Applying genome scale metabolic models integrated with OMICs technologies for improvemwent of commercial CHO cell culture process

Although metabolic flux analysis has been established in microbial fermentation, their application in CHO cell culture is sparse. In general CHO cell culture process development is highly rely on empirical experience with limited cell and metabolite data without good mechanism understanding. The purpose of this research is to apply genome scale metabolic modeling for CHO cell culture process improvement. Recently we found that several medium components had significant impact on mAb production by BMSCHO1, a proprietary cell line (Fig. 1). Some of medium components at a low concentration, though within normal ranges for CHO cell culture, caused the BMSCHO1 crashed. Meanwhile some of the other medium components at a low concentration did not cause cell crash, but significantly decreased productivity. The preliminary genetic test results indicated no change in DNA copy number and southern blot integration profile under different medium conditions. Currently we are investigating both supernatant and cell pellets for metabolomics analysis using NMR and LCMS, and assessing epigenetic characteristics. In addition, transcriptomics data have been analyzed by RNA sequence and RT-PCR. Genome-scale modeling integrated with these OMICS datasets have been built and analyzed. In the presentation, we plan to share the investigation details of commercial cell-line and manufacturing process based on the application of genome scale modeling integrated with OMICS technology. Please click Additional Files below to see the full abstract

Antifungal mechanisms of the antagonistic bacterium Bacillus mojavensis UTF-33 and its potential as a new biopesticide

Biological control has gradually become the dominant means of controlling fungal disease over recent years. In this study, an endophytic strain of UTF-33 was isolated from acid mold (Rumex acetosa L.) leaves. Based on 16S rDNA gene sequence comparison, and biochemical and physiological characteristics, this strain was formally identified as Bacillus mojavensis. Bacillus mojavensis UTF-33 was sensitive to most of the antibiotics tested except neomycin. Moreover, the filtrate fermentation solution of Bacillus mojavensis UTF-33 had a significant inhibitory effect on the growth of rice blast and was used in field evaluation tests, which reduced the infestation of rice blast effectively. Rice treated with filtrate fermentation broth exhibited multiple defense mechanisms in response, including the enhanced expression of disease process-related genes and transcription factor genes, and significantly upregulated the gene expression of titin, salicylic acid pathway-related genes, and H2O2 accumulation, in plants; this may directly or indirectly act as an antagonist to pathogenic infestation. Further analysis revealed that the n-butanol crude extract of Bacillus mojavensis UTF-33 could retard or even inhibit conidial germination and prevent the formation of adherent cells both in vitro and in vivo. In addition, the amplification of functional genes for biocontrol using specific primers showed that Bacillus mojavensis UTF-33 expresses genes that can direct the synthesis of bioA, bmyB, fenB, ituD, srfAA and other substances; this information can help us to determine the extraction direction and purification method for inhibitory substances at a later stage. In conclusion, this is the first study to identify Bacillus mojavensis as a potential agent for the control of rice diseases; this strain, and its bioactive substances, have the potential to be developed as biopesticides

Comparison and Synthesis of Precipitation Data from CloudSat CPR and GPM KaPR

Employing different bands of radar to detect precipitation information in identical regions enables the acquisition of a more comprehensive precipitation cloud structure, thereby refining the continuity and completeness of precipitation measurements. This study first compared the coincident data from CloudSat W-band cloud profiling radar (CPR) and Global Precipitation Measurement Mission (GPM) Ka-band precipitation radar (KaPR) from 2014 to 2017, and then a synthesis of the radar reflectivity from CPR and KaPR was attempted to obtain a complete cloud and precipitation structure. The findings of the reflectivity comparisons indicated that the echo-top height identified by CPR is on average 3.6 to 4.2 km higher than that from KaPR, due to the higher sensitivity. Because of strong attenuation of CPR by liquid-phase particles, the reflectivity below the height of the melting layer usually shows an opposite gradient to KaPR with decreasing altitude. The difference in the near-surface rain rates of CPR and KaPR was found to be related to reflectivity gradients in the vertical direction, and the larger the reflectivity gradients, the greater the differences in near-surface rain rates. For better representing the complete vertical structure of precipitation clouds and improving the consistency of the reflectivity and precipitation rate, the radar reflectivity was weighted, synthesized from CPR and KaPR based on the gradient difference of the reflectivity from the two radars. We presented the synthesis results for a stratiform cloud and a deep convective case, and Spearman’s rank correlation coefficient (rs) between the GPM combined radiometer precipitation rate and the radar reflectivity was utilized to analyze the performance of the synthesis. The consistency between synthesized reflectivity and precipitation rate in the non-liquid phase was improved compared with KaPR, and the rs of the ice and mixed phases was increased by about 12% and 10%, respectively

