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1
Yang, Yepeng, Zaixing Jiang, Jianguo Zhang, Zongxuan Zhang, and Chun Yang. "Control Effect of Deposition Processes on Shale Lithofacies and Reservoirs Characteristics in the Eocene Shahejie Formation (Es4s), Dongying Depression, China." Energies 16, no. 5 (February 24, 2023): 2200. http://dx.doi.org/10.3390/en16052200.
Abstract:
The lacustrine fine-grained sedimentary rocks in the upper interval of the fourth member of the Eocene Shahejie Formation (Es4s) in the Dongying Depression are important shale oil exploration targets in Bohai Bay Basin. They are widely distributed and rich in organic matter. In this study, samples were observed under the optical microscope and FESEM, combined with geochemical test and physical property analysis to study the sedimentary characteristics and reservoir characteristics of them. Nine lithofacies are recognized based on the mineral composition, the content of organic matter and the beddings. The middle-high organic laminated calcareous fine-grained sedimentary rocks (LF1) and the middle-high organic laminated mixed fine-grained sedimentary rocks (LF2) resulted from seasonal sediment variations and settled by suspension in the deep lake. The middle-high organic flaggy mixed fine-grained sedimentary rocks (LF3), the middle-high organic flaggy calcareous fine-grained sedimentary rocks (LF4), the middle-high organic massive calcareous fine-grained sedimentary rocks (LF5) and the middle organic massive mixed fine-grained sedimentary rocks (LF6) were formed by redeposition. The low organic massive argillaceous fine-grained sedimentary rocks (LF7), the low organic massive felsic fine-grained sedimentary rocks (LF8) and the low organic massive mixed fine-grained sedimentary rocks (LF9) are affected by the terrigenous input events. The pore structures vary in different beddings which are influenced by the kinds and arrangement of minerals and particles. In the laminated lithofacies, the ink-bottle-shaped pores are dominant. In the flaggy and massive lithofacies, the ink-bottle-shaped pores and the slit-shaped pores coexist. LF1 and LF2 are the best target for shale oil exploration and the LF3, LF4, LF5 and LF6 are the second. The deposition processes control the lithofacies and reservoir characteristics of the fined-grained sedimentary rocks.
2
Tam, Lai-Wa, Paul T. Ranum, and Paul A. Lefebvre. "CDKL5 regulates flagellar length and localizes to the base of the flagella in Chlamydomonas." Molecular Biology of the Cell 24, no. 5 (March 2013): 588–600. http://dx.doi.org/10.1091/mbc.e12-10-0718.
Abstract:
The length of Chlamydomonas flagella is tightly regulated. Mutations in four genes—LF1, LF2, LF3, and LF4—cause cells to assemble flagella up to three times wild-type length. LF2 and LF4 encode protein kinases. Here we describe a new gene, LF5, in which null mutations cause cells to assemble flagella of excess length. The LF5 gene encodes a protein kinase very similar in sequence to the protein kinase CDKL5. In humans, mutations in this kinase cause a severe form of juvenile epilepsy. The LF5 protein localizes to a unique location: the proximal 1 μm of the flagella. The proximal localization of the LF5 protein is lost when genes that make up the proteins in the cytoplasmic length regulatory complex (LRC)—LF1, LF2, and LF3—are mutated. In these mutants LF5p becomes localized either at the distal tip of the flagella or along the flagellar length, indicating that length regulation involves, at least in part, control of LF5p localization by the LRC.
3
Wea, Redempta, Bernadete Barek Koten, and Christian Abimayu Morelaka. "Kandungan Energi Bruto, Energi Tercerna dan Energi Metabolis Pakan Cair Fermentasi Berbahan Biji Asam Utuh pada Babi Grower." Jurnal Ilmu Peternakan dan Veteriner Tropis (Journal of Tropical Animal and Veterinary Science) 11, no. 2 (July 30, 2021): 131. http://dx.doi.org/10.46549/jipvet.v11i2.156.
Abstract:
Tamarind seeds have a high energy content but have limited use for pigs because the seed coat is tough and contains anti-nutrient tannins. Therefore, liquid feed fermentation technology is carried out. The aim of this research was to assess the gross energy, digestible energy, and metabolic energy content of liquid feed fermentation (Lff) with different fermentation times in growing pigs. The research materials were whole tamarind seeds, bran, corn, meat and bone meal, and soybean meal. The study used a completely randomized design and consisted of 5 treatments and 5 replications. Treatment = Lf0: Lff time 0 days; Lf1: Lff for 7 days, Lf2: Lff for 14 days, Lf3: Lff for 21days, Lf4: Lff for 28 days fermentation. The research variables were the energy content of the ration and the prediction of digestible energy and metabolic energy value. Data were analyzed using analysis of variance and Duncan's advanced test. The results showed that the Lff with different fermentation time had a significant effect (P <0,05) on gross energy, digestible energy, and metabolic energy value. The best value of energy is Lff for 21 days. It was concluded that the time for fermentation of liquid feed made from tamarind seeds which can produce good energy content, digestibility, and metabolic energy is 21 days.
4
Tang, Jing, Jianbo Fu, Yunxia Wang, Bo Li, Yinghong Li, Qingxia Yang, Xuejiao Cui, et al. "ANPELA: analysis and performance assessment of the label-free quantification workflow for metaproteomic studies." Briefings in Bioinformatics 21, no. 2 (January 15, 2019): 621–36. http://dx.doi.org/10.1093/bib/bby127.
Abstract:
Abstract Label-free quantification (LFQ) with a specific and sequentially integrated workflow of acquisition technique, quantification tool and processing method has emerged as the popular technique employed in metaproteomic research to provide a comprehensive landscape of the adaptive response of microbes to external stimuli and their interactions with other organisms or host cells. The performance of a specific LFQ workflow is highly dependent on the studied data. Hence, it is essential to discover the most appropriate one for a specific data set. However, it is challenging to perform such discovery due to the large number of possible workflows and the multifaceted nature of the evaluation criteria. Herein, a web server ANPELA (https://idrblab.org/anpela/) was developed and validated as the first tool enabling performance assessment of whole LFQ workflow (collective assessment by five well-established criteria with distinct underlying theories), and it enabled the identification of the optimal LFQ workflow(s) by a comprehensive performance ranking. ANPELA not only automatically detects the diverse formats of data generated by all quantification tools but also provides the most complete set of processing methods among the available web servers and stand-alone tools. Systematic validation using metaproteomic benchmarks revealed ANPELA’s capabilities in 1 discovering well-performing workflow(s), (2) enabling assessment from multiple perspectives and (3) validating LFQ accuracy using spiked proteins. ANPELA has a unique ability to evaluate the performance of whole LFQ workflow and enables the discovery of the optimal LFQs by the comprehensive performance ranking of all 560 workflows. Therefore, it has great potential for applications in metaproteomic and other studies requiring LFQ techniques, as many features are shared among proteomic studies.
5
Mehta, Subina, Caleb W. Easterly, Ray Sajulga, Robert J. Millikin, Andrea Argentini, Ignacio Eguinoa, Lennart Martens, et al. "Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform." Proteomes 8, no. 3 (July 8, 2020): 15. http://dx.doi.org/10.3390/proteomes8030015.
