its unique selectivity. The metastable liquid crystal, used at 80 °C, has also exhibited an original behavior by its stability after several weeks of use at the same temperature, maintaining constant retention factors and selectivity.

Rouse 2D Diffusion of Polymer Chains in Low Density Precursor Films of Polybutadiene Melts.

We took advantage of pseudopartial wetting to promote the spreading of precursor films whose surface density smoothly decays to zero away from a sessile droplet. By following the spreading dynamics of semidilute precursor films of polybutadiene melts on silicon wafers, we measure molecular diffusion coefficients for different molar masses and temperatures. For homopolymers, chains follow a thermally activated 2D Rouse diffusion mechanism, with an activation energy revealing polymer segment interactions with the surface. This Rouse model is generalized to chains with specific terminal groups.

Epigenetic changes and their relationship to somaclonal variation: a need to monitor the micropropagation of plantation crops.

Chromatin modulation plays important roles in gene expression regulation and genome activities. In plants, epigenetic changes, including variations in histone modification and DNA methylation, are linked to alterations in gene expression. Despite the significance and potential of in vitro cell and tissue culture systems in fundamental research and marketable applications, these systems threaten the genetic and epigenetic networks of intact plant organs and tissues. Cell and tissue culture applications can lead to DNA variations, methylation alterations, transposon activation, and finally, somaclonal variations. In this review, we discuss the status of the current understanding of epigenomic changes that occur under in vitro conditions in plantation crops, including coconut, oil palm, rubber, cotton, coffee and tea. It is hoped that comprehensive knowledge of the molecular basis of these epigenomic variations will help researchers develop strategies to enhance the totipotent and embryogenic capabilities of tissue culture systems for plantation crops.

GanoCare® Improves Oil Palm Growth and Resistance against Ganoderma Basal Stem Rot Disease in Nursery and Field Trials.

Basal stem rot (BSR) caused by Ganoderma boninense is a major threat to sustainable oil palm production especially in Southeast Asia and has brought economic losses to the oil palm industry around the world. With no definitive cure at present, this study introduces a new fertilizer technology called GanoCare®, as an effort to suppress BSR incidence in oil palm. Experiments were carried out to evaluate the effect of GanoCare® on growth, physiology, and BSR disease suppression using sitting technique in the oil palm nursery stage. A follow-up using similar treatments was carried out in the field to test on severity of Ganoderma using baiting technique under natural condition. Treatments tested were 10 g/month and 30 g/three months given as pretreatment only or continuous treatment. Results showed that GanoCare® increased the height, bulb diameter, leaf area, chlorophyll content, photosynthesis rate, and fresh and dry weight of the leaf, bole, and root of oil palm seedlings in the nursery trial. Seedlings treated with GanoCare® exhibited reduced percentage of disease severity, incidence, and dead seedlings, compared to the control. In nursery and field, lowest percentage of dead seedlings due to Ganoderma was found in seedlings given combination of pretreatment and continuous treatment of 30 g/three months (T4) with 5.56 and 6.67%, while control seedlings significantly marked the maximum percentage of 94.45 and 93.33%. The most successful treatment in both nursery and field was T4 with disease reductions of 77.78 and 82.36%, respectively, proving that nutrients contained in GanoCare® are essential in allowing better development of a strong defense system in the seedlings.

Discrimination of diesel fuels marketed in Morocco using FTIR, GC-MS analysis and chemometrics methods.

The purpose of this study was to perform a discrimination and classification of diesel samples from the four major suppliers of petroleum products in Morocco using Fourier Transform Infrared Spectroscopy (FTIR), Gas Chromatography coupled with Mass Spectrometry (GC-MS) and chemometrics tools. Eighty diesel samples were collected from different gas stations owned by the four biggest brands in the Moroccan market. Principal Component Analysis (PCA) was performed to depict the similarities between the samples and check the presence of outliers. Partial Least Squares Discriminant Analysis (PLS-DA) models were set up for the discrimination and the classification of the four groups of samples (i.e., diesel suppliers). The models proposed in this study, were characterized by good prediction abilities, especially the FTIR-PLSDA model that was characterized by 100% of accurate discrimination of the four groups. The approach of analysis showed that the FTIR spectra can provide a cheap and rapid means for the determination of the diesel origin and to ensure the traceability of diesel products marketed in Morocco with respect for the rules of the green chemistry.

Adaptation of the metabolomics profile of rice after Pyricularia oryzae infection.

Pyricularia oryzae (P. oryzae), one of the most devastating fungal pathogens, is the cause of blast disease in rice. Infection with a blast fungus induces biological responses in the host plant that lead to its survival through the termination or suppression of pathogen growth, and metabolite compounds play vital roles in plant interactions with a wide variety of other organisms. Numerous studies have indicated that rice has a multi-layered plant immune system that includes pre-developed (e.g., cell wall and phytoanticipins), constitutive and inducible (phytoalexins) defence barriers against stresses. Significant progress towards understanding the basis of the molecular mechanisms underlying the defence responses of rice to P. oryzae has been achieved. Nonetheless, even though the important metabolites in the responses of rice to pathogens have been identified, their exact mechanisms and their contributions to plant immunity against blast fungi have not been elucidated. The purpose of this review is to summarize and discuss recent advances towards the understanding of the integrated metabolite variations in rice after P. oryzae invasion.

Zwitterionic polymer ligands: an ideal surface coating to totally suppress protein-nanoparticle corona formation?

