Adequate Purity Research Articles

Phase-separated solvothermal high yields recovery of lithium and cobalt cathode precursors from end-of-life LiCoO2 lithium-ion batteries

Lithium-ion batteries (LIBs) recycling is one of the most urgent challenges affecting this technological sector. Indeed, their continuously growing production and demand is already leading to the creation of large volumes of end-of-life LIBs (EoL-LIBs). At the same time, the growing demand for LIBs is not sustainable from the point of view of supply of the critical raw materials needed to produce the essential components of LIBs. The development of efficient and sustainable recycling strategies provides a solution to these two urgent issues. Here we propose a new ternary deep eutectic solvent (DES) composition based on choline chloride, citric acid, and ethylene glycol in molar ratio 1:1:1 for the reductive degradation of LiCoO2 cathode. The optimized leaching process (5g of DES for 100 mg of black mass for 30 min at 140 °C) leads to the full degradation of the cathode with extraction yields above 97% for both Li and Co. Simple electrochemical tests confirm irreversible DES degradation, making its recovery and reuse impractical. We demonstrate that a subsequent thermal treatment, using DES as a sacrificial agent, allows to separate and recover Co3O4 and LiCl with adequate purity to be exploited for LiCoO2 resynthesis. As a proof of concept, a new batch of LiCoO2 is synthesized and used for new cells’ assembly. The performance of the resynthesized material is comparable with that of the commercial benchmark material, demonstrating the possibility of a full closed-loop recycling route.

Principles and Limitations of miRNA Purification and Analysis in Whole Blood Collected during Ablation Procedure from Patients with Atrial Fibrillation.

Background: MicroRNA (miRNA) have the potential to be non-invasive and attractive biomarkers for a vast number of diseases and clinical conditions; however, a reliable analysis of miRNA expression in blood samples meets a number of methodological challenges. In this report, we presented and discussed, specifically, the principles and limitations of miRNA purification and analysis in blood plasma samples collected from the left atrium during an ablation procedure on patients with atrial fibrillation (AF). Materials and Methods: Consecutive patients hospitalized in the First Department of Cardiology for pulmonary vein ablation were included in this study (11 with diagnosed paroxysmal AF, 14 with persistent AF, and 5 without AF hospitalized for left-sided WPW ablation-control group). Whole blood samples were collected from the left atrium after transseptal puncture during the ablation procedure of AF patients. Analysis of the set of miRNA molecules was performed in blood plasma samples using the MIHS-113ZF-12 kit and miScript microRNA PCR Array Human Cardiovascular Disease. Results: The miRNS concentrations were in the following ranges: paroxysmal AF: 7-23.1 ng/µL; persistent AF: 4.9-66.8 ng/µL; controls: 6.3-10.6 ng/µL. The low A260/280 ratio indicated the protein contamination and the low A260/A230 absorbance ratio suggested the contamination by hydrocarbons. Spectrophotometric measurements also indicated low concentration of nucleic acids (<10 ng/µL). Further steps of analysis revealed that the concentration of cDNA after the Real-Time PCR (using the PAXgene RNA Blood kit) reaction was higher (148.8 ng/µL vs. 68.4 ng/µL) and the obtained absorbance ratios (A260/A280 = 2.24 and A260/A230 = 2.23) indicated adequate RNA purity. Conclusions: Although developments in miRNA sequencing and isolation technology have improved, detection of plasma-based miRNA, low RNA content, and sequencing bias introduced during library preparation remain challenging in patients with AF. The measurement of the quantity and quality of the RNA obtained is crucial for the interpretation of an efficient RNA isolation.

Characterization and Calibration of Cold-Alcohol Plasma Fractionation Intermediates by Kjeldahl Digestion and Digital Refractometry

Background Almost 80 years after implementation of the industrial ethanol fractionation process, based on the pioneering work of Edwin J. Cohn's research group, it has not lost its importance in providing life-saving biotherapies to patients. The focus has shifted from albumin, which was first used to treat intensive care patients, to immunoglobulin G preparations. Nowadays the latter enables effective, life-long treatment of patients suffering from immunodeficiencies. Ethanol concentration, pH, temperature, protein, and salt concentration are diligently varied during the Cohn fractionation process to finally yield fractions in which the main plasma proteins are enriched at adequate purity. Total protein concentration of the intermediates, probably not as important as ethanol levels and pH, has nevertheless an indisputable influence on the process’ performance Objectives Total protein measurement is therefore a valuable in process-control for versatile process performance monitoring. For this purpose, we investigated the application of analytical digital refractometry. Design For our pilot study, we used six consecutive batches of nine relevant intermediates covering Takeda's whole industrial-scale Cohn Fractionation process. Methods Total protein concentrations of the intermediates were measured with the method of Kjehldal to obtain reference data and digital analytical refractometry, using 10-kDa ultrafiltration to obtain a protein free permeate serving as a sample-specific blank. Results and Conclusions Specific refractive index increment dn/dc values, allowing the calculation of the total protein concentrations by refractive index measurement, were obtained for the Cohn Fractionation intermediates investigated. Thus, analytical digital refractometry, a simple, fast, and robust technique, was shown to be fit for this purpose.