Abstract:
For mass spectrometry-based peptide and protein quantification, label-free quantification (LFQ) based on precursor mass peak (MS1) intensities is considered reliable due to its dynamic range, reproducibility, and accuracy. LFQ enables peptide-level quantitation, which is useful in proteomics (analyzing peptides carrying post-translational modifications) and multi-omics studies such as metaproteomics (analyzing taxon-specific microbial peptides) and proteogenomics (analyzing non-canonical sequences). Bioinformatics workflows accessible via the Galaxy platform have proven useful for analysis of such complex multi-omic studies. However, workflows within the Galaxy platform have lacked well-tested LFQ tools. In this study, we have evaluated moFF and FlashLFQ, two open-source LFQ tools, and implemented them within the Galaxy platform to offer access and use via established workflows. Through rigorous testing and communication with the tool developers, we have optimized the performance of each tool. Software features evaluated include: (a) match-between-runs (MBR); (b) using multiple file-formats as input for improved quantification; (c) use of containers and/or conda packages; (d) parameters needed for analyzing large datasets; and (e) optimization and validation of software performance. This work establishes a process for software implementation, optimization, and validation, and offers access to two robust software tools for LFQ-based analysis within the Galaxy platform.
6
Asleson, Catherine M., and Paul A. Lefebvre. "Genetic Analysis of Flagellar Length Control in Chlamydomonas reinhardtii: A New Long-Flagella Locus and Extragenic Suppressor Mutations." Genetics 148, no. 2 (February 1, 1998): 693–702. http://dx.doi.org/10.1093/genetics/148.2.693.
Abstract:
Abstract Flagellar length in the biflagellate alga Chlamydomonas reinhardtii is under constant and tight regulation. A number of mutants with defects in flagellar length control have been previously identified. Mutations in the three long-flagella (lf) loci result in flagella that are up to three times longer than wild-type length. In this article, we describe the isolation of long-flagellar mutants caused by mutations in a new LF locus, LF4. lf4 mutations were shown to be epistatic to lf1, while lf2 was found to be epistatic to lf4 with regard to the flagellar regeneration defect. Mutations in lf4 were able to suppress the synthetic flagella-less phenotype of the lf1, lf2 double mutant. In addition, we have isolated four extragenic suppressor mutations that suppress the long-flagella phenotype of lf1, lf2, or lf3 double mutants.
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Álvarez, María Dolores, Arancha Saiz, Beatriz Herranz, and Susana Cofrades. "Olive Pomace Oil Structuring for the Development of Healthy Puff Pastry Laminating Fats: The Effect of Chilling Storage on the Quality of Baked Products." Foods 13, no. 4 (February 16, 2024): 603. http://dx.doi.org/10.3390/foods13040603.
Abstract:
Developing puff pastry (PP) laminating fats (LFs) with sustainable structured olive pomace oil (OPO) could contribute to its increased valorization. This study evaluated the physicochemical stability of four OPO-based LFs or margarines and the performance of their baked PP counterparts during two months of chilling storage at 4 °C. LF samples, developed at the laboratory scale, contained 41% (LF1 and LF2) OPO and 31% (LF3 and LF4) OPO together with 10% cocoa butter when using two static initial crystallization conditions (room temperature for LF1 and LF3, freezer for LF2 and LF4) before storage. During the storage period, the proximate composition, thermal and dynamic rheological properties, firmness and spreadability, oil-binding capacity, color, and lipid oxidation of the four LF samples were examined, along with the baking performance and textural properties of the PP counterparts. The initial cooling rate had minimal significance. Cocoa butter negatively influenced post-crystallization processes occurring in OPO-based LF3 and LF4, resulting in increased hardness and reduced performance after 18 days of storage, attributed, at least partially, to a high amount of 1,3-dipalmitoyl-2-oleoyl-glycerol (POP), mainly from cocoa butter. Conversely, OPO-based LF1 and LF2 maintained their quality and were stable for two months without apparent granular crystal formation.
8
Tang, Jing, Yang Zhang, Jianbo Fu, Yunxia Wang, Yi Li, Qingxia Yang, Lixia Yao, Weiwei Xue, and Feng Zhu. "Computational Advances in the Label-free Quantification of Cancer Proteomics Data." Current Pharmaceutical Design 24, no. 32 (January 15, 2019): 3842–58. http://dx.doi.org/10.2174/1381612824666181102125638.
Abstract:
Background: Due to its ability to provide quantitative and dynamic information on tumor genesis and development by directly profiling protein expression, the proteomics has become intensely popular for characterizing the functional proteins driving the transformation of malignancy, tracing the large-scale protein alterations induced by anticancer drug, and discovering the innovative targets and first-in-class drugs for oncologic disorders. Objective: To quantify cancer proteomics data, the label-free quantification (LFQ) is frequently employed. However, low precision, poor reproducibility and inaccuracy of the LFQ of proteomics data have been recognized as the key “technical challenge” in the discovery of anticancer targets and drugs. In this paper, the recent advances and development in the computational perspective of LFQ in cancer proteomics were therefore systematically reviewed and analyzed. Methods: PubMed and Web of Science database were searched for label-free quantification approaches, cancer proteomics and computational advances. Results: First, a variety of popular acquisition techniques and state-of-the-art quantification tools are systematically discussed and critically assessed. Then, many processing approaches including transformation, normalization, filtering and imputation are subsequently discussed, and their impacts on improving LFQ performance of cancer proteomics are evaluated. Finally, the future direction for enhancing the computation-based quantification technique for cancer proteomics are also proposed. Conclusion: There is a dramatic increase in LFQ approaches in recent year, which significantly enhance the diversity of the possible quantification strategies for studying cancer proteomics.
9
Sivakova, Barbara, Jan Jurcik, Veronika Lukacova, Tomas Selicky, Ingrid Cipakova, Peter Barath, and Lubos Cipak. "Label-Free Quantitative Phosphoproteomics of the Fission Yeast Schizosaccharomyces pombe Using Strong Anion Exchange- and Porous Graphitic Carbon-Based Fractionation Strategies." International Journal of Molecular Sciences 22, no. 4 (February 9, 2021): 1747. http://dx.doi.org/10.3390/ijms22041747.
Abstract:
The phosphorylation of proteins modulates various functions of proteins and plays an important role in the regulation of cell signaling. In recent years, label-free quantitative (LFQ) phosphoproteomics has become a powerful tool to analyze the phosphorylation of proteins within complex samples. Despite the great progress, the studies of protein phosphorylation are still limited in throughput, robustness, and reproducibility, hampering analyses that involve multiple perturbations, such as those needed to follow the dynamics of phosphoproteomes. To address these challenges, we introduce here the LFQ phosphoproteomics workflow that is based on Fe-IMAC phosphopeptide enrichment followed by strong anion exchange (SAX) and porous graphitic carbon (PGC) fractionation strategies. We applied this workflow to analyze the whole-cell phosphoproteome of the fission yeast Schizosaccharomyces pombe. Using this strategy, we identified 8353 phosphosites from which 1274 were newly identified. This provides a significant addition to the S. pombe phosphoproteome. The results of our study highlight that combining of PGC and SAX fractionation strategies substantially increases the robustness and specificity of LFQ phosphoproteomics. Overall, the presented LFQ phosphoproteomics workflow opens the door for studies that would get better insight into the complexity of the protein kinase functions of the fission yeast S. pombe.
10
Johannsen, Christina, Christian J. Koehler, and Bernd Thiede. "Comparison of LFQ and IPTL for Protein Identification and Relative Quantification." Molecules 26, no. 17 (September 2, 2021): 5330. http://dx.doi.org/10.3390/molecules26175330.
