Deep Learning Insights into the Dynamic Effects of Photodynamic Therapy on Cancer Cells.

Photodynamic therapy (PDT) shows promise in tumor treatment, particularly when combined with nanotechnology. This study examines the impact of deep learning, particularly the Cellpose algorithm, on the comprehension of cancer cell responses to PDT. The Cellpose algorithm enables robust morphological analysis of cancer cells, while logistic growth modelling predicts cellular behavior post-PDT. Rigorous model validation ensures the accuracy of the findings. Cellpose demonstrates significant morphological changes after PDT, affecting cellular proliferation and survival. The reliability of the findings is confirmed by model validation. This deep learning tool enhances our understanding of cancer cell dynamics after PDT. Advanced analytical techniques, such as morphological analysis and growth modeling, provide insights into the effects of PDT on hepatocellular carcinoma (HCC) cells, which could potentially improve cancer treatment efficacy. In summary, the research examines the role of deep learning in optimizing PDT parameters to personalize oncology treatment and improve efficacy.

PXMP4 promotes gastric cancer cell epithelial-mesenchymal transition via the PI3K/AKT signaling pathway.

BACKGROUND: Peroxisomal membrane protein 4 (PXMP4), a member of the peroxisome membrane protein PXMP2/4 family, participates in the progression of several malignant cancers. Nevertheless, the effect of PXMP4 in the development of gastric cancer (GC) is still unknown. As a result, the focus of this investigation was to elucidate the potential mechanisms of PXMP4 in GC. METHODS AND RESULTS: Firstly, bioinformatics analysis results showed higher expression of PXMP4 in GC tissues. Secondly, clinical analysis of 57 patients with GC revealed correlations between PXMP4 expression and differentiation, depth of invasion, as well as TNM stage. Furthermore, individuals with elevated PXMP4 expression in GC exhibited an unfavorable prognosis. In vitro data showed the involvement of knockdown/overexpression of PXMP4 in the proliferation, invasion, and migration of GC cells, and triggering the epithelial-mesenchymal transition (EMT) of GC cells through the activation of the PI3K/AKT signaling pathway. LY294002, a PI3K/AKT inhibitor, inhibited the expression of PI3K/AKT-related proteins but did not affect the expression of PXMP4. CONCLUSIONS: These findings indicate that PXMP4 potentially functions as an upstream molecule in the PI3K/AKT pathway, governing the EMT process in GC.

A study of the role of multiple layer-by-layer assembled bionic extracellular matrix in promoting wound healing via activation of the Wnt signaling pathway.

Wound healing is a multicellular collaborative process in which the adhesion and proliferation of fibroblasts in the wound is the basis for ensuring rapid wound healing, and in this process, it can promote the regeneration and remodeling of tissue and extracellular matrix. Studies have shown that Arg-Gly-Asp adhesive peptide (RGD) and basic fibroblast growth factor (bFGF) can stimulate the adhesion and proliferation of fibroblasts by activating the Wnt/ß-catenin signaling pathway, respectively. This study adopts the principle of layer-by-layer self-assembly, and the binding force formed by electrostatic attraction and Schiff base was used to combine bFGF and RGD with collagen membrane to form a biomimetic membrane that is non-cytotoxic with strong biocompatibility that could promote soft tissue healing. The surface characteristics of MLCM and the sustained release concentration of bFGF in vitro were measured, and the effects of MLCM on cell viability, proliferation, migration, and wound healing by means of Wnt/catenin pathways were studied through cell experiments and animal experiments under the comparison of negative control groups and positive control groups. The results showed that MLCM could stimulate wound healing more actively and had a positive effect on cell activity, proliferation, and migration. During wound healing, MLCM activates the Wnt/ß-catenin signaling pathway and inhibition of Wnt/ß-catenin signaling pathway significantly reduces the positive effects of MLCM on wound healing.

QTL mapping and candidate gene analysis for yield and grain weight/size in Tartary buckwheat.