Investigation of the Structural, Dielectric, Magnetic, and Magnetoelectric Properties of Nd-Substituted Sr3Co2Fe24O41 Z-Hexaferrite

The Neodymium (Nd) substituted Sr-based Z-Hexaferrites having composition Sr3-xNdxCo2Fe24O41 (x = 0, 0.15, 0.30 and 0.45) corresponding to pristine, 5, 10 and 15% substitution were prepared using solid-state reaction method in pre-optimized rare Earth metal solubility range (x ≤ 0.45) and labeled as SCFO, SNCFO5, SNCFO10 and SNCFO15, respectively. X-ray diffractometer and Scanning Electron Microscopy (SEM) were utilized to investigate the prepared samples’ structure and grain morphology. The X-ray diffraction (XRD) patterns confirmed Z-hexaferrite formation with adequate phase purity. Dielectric measurements exhibited a relaxation-type, frequency-dependent, and thermally activated dielectric response across all prepared samples. In Nd substituted SCFO, the obtained value of coercivity (Hc) ranges from 52.2–68.45 oersted, confirming a soft magnetic behavior. Magnetoelectric coupling coefficient(α) recorded at room temperature has a maximum value of 0.2133 mV cm−1Oe−1 for the pristine sample and this value of α varies with Nd substitution for all prepared samples.

Protein separation by sequential selective complex coacervation

In food manufacturing and particular biomedical products selected proteins are often required. Obtaining the desired proteins in a pure form from natural resources is therefore important, but often very challenging. Herein, we design a sequential coacervation process that allows to efficiently isolate and purify proteins with different isoelectric points (pIs) from a mixed solution, namely Bovine Serum Albumin (BSA, pI = 4.9) and Peroxidase from Horseradish (HRP, pI = 7.2). The key to separation is introducing a suitable polyelectrolyte that causes selective complex coacervation at appropriate pH and ionic strength. Specifically, polyethyleneimine (PEI), when added into the mixture at pH 6.0, produces a coacervation which exclusively contains BSA, leading to a supernatant solution containing 100 % HRP with a purity of 91 %. After separating the dilute and dense phases, BSA is recovered by adding poly(acrylic acid) (PAA) to the concentrated phase, which displaces BSA from the complex because it interacts more strongly with PEI. The supernatant phase after this step contains approximately 75 % of the initial amount of BSA with a purity of 99 %. Our results confirm that coacervation under well-defined conditions can be selective, enabling separation of proteins with adequate purity. Therefore, the established approach demonstrates a facile and sustainable strategy with potential for protein separation at industrial scale.

Germline variants in non-BRCA1/2 homologous recombination-related genes and ovarian cancer: Analysis of tumor phenotype and survival.