Abstract:
(1) Background: Mass spectrometry-based quantitative proteome profiling is most commonly performed by label-free quantification (LFQ), stable isotopic labeling with amino acids in cell culture (SILAC), and reporter ion-based isobaric labeling methods (TMT and iTRAQ). Isobaric peptide termini labeling (IPTL) was described as an alternative to these methods and is based on crosswise labeling of both peptide termini and MS2 quantification. High quantification accuracy was assumed for IPTL because multiple quantification points are obtained per identified MS2 spectrum. A direct comparison of IPTL with other quantification methods has not been performed yet because IPTL commonly requires digestion with endoproteinase Lys-C. (2) Methods: To enable tryptic digestion of IPTL samples, a novel labeling for IPTL was developed that combines metabolic labeling (Arg-0/Lys-0 and Arg-d4/Lys-d4, respectively) with crosswise N-terminal dimethylation (d4 and d0, respectively). (3) Results: The comparison of IPTL with LFQ revealed significantly more protein identifications for LFQ above homology ion scores but not above identity ion scores. (4) Conclusions: The quantification accuracy was superior for LFQ despite the many quantification points obtained with IPTL.
11
Lê, Hoàng Long, Lệnh Lương Lê, Thị Hương Phạm, Thị Hà My Bùi, Thị Hường Ngô, and Thị Nhung Viên. "GIÁ TRỊ CỦA SIÊU ÂM ĐỊNH LƯỢNG MỠ GAN BẰNG KỸ THUẬT LFQ ĐỂ ĐÁNH GIÁ GAN NHIỄM MỠ CÓ THAM CHIẾU VỚI MRI-PDFF." VietNam Military Medical Unisversity 49 (April 17, 2024): 213–22. http://dx.doi.org/10.56535/jmpm.v49.801.
Abstract:
Mục tiêu: Xác định giá trị của siêu âm định lượng mỡ gan bằng kỹ thuật LFQ để đánh giá gan nhiễm mỡ (GNM). Phương pháp nghiên cứu: Nghiên cứu tiến cứu, mô tả cắt ngang trên 38 bệnh nhân (BN), tất cả được làm siêu âm mode B, đo hệ số suy giảm AC bằng kỹ thuật LFQ và chụp MRI-PDFF tại Phòng khám Đa khoa 360 Lê Hoàn từ tháng 9/2023 - 12/2023. So sánh kết quả siêu âm LFQ với kết quả MRI-PDFF. Kết quả: 13 BN gan không nhiễm mỡ (34,2%) và 25 BN GNM (65,8%) được xác định trên MRI-PDFF với FF lần lượt là < 5,2% và ³ 5,2%. Trong số 25 BN có GNM trên MRI-PDFF, có 8 BN (32,0%) không có thừa cân hay béo phì BMI < 23 kg/m2. Siêu âm mode B chỉ xác nhận 16/25 BN (64,0%) trong số BN được xác định GNM trên MRI-PDFF. Giá trị ngưỡng của hệ số suy giảm AC bằng kỹ thuật LFQ là 0,62; 0,66 và 0,66 dB/cm/MHz tương ứng lần lượt với S1 (FF ³ 5,2%), S2 (FF ³ 11,3%) và S3 (FF ³ 17,1%) trên MRI-PDFF. Phân tích đường cong ROC chỉ ra độ nhạy (Se), độ đặc hiệu (Sp), giá trị ngưỡng (cut-off) của AC cũng như AUC lần lượt là 76,6%, 45,2%, 0,62, 0,766 tương ứng với ³ S1 và 80,0%, 65,7%, 0,66, 0,909 tương ứng với ³ S2. Kết luận: Siêu âm định lượng mỡ gan với kỹ thuật LFQ bằng cách đo hệ số suy giảm AC có giá trị trong đánh giá GNM. Đây là kỹ thuật đơn giản, dễ thực hiện trên hệ thống siêu âm sẵn có, chi phí thấp, có thể áp dụng rộng rãi.
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Dragonieri, Silvano, Sean Galloway, Vitaliano Nicola Quaranta, Andrea Portacci, Maria Rosaria Vulpi, Carla Santomasi, Agnese Caringella, and Giovanna Elisiana Carpagnano. "Assessment of Five Questionnaires for Chronic Obstructive Pulmonary Disease in a Southern Italian Population: A Proof-of-Concept Study." Medicina 59, no. 7 (July 5, 2023): 1252. http://dx.doi.org/10.3390/medicina59071252.
Abstract:
Background and Objectives: Chronic obstructive pulmonary disease (COPD) is a growing burden to society, and remains underdiagnosed in Italy. This study aimed at evaluating five validated screening questionnaires to consider which one was the most accurate, and the optimal cut-off score for each to be considered for the Southern Italian population. Materials and Methods: A total of 144 patients were recruited in the study. The age range was 46–85 years. All subjects underwent spirometry, and completed the five questionnaires: CDQ, LFQ, COPD-PS, COPD-SQ, and CAPTURE. Receiver-operator curves (ROC) were drawn for each questionnaire. The area under the curve (AUC), sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), values for the optimal cut-off score and previously recommended score were calculated and compared. Results: Of the questionnaires, the CDQ, LFQ, and COPD-SQ had significant differences between COPD (n = 86) and non-COPD (n = 52) groups. The AUCs for each questionnaire with (95%CI) were: CAPTURE, 0.602 (0.431–0.773); CDQ, 0.714 (0.555–0.872); LFQ, 0.331 (0.183–0.479; COPD-PS, 0.652 (0.497–0.807); and COPD-SQ, 0.679 (0.520–0.837). Only the CDQ and COPD-SQ had significant AUC screening characteristics. The optimal cut-off values for the CDQ, LFQ, and COPD-PS were modified to 22, 10, and 4, respectively. The COPD-SQ remained at 17. Conclusion: The CDQ and COPD-SQ can discriminate between individuals with and without COPD in the Italian population. The CDQ has a moderate screening accuracy, and the COPD-PS and COPD-SQ have low accuracy, when the optimal cut-off scores are used. Of the five questionnaires assessed, the CDQ and COPD-SQ questionnaires could be used for screening for COPD in the Southern Italian population.
13
Syifa, Nailis, Jhih-Tian Yang, Chang-Shiann Wu, Miao-Hsia Lin, Wan-Ling Wu, Cheng-Wei Lai, Sheng-Hsuan Ku, et al. "Phosphoproteomics and Bioinformatics Analyses Reveal Key Roles of GSK-3 and AKAP4 in Mouse Sperm Capacitation." International Journal of Molecular Sciences 21, no. 19 (October 2, 2020): 7283. http://dx.doi.org/10.3390/ijms21197283.
Abstract:
Protein phosphorylation can induce signal transduction to change sperm motility patterns during sperm capacitation. However, changes in the phosphorylation of sperm proteins in mice are still incompletely understood. Here, capacitation-related phosphorylation in mouse sperms were firstly investigated by label-free quantitative (LFQ) phosphoproteomics coupled with bioinformatics analysis using ingenuity pathway analysis (IPA) methods such as canonical pathway, upstream regulator, and network analysis. Among 1632 phosphopeptides identified at serine, threonine, and tyrosine residues, 1050 novel phosphosites, corresponding to 402 proteins, were reported. Gene heatmaps for IPA canonical pathways showed a novel role for GSK-3 in GP6 signaling pathways associated with capacitation for 60 min. At the same time, the reduction of the abundant isoform-specific GSK-3α expression was shown by western blot (WB) while the LFQ pY of this isoform slightly decreased and then increased. The combined results from WB and LFQ methods explain the less inhibitory phosphorylation of GSK-3α during capacitation and also support the predicted increases in its activity. In addition, pAKAP4 increased at the Y156 site but decreased at the Y811 site in a capacitated state, even though IPA network analysis and WB analysis for overall pAKAP revealed upregulated trends. The potential roles of GSK-3 and AKAP4 in fertility are discussed.