BACKGROUND: Grain weight/size influences not only grain yield (GY) but also nutritional and appearance quality and consumer preference in Tartary buckwheat. The identification of quantitative trait loci (QTLs)/genes for grain weight/size is an important objective of Tartary buckwheat genetic research and breeding programs. RESULTS: Herein, we mapped the QTLs for GY, 1000-grain weight (TGW), grain length (GL), grain width (GW) and grain length-width ratio (L/W) in four environments using 221 recombinant inbred lines (XJ-RILs) derived from a cross of 'Xiaomiqiao × Jinqiaomai 2'. In total, 32 QTLs, including 7 for GY, 5 for TGW, 6 for GL, 11 for GW and 3 for L/W, were detected and distributed in 24 genomic regions. Two QTL clusters, qClu-1-3 and qClu-1-5, located on chromosome Ft1, were revealed to harbour 7 stable major QTLs for GY (qGY1.2), TGW (qTGW1.2), GL (qGL1.1 and qGL1.4), GW (qGW1.7 and qGW1.10) and L/W (qL/W1.2) repeatedly detected in three and above environments. A total of 59 homologues of 27 known plant grain weight/size genes were found within the physical intervals of qClu-1-3 and qClu-1-5. Six homologues, FtBRI1, FtAGB1, FtTGW6, FtMADS1, FtMKK4 and FtANT, were identified with both non-synonymous SNP/InDel variations and significantly differential expression levels between the two parents, which may play important roles in Tatary buckwheat grain weight/size control and were chosen as core candidate genes for further investigation. CONCLUSIONS: Two stable major QTL clusters related to grain weight/size and six potential key candidate genes were identified by homology comparison, SNP/InDel variations and qRT‒qPCR analysis between the two parents. Our research provides valuable information for improving grain weight/size and yield in Tartary buckwheat breeding.

The compensation incentive effect of athletes: A structural equation model.

This study explores the compensation incentive effect of athletes. Based on the related literature, we proposed theoretical hypotheses on the compensation incentive effect and established an assessment index system of the compensation incentive effect for athletes. A structural equation model was used to test the survey data of 352 athletes in six provinces to discover the truth of the compensation incentive effect. The results suggested that direct economic compensation satisfaction, direct non-economic compensation satisfaction, and indirect non-economic compensation satisfaction had significant positive effects on the compensation incentive effect of athletes, while indirect economic compensation satisfaction showed no significant effect. Moreover, the evaluation results of athletes' compensation incentive effect showed that direct economic compensation satisfaction contributed the most to the influence factor of the compensation incentive effect. Therefore, the evaluation of athletes' compensation incentive effect should focus on variables of direct economic compensation satisfaction, i.e., basic compensation satisfaction, bonus income satisfaction, and subsidy satisfaction. Finally, some strategies and recommendations were suggested to improve the compensation design for athletes.

Age and gender differences in static and dynamic balance of Chinese preschool children.

Objectives: Balance is a crucial ability of early age, but there is conflicting evidence with regard to age and gender differences in preschool children's balance ability. Additionally, there are several tools available to measure balance, yet, wide variation in their use has restricted the capacity to synthesize the reference values. Therefore, the primary purpose of this study was to investigate the balance ability of preschool-aged children and determine how it is moderated by age and gender. The analysis pertained to determining whether different testing methods affect the results of static or dynamic balancing ability to provide a basis for normative balance ability data for healthy boys and girls between 3 and 6 years of age. Method: Six hundred and nineteen preschool children (296 boys and 323 girls) aged 3-6 years participated in the study. The static balance (SB) was assessed with children standing on one leg (OST) and in a tandem stance (TS) with respect to time. The balance beam test (BBT) and functional reach test (FRT) were used to evaluate dynamic balance (DB) by measuring the time spent and the distance reached, respectively. Result: The results revealed significant differences in OST with respect to gender (η2 = 0.037, p < 0.001), TS (η2 = 0.026, p < 0.001) and FRT (η2 = 0.016, p = 0.002); the girls performed better than boys on most balance tests except on BBT (η2 = 0.000, p = 0.596). Age had positive effects on the static and dynamic balance performance on the OST (η2 = 0.336, p < 0.001), TS (η2 = 0.205, p < 0.001), BBT (η2 = 0.367, p < 0.001) and FRT (η2 = 0.392, p < 0.001). Older children performed better than their younger counterparts. No significant interactions between age groups and sex were found. Conclusion: This study revealed that static and dynamic balance stability in preschool-aged children was affected by gender and age. Gender dimorphism is present in preschool children, older girls displayed better postural stability than boys, and balance performance improved with age. In addition, the study provides age- and gender-specific balance performance reference values for preschool children across multiple methods, which can be used to monitor static and dynamic balance development.