5565 Background: BRCA1/2-associated ovarian cancer (OC) exhibits homologous recombination (HR)-deficiency (HRD) and a better prognosis than BRCA1/2-wildtype (WT) OC. However, it is unclear if patients with germline pathogenic variants (gPV) in other HR-related genes have a similar tumor phenotype. We sought to define OC molecular features from patients with gPV in other HR genes and analyze survival compared to patients with BRCA1/2 and WT OC. Methods: We identified patients with OC treated at our institution who underwent tumor-normal sequencing using MSK-IMPACT targeting 341-505 cancer-related genes with germline analysis of ≥76 genes from 7/2015-12/2020. Biallelic inactivation was inferred via assessments of loss of heterozygosity (LOH) at gPV in non- BRCA1/2 HR-related genes ( ATM, BARD1, BRIP1, FANCA, FANCC, NBN, PALB2, RAD50, RAD51B, RAD51C, and RAD51D). Clinical characteristics were compared to patients with BRCA1/2-associated and WT OC using non-parametric tests. Progression-free (PFS) and overall-survival (OS) were calculated from date of pathologic diagnosis using the Kaplan-Meier method. Left truncation at date of MSK-IMPACT consent was applied. Whole-exome sequencing (WES) was performed in a subset of OCs. Results: Of 882 patients with OC, 56 (6.3%) had gPV in non- BRCA1/2 HR-related genes compared to 95 (10.8%) patients with BRCA1-associated OC (58 germline, 37 somatic) and 59 (6.7%) patients with BRCA2-associated OC (40 germline, 19 somatic). Patients with a deleterious genetic alteration were diagnosed with OC at younger age and more likely to have high-grade serous histology compared to the WT group (p &lt; 0.01). High rates of biallelic alterations were observed amongst gPV in BRIP1 (11/13), PALB2 (3/4), RAD51B (3/4), RAD51C (3/4), and RAD51D (8/10), and WES was performed in a subset (n = 27) of tumors from these patients with adequate tumor purity (&gt;30%). We observed a higher tumor mutational burden (TMB), median 2.5 (1.1-6.0) vs. 1.2 (0.6-2.6) mut/Mb, and enrichment of HRD mutational signatures in tumors associated with PALB2 and RAD51B/C/D compared with BRIP1 (p &lt; 0.01), although markers of telomeric-allelic imbalance (TAI), large-scale state transitions (LST) and fraction of genome altered (FGA) were similar. PFS and OS varied by gene group with best survival in BRCA1/2-associated OC, even after adjustment for clinical covariates in multivariable models (p &lt; 0.01). Although we observed heterogeneity in PFS and OS for those with gPV in other HR-related genes by biallelic status and HRD phenotype, none had significantly better survival than those with WT OC. Conclusions: OCs associated with gPV in non- BRCA1/2 HR-related genes represent a heterogenous group. OCs in those with gPV in PALB2 and RAD51B/C/D preferentially harbored biallelic alterations and displayed an HRD phenotype.

A novel brick for bispecific antibody construction.

In recent years, the development of bispecific antibodies (bsAbs) has become a major trend in the biopharmaceutical industry. By simultaneously engaging two molecular targets, bsAbs have exhibited unique mechanisms of action that could lead to clinical benefits unattainable by conventional monoclonal antibodies. The type of structure used to construct a bsAb directly influences the distance, angle, degree of freedom, and affinity between the two antibody binding sites and the interaction between the two antigens or the cells where the antigens are located, which have been bound by the antibody. Consequently, the structure of the bsAb is one of the most vital factors affecting its function. Herein, we reported for the first time a novel basic module bsAb format, VFV (Variable domain-Fab-Variable domain). And then, the feasibility of the VFV format was demonstrated by constructing a series of engager-like basic module bsAbs. Next, a series of VFV bsAbs containing Fc (VFV-Ig), Fab (VFV-Fab), or Hinge (VFV-Hinge) were developed based on Hxb module, and all of them had adequate purity and activity. Finally, a T cell engager bsAb with the potential to overcome on-target off-tumor activity was constructed according to the structural characteristics of VFV, which validated that the VFV module can be used as a new brick for the construction of various bsAbs. In a word, the successful construction of this bsAb format for the first time not only enriches the arsenal of the bsAb format, but also provides inspiration for the construction of new bsAbs. Nevertheless, we are fully aware that as a proof-of-concept study, this paper has many shortcomings, and there is still a lot of work to be done to determine whether VFV can serve as a platform for drug development.

A Simplified and Efficient Method for Production of Manganese Ferrite Magnetic Nanoparticles and Their Application in DNA Isolation.

A simplified, fast, and effective production method has been developed for the synthesis of manganese ferrite (MnFe2O4) magnetic nanoparticles (MNPs). In addition to the wide applicability of MnFe2O4 MNPs, this work also reports their application in DNA isolation for the first time. An ultrasonic-cavitation-assisted combustion method was applied in the synthesis of MnFe2O4 MNPs at different furnace temperatures (573 K, 623 K, 673 K, and 773 K) to optimize the particles' properties. It was shown that MnFe2O4 nanoparticles synthesized at 573 K consist of a spinel phase only with adequate size and zeta potential distributions and superparamagnetic properties. It was also demonstrated that superparamagnetic manganese ferrite nanoparticles bind DNA in buffer with a high NaCl concentration (2.5 M), and the DNA desorbs from the MNPs by decreasing the NaCl concentration of the elution buffer. This resulted in a DNA yield comparable to that of commercial DNA extraction products. Both the DNA concentration measurements and electrophoresis confirmed that a high amount of isolated bacterial plasmid DNA (pDNA) with adequate purity can be extracted with MnFe2O4 (573 K) nanoparticles by applying the DNA extraction method proposed in this article.