14
Fragoulopoulou, Maria. "Uniqueness of topology for semisimple ${\rm LFQ}$-algebras." Proceedings of the American Mathematical Society 117, no. 4 (April 1, 1993): 963. http://dx.doi.org/10.1090/s0002-9939-1993-1101981-x.
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Rand, Jacob H., Xiao-Xuan Wu, Lucia R. Wolgast, Douglas M. Taatjes, and Stephen R. Master. "Discovery of Unexpected Phospholipid-Binding Proteins in Antiphospholipid Syndrome Patients." Blood 142, Supplement 1 (November 28, 2023): 5393. http://dx.doi.org/10.1182/blood-2023-182506.
Abstract:
INTRODUCTION: The antiphospholipid syndrome (APS), initially described nearly 4 decades ago, remains enigmatic with unclear pathophysiology. In addition to the lack of a mechanistic diagnostic test, APS exhibits considerable phenotypic heterogeneity, including the occurrence of “non-consensus” clinical manifestations (i.e. other than vascular thrombosis and pregnancy complications). Despite the evidence that phospholipid-binding factors are highly likely to be central to APS pathogenesis, the full complement of phospholipid-binding proteins has yet to be systemically assayed. Proteomic profiling by label-free quantitation (LFQ) may identify patterns of protein binding to phospholipid that are central to APS pathogenesis and thereby elucidate a basis for the heterogeneous clinical presentations of APS. METHODS: C18 silica beads were coated with phospholipid by incubation with a suspension of 30% phosphatidylserine/70% phosphatidylcholine. Plasmas from 4 groups: 1) APS patients (n=11), 2) APL positive patients who lacked clinical manifestations (“APL”) (n=11), 3) non-APL patients with thrombosis (“nonAPL”)(n=11), and 4) normal healthy controls (“normal”) (n=6) were incubated with the phospholipid-coated beads, and eluates were processed by gel electrophoresis followed by tryptic digestion. The resulting peptides were analyzed by LC-MS/MS on a Thermo Orbitrap Fusion Lumos. Protein identification, false discovery rate (FDR) estimation, and LFQ were performed using Proteome Discoverer 2.2 (Thermo). LFQ values were normalized by overall peptide abundance, and relative quantitation was obtained. Groupwise comparisons were performed using PD 2.2 in order to identify differentially enriched proteins. RESULTS: A total of 1,210 proteins were identified, with 875 proteins identified at high confidence (q<0.01). Based on gel electrophoresis, all samples had comparable amounts of total protein, and normalization of LFQ data on the basis of total proteins was therefore performed. Differentially expressed proteins between groups were identified using both fold-change and -log p value cutoffs (Figure 1a). Primary analysis focused on identifying proteins that were consistently preferentially bound from the APS plasmas compared to the normal controls. Novel findings included the following proteins related to coagulation, immune response, and to lipid binding that bound preferentially from APS plasmas compared to normal plasmas (APS:control ratios shown in parentheses): coagulation factor VII (10.4), heparin cofactor 2 (9.6), CD14 (6.1), apolipoprotein L1 (6.0), and apolipoprotein L2 (5.5). Additional proteins that preferentially bound from APS plasmas included OAF (13.7), BRSK1 (13.2), MINPP1 (12.5), fetuin B (10.5), SHBG (8.9), ADAMTS-like protein 4 (8.5), SERPIN A4 (7.6), alpha-2-HS glycoprotein (6.7) and inter-alpha-trypsin inhibitor heavy chains (H3, H4 and H1; 8.5, 6.6, 6.5 respectively). Consistent with prior knowledge of APS, and validating this LFQ approach immunoglobulins and complement proteins were also among the preferentially bound proteins and included: Ig heavy chain 1-3 (15.6), complement C9 (13.3), complement C4-B, (7.1), complement component C8 beta chain (5.6), Ig kappa variable 1D-8 (5.6), and Ig lambda-like polypeptide 1 (3.9). Interestingly, a number of identified proteins showed intermediate abundance (between APS and control) in the APL positive patients without clinical manifestations (“APL”) and APL negative patients with thrombosis (“nonAPL”) (see figure 1B-D for examples), suggesting a potential dose response effect. CONCLUSIONS: 1) These results are a first demonstration of concept for the ability of LFQ proteomics to address the complexity of APS through analysis of phospholipid-bound proteins. 2) A number of phospholipid-binding proteins, many of which have not been previously implicated in APS pathogenesis, are preferentially present in APS patient plasma 3) Some plasmas from APL and non-APL patients also show increased binding of some of these proteins compared to the normal controls, suggesting that LFQ may identify markers for subgroups of patients within these 2 categories.
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Goyes, Alirio Rodrigo Bastidas, Andrés Felipe Barragán Amado, Maria Mónica Martinez, Natalia Pinzón Villamil, and Arsanios Martin Daniel. "Validation and reproducibility of the lung function questionnaire (LFQ) for the diagnosis of COPD in Colombia." Pneumologia 69, no. 1 (July 27, 2020): 37–46. http://dx.doi.org/10.2478/pneum-2020-0010.
Abstract:
AbstractIntroductionThe development of clinical prediction scales and their use can reduce under-diagnosis and increase early detection of chronic obstructive pulmonary disease (COPD). The performance of clinical prediction scales in Colombia is unknown. The objective of this study is to evaluate the validity and reproducibility of the lung function questionnaire (LFQ) in Colombia.MethodA cross-sectional study was performed, with analysis of diagnostic validity and reliability in people over 40 years of age who underwent a spirometry test. The LFQ questionnaire was applied. To assess reproducibility, the test was carried out at two time points: first at the initial consultation; and then 1 day to 1 week after the previous application. Spirometry was performed immediately after the initial questionnaire, meeting the American Thoracic Society criteria.ResultsAmong the 1996 subjects included in the analysis, the average age was 65 years (SD: 11.97 years), prevalence of COPD was 21.3%, the intra-class correlation coefficient between the two time points was 0.844 (95% CI: 0.863–0.901) (p < 0.001), and kappa was 0.797 for the dichotomous outcome ≤18 COPD risk points (p < 0.001), validity analysis using the area under the receiver operating characteristic curve for the population evaluated was 0.715 (95% CI: 0.685–0.745); the dichotomous outcome of the questionnaire ≤18 points was as follows: sensitivity – 91.18% (95% CI: 88.0–94.3); specificity – 32.41% (95% CI: 29.8–35.0); positive predictive value – 26.7% (95% CI: 24.1–29.3); negative predictive value – 93.15% (95% CI: 90.7–95.6); likelihood ratio (LR) +: 1.34 (95% CI: 1.28–1.42), LR– 0.27 (95% CI: 0.19–0.39); number needed to diagnose: 4; number needed to misdiagnose: 2 (p < 0.001).ConclusionThe LFQ questionnaire has good performance for the diagnosis of COPD, especially in populations without previous respiratory symptoms or usual risk factors, optimising the use of spirometry to increase its detection.
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Qureshi, Kamil A., Mohamad Arif, Abdul Basit, Sajjad Ahmad, Hammad Tariq Janjuhah, and George Kontakiotis. "Sedimentological Controls on the Reservoir Characteristics of the Mid-Triassic Tredian Formation in the Salt and Trans-Indus Surghar Ranges, Pakistan: Integration of Outcrop, Petrographic, and SEM Analyses." Journal of Marine Science and Engineering 11, no. 5 (May 10, 2023): 1019. http://dx.doi.org/10.3390/jmse11051019.