In the last few years, zwitterionic polymers have been developed as antifouling surface coatings. However, their ability to completely suppress protein adsorption at the surface of nanoparticles in complex biological media remains undemonstrated. Here we investigate the formation of hard (irreversible) and soft (reversible) protein corona around model nanoparticles (NPs) coated with sulfobetaine (SB), phosphorylcholine (PC) and carboxybetaine (CB) polymer ligands in model albumin solutions and in whole serum. We show for the first time a complete absence of protein corona around SB-coated NPs, while PC- and CB-coated NPs undergo reversible adsorption or partial aggregation. These dramatic differences cannot be described by naïve hard/soft acid/base electrostatic interactions. Single NP tracking in the cytoplasm of live cells corroborate these in vitro observations. Finally, while modification of SB polymers with additional charged groups lead to consequent protein adsorption, addition of small neutral targeting moieties preserves antifouling and enable efficient intracellular targeting.

Improvement of Drought Tolerance in Rice (Oryza sativa L.): Genetics, Genomic Tools, and the WRKY Gene Family.

Drought tolerance is an important quantitative trait with multipart phenotypes that are often further complicated by plant phenology. Different types of environmental stresses, such as high irradiance, high temperatures, nutrient deficiencies, and toxicities, may challenge crops simultaneously; therefore, breeding for drought tolerance is very complicated. Interdisciplinary researchers have been attempting to dissect and comprehend the mechanisms of plant tolerance to drought stress using various methods; however, the limited success of molecular breeding and physiological approaches suggests that we rethink our strategies. Recent genetic techniques and genomics tools coupled with advances in breeding methodologies and precise phenotyping will likely reveal candidate genes and metabolic pathways underlying drought tolerance in crops. The WRKY transcription factors are involved in different biological processes in plant development. This zinc (Zn) finger protein family, particularly members that respond to and mediate stress responses, is exclusively found in plants. A total of 89 WRKY genes in japonica and 97 WRKY genes in O. nivara (OnWRKY) have been identified and mapped onto individual chromosomes. To increase the drought tolerance of rice (Oryza sativa L.), research programs should address the problem using a multidisciplinary strategy, including the interaction of plant phenology and multiple stresses, and the combination of drought tolerance traits with different genetic and genomics approaches, such as microarrays, quantitative trait loci (QTLs), WRKY gene family members with roles in drought tolerance, and transgenic crops. This review discusses the newest advances in plant physiology for the exact phenotyping of plant responses to drought to update methods of analysing drought tolerance in rice. Finally, based on the physiological/morphological and molecular mechanisms found in resistant parent lines, a strategy is suggested to select a particular environment and adapt suitable germplasm to that environment.

Antioxidant Enzyme Activities and Secondary Metabolite Profiling of Oil Palm Seedlings Treated with Combination of NPK Fertilizers Infected with Ganoderma boninense.

Oil palm (Elaeis guineensis Jacq) is one of the major sources of edible oil. Reducing the effect of Ganoderma, main cause of basal stem rot (BSR) on oil palm, is the main propose of this study. Understanding the oil palm defense mechanism against Ganoderma infection through monitoring changes in the secondary metabolite compounds levels before/after infection by Ganoderma under different fertilizing treatment is required. Oil palm requires macro- and microelements for growth and yield. Manipulating the nutrient for oil palm is a method to control the disease. The 3-4-month-old oil palm seedlings were given different macronutrient treatments to evaluate induction of defense related enzymes and production of secondary metabolite compounds in response to G. boninense inoculation. The observed trend of changes in the infected and uninfected seedlings was a slightly higher activity for ß-1,3-glucanases, chitinase, peroxidase, and phenylalanine ammonia-lyase during the process of pathogenesis. It was found that PR proteins gave positive response to the interaction between oil palm seedlings and Ganoderma infection. Although the responses were activated systematically, they were short-lasting as the changes in enzymes activities appeared before the occurrence of visible symptoms. Effect of different nutrients doses was obviously observed among the results of the secondary metabolite compounds. Many identified/unidentified metabolite compounds were presented, of which some were involved in plant cell defense mechanism against pathogens, mostly belonging to alkaloids with bitter-tasting nitrogenous-compounds, and some had the potential to be used as new markers to detect basal stem rot at the initial step of disease.

Contribution of transposable elements in the plant's genome.

Plants maintain extensive growth flexibility under different environmental conditions, allowing them to continuously and rapidly adapt to alterations in their environment. A large portion of many plant genomes consists of transposable elements (TEs) that create new genetic variations within plant species. Different types of mutations may be created by TEs in plants. Many TEs can avoid the host's defense mechanisms and survive alterations in transposition activity, internal sequence and target site. Thus, plant genomes are expected to utilize a variety of mechanisms to tolerate TEs that are near or within genes. TEs affect the expression of not only nearby genes but also unlinked inserted genes. TEs can create new promoters, leading to novel expression patterns or alternative coding regions to generate alternate transcripts in plant species. TEs can also provide novel cis-acting regulatory elements that act as enhancers or inserts within original enhancers that are required for transcription. Thus, the regulation of plant gene expression is strongly managed by the insertion of TEs into nearby genes. TEs can also lead to chromatin modifications and thereby affect gene expression in plants. TEs are able to generate new genes and modify existing gene structures by duplicating, mobilizing and recombining gene fragments. They can also facilitate cellular functions by sharing their transposase-coding regions. Hence, TE insertions can not only act as simple mutagens but can also alter the elementary functions of the plant genome. Here, we review recent discoveries concerning the contribution of TEs to gene expression in plant genomes and discuss the different mechanisms by which TEs can affect plant gene expression and reduce host defense mechanisms.