Rapid Purification and Formulation of Radiopharmaceuticals via Thin-Layer Chromatography.

Before formulating radiopharmaceuticals for injection, it is necessary to remove various impurities via purification. Conventional synthesis methods involve relatively large quantities of reagents, requiring high-resolution and high-capacity chromatographic methods (e.g., semi-preparative radio-HPLC) to ensure adequate purity of the radiopharmaceutical. Due to the use of organic solvents during purification, additional processing is needed to reformulate the radiopharmaceutical into an injectable buffer. Recent developments in microscale radiosynthesis have made it possible to synthesize radiopharmaceuticals with vastly reduced reagent masses, minimizing impurities. This enables purification with lower-capacity methods, such as analytical HPLC, with a reduction of purification time and volume (that shortens downstream re-formulation). Still, the need for a bulky and expensive HPLC system undermines many of the advantages of microfluidics. This study demonstrates the feasibility of using radio-TLC for the purification of radiopharmaceuticals. This technique combines high-performance (high-resolution, high-speed separation) with the advantages of a compact and low-cost setup. A further advantage is that no downstream re-formulation step is needed. Production and purification of clinical scale batches of [18F]PBR-06 and [18F]Fallypride are demonstrated with high yield, purity, and specific activity. Automating this radio-TLC method could provide an attractive solution for the purification step in microscale radiochemistry systems.

Low-Input High-Molecular-Weight DNA Extraction for Long-Read Sequencing From Plants of Diverse Families.

Long-read DNA sequencing technologies require high molecular weight (HMW) DNA of adequate purity and integrity, which can be difficult to isolate from plant material. Plant leaves usually contain high levels of carbohydrates and secondary metabolites that can impact DNA purity, affecting downstream applications. Several protocols and kits are available for HMW DNA extraction, but they usually require a high amount of input material and often lead to substantial DNA fragmentation, making sequencing suboptimal in terms of read length and data yield. We here describe a protocol for plant HMW DNA extraction from low input material (0.1 g) which is easy to follow and quick (2.5 h). This method successfully enabled us to extract HMW from four species from different families (Orchidaceae, Poaceae, Brassicaceae, Asteraceae). In the case of recalcitrant species, we show that an additional purification step is sufficient to deliver a clean DNA sample. We demonstrate the suitability of our protocol for long-read sequencing on the Oxford Nanopore Technologies PromethION® platform, with and without the use of a short fragment depletion kit.

Synthesis, characterization and antimicrobial activity of novel tetrazoles clubbed with pyrimidine

An attempt was made to synthesize pyrimidine tetrazole derivatives of pharmaceutical interest by oxidative cyclization of chalcones with adequate yield and purity, prompted by the diversity of their wider usage and the fact that they are an integral part of genetic content. The present work involves the reaction of 5-(2,6-dimethylphenyl)-1H-tetrazole with acetic anhydride to yield 1-[5-(2,6-dimethylphenyl)-1H-tetrazol-1-yl] ethanone (1) and which then treated with different aromatic aldehydes in presence of alkaline medium to chalcones (2a-f). Reaction of chalcones (2a-f) with urea and thiourea to produce 5-[5-(2,6-dimethylphenyl)-1H-tetrazol-1-yl]-4-(substituted aryl ) pyrimidin-2-ol (3a-f) and 5-[5-(2,6-dimethylphenyl)-1H-tetrazol-1-yl]-4-(substituted aryl) pyrimidin-2-thiol (4a-f) respectively. All compounds were characterized by infrared spectroscopy (IR), H nuclear magnetic resonance (NMR), and mass spectrometry (MS) to prove the structure and assessed in vitro for their efficacy as antibacterial and antifungal activity against four bacteria. The compounds 3c, 3d and 3f and compounds 4c, 4d and 4f possess very good activity against and E. coli and the compounds 3e, 3c and 3a and compounds 4e,4b and 4c possess very good activity against fungi and .