Estimating the impact of ground ozone concentrations on crop yields across China from 2014 to 2018: A multi-model comparison.

Ground level ozone exerts a strong impact on crop yields, yet how to properly quantify ozone induced yield losses in China remains challenging. To this end, we employed a series of O3-crop models to estimate ozone induced yield losses in China from 2014 to 2018. The outputs from all models suggested that the total Relative Yield Losses (RYL) of wheat in China from 2014 to 2018 was 18.4%-49.3% and the total RYL of rice was 6.2%-52.9%. Consequently, the total Crop Production Losses (CPL) of wheat and rice could reach 63.9-130.4 and 28.3-35.4 million tons, and the corresponding Total Economic Losses (TEL) could reach 20.5-44.7 and 11.0-15.3 billion dollars, stressing the great importance and urgency of national ozone management. Meanwhile, the estimation outputs highlighted the large variations between different regional O3-crop models when applying to large scales. Instead of applying one unified O3-crop models to all regions across China, we also explored the strategy of employing specific O3-crop models in corresponding (and neighboring) regions to estimate ozone induced yield loss in China. The comparison of two strategies suggested that the mean value from multiple models may still present an inconsistent over/underestimation trend for different crops. Therefore, it is a preferable strategy to employ corresponding O3-crop models in different regions for estimating the national crop losses caused by ozone pollution. However, the severe lack of regional O3-crop models in most regions across China makes a robust estimation of national yield losses highly challenging. Given the large variations between O3-crop interactions across regions, a systematic framework with massive regional O3-crop models should be properly designed and implemented.

Mapping QTLs for 1000-grain weight and genes controlling hull type using SNP marker in Tartary buckwheat (Fagopyrum tataricum).

BACKGROUND: Tartary buckwheat (Fagopyrum tataricum), an important pseudocereal crop, has high economic value due to its nutritional and medicinal properties. However, dehulling of Tartary buckwheat is difficult owing to its thick and tough hull, which has greatly limited the development of the Tartary buckwheat processing industry. The construction of high-resolution genetic maps serves as a basis for identifying quantitative trait loci (QTLs) and qualitative trait genes for agronomic traits. In this study, a recombinant inbred lines (XJ-RILs) population derived from a cross between the easily dehulled Rice-Tartary type and Tartary buckwheat type was genotyped using restriction site-associated DNA (RAD) sequencing to construct a high-density SNP genetic map. Furthermore, QTLs for 1000-grain weight (TGW) and genes controlling hull type were mapped in multiple environments. RESULTS: In total, 4151 bin markers comprising 122,185 SNPs were used to construct the genetic linkage map. The map consisted of 8 linkage groups and covered 1444.15 cM, with an average distance of 0.35 cM between adjacent bin markers. Nine QTLs for TGW were detected and distributed on four loci on chromosome 1 and 4. A major locus detected in all three trials was mapped in 38.2-39.8 cM region on chromosome 1, with an LOD score of 18.1-37.0, and explained for 23.6-47.5% of the phenotypic variation. The genes controlling hull type were mapped to chromosome 1 between marker Block330 and Block331, which was closely followed by the major locus for TGW. The expression levels of the seven candidate genes controlling hull type present in the region between Block330 and Block336 was low during grain development, and no significant difference was observed between the parental lines. Six non-synonymous coding SNPs were found between the two parents in the region. CONCLUSIONS: We constructed a high-density SNP genetic map for the first time in Tartary buckwheat. The mapped major loci controlling TGW and hull type will be valuable for gene cloning and revealing the mechanism underlying grain development and easy dehulling, and marker-assisted selection in Tartary buckwheat.

Transcriptome-Wide Analysis of Nitrogen-Regulated Genes in Tea Plant (Camellia sinensis L. O. Kuntze) and Characterization of Amino Acid Transporter CsCAT9.1.