Abstract:
The current study uses an integrated lithofacies, optical microscopy, and scanning electron microscopy (SEM) analysis to investigate the sedimentary processes, depositional architecture, and reservoir rock potential of the Tredian Formation’s (Mid-Triassic) mixed siliciclastic and carbonate succession in the Salt and Trans-Indus Ranges. The formation has been divided litho-stratigraphically into two components: the lower Landa Member, which consists of fine-grained sandstone and shale, and the upper Khatkiara Member, which consists of coarse-grained sandstone. Based on sedimentary structures and lithology, four distinct types of lithofacies are identified. Two lithofacies representing sandstones interbedded with shale (LF1) and thick-bedded sandstone (LF2) lithofacies suggestive of fluvio-deltaic settings are among them. Another two lithofacies of thin-bedded sandstone (LF3) and dolomite (LF4) suggest a tidal flat depositional environment, correspondingly. The petrographic examination of the Tredian sandstones indicates a lithology ranging from sub-feldspathic arenite to feldspathic arenite with moderate packing. The presence of primary calcite cement, silica cement, and iron oxide/hydroxide cements were shown by the diagenetic investigation, which was supported by SEM studies. In addition, secondary cements include ferroan-dolomite, chlorite, and illite, which is linked with chemical alteration of unstable grains. The paragenetic sequence depicts the diagenetic evolution of the Tredian sandstone from early to late diagenetic phases. The reservoir quality of the LF1 and LF4 lithofacies has been destroyed by early-stage calcite cementation, but the lithofacies LF2 and LF3 have a strong reservoir potential owing to the scarcity of calcite cement, dissolution of unstable feldspar grains, and grain fracture.
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MAHADEVAN, GOPALAN, PALANIVEL BHARATHIRAJAN, VELAYUTHAM RAVI, MOJTABA POULADI, and MARYAM MIRZAEI VAND KHANGHAH. "Short Communication: Age and growth of elongated mudskipper, Pseudapocryptes elongatus (Cuvier, 1816) from Sundarbans, India." Biodiversitas Journal of Biological Diversity 20, no. 1 (December 4, 2018): 85–90. http://dx.doi.org/10.13057/biodiv/d200111.
Abstract:
Mahadevan G, Bharathirajan P, Ravi V, Pouladi M, Mirzaei Vand Khanghah M. 2019. Short Communication: Age and growth of elongated mudskipper, Pseudapocryptes elongatus (Cuvier, 1816) from Sundarbans, India. Biodiversitas 20: 85-90. The estimation of age and mathematical expression of fish growth is complex and debated subject in fishery sciences. Growth parameters of elongated mudskipper, Pseudapocryptes elongatus were estimated based on the length frequency data using FiSAT II software (several tools such as Powell-Wetherall method, ELEFAN and von Bertalanffy growth estimates). Samples were collected from Sundarbans mangroves using gill and cast nets and by hand picking. The length-frequency (LFQ) of P.elongatus was recorded from January 2014 to December 2015 and the above tools estimated the growth parameters (L∞, K and t0) from the progression of LFQ modes through time. L∞ and K values of males were 220.50 mm and 1.3 yr-1, respectively and similarly, L∞ and K values of females were 221.05 mm and 1.21 yr-1, respectively. The t0 values estimated for males and females were-0.1915 years and-0.1661 years, respectively. The estimated growth performance index (Φ) values for males and females of P. elongatus were 4.394 and 4.503, respectively. The lifespan of both the sexes was found to be 4+ years.
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Sommella, Eduardo, Valeria Capaci, Michelangelo Aloisio, Emanuela Salviati, Pietro Campiglia, Giuseppe Molinario, Danilo Licastro, et al. "A Label-Free Proteomic Approach for the Identification of Biomarkers in the Exosome of Endometrial Cancer Serum." Cancers 14, no. 24 (December 19, 2022): 6262. http://dx.doi.org/10.3390/cancers14246262.
Abstract:
Endometrial cancers (ECs) are mostly adenocarcinomas arising from the inner part of the uterus. The identification of serum biomarkers, either soluble or carried in the exosome, may be useful in making an early diagnosis. We used label-free quantification mass spectrometry (LFQ-MS)-based proteomics to investigate the proteome of exosomes in the albumin-depleted serum from 12 patients with EC, as compared to 12 healthy controls. After quantification and statistical analysis, we found significant changes in the abundance (p < 0.05) of 33 proteins in EC vs. control samples, with a fold change of ≥1.5 or ≤0.6. Validation using Western blotting analysis in 36 patients with EC as compared to 36 healthy individuals confirmed the upregulation of APOA1, HBB, CA1, HBD, LPA, SAA4, PF4V1, and APOE. A multivariate logistic regression model based on the abundance of these proteins was able to separate the controls from the EC patients with excellent sensitivity levels, particularly for stage 1 ECs. The results show that using LFQ-MS to explore the specific proteome of serum exosomes allows for the identification of biomarkers in EC. These observations suggest that PF4V1, CA1, HBD, and APOE represent biomarkers that are able to reach the clinical stage, after a validation phase.
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Davidson, Jennilee M., Stephanie L. Rayner, Sidong Liu, Flora Cheng, Antonio Di Ieva, Roger S. Chung, and Albert Lee. "Inter-Regional Proteomic Profiling of the Human Brain Using an Optimized Protein Extraction Method from Formalin-Fixed Tissue to Identify Signaling Pathways." International Journal of Molecular Sciences 24, no. 5 (February 21, 2023): 4283. http://dx.doi.org/10.3390/ijms24054283.
Abstract:
Proteomics offers vast potential for studying the molecular regulation of the human brain. Formalin fixation is a common method for preserving human tissue; however, it presents challenges for proteomic analysis. In this study, we compared the efficiency of two different protein-extraction buffers on three post-mortem, formalin-fixed human brains. Equal amounts of extracted proteins were subjected to in-gel tryptic digestion and LC-MS/MS. Protein, peptide sequence, and peptide group identifications; protein abundance; and gene ontology pathways were analyzed. Protein extraction was superior using lysis buffer containing tris(hydroxymethyl)aminomethane hydrochloride, sodium dodecyl sulfate, sodium deoxycholate, and Triton X-100 (TrisHCl, SDS, SDC, Triton X-100), which was then used for inter-regional analysis. Pre-frontal, motor, temporal, and occipital cortex tissues were analyzed by label free quantification (LFQ) proteomics, Ingenuity Pathway Analysis and PANTHERdb. Inter-regional analysis revealed differential enrichment of proteins. We found similarly activated cellular signaling pathways in different brain regions, suggesting commonalities in the molecular regulation of neuroanatomically-linked brain functions. Overall, we developed an optimized, robust, and efficient method for protein extraction from formalin-fixed human brain tissue for in-depth LFQ proteomics. We also demonstrate herein that this method is suitable for rapid and routine analysis to uncover molecular signaling pathways in the human brain.
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Hutchings, Charlotte, Charlotte S. Dawson, Thomas Krueger, Kathryn S. Lilley, and Lisa M. Breckels. "A Bioconductor workflow for processing, evaluating, and interpreting expression proteomics data." F1000Research 12 (October 24, 2023): 1402. http://dx.doi.org/10.12688/f1000research.139116.1.