Circulating Cell-Free DNA (ccfDNA) Isolation from Patients with Diffuse Large B-Cell Lymphoma (DLBCL): Comparative Analysis of Commercial Kits

Introduction: Isolation of circulating cell-free DNA (ccfDNA) and circulating tumor DNA (ctDNA) are useful methodologies for studies of neoplastic genetic material and can provide information about cancer heterogeneity, prognosis and minimal residual disease (MRD) [1,2]. Therefore, the recovery of ccfDNA in sufficient quantity and adequate purity is crucial to provide accurate and reproducible results. In this study, we investigate the efficiency of four different commercial kits to recover short fragments of DNA compatible with the ccfDNA.Methods: Ten mL of total peripheral blood from seven patients with Diffuse Large B-Cell Lymphoma (DLBCL) were collected in EDTA and were immediately processed. Plasma was obtained by centrifugation at 1.900 x g for 10 min at 4 ºC, followed by other centrifugation at 20.000 x g for 10 min at 4 ºC to remove cellular debris. Aliquots of 1.0 mL of plasma were stored at -80 ºC until ccfDNA extraction. The ccfDNA extraction was performed using the same samples by the following kits: QIAamp MinElute ccfDNA kit (CFDNA - Qiagen, Hilden, Germany), QIAamp DNA Mini Kit (QBLOOD - Qiagen, Hilden, Germany), Illustra Blood GenomicPrep Mini Spin Kit (GE - GE Healthcare Bio-Sciences Corp, UK) and ccfDNA isolation kit Quick-ccfDNA Serum & Plasma Kit (ZYMO - Zymo Research, Irvine, USA) [Table 1] according to the manufacturer's recommendations. The ccfDNA obtained was eluted in 30 µL of elution buffer for the subsequent experiments. The measurement of the ccfDNA obtained for each kit was performed in a Qubit 2.0 fluorometer using Qubit dsDNA HS assay kit (Thermo Fischer Scientific, Waltham, USA). The analysis of integrity, purity and the size of the fragments of DNA were performed in the Agilent 2100 Bioanalyzer (Agilent Technologies, Germany) equipment using the High Sensitivity DNA kit (Agilent Technologies, Germany).Results: The results obtained for each commercial kit in the Qubit-analysis were: CFDNA (0.27 ng/uL), QBLOOD (0.26 ng/uL), ZYMO (0.03 ng/uL) and GE (0.02 ng/uL) [Figure 1]. The Bionalyzer eletrophoresis showed that CFDNA kit was able to recover two different fragments sizes of ccfDNA one of 360-380 bp (0.114 ng/uL) and other of 160-180 bp (1.808 ng/uL). The DNA recovered with QBLOOD revealed sizes of 360-380 bp (0.031 ng/uL) and 160-180 bp (0.079 ng/uL). Both kits, GE and ZYMO were not able to isolate fragments of DNA smaller than 10.380 pb .Conclusion: We demonstrated that QIAamp MinElute ccfDNA kit (CFDNA) was capable to recovery high quantity of small fragments of DNA compatible with ccfDNA. This result supports the use of protocols based in magnetic beads in experiments working with ccfDNA. Additionally, we highlight the importance to verify the quality and not only the quantity of the DNA extracted to confirm the presence of ccfDNA. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

CIRCULATING CELL-FREE DNA (CCFDNA) ISOLATION FROM PATIENTS WITH DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL): COMPARATIVE ANALYSIS OF COMMERCIAL KITS

Introduction Isolation of circulating cell-free DNA (ccfDNA) and circulating tumor DNA (ctDNA) are useful methodologies for studies of neoplastic genetic material and can provide information about cancer heterogeneity, prognosis and minimal residual disease (MRD). Therefore, the recovery of ccfDNA in sufficient quantity and adequate purity is crucial to provide accurate and reproducible results. In this study, we investigate the efficiency of four different commercial kits to recover short fragments of DNA compatible with the ccfDNA. Methods Ten mL of total peripheral blood from seven patients with Diffuse Large B-Cell Lymphoma (DLBCL) were collected in EDTA and were immediately processed. Plasma was obtained by centrifugation at 1.900 x g for 10 min at 4 °C, followed by other centrifugation at 20.000 x g for 10 min at 4 °C to remove cellular debris. Aliquots of 1.0 mL of plasma were stored at -80 °C until ccfDNA extraction. The ccfDNA extraction was performed using the same samples by the following kits: QIAamp MinElute ccfDNA kit (CFDNA - Qiagen, Hilden, Germany), QIAamp DNA Mini Kit (QBLOOD - Qiagen, Hilden, Germany), Illustra Blood GenomicPrep Mini Spin Kit (GE - GE Healthcare Bio-Sciences Corp, UK) and ccfDNA isolation kit Quick-ccfDNA Serum & Plasma Kit (ZYMO - Zymo Research, Irvine, USA) according to the manufacturer's recommendations. The ccfDNA obtained was eluted in 30 μL of elution buffer for the subsequent experiments. The measurement of the ccfDNA obtained for each kit was performed in a Qubit 2.0 fluorometer using Qubit dsDNA HS assay kit (Thermo Fischer Scientific, Waltham, USA). The analysis of integrity, purity and the size of the fragments of DNA were performed in the Agilent 2100 Bioanalyzer (Agilent Technologies, Germany) equipment using the High Sensitivity DNA kit (Agilent Technologies, Germany). Results The results obtained for each commercial kit in the Qubit-analysis were: CFDNA (0.27 ng/uL), QBLOO D (0.26 ng/uL), ZYMO (0.03 ng/uL) and GE (0.02 ng/uL). The Bionalyzer eletrophoresis showed that CFDNA kit was able to recover two different fragments sizes of ccfDNA one of 360–380 bp (0.114 ng/uL) and other of 160-180 bp (1.808 ng/uL). The DNA recovered with QBLOOD revealed sizes of 360-380 bp (0.031 ng/uL) and 160-180 bp (0.079 ng/uL). Both kits, GE and ZYMO were not able to isolate fragments of DNA smaller than 10.380 pb. Conclusion We demonstrated that QIAamp MinElute ccfDNA kit (CFDNA) was capable to recovery high quantity of small fragments of DNA compatible with ccfDNA. This result supports the use of protocols based in magnetic beads in experiments working with ccfDNA. Additionally, we highlight the importance to verify the quality and not only the quantity of the DNA extracted to confirm the presence of ccfDNA.

