Dataset of above and below ground traits assessed in Durum wheat cultivars grown under Mediterranean environments differing in water and temperature conditions.

Ideotypic characteristics of durum wheat associated with higher yield under different water and temperature regimes were studied under Mediterranean conditions. The focus of this paper is to provide raw and supplemental data from the research article entitled "Durum wheat ideotypes in Mediterranean environments differing in water and temperature conditions" [1], which aims to define specific durum wheat ideotypes according to their responses to different agronomic conditions. In this context, six modern (i.e. post green revolution) genotypes with contrasting yield performance (i.e. high vs low yield) were grown during two consecutive years under different treatments: (i) winter planting under support-irrigation conditions, (ii) winter planting under rainfed conditions, (iii) late planting under support-irrigation. Trials were conducted at the INIA station of Colmenar de Oreja (Madrid). Different traits were assessed to inform about water status (canopy temperature at anthesis and stable carbon isotope composition (δ13C) of the flag leaf and mature grains), root performance (root traits and the oxygen isotope composition (δ18O) in the stem base water), phenology (days from sowing to heading), nitrogen status/photosynthetic capacity (nitrogen content and stable isotope composition (δ15N) of the flag leaf and mature grain together with the pigment contents and the nitrogen balance index (NBI) of the flag leaf), crop growth (plant height (PH) and the normalized difference vegetation index (NDVI) at anthesis), grain yield and agronomic yield components. For most of the parameters assessed, data analysis demonstrated significant differences among genotypes within each treatment. The level of significance was determined using the Tukey-b test on independent samples, and ideotypes were modelled from the results of principle component analysis. The present data shed light on traits that help to define specific ideotype characteristics that confer genotypic adaptation to a wide range of agronomic conditions produced by variations in planting date, water conditions and season.

Mapping nucleosome and chromatin architectures: A survey of computational methods.

With ever-growing genomic sequencing data, the data variabilities and the underlying biases of the sequencing technologies pose significant computational challenges ranging from the need for accurately detecting the nucleosome positioning or chromatin interaction to the need for developing normalization methods to eliminate systematic biases. This review mainly surveys the computational methods for mapping the higher-resolution nucleosome and higher-order chromatin architectures. While a detailed discussion of the underlying algorithms is beyond the scope of our survey, we have discussed the methods and tools that can detect the nucleosomes in the genome, then demonstrated the computational methods for identifying 3D chromatin domains and interactions. We further illustrated computational approaches for integrating multi-omics data with Hi-C data and the advance of single-cell (sc)Hi-C data analysis. Our survey provides a comprehensive and valuable resource for biomedical scientists interested in studying nucleosome organization and chromatin structures as well as for computational scientists who are interested in improving upon them.

Quantification and identification analysis of Ziziphus jujuba Mill. peel pigmentation at different developmental stages.

The fruit peel of a color mutant jujube cultivar, 'Sanbianhong' (SBF), was investigated using an ultra-high performance liquid chromatography quadrupole Orbitrap mass spectrometry (UHPLC-Q-Orbitrap MS) at five ripening stages (S1, Young fruit stage; S2, swelling stage; S3, white-mature stage; S4, pre-mature stage and S5, mature stage). Lutein, ß-carotene, chlorophyll a, chlorophyll b, and 13 anthocyanins were identified. Chlorophyll a and cyanidin 3-O-galactoside were considered key color metabolites in S1 with the content of 1.083 mg/g of fresh weight (FW) and 4.585 mg/g of FW, respectively. Delphinidin (0.488 mg/g FW) and cyanidin (6.259 mg/g FW) were identified as the key pigments in S3. Delphinidin 3-O-glucoside (0.256 mg/g FW) was identified as the key anthocyanin in maturity S5. Herein, the identification and quantitation of pigment-related metabolites of SBF were studied for the first time, and the results provide a theoretical basis for understanding the pigment changes of jujube fruit during ripening.

Preliminary exploration of response the course of radiotherapy for stage III non-small cell lung cancer based on longitudinal CT radiomics features.

PURPOSE: Explore the longitudinal CT-based radiomics to demonstrate the changing trend of radiotherapy response and to determine at which point after the onset of treatment radiomics exhibit the greatest change for stage III NSCLC patients. METHODS AND MATERIALS: Ten stage III NSCLC patients in line with inclusion criteria were enrolled retrospectively, each of whom received radiotherapy or concurrent chemo-radiotherapy and performed eight series of follow-up CT imaging. Longitudinal radiomics were extracted on region of interest from the eight registered images, then two steps were conducted to select significant features as indicators of tumor change: 1) stable features were selected by Kendall rank correlation; 2) texture feature types with a steadily changing trend were retained and intensity features with stable change trends were selected to represent the large number of them. Next, the trend and rate of tumor change were analyzed using the Delta method and Curve-fitting method. Finally, the statistics in the distribution of stable features in patients were calculated. RESULTS: 675 stable features were selected from a total number of 1371 radiomics features, then 12 texture features types were retained and three intensity features were chosen to represent their own category. Among the final selected feature types, it was found that the two time points were weeks 1 and 3 with the higher rate of change. One patient had very few stable tumor features out of a total of 101 features, and the rate of change of features of another patient was conspicuously higher than the average level with number of 301 features. CONCLUSION: The longitudinal CT radiomics could demonstrate the change trend of tumor and at which point exhibit the greatest change during radiotherapy, and potentially be used for treatment decisions concerning adaptive radiotherapy.