An Enhanced Spatial and Temporal Data Fusion Model for Fusing Landsat and MODIS Surface Reflectance to Generate High Temporal Landsat-Like Data

Remotely sensed data, with high spatial and temporal resolutions, can hardly be provided by only one sensor due to the tradeoff in sensor designs that balance spatial resolutions and temporal coverage. However, they are urgently needed for improving the ability of monitoring rapid landscape changes at fine scales (e.g., 30 m). One approach to acquire them is by fusing observations from sensors with different characteristics (e.g., Enhanced Thematic Mapper Plus (ETM+) and Moderate Resolution Imaging Spectroradiometer (MODIS)). The existing data fusion algorithms, such as the Spatial and Temporal Data Fusion Model (STDFM), have achieved some significant progress in this field. This paper puts forward an Enhanced Spatial and Temporal Data Fusion Model (ESTDFM) based on the STDFM algorithm, by introducing a patch-based ISODATA classification method, the sliding window technology, and the temporal-weight concept. Time-series ETM+ and MODIS surface reflectance are used as test data for comparing the two algorithms. Results show that the prediction ability of the ESTDFM algorithm has been significantly improved, and is even more satisfactory in the near-infrared band (the contrasting average absolute difference [AAD]: 0.0167 vs. 0.0265). The enhanced algorithm will support subsequent research on monitoring land surface dynamic changes at finer scales

The influence of hydraulic characteristics on algal bloom in three gorges reservoir, China: a combination of cultural experiments and field monitoring

It is essential to understand the mechanism of algal bloom and develop effect measures to control the hazard in aquatic environment, such as large reservoirs. In this study, a series of experiments, along with field observation from 2007 to 2016, were carried out to identify the hydrodynamic parameters that drive the algal bloom in the Three Gorges Reservoir (TGR), China, and their threshold values were determined. The results show that algae concentration was markedly diluted with a short retention time, and the threshold value of the retention time to avoid algal bloom was approximately less than 3 days. With strong stratification, the algae concentration was able to approach to the level of algal bloom in 10 days, even when the water temperature is lower than 12 °C. The ratio of mixing depth to euphotic depth (Zm/Ze) had significant negative correlations with both algae concentration and algae specific growth rate (SGR). The field monitoring data indicated that Zm/Ze is an important hydrodynamic parameter which sensitively affects algae growth and concentration. This study made the first attempt to determine Zm/Ze >2.8 to restrain algal bloom in the TGR. Our findings shed light on the influence of critical depth on the algal bloom in the TGR, and the results can serve to control algal bloom in reservoirs through discharge operation

Molecular characterization and function analysis of the rice OsDUF1664 family

The functions of a large number of genes, including gene families with domains of unknown functions (DUF), still remain unclear. In this study, we analyzed four members of OsDUF1664 (OsDUF1664.1-OsDUF1664.4) in rice Nipponbare. By phylogenetic analysis, DUF1664 members in rice and Arabidopsis were classified into three major groups (I, II, III). Under drought conditions, the expression level of OsDUF1664.3 in rice was significantly elevated. Overexpression of OsDUF1664.3 in Escherichia coli led to a significant enhancement of catalase (CAT) and peroxidase (POD) activities, and improved bacterial resistance to drought. The results of this study will provide important information for further study of the function of the OsDUF1664 family in rice