Abstract:
Background: Expression proteomics involves the global evaluation of protein abundances within a system. In turn, differential expression analysis can be used to investigate changes in protein abundance upon perturbation to such a system. Methods: Here, we provide a workflow for the processing, analysis and interpretation of quantitative mass spectrometry-based expression proteomics data. This workflow utilizes open-source R software packages from the Bioconductor project and guides users end-to-end and step-by-step through every stage of the analyses. As a use-case we generated expression proteomics data from HEK293 cells with and without a treatment. Of note, the experiment included cellular proteins labelled using tandem mass tag (TMT) technology and secreted proteins quantified using label-free quantitation (LFQ). Results: The workflow explains the software infrastructure before focusing on data import, pre-processing and quality control. This is done individually for TMT and LFQ datasets. The application of statistical differential expression analysis is demonstrated, followed by interpretation via gene ontology enrichment analysis. Conclusions: A comprehensive workflow for the processing, analysis and interpretation of expression proteomics is presented. The workflow is a valuable resource for the proteomics community and specifically beginners who are at least familiar with R who wish to understand and make data-driven decisions with regards to their analyses.
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Fragão-Marques, Mariana, Rui Vitorino, Isaac Barroso, Inês Falcão-Pires, Adelino Leite-Moreira, and Fábio Trindade. "Pericardial Fluid Annexin A1 Is a Marker of Atrial Fibrillation in Aortic Stenosis: A Proteomics Analysis." Journal of Personalized Medicine 12, no. 2 (February 11, 2022): 264. http://dx.doi.org/10.3390/jpm12020264.
Abstract:
Atrial fibrillation (AF) is the most common arrhythmia with adverse clinical outcomes. Pericardial fluid (PF) mirrors the heart’s pathophysiological status due to its proximity. This study aimed to characterise the PF proteome to identify new biomarkers of disease. Eighty-three patients submitted to aortic valve replacement surgery with severe aortic stenosis were selected, and their baseline echocardiographic and clinical variables were documented. Thirteen samples were selected blindly for proteome characterisation following a shotgun (GeLC–MS/MS) and a label-free quantification approach (LFQ). According to previous AF history, a partial least squares discriminant analysis (PLS-DA) was conducted, and the top 15 variables important in projection were identified. To inquire potential biomarkers, ROC curves were designed using LFQ data. Target proteins were further validated by ELISA, in both pericardial fluid and serum. Proteome analysis uncovered nine proteins up- and downregulated ≥2-fold. Annexin A1, annexin A2, and vimentin were among the top 15 most important variables for group discrimination in PLS-DA. Protein—protein interaction and gene ontology enrichment analysis presented functional interaction among identified proteins, which were all part of focal adhesion sites. Annexin A1 was increased in the pericardial fluid of AF patients but not in serum when quantified by ELISA. Annexin A1 is a novel pericardial fluid biomarker of AF in patients with severe aortic stenosis.
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Rende, Umut, Seong Beom Ahn, Subash Adhikari, Edward S. X. Moh, Carol A. Pollock, Sonia Saad, and Anna Guller. "Deciphering the Kidney Matrisome: Identification and Quantification of Renal Extracellular Matrix Proteins in Healthy Mice." International Journal of Molecular Sciences 24, no. 3 (February 1, 2023): 2827. http://dx.doi.org/10.3390/ijms24032827.
Abstract:
Precise characterization of a tissue’s extracellular matrix (ECM) protein composition (matrisome) is essential for biomedicine. However, ECM protein extraction that requires organ-specific optimization is still a major limiting factor in matrisome studies. In particular, the matrisome of mouse kidneys is still understudied, despite mouse models being crucial for renal research. Here, we comprehensively characterized the matrisome of kidneys in healthy C57BL/6 mice using two ECM extraction methods in combination with liquid chromatography tandem mass spectrometry (LC-MS/MS), protein identification, and label-free quantification (LFQ) using MaxQuant. We identified 113 matrisome proteins, including 22 proteins that have not been previously listed in the Matrisome Database. Depending on the extraction approach, the core matrisome (structural proteins) comprised 45% or 73% of kidney ECM proteins, and was dominated by glycoproteins, followed by collagens and proteoglycans. Among matrisome-associated proteins, ECM regulators had the highest LFQ intensities, followed by ECM-affiliated proteins and secreted factors. The identified kidney ECM proteins were primarily involved in cellular, developmental and metabolic processes, as well as in molecular binding and regulation of catalytic and structural molecules’ activity. We also performed in silico comparative analysis of the kidney matrisome composition in humans and mice based on publicly available data. These results contribute to the first reference database for the mouse renal matrisome.
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Cehofski, Lasse Jørgensen, Anders Kruse, Alexander Nørgård Alsing, Benn Falch Sejergaard, Jonas Ellegaard Nielsen, Shona Pedersen, Danson Vasanthan Muttuvelu, Svend Kirkeby, Bent Honoré, and Henrik Vorum. "Aflibercept Intervention in Experimental Branch Retinal Vein Occlusion Results in Upregulation of DnaJ Homolog Subfamily C Member 17." Journal of Ophthalmology 2021 (March 6, 2021): 1–9. http://dx.doi.org/10.1155/2021/6690260.
Abstract:
Aflibercept is an inhibitor of vascular endothelial growth factor (VEGF) used to treat macular edema following branch retinal vein occlusion (BRVO). Despite well-documented efficacy, there is limited knowledge about proteome changes following aflibercept intervention in BRVO. Proteome changes may provide insights into mechanisms of action as well as aspects related to safety profile. In seven Danish Landrace pigs, BRVO was induced with a well-established experimental model of argon laser-induced BRVO. BRVO was induced in both eyes. Three days after the induced BRVO, aflibercept was injected intravitreally in the right eyes, while the left eyes received intravitreal isotonic saline water. Retinas were collected 15 days after the induced BRVO and analyzed with label-free quantification liquid chromatography tandem mass spectrometry (LFQ LC-MS/MS). Fourteen proteins were changed in expression following aflibercept intervention in the BRVO model. LFQ LC-MS/MS identified an upregulation of DnaJ homolog subfamily C member 17 (DNAJC17) (fold change = 6.19) and a modest downregulation of isoform 2 of the protein encoded by N-myc downstream regulated gene 2 (NDRG2) (fold change = 0.40). NDRG2 was unchanged by Western blotting. In the additional significantly regulated proteins, only discrete changes were observed (fold changes 0.52–1.59). Our study is the first to report an association between aflibercept intervention and the heat shock protein DNAJC17. Our results indicate that the role of heat shock proteins in the treatment of BRVO should be further explored.
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Altshuler, Lori, Jim Mintz, and Kristin Leight. "The Life Functioning Questionnaire (LFQ): a brief, gender-neutral scale assessing functional outcome." Psychiatry Research 112, no. 2 (October 2002): 161–82. http://dx.doi.org/10.1016/s0165-1781(02)00180-4.
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Fu, Jianbo, Yongchao Luo, Minjie Mou, Hongning Zhang, Jing Tang, Yunxia Wang, and Feng Zhu. "Advances in Current Diabetes Proteomics: From the Perspectives of Label- free Quantification and Biomarker Selection." Current Drug Targets 21, no. 1 (December 20, 2019): 34–54. http://dx.doi.org/10.2174/1389450120666190821160207.