Identification of potential plasma biomarkers in early-stage nasopharyngeal carcinoma-derived exosomes based on RNA sequencing

BackgroundEarly diagnosis of nasopharyngeal carcinoma (NPC) is vital to improve the prognosis of these patients. However, early diagnosis of NPC is typically challenging. Therefore, we explored the pathogenetic roles and associated mechanisms of exosomes in plasma of patients with early-stage NPC.MethodsExosomes in plasma were extracted by ultra-high-speed centrifugation. Western blot and transmission electron microscopy (TEM) were used to verify the purity of exosomes. The sequencing data (6 plasma samples from healthy volunteers vs. 6 NPC plasma samples) were analyzed by principal component analysis (PCA), DESeq2, gene ontology (GO), Kyoto encyclopedia of genes and genomes (KEGG), and TargetScan. The differentially expressed miRNAs (DEmiRNAs) were obtained from the dataset (GSE118720) downloaded from the Gene Expression Omnibus (GEO) repository. Additionally, the datasets downloaded from the GEO database (GSE12452, GSE13597, GSE53819, GSE64634) were used to predict the target genes and functions of hsa-miR-1301-3p. qPCR was applied to verify the differences in the expressions of hsa-miR-1301-3p between 10 normal plasma and 10 NPC plasma samples.ResultsWestern blot, TEM, and Nanoparticle Tracking Analysis showed adequate purity of the extracted exosomes. RNA-seq analysis revealed 21 upregulated miRNAs, and 10 downregulated miRNAs in plasma exosomes of early-stage NPC patients. GO analysis showed that the target genes of DEmiRNAs were mainly enriched in DNA synthesis and transcription regulation. KEGG analysis revealed that DEmiRNAs were mainly enriched in PI3K-Akt and MAPK signaling pathways. Moreover, the expression of hsa-mir-1301-3p was verified to be significantly upregulated in enlarged samples of plasma exosomes.ConclusionsWe identified several DEmiRNAs extracted from tumor-derived exosomes between normal plasma and early-stage NPC plasma. Bioinformatics analyses indicated that these DEmiRNAs may be related to NPC development. Our study may provide novel insights into underlying biomarkers and mechanisms of plasma exosomes in early-stage NPC.

Preparation and Uses of Chlorinated Glycerol Derivatives.

Crude glycerol (C3H8O3) is a major by-product of biodiesel production from vegetable oils and animal fats. The increased biodiesel production in the last two decades has forced glycerol production up and prices down. However, crude glycerol from biodiesel production is not of adequate purity for industrial uses, including food, cosmetics and pharmaceuticals. The purification process of crude glycerol to reach the quality standards required by industry is expensive and dificult. Novel uses for crude glycerol can reduce the price of biodiesel and make it an economical alternative to diesel. Moreover, novel uses may improve environmental impact, since crude glycerol disposal is expensive and dificult. Glycerol is a versatile molecule with many potential applications in fermentation processes and synthetic chemistry. It serves as a glucose substitute in microbial growth media and as a precursor in the synthesis of a number of commercial intermediates or fine chemicals. Chlorinated derivatives of glycerol are an important class of such chemicals. The main focus of this review is the conversion of glycerol to chlorinated derivatives, such as epichlorohydrin and chlorohydrins, and their further use in the synthesis of additional downstream products. Downstream products include non-cyclic compounds with allyl, nitrile, azide and other functional groups, as well as oxazolidinones and triazoles, which are cyclic compounds derived from ephichlorohydrin and chlorohydrins. The polymers and ionic liquids, which use glycerol as an initial building block, are highlighted, as well.