The vigor of tea plants (Camellia sinensis) and tea quality are strongly influenced by the abundance and forms of nitrogen, principally NO3-, NH4+, and amino acids. Mechanisms to access different nitrogen sources and the regulatory cues remain largely elusive in tea plants. A transcriptome analysis was performed to categorize differentially expressed genes (DEGs) in roots and young leaves during the early response to four nitrogen treatments. Relative to the continuously nitrogen-replete control, the three nitrogen-deprived and resupplied treatments shared 237 DEGs in the shoots and 21 DEGs in the root. Gene-ontology characterization revealed that transcripts encoding genes predicted to participate in nitrogen uptake, assimilation, and translocation were among the most differentially expressed after exposure to the different nitrogen regimes. Because of its high transcript level regardless of nitrogen condition, a putative amino acid transporter, TEA020444/CsCAT9.1, was further characterized in Arabidopsis and found to mediate the acquisition of a broad spectrum of amino acids, suggesting a role in amino acid uptake, transport, and deposition in sinks as an internal reservoir. Our results enhance our understanding of nitrogen-regulated transcript level patterns in tea plants and pinpoint candidate genes that function in nitrogen transport and metabolism, allowing tea plants to adjust to variable nitrogen environments.

Influence of meteorological conditions on PM2.5 concentrations across China: A review of methodology and mechanism.

Air pollution over China has attracted wide interest from public and academic community. PM2.5 is the primary air pollutant across China. Quantifying interactions between meteorological conditions and PM2.5 concentrations are essential to understand the variability of PM2.5 and seek methods to control PM2.5. Since 2013, the measurement of PM2.5 has been widely made at 1436 stations across the country and more than 300 papers focusing on PM2.5-meteorology interactions have been published. This article is a comprehensive review on the meteorological impact on PM2.5 concentrations. We start with an introduction of general meteorological conditions and PM2.5 concentrations across China, and then seasonal and spatial variations of meteorological influences on PM2.5 concentrations. Next, major methods used to quantify meteorological influences on PM2.5 concentrations are checked and compared. We find that causality analysis methods are more suitable for extracting the influence of individual meteorological factors whilst statistical models are good at quantifying the overall effect of multiple meteorological factors on PM2.5 concentrations. Chemical Transport Models (CTMs) have the potential to provide dynamic estimation of PM2.5 concentrations by considering anthropogenic emissions and the transport and evolution of pollutants. We then comprehensively examine the mechanisms how major meteorological factors may impact the PM2.5 concentrations, including the dispersion, growth, chemical production, photolysis, and deposition of PM2.5. The feedback effects of PM2.5 concentrations on meteorological factors are also carefully examined. Based on this review, suggestions on future research and major meteorological approaches for mitigating PM2.5 pollution are made finally.

Genome-wide selection footprints and deleterious variations in young Asian allotetraploid rapeseed.

Brassica napus (AACC, 2n = 38) is an important oilseed crop grown worldwide. However, little is known about the population evolution of this species, the genomic difference between its major genetic groups, such as European and Asian rapeseed, and the impacts of historical large-scale introgression events on this young tetraploid. In this study, we reported the de novo assembly of the genome sequences of an Asian rapeseed (B. napus), Ningyou 7, and its four progenitors and compared these genomes with other available genomic data from diverse European and Asian cultivars. Our results showed that Asian rapeseed originally derived from European rapeseed but subsequently significantly diverged, with rapid genome differentiation after hybridization and intensive local selective breeding. The first historical introgression of B. rapa dramatically broadened the allelic pool but decreased the deleterious variations of Asian rapeseed. The second historical introgression of the double-low traits of European rapeseed (canola) has reshaped Asian rapeseed into two groups (double-low and double-high), accompanied by an increase in genetic load in the double-low group. This study demonstrates distinctive genomic footprints and deleterious SNP (single nucleotide polymorphism) variants for local adaptation by recent intra- and interspecies introgression events and provides novel insights for understanding the rapid genome evolution of a young allopolyploid crop.

Understanding long-term variations of meteorological influences on ground ozone concentrations in Beijing During 2006-2016.