Abstract:
Background: Due to its prevalence and negative impacts on both the economy and society, the diabetes mellitus (DM) has emerged as a worldwide concern. In light of this, the label-free quantification (LFQ) proteomics and diabetic marker selection methods have been applied to elucidate the underlying mechanisms associated with insulin resistance, explore novel protein biomarkers, and discover innovative therapeutic protein targets. Objective: The purpose of this manuscript is to review and analyze the recent computational advances and development of label-free quantification and diabetic marker selection in diabetes proteomics. Methods: Web of Science database, PubMed database and Google Scholar were utilized for searching label-free quantification, computational advances, feature selection and diabetes proteomics. Results: In this study, we systematically review the computational advances of label-free quantification and diabetic marker selection methods which were applied to get the understanding of DM pathological mechanisms. Firstly, different popular quantification measurements and proteomic quantification software tools which have been applied to the diabetes studies are comprehensively discussed. Secondly, a number of popular manipulation methods including transformation, pretreatment (centering, scaling, and normalization), missing value imputation methods and a variety of popular feature selection techniques applied to diabetes proteomic data are overviewed with objective evaluation on their advantages and disadvantages. Finally, the guidelines for the efficient use of the computationbased LFQ technology and feature selection methods in diabetes proteomics are proposed. Conclusion: In summary, this review provides guidelines for researchers who will engage in proteomics biomarker discovery and by properly applying these proteomic computational advances, more reliable therapeutic targets will be found in the field of diabetes mellitus.
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Margalit, Anatte, James C. Carolan, David Sheehan, and Kevin Kavanagh. "The Aspergillus fumigatus Secretome Alters the Proteome of Pseudomonas aeruginosa to Stimulate Bacterial Growth: Implications for Co-infection." Molecular & Cellular Proteomics 19, no. 8 (May 23, 2020): 1346–59. http://dx.doi.org/10.1074/mcp.ra120.002059.
Abstract:
Individuals with cystic fibrosis are susceptible to co-infection by Aspergillus fumigatus and Pseudomonas aeruginosa. Despite the persistence of A. fumigatus in the cystic fibrosis lung P. aeruginosa eventually predominates as the primary pathogen. Several factors are likely to facilitate P. aeruginosa colonization in the airways, including alterations to the microbial environment. The cystic fibrosis airways are hypoxic, nitrate-rich environments, and the sputum has higher amino acid concentrations than normal. In this study, significant growth proliferation was observed in P. aeruginosa when the bacteria were exposed to A. fumigatus culture filtrates (CuF) containing a high nitrate content. Proteomic analysis of the A. fumigatus CuF identified a significant number of environment-altering proteases and peptidases. The molecular mechanisms promoting bacterial growth were investigated using label-free quantitative (LFQ) proteomics to compare the proteome of P. aeruginosa grown in the A. fumigatus CuF and in CuF produced by a P. aeruginosa-A. fumigatus co-culture, to that cultured in P. aeruginosa CuF. LFQ proteomics revealed distinct changes in the proteome of P. aeruginosa when cultured in the different CuFs, including increases in the levels of proteins involved in denitrification, stress response, replication, amino acid metabolism and efflux pumps, and a down-regulation of pathways involving ABC transporters. These findings offer novel insights into the complex dynamics that exist between P. aeruginosa and A. fumigatus. Understanding the molecular strategies that enable P. aeruginosa to predominate in an environment where A. fumigatus exists is important in the context of therapeutic development to target this pathogen.
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Dustin, Michael, Ahmed Saadawi, Viveka Mayya, Pablo Cespedes, Salvatore Valvo, Lina Chen, and Philippos Demetriou. "Dissection of T-cell tolerance induction by dendritic cell surface glycoproteins." Journal of Immunology 204, no. 1_Supplement (May 1, 2020): 143.1. http://dx.doi.org/10.4049/jimmunol.204.supp.143.1.
Abstract:
Abstract Tolerogenic dendritic cells (DC) induce T-cell clonal deletion, anergy, generation and activation of regulatory T cells. In vitro production of TolDC has been accomplished, however the full molecular circuitry is not known. We aim to decipher the chemical signals and physical characteristics leading to T-cell tolerance in an artificial system. We have performed surface proteomic analysis of human peripheral blood cDC2 subset without and with in vitro stimulation with polyIC in vitro. The surface proteomics is based on biotinylation of sialic acids and the signal strength was 55-fold higher in the resting compared to the activated condition, presumably due to decreased sialation of glycoproteins in the activated cDC2. We found that label free quantification (LFQ), corrected for differences in sialation, agreed well with quantitative surface expression by flow cytometry. We combined the two datasets and ranked the top 120 glycoproteins with extracellular domains (ECD) > 60 amino acids by LFQ with approximately one third invariant, one third up-regulated/induced and one one-third down-regulated/lost on activation. The 120 ECD were expressed in HEK293 cells with C-terminal 10His tags and purified by Ni2+ affinity chromatography. Supported lipids bilayers (SLB) representing the tolerogenic and activating DC are being designed with different combinations of the 120 ECDs. We will adjust sialation to match resting and activated states. The SLB compositions will be tested for immunological synapse formation (fluorescent self-pMHC/CD80, ICAM-1 and CD58 for the cSMAC, pSMAC and dSMAC) and tolerance/activation spectrum with identification of relevant molecular combinations by machine learning.
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Nafar, Mohsen, Shiva Samavat, Nooshin Dalili, Shiva Kalantari, Leonard Foster, Kyung-Mee Moon, and Somaye-Sadat Heidari. "Identification of Potential Predictive and Diagnostic Urinary Biomarkers for Acute Rejection in Renal Transplant Recipients: A Proteomics Study." OBM Transplantation 07, no. 03 (July 7, 2023): 1–33. http://dx.doi.org/10.21926/obm.transplant.2303191.
Abstract:
Acute rejection (AR) is one of the main predictors of long-term survival of allograft. The development of noninvasive diagnostic biomarkers of AR is an unmet need for the timely detection. This study aimed to identify novel detective biomarkers of AR by analyzing the urine proteome profile of transplant patients. Forty-two transplant patients including 30 biopsy-proven AR patients (including antibody and T-cell mediated rejection) and 12 transplant patients with stable renal function (control group) were enrolled. Label-free quantification (LFQ) proteomics technique was performed on urine samples. Multivariate statistical analysis was applied for biomarker identification. The ELISA method validated EGF (epidermal growth factor) from the top 10 candidate biomarkers in an independent cohort. Gene ontology and possible pathways were also analyzed. LFQ analysis revealed 453 identified proteins differentially expressed between groups that mainly participated in complement and coagulation pathways and proteolysis. Ten proteins with the highest AUCs (Area under the ROC Curve) were identified as candidate diagnostic biomarkers. Candidate biomarkers were mainly associated with extracellular matrix (ECM) degradation and epithelial-to-mesenchymal transition (EMT). Reduction of urinary EGF measured by ELISA in an independent group confirmed proteomics results. We introduced a unique set of diagnostic urinary biomarkers for AR. Interactions of biomarkers and validation of EGF among biomarker panels revealed that ECM remodeling and EMT might be the consequence of immunological processes in AR. If validated as a panel, the mentioned biomarkers might shed light on the pathogenesis of chronic injury after AR and point out the potential treatment strategies.
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Ortigues, Isabelle, T. Smith, M. Gill, S. B. Cammell, and N. W. Yarrow. "The effect of fishmeal supplementation of a straw-based diet on growth and calorimetric efficiency of growth in heifers." British Journal of Nutrition 64, no. 3 (November 1990): 639–51. http://dx.doi.org/10.1079/bjn19900067.