Optimization of parameters affecting on CHO cell culture producing recombinant erythropoietin

Several factors may affect erythropoietin (EPO) sugar structures including designing cell culture procedure, pH, concentration of additives, dissolved oxygen, and other physicochemical parameters. In this study, we investigated the influence of changes in effective parameters and compounds on the growth rate of Chinese hamster ovary cell (CHO) cells producing recombinant EPO. Cell culture was performed at different temperature, buffering conditions, and varied concentrations of additives such as pyruvic acid, insulin, GlutaMAX, and sodium butyrate. Results indicated that the optimal temperature and pH were 37 °C and 7.2, respectively. Also, optimal concentrations for pyruvic acid, butyrate, glutamate, and insulin were obtained to be 20 mM, 1 mM, 2 mM, and 40 μg/mL, respectively. Then, cell culture was performed in microcarrier-coated spinner flasks under the optimized condition. The results showed recombinant human EPO (rhEPO) production with adequate purity. Optimization of physicochemical conditions and culture media are important factors to improve the quantity and quality of protein products. This study showed that cell growth and recombinant EPO protein production significantly increased under the optimized conditions. The results of this research can also be used in scale-up to increase the efficiency of EPO production. Abbreviations: EPO: erythropoietin; CHO cell: Chinese hamster ovary cell; rhEPO: recombinant human EPO; DMEM: modified eagle’s medium; FBS: fetal bovine serum; SDS-PAGE: sodium dodecyl sulfate–polyacrylamide gel electrophoresis; IGF-1: insulin-like growth factor 1

Abstract A60: Integrated proteogenomic characterization of pancreatic ductal adenocarcinoma

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor survival rates. Towards understanding the underlying molecular alterations that drive the PDAC oncogenesis, we conducted the first comprehensive proteogenomic analysis of 76 pancreatic tumors and 44 adjacent normal tissues (NATs). Proteomics, whole-genome sequencing, whole-exome sequencing, methylation, and RNA-seq were performed on these tissues to facilitate an integrated proteogenomic analysis and determine the impact of genomic alterations on protein expression. Genomic analysis showed that 89% of tumor samples had a detectable KRAS hotspot mutation, close to the mutation rate reported by TCGA. TP53 (56%), SMAD4 (18%), and CDKN2A (17%) rates were lower, but also close to those in the TCGA cohort, suggesting adequate tumor purity percentages in most of our samples. Additionally, we applied several deconvolution methods, including ESTIMATE and EDec, to estimate tumor purity and cell type composition using transcriptomics and DNA methylation data. These purity estimates correlated with KRAS variant allele frequency (VAF). RNA-based subtyping identified a balanced collection of subtypes consistent with previous reports in PDAC. However, gene expression and protein abundance were not correlated with the mean Spearman correlation of 0.23. Highly correlated pathways included pancreatic secretion, protein digestion and absorption, and allograft rejection, while pathways with low correlation encompassed oxidative phosphorylation and cytoskeleton organization during mitosis. Interestingly, mutations did not have a strong cis impact on the overall proteome level. However, we observed significant increases in BAX and DNMT1 protein levels associated with TP53 mutations. Tumor-normal analyses revealed tumor-specific gene and protein expression, including EMT, cell adhesion, and keratin genes. Proteomic analysis identified several druggable events in ERBB2, SYK, PAK1, PDPK1, and EPHA2. Using cell surface marker gene expression, we identified and classified our samples into four immune subtypes: NK- excluded, NK+ excluded, immune desert, and inflamed. PLEK, WAS, CD48, ALDOA, and ASPH had highly differential protein levels in inflamed tumors, among others. We further identified that protein levels of INTS14, SULF2, and PTPMT1, among others, were associated with patient survival, demonstrating the prognostic value of proteomics over RNA alone. Additionally, we are characterizing an additional 81 pancreatic tumors and 58 NATs using our deep proteogenomic analysis and post-translational modifications, aiming to verify the preliminary findings and to investigate the roles of cell signaling network and cell surface receptors on PDAC oncogenesis. This integrated proteogenomic characterization of PDAC will be a valuable resource for the community, paving the way for the discovery of novel therapeutic targets. Citation Format: Kyung Cho Cho, Ralph Hruban, Hui Zhang, Chen Huang, Bing Zhang, Daniel Cui Zhou, Li Ding, Emily Boja, Investigators from the Clinical Proteomic Tumor Analysis Consortium. Integrated proteogenomic characterization of pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr A60.