Continuous direct compression: Development of an empirical predictive model and challenges regarding PAT implementation.

In this study, an empirical predictive model was developed based on the quantitative relationships between blend properties, critical quality attributes (CQA) and critical process parameters (CPP) related to blending and tableting. The blend uniformity and API concentration in the tablets were used to elucidate challenges related to the processability as well as the implementation of PAT tools. Thirty divergent ternary blends were evaluated on a continuous direct compression line (ConsiGma™ CDC-50). The trials showed a significant impact of the impeller configuration and impeller speed on the blending performance, whereas a limited impact of blend properties was observed. In contrast, blend properties played a significant role during compression, where changes in blend composition significantly altered the tablet quality. The observed correlations allowed to develop an empirical predictive model for the selection of process configurations based on the blend properties, reducing the number of trial runs needed to optimize a process and thus reducing development time and costs of new drug products. Furthermore, the trials elucidated several challenges related to blend properties that had a significant impact on PAT implementation and performance of the CDC-platform, highlighting the importance of further process development and optimization in order to solve the remaining challenges.

Continuous twin screw granulation: Impact of microcrystalline cellulose batch-to-batch variability during granulation and drying - A QbD approach.

Despite significant advances in the research domain of continuous twin screw granulation, limited information is currently available on the impact of raw material properties, especially considering batch-to-batch variability. The importance of raw material variability and subsequent mitigation of the impact of this variability on the manufacturing process and drug product was recently stressed in the Draft Guidance for Industry on Quality Considerations for Continuous Manufacturing by the U.S. Food and Drug Administration (FDA). Therefore, this study assessed the impact of microcrystalline cellulose (MCC) batch-to-batch variability and process settings in a continuous twin screw wet granulation and semi-continuous drying line. Based on extensive raw material characterization and subsequent principal component analysis, raw material variability was quantitatively introduced in the design of experiments approach by means of t1 and t2 scores. L/S ratio had a larger effect on critical granule attributes and processability than screw speed and drying time. A large impact of the t1 and t2 scores was found, indicating the importance of raw material attributes. For the studied formulation, it was concluded that MCC batches with a low water binding capacity, low moisture content and high bulk density generated granules with the most desirable quality attributes. Additionally, an innovative and quantitative approach towards mitigating batch-to-batch variability of raw materials was proposed, which is also applicable for additional excipients and APIs.

Raman spectroscopy links differentiating osteoblast matrix signatures to pro-angiogenic potential.

Mineralization of bone is achieved by the sequential maturation of the immature amorphous calcium phase to mature hydroxyapatite (HA) and is central in the process of bone development and repair. To study normal and dysregulated mineralization in vitro, substrates are often coated with poly-l-lysine (PLL) which facilitates cell attachment. This study has used Raman spectroscopy to investigate the effect of PLL coating on osteoblast (OB) matrix composition during differentiation, with a focus on collagen specific proline and hydroxyproline and precursors of HA. Deconvolution analysis of murine derived long bone OB Raman spectra revealed collagen species were 4.01-fold higher in OBs grown on PLL. Further, an increase of 1.91-fold in immature mineral species (amorphous calcium phosphate) was coupled with a 9.32-fold reduction in mature mineral species (carbonated apatite) on PLL versus controls. These unique low mineral signatures identified in OBs were linked with reduced alkaline phosphatase enzymatic activity, reduced Alizarin Red staining and altered osteogenic gene expression. The promotion of immature mineral species and restriction of mature mineral species of OB grown on PLL were linked to increased cell viability and pro-angiogenic vascular endothelial growth factor (VEGF) production. These results demonstrate the utility of Raman spectroscopy to link distinct matrix signatures with OB maturation and VEGF release. Importantly, Raman spectroscopy could provide a label-free approach to clinically assess the angiogenic potential of bone during fracture repair or degenerative bone loss.

1H NMR-based metabolomic study of metabolic profiling for pollinosis.

BACKGROUND: Allergic rhinitis is the main symptom of pollinosis, relieved by non-specific treatment universally. This study aimed to find the changes of serum metabolites between the seizure and remission periods of pollinosis and provide assistance in the diagnosis and/or therapy. METHODS: Metabonomics based on 1H nuclear magnetic resonance (NMR) was used to study the 37 serum samples of pollinosis patients. RESULTS: We believed that the decreased levels of isoleutine, leutine, valine, 3-hydroxybutyric acid, allo-threonine, alanine, methionine, glutamine, lysine, glycine, l-tyrosine, histidine, phenylalanine, lactate, acetate, O-acetylcholine, creatine and creatinine and the increased level of N-acetylglutamine at the seizure stage were statistically significant. CONCLUSIONS: Pollinosis could change the metabolic profiles of energy, amino acid and lipid in patients, which might be the diagnosis and/or prognosis markers for hay fever patients.