Recently, ground ozone has become one major airborne pollutant and the frequency of ozone-induced pollution episodes has increased rapidly across China. However, due to the lack of long-term observation data, relevant research on the characteristics and influencing factors of urban ozone concentrations remains limited. Based on ground ozone observation data during 2006-2016, we quantified the causality influence of individual meteorological factors on ozone concentrations in Beijing using a convergent cross mapping (CCM) method. The result indicated that the influence of each meteorological factor on ozone concentrations varied significantly across seasons and years. At the inter-annual scale, all-year meteorological influences on ozone concentrations were much more stable than seasonal meteorological influences. At the seasonal scale, meteorological influences on ozone concentrations were stronger in spring and autumn. Amongst multiple individual factors, temperature was the key meteorological influencing factor for ozone concentrations in all seasons except winter, when wind, humidity and SSD exerted major influences on ozone concentrations. In addition to temperature, air pressure was another meteorological factor that exerted strong influences on ozone concentrations. At both the inter-annual and seasonal scale, the influence of temperature and humidity on ozone concentrations was generally stable whilst that of other factors experienced large variations. Different from PM2.5, meteorological influences on ozone concentrations were relatively weak in summer, when ozone concentrations were the highest in Beijing. Given the generally stable meteorological influences on ozone concentrations and human-induced emissions of VOCs and NOx across seasons, warming induced notable increase in summertime biogenic emissions of VOCs and NOx can be a major driver for the increasing ozone pollution episodes. This research provides useful references for understanding long-term meteorological influences on ozone concentrations in mega cities in China.

A genome-scale metabolic network alignment method within a hypergraph-based framework using a rotational tensor-vector product.

Biological network alignment aims to discover important similarities and differences and thus find a mapping between topological and/or functional components of different biological molecular networks. Then, the mapped components can be considered to correspond to both their places in the network topology and their biological attributes. Development and evolution of biological network alignment methods has been accelerated by the rapidly increasing availability of such biological networks, yielding a repertoire of tens of methods based upon graph theory. However, most biological processes, especially the metabolic reactions, are more sophisticated than simple pairwise interactions and contain three or more participating components. Such multi-lateral relations are not captured by graphs, and computational methods to overcome this limitation are currently lacking. This paper introduces hypergraphs and association hypergraphs to describe metabolic networks and their potential alignments, respectively. Within this framework, metabolic networks are aligned by identifying the maximal Z-eigenvalue of a symmetric tensor. A shifted higher-order power method was utilized to identify a solution. A rotational strategy has been introduced to accelerate the tensor-vector product by 250-fold on average and reduce the storage cost by up to 1,000-fold. The algorithm was implemented on a spark-based distributed computation cluster to significantly increase the convergence rate further by 50- to 80-fold. The parameters have been explored to understand their impact on alignment accuracy and speed. In particular, the influence of initial value selection on the stationary point has been simulated to ensure an accurate approximation of the global optimum. This framework was demonstrated by alignments among the genome-wide metabolic networks of Escherichia coli MG-1655 and Halophilic archaeon DL31. To our knowledge, this is the first genome-wide metabolic network alignment at both the metabolite level and the enzyme level. These results demonstrate that it can supply quite a few valuable insights into metabolic networks. First, this method can access the driving force of organic reactions through the chemical evolution of metabolic network. Second, this method can incorporate the chemical information of enzymes and structural changes of compounds to offer new way defining reaction class and module, such as those in KEGG. Third, as a vertex-focused treatment, this method can supply novel structural and functional annotation for ill-defined molecules. The related source code is available on request.

Understanding the Influence of Crop Residue Burning on PM2.5 and PM10 Concentrations in China from 2013 to 2017 Using MODIS Data.

In recent years, particulate matter (PM) pollution has increasingly affected public life and health. Therefore, crop residue burning, as a significant source of PM pollution in China, should be effectively controlled. This study attempts to understand variations and characteristics of PM10 and PM2.5 concentrations and discuss correlations between the variation of PM concentrations and crop residue burning using ground observation and Moderate Resolution Imaging Spectroradiometer (MODIS) data. The results revealed that the overall PM concentration in China from 2013 to 2017 was in a downward tendency with regional variations. Correlation analysis demonstrated that the PM10 concentration was more closely related to crop residue burning than the PM2.5 concentration. From a spatial perspective, the strongest correlation between PM concentration and crop residue burning existed in Northeast China (NEC). From a temporal perspective, the strongest correlation usually appeared in autumn for most regions. The total amount of crop residue burning spots in autumn was relatively large, and NEC was the region with the most intense crop residue burning in China. We compared the correlation between PM concentrations and crop residue burning at inter-annual and seasonal scales, and during burning-concentrated periods. We found that correlations between PM concentrations and crop residue burning increased significantly with the narrowing temporal scales and was the strongest during burning-concentrated periods, indicating that intense crop residue burning leads to instant deterioration of PM concentrations. The methodology and findings from this study provide meaningful reference for better understanding the influence of crop residue burning on PM pollution across China.