Molecular characterization and function analysis of the rice OsDUF617 family

With the advance of sequencing technology, the number of sequenced genomes has been rapidly increasing. However, the functions of a large number of genes, including gene families with domains of unknown functions (DUF), still remain unclear. In this study, we analysed eight members of OsDUF617 (OsDUF617.1-OsDUF617.8) in rice Nipponbare. By phylogenetic analysis, all these OsDUF617 proteins could be classified into three major groups (I, II, III). We used real-time polymerase chain reaction to examine the expression of all these OsDUF617 members in 15 distinct rice tissues. The expression of these members under various abiotic stress and abscisic acid (ABA) conditions was also examined. Under drought conditions, the expression level of OsDUF617.8 in rice was significantly elevated. Overexpression of OsDUF617.8 in Escherichia coli led to a significant enhancement of catalase (CAT) and peroxidase (POD) activities, and improved bacterial resistance to osmotic stress. The results of this study will provide important information for further study of the function of the OsDUF617 family in rice. Supplemental data for this article is available online at 10.1080/13102818.2021.1934541

Molecular characterization and function analysis of the rice OsDUF829 family

Although the number of sequenced plant genomes has been rapidly increasing, many plant proteins in public databases are recognized as proteins with domains of unknown function (DUF). The domain of unknown function DUF829 family consists of plant proteins with an average length of around 220 residues. In this study, we attempted to uncover the biological functions of four DUF829 members (OsDUF829.1–OsDUF829.4) in rice Nipponbare. We classified these proteins into three groups (group I, II and III) using phylogenetic analysis. Real time polymerase chain reaction (PCR) showed that the expression patterns of the four OsDUF829 family members were different in 15 different rice tissues. Under salt and heat stress conditions, the expression level of OsDUF829.2 and OsDUF829.4 was significantly elevated. Overexpression of OsDUF829.2 and OsDUF829.4 in Escherichia coli significantly improved the resistance to salt stress. The obtained results provide important implications for further functional studies of the OsDUF829 family in rice

Assessment of the Divergent Influence of Natural and Non-Seasonal Hydrological Fluctuations on Functional Traits and Niche Characteristics of Plant Guilds along the Xiangxi River, China

The reservoir water level fluctuation zones (RWLFZs) and the natural riparian zones (NRZs) are two riparian ecosystems with dramatically opposite hydrological rhythms that notably influence the plant guilds. However, little is known about the discrepancies of the functional traits and niche characteristics of plant guilds in the RWLFZs and NRZs under different flooding rhythms. The aims of this study were to assess the divergent influence of natural and non-seasonal hydrological fluctuations on functional traits and niche characteristics of plant guilds. The results showed that 78 vascular plant species were identified in the riparian zones of the Xiangxi River basin. The dominant species were annuals in the two riparian ecosystems and their percentage increased temporally from 65.79% in the NRZs to 67.34% in the RWLFZs. Compared with the NRZs, the specific leaf area, vegetation coverage and the aboveground biomass in the RWLFZs significantly increased by 74%, 27% and 19.6%, respectively, while the water-use efficiency of the RWLFZ decreased by 59.6% and there was no significant difference in the net photosynthetic rate between them, which showed that annuals in the RWLFZs adopted the R adaptation strategy of being fast-growing with a short lifespan and quickly acquiring and investing resources by altering leaf morphology, including expanding the leaf area. The Simpson dominance index of RWLFZs was significantly higher than that of NRZ. Thus, counter-seasonally hydrological alterations had significant effects on functional traits of dominant species in the RWFLZs. Moreover, the highly adaptable and widely distributed species with larger niche breadths and high important values usually had a higher niche overlap value in the RWLFZs than in the NRZs, which showed that the competition in the plant communities after experiencing anti-seasonal flooding was much more intraspecific than interspecific and would facilitate the expansion of species niches. Our findings imply that the species with large niche breadths and high important values should be prioritized in ecological restoration efforts in the newly formed hydro-fluctuation zones of the TGR