Comprehensive relative quantitative metabolomics analysis of lycopodium alkaloids in different tissues of Huperzia serrata.

Qian ceng Ta, the whole plant of Huperzia serrata, is an important landscape and medicinal herbs and contains abundant bioactive lycopodium alkaloids. Although the structures of more than 100 lycopodium alkaloids in Huperzia serrata have been isolated and identified, the content and distribution of these alkaloids in different tissues are still unclear. In current study, an ultra-performance liquid chromatography-mass spectrometry based comprehensive metabolomics strategy was developed, including the extraction, separation, identification, and statistical analysis. The results showed that different types lycopodium alkaloids could be separated at different time-windows, which was helpful for further metabolite identification. Peak4388 and peak3954 were metabolite biomarkers for the different tissues according to the principle component analysis and partial least squares-discriminant analysis model. A computational tool based in-house database was also built up and used for putative identification. Of the 2354 true peaks after four-step filtration, 118 peaks were putatively identified as lycopodium alkaloids by using in-house database, and four of which was identified by authentic standards. Alternatively, another computational software was used to predict the fragmentation pattern, to dereplicate the structure of identified peaks, and identified the peak3585 to N-methylhuperzine A. The integration of both computational tools could be used for more metabolites identification.

Unraveling the efficiency of RAPD and SSR markers in diversity analysis and population structure estimation in common bean.

Increase in food production viz-a-viz quality of food is important to feed the growing human population to attain food as well as nutritional security. The availability of diverse germplasm of any crop is an important genetic resource to mine the genes that may assist in attaining food as well as nutritional security. Here we used 15 RAPD and 23 SSR markers to elucidate diversity among 51 common bean genotypes mostly landraces collected from the Himalayan region of Jammu and Kashmir, India. We observed that both the markers are highly polymorphic. The discriminatory power of these markers was determined using various parameters like; percent polymorphism, PIC, resolving power and marker index. 15 RAPDs produced 171 polymorphic bands, while 23 SSRs produced 268 polymorphic bands. SSRs showed a higher PIC value (0.300) compared to RAPDs (0.243). Further the resolving power of SSRs was 5.241 compared to 3.86 for RAPDs. However, RAPDs showed a higher marker index (2.69) compared to SSRs (1.279) that may be attributed to their higher multiplex ratio. The dendrograms generated with hierarchical UPGMA cluster analysis grouped genotypes into two main clusters with various degrees of sub clustering within the cluster. Here we observed that both the marker systems showed comparable accuracy in grouping genotypes of common bean according to their area of cultivation. The model based STRUCTURE analysis using 15 RAPD and 23 SSR markers identified a population with 3 sub-populations which corresponds to distance based groupings. High level of genetic diversity was observed within the population. These findings have further implications in common bean breeding as well as conservation programs.

â¿¿Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples.

Large biobanks exist worldwide containing formalin-fixed, paraffin-embedded samples and samples stored in RNAlater. However, the impact of tissue preservation on the result of a quantative proteome analysis remains poorly described. Human colon mucosal biopsies were extracted from the sigmoideum and either immediately frozen, stabilized in RNAlater, or stabilized by formalin-fixation. In one set of biopsies, formalin stabilization was delayed for 30 min. The protein content of the samples was characterized by high throughput quantitative proteomics. We were able to identify a similar high number of proteins in the samples regardless of preservation method, with only minor differences in protein quantitation.

Proapoptotic activity of aflatoxin B1 and sterigmatocystin in HepG2 cells.

Aflatoxin B1 (AFB1) and sterigmatocystin (ST) are two hepatocarcinogenic mycotoxins that are commonly coexisted in cereal grains, and their co-proapoptotic activity in HepG2 cells was studied. The values of IC50, which is the dosage of mycotoxin resulting in a 50% cell growth inhibition measured by a sulforhodamine B (SRB) colorimetric assay, were 16.9 µM and 7.3 µM for AFB1 and ST, respectively. Additively and dose-dependently, cell apoptosis-related toxicity endpoints of double strand DNA and ATP content were decreased while the intracellular ROS and mitochondria membrane permeability (MMP) were increased. Consistently, when cell cycle is arrest at G0/G1 or S phase by AFB1 and/or ST, the experimental results from flow cytometry assay demonstrated that the rate of cell apoptosis and mitochondrial membrane potential were also additively increased and decreased, respectively, in a dose-dependent manner. Thus, the integrity of mitochondria (MMP and membrane potential) that is the central component of cell apoptosis is disrupted by AFB1 and ST in an additive manner. With the immunocytochemistry analysis showing increased expression of apoptosis-related proteins of Bax, Caspase-3 and p53 and decreased expression of Bcl-2 protein, an additive nature of the co-proapoptotic activity of AFB1 and ST was revealed.