Assembly and comparison of two closely related Brassica napus genomes.

As an increasing number of plant genome sequences become available, it is clear that gene content varies between individuals, and the challenge arises to predict the gene content of a species. However, genome comparison is often confounded by variation in assembly and annotation. Differentiating between true gene absence and variation in assembly or annotation is essential for the accurate identification of conserved and variable genes in a species. Here, we present the de novo assembly of the B. napus cultivar Tapidor and comparison with an improved assembly of the Brassica napus cultivar Darmor-bzh. Both cultivars were annotated using the same method to allow comparison of gene content. We identified genes unique to each cultivar and differentiate these from artefacts due to variation in the assembly and annotation. We demonstrate that using a common annotation pipeline can result in different gene predictions, even for closely related cultivars, and repeat regions which collapse during assembly impact whole genome comparison. After accounting for differences in assembly and annotation, we demonstrate that the genome of Darmor-bzh contains a greater number of genes than the genome of Tapidor. Our results are the first step towards comparison of the true differences between B. napus genomes and highlight the potential sources of error in future production of a B. napus pangenome.

A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome.

KEY MESSAGE: The Brassica napus Illumina array provides genome-wide markers linked to the available genome sequence, a significant tool for genetic analyses of the allotetraploid B. napus and its progenitor diploid genomes. A high-density single nucleotide polymorphism (SNP) Illumina Infinium array, containing 52,157 markers, was developed for the allotetraploid Brassica napus. A stringent selection process employing the short probe sequence for each SNP assay was used to limit the majority of the selected markers to those represented a minimum number of times across the highly replicated genome. As a result approximately 60 % of the SNP assays display genome-specificity, resolving as three clearly separated clusters (AA, AB, and BB) when tested with a diverse range of B. napus material. This genome specificity was supported by the analysis of the diploid ancestors of B. napus, whereby 26,504 and 29,720 markers were scorable in B. oleracea and B. rapa, respectively. Forty-four percent of the assayed loci on the array were genetically mapped in a single doubled-haploid B. napus population allowing alignment of their physical and genetic coordinates. Although strong conservation of the two positions was shown, at least 3 % of the loci were genetically mapped to a homoeologous position compared to their presumed physical position in the respective genome, underlying the importance of genetic corroboration of locus identity. In addition, the alignments identified multiple rearrangements between the diploid and tetraploid Brassica genomes. Although mostly attributed to genome assembly errors, some are likely evidence of rearrangements that occurred since the hybridisation of the progenitor genomes in the B. napus nucleus. Based on estimates for linkage disequilibrium decay, the array is a valuable tool for genetic fine mapping and genome-wide association studies in B. napus and its progenitor genomes.

Linkage and regional association analysis reveal two new tightly-linked major-QTLs for pod number and seed number per pod in rapeseed (Brassica napus L.).

To facilitate the pseudochromosomes assembly and gene cloning in rapeseed, we developed a reference genetic population/map (named BnaZNF2) from two sequenced cultivars, Zhongshuang11 and No.73290, those exhibit significant differences in many traits, particularly yield components. The BnaZNF2 genetic map exhibited perfect collinearity with the physical map of B. napus, indicating its high quality. Comparative mapping revealed several genomic rearrangements between B. napus and B. rapa or B. oleracea. A total of eight and 16 QTLs were identified for pod number and seed number per pod, respectively, and of which three and five QTLs are identical to previously identified ones, whereas the other five and 11 are novel. Two new major QTL respectively for pod number and seed number per pod, qPN.A06-1 and qSN.A06-1 (R(2 )= 22.8% and 32.1%), were colocalised with opposite effects, and only qPN.A06-1 was confirmed and narrowed by regional association analysis to 180 kb including only 33 annotated genes. Conditional QTL analysis and subsequent NILs test indicated that tight linkage, rather than pleiotropy, was the genetic causation of their colocalisation. Our study demonstrates potential of this reference genetic population/map for precise QTL mapping and as a base for positional gene cloning in rapeseed.