Tumor mutational burden.

Tumor mutational burden.

Extraction, characterization and technological properties of white garland-lily starch

The white garland-lily rhizomes represent a potential source for starch extraction. Thus, the present study aimed to contribute with new data about the starch extraction yield and to characterize the chemical-structural, thermal and technological properties of the white garland-lily starch. The rhizomes harvested in the dry season presented greater starch yields (22.0 g 100 g−1) than in the early summer (6.9 ± 0.5 g 100 g−1) (d.b). The starch presented adequate purity (97.67 g 100 g−1), the granules were flat, with the thickness varying from 2 to 6 μm and length between 12 and 38 μm, and they showed no birefringence. They presented an amylose content of 59.16 g 100 g−1, crystallinity of 19.30% and type B starch. The C13 CP/MAS spectrum presented an amorphous pattern although indicating a transition to type V. This was a product with moderate swelling power and a high gelatinization peak temperature (76.78 °C). The extraction of white garland-lily starch is feasible in the dry season when it has chemical-structural, thermal and technological properties suitable for use in the food industry, related to its high amorphous starch content.

Abstract P3-06-01: Clonal evolution and heterogeneity in breast tumors treated with neoadjuvant HER2-targeted therapy

Abstract Background: Understanding to what extent a breast tumor's genetic composition may change over the course of a few months of neoadjuvant therapy has implications for optimal therapeutic approach. However, genomic changes observed across treatment may result from either treatment-induced clonal evolution or geographically disparate sampling of a heterogeneous tumor. We sought to characterize the geographic heterogeneity in primary breast tumors, and to incorporate this information into analysis of clonal evolution with neoadjuvant therapy. Methods: We assembled the largest cohort to date of multi-region (n=2-3) whole-exome sequenced (WES) or whole-genome sequenced untreated primary breast tumors with matched normal and adequate tumor purity for analysis: four tumors with data generated for this study and five tumors compiled from three previous studies. We also generated the first cohort of multi-region (n=2-6) WES breast tumors post-neoadjuvant HER2-targeted therapy and chemotherapy, sequencing one region from a pre-treatment diagnostic specimen, multiple regions from the post-treatment surgical specimen, and matched normal for five HER2+ breast tumors that did not achieve a pathologic complete response. We used an agent-based model of spatial tumor growth to investigate whether the mutational patterns we observed with treatment were consistent with pre-existing heterogeneity or treatment-induced selection. Results: In untreated primary breast tumors, on average 30% (range 1-70%) of apparently clonal mutations from a single region were absent or rare in a second, spatially disparate region (high-frequency regional, or HFR). Intra-tumor heterogeneity was similar post-treatment (HFR 28%, range 10-54%), and was higher in breast tumors than in previously analyzed colon, brain, lung, and esophageal tumors. Simulation studies confirmed that with high heterogeneity as observed in breast tumors, analysis of one pre-treatment and one post-treatment region could not distinguish treatment-induced clonal evolution from pre-existing heterogeneity; however, obtaining at least two post-treatment regions allowed for detection of clonal shifts with treatment. Analysis of multi-region data revealed that clonal replacement occurred with neoadjuvant therapy in two of the five tumors. Candidate causes of therapeutic resistance included amplifications in CCND1, ERBB4, and MYC in one subclone, and functional protein-altering mutations in ERCC2, SMO, and WT1 in another. Mathematical modeling suggested that these putative resistant subclones comprised 0.02-12.5% of the overall pre-treatment cell population, substantially larger than previous estimates of resistant tumor clone size. Conclusions: WES data from multiple regions of untreated and treated primary breast tumors revealed considerable heterogeneity that remained present throughout treatment with chemotherapy and HER2-targeted therapy, even while major clonal sweeps took place in a minority of tumors. Obtaining at least two samples for analysis from breast tumors post-neoadjuvant therapy may reveal the tumor's evolutionary path and, especially as increasing numbers of molecular and immune therapeutic targets are identified, inform new clinical strategies. Citation Format: Caswell-Jin JL, McNamara K, Reiter JG, Sun R, Hu Z, Ma Z, Suarez CJ, Tilk S, Raghavendra A, Forte V, Chin S-F, Bardwell H, Provenzano E, Caldas C, Lang J, West R, Tripathy D, Press MF, Curtis C. Clonal evolution and heterogeneity in breast tumors treated with neoadjuvant HER2-targeted therapy [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-06-01.