CeCaFDB: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13C-fluxomics.

The Central Carbon Metabolic Flux Database (CeCaFDB, available at http://www.cecafdb.org) is a manually curated, multipurpose and open-access database for the documentation, visualization and comparative analysis of the quantitative flux results of central carbon metabolism among microbes and animal cells. It encompasses records for more than 500 flux distributions among 36 organisms and includes information regarding the genotype, culture medium, growth conditions and other specific information gathered from hundreds of journal articles. In addition to its comprehensive literature-derived data, the CeCaFDB supports a common text search function among the data and interactive visualization of the curated flux distributions with compartmentation information based on the Cytoscape Web API, which facilitates data interpretation. The CeCaFDB offers four modules to calculate a similarity score or to perform an alignment between the flux distributions. One of the modules was built using an inter programming algorithm for flux distribution alignment that was specifically designed for this study. Based on these modules, the CeCaFDB also supports an extensive flux distribution comparison function among the curated data. The CeCaFDB is strenuously designed to address the broad demands of biochemists, metabolic engineers, systems biologists and members of the -omics community.

[Evaluation of nutrient level and its factors of breast milk in Shenzhen City].

OBJECTIVE: To investigate the nutrient level for Fat and Nutrient Elements (Ca, K, Na, Mg, Fe and Zn) in Breast Milk and its factors in Shenzhen, China. Eventually we can evaluate the nutrient study for local infants and provide a more reasonable basis for infants breast-feeding. METHODS: 235 breast milk (1 - 2 months postpartum) samples were collected in three districts of Shenzhen during the year of 2011 to 2013. Fat content was analyzed by Soxlet Extraction System, and elements contents were determined by ICP - OES. RESULTS: The average content of fat was 3.73 g/100 ml. The average concentrations of Ca, K, Na, Mg, Fe and Zn in breast milk from Shenzhen were 296.55, 531.45, 188.96, 28.22, 0.27 and 2.36 mg/L, respectively. CONCLUSION: The average contents of fat and elements of Ca, K in the breast milk from Shenzhen were within the reference ranges provided by the World Health Organization (WHO). However, the levels for element of Fe and Mg were much lower than the reference ranges, and the levels for Na and Zn were relative higher when compared with the standard. No significant difference in six nutrients among three districts in Shenzhen were found, however, the significant difference in each element was found compared with that from other cities or countries. Furthermore Zinc daily intake for local infant reached the level of recommended nutrient intake (RNI), however other nutrients were under the adequate intake level (AI) which was set by Chinese nutrition society (CNS).

Quantitative trait loci that control the oil content variation of rapeseed (Brassica napus L.).

KEY MESSAGE: This report describes an integrative analysis of seed-oil-content quantitative trait loci (QTL) in Brassica napus , using a high-density genetic map to align QTL among different populations. Rapeseed (Brassica napus) is an important source of edible oil and sustainable energy. Given the challenge involved in using only a few genes to substantially increase the oil content of rapeseed without affecting the fatty acid composition, exploitation of a greater number of genetic loci that regulate the oil content variation among rapeseed germplasm is of fundamental importance. In this study, we investigated variation in the seed-oil content among two related genetic populations of Brassica napus, the TN double-haploid population and its derivative reconstructed-F2 population. Each population was grown in multiple experiments under different environmental conditions. Mapping of quantitative trait loci (QTL) identified 41 QTL in the TN populations. Furthermore, of the 20 pairs of epistatic interaction loci detected, approximately one-third were located within the QTL intervals. The use of common markers on different genetic maps and the TN genetic map as a reference enabled us to project QTL from an additional three genetic populations onto the TN genetic map. In summary, we used the TN genetic map of the B. napus genome to identify 46 distinct QTL regions that control seed-oil content on 16 of the 19 linkage groups of B. napus. Of these, 18 were each detected in multiple populations. The present results are of value for ongoing efforts to breed rapeseed with high oil content, and alignment of the QTL makes an important contribution to the development of an integrative system for genetic studies of rapeseed.