Abstract:
Thirty-two 160 kg dairy heifers were used to measure the effects of increasing dietary protein content on growth and heat production. A basal diet containing (g/kg) 550 sodium hydroxide-treated straw, 220 barley, 220 sugarbeet pulp and 10 urea was offered with 0, 76 and 152 g fishmeal/kg dry matter of the basal diet (F0, F1 and F2 levels respectively). The three diets were each given at two levels of feeding (low, L; high, H): 57.6 g/d per kg metabolic body-weight (W0.75) for the LF0 diet and 74.7 g/d per kg W0.75 for the HFO diet. Apparent digestibility of the diets increased in response to the addition of fishmeal. Mean dry matter digestibility values were 0.67, 0.67, 0.69, 0.66, 0.68 and 0.69 and those for acid-detergent fibre digestibility were 0.60, 0.63, 0.66, 0.58, 0.60 and 0.65 for diets LF0, LF1, LF2, HF0, HF1 and HF2 respectively. Nitrogen retention increased in response to both fishmeal and feeding level. Live-weight gains were 170, 296, 434 g/d for the LF0, LF1 and LF2 diets and 468, 651 and 710 g/d for the HF0, HF1 and HF2 diets respectively. There were significant effects of increasing the plane of feeding and the level of fishmeal in the diet on live-weight gain. Dietary effects on live-weight gains were accompanied by increases in mean energy retention of 23, 45, 82, 94, 160 and 152 kJ/d per kg W0.75 for diets LF0, LF1, LF2, HF0, HF1 and HF2 respectively, but no definite evidence was obtained that dietary supplementation with fishmeal modified the efficiency of utilization of metabolizable energy for growth.
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Avcı, Sertan, and Engin Yurtseven. "The Effect of Irrigation Water Quality and Leaching Ratio on Some Yield Parameters in Alfalfa (Medicago Sativa L.)." Turkish Journal of Agriculture - Food Science and Technology 10, no. 6 (July 7, 2022): 1186–90. http://dx.doi.org/10.24925/turjaf.v10i6.1186-1190.5323.
Abstract:
This study was carried out over the experimental fields of Ankara University, Faculty of Agriculture Gümüşdere Campus. Experiments were conducted with 3 different irrigation water salinity levels (S1=0.25 dS/m – control/tap water, S2=1.5 dS/m, S3=3.0 dS/m) and 4 different leaching ratios (LF1=10%, LF2 =20%, LF3 = 35%, LF4=50%) in randomized plots factorial experimental design with 3 replications. Totally, 36 (3×4×3) lysimeters were used in present experiments. Plant height, fresh and dry herbage yield and total ash content of alfalfa plants were analyzed. With increasing salinity levels, plant height, fresh and dry herbage yields decreased and total ash contents increased. Positive effects of leaching applications were observed, but this effect was not found to be significant. The main reason for this situation may be the necessity of a good drainage system for a good leaching application.
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Curry, Erin, Megan E. Philpott, Jessye Wojtusik, Wendy D. Haffey, Michael A. Wyder, Kenneth D. Greis, and Terri L. Roth. "Label-Free Quantification (LFQ) of Fecal Proteins for Potential Pregnancy Detection in Polar Bears." Life 12, no. 6 (May 27, 2022): 796. http://dx.doi.org/10.3390/life12060796.
Abstract:
Reliable pregnancy diagnostics would be beneficial for monitoring polar bear (Ursus maritimus) populations both in situ and ex situ, but currently there is no method of non-invasive pregnancy detection in this species. Recent reports in several carnivore species described the identification of fecal proteins that may serve as pregnancy biomarkers; however, repeatability has been limited. The objective of the current analysis was to utilize an unbiased, antibody-free, label-free method for the identification and quantification of fecal proteins to determine if differences associated with pregnancy are detectable in polar bears. Protein was extracted from fecal samples (n = 48) obtained from parturient (n = 6) and non-parturient (n = 6) profiles each at four timepoints: pre-breeding season, embryonic diapause, early placental pregnancy, and mid-placental pregnancy. Protein was prepared and analyzed on the Thermo Orbitrap Eclipse nanoLC-MS/MS system. A total of 312 proteins was identified and quantified; however, coefficients of variation (CV) were high for both abundance ratio variability (384.8 ± 61.0% SEM) and within group variability (86.8 ± 1.5%). Results of this study suggest that the inconsistencies in specific protein concentrations revealed previously by antibody-based assays may not be due to that methodology’s limitations, but rather, are reflective of true variation that exists among samples.
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Schelletter, Louise, Stefan Albaum, Stefan Walter, Thomas Noll, and Raimund Hoffrogge. "Clonal variations in CHO IGF signaling investigated by SILAC-based phosphoproteomics and LFQ-MS." Applied Microbiology and Biotechnology 103, no. 19 (August 16, 2019): 8127–43. http://dx.doi.org/10.1007/s00253-019-10020-z.
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Jha, P. "Plancton exógeno como alimento para la cría intensiva del ciprínido ornamental Epalzeorhynchus frenatus." Archivos de Zootecnia 59, no. 225 (October 3, 2010): 11–20. http://dx.doi.org/10.21071/az.v59i225.4887.
Abstract:
Para explorar la utilidad de diferentes regímenes de manejo para intensificar la cría del ciprínido Epalzeorhynchus frenatus, larvas del pez (0,18 ± 0,014 g) fueron cultivadas durante tres meses (18 febrero-18 mayo 2007) en tanques de hormigón, de acuerdo con seis tratamientos: tres regímenes con alimento vivo en los que los peces se mantuvieron a una densidad de 0,3 (LF1); 0,5 (LF2); y 1,0 pez/l (LF3); y otros tres regímenes con alimentación tradicional (granulada) en los que los peces se mantuvieron a una densidad de 0,3 (TD1); 0,5 (TD2); 1,0 pez/l (TD3). Se introdujo plancton exógeno en los tanques con alimento vivo. Se hicieron tres repeticiones por tratamiento en las que los peces fueron alimentados cada día ligeramente en exceso del nivel de saciedad, para eliminar la posibilidad de que el suministro de alimento fuera un factor limitante del crecimiento. Los valores del oxígeno disuelto fueron más altos en el tratamiento LF1, seguido por LF2, TD1, LF3, TD2 y TD3 (p
35
Koch, Marco, Thomas Butt, Wudong Guo, Xue Li, Yirong Chen, Diana Tan, and Gordon G. Liu. "OP366 Characterizing The Population At Risk Of Chronic Obstructive Pulmonary Disease In China Using A Real-World Population Survey." International Journal of Technology Assessment in Health Care 36, S1 (December 2020): 7. http://dx.doi.org/10.1017/s026646232000104x.
Abstract:
IntroductionChronic obstructive pulmonary disease (COPD) is a leading cause of morbidity and mortality in China. However, early identification of patients with COPD in the community is challenging. This study used a real-world survey of the Chinese urban adult population to estimate the prevalence of COPD diagnosis or COPD-risk, examine the health outcomes and healthcare resource use of these groups, and investigate the sociodemographic factors associated with these statuses.MethodsRespondents to the 2017 National Health and Wellness Survey in China (n = 19,994) were classified into: COPD (diagnosed), COPD-risk (undiagnosed), and control (undiagnosed, not at-risk) using their self-reported diagnosis and Lung Function Questionnaire (LFQ) score. These groups were compared by healthcare resource use and health outcomes (EuroQol [EQ-5D] and Work Productivity and Activity Impairment questionnaires). Factors associated with being in these groups were investigated using pairwise comparisons (t-tests and chi-square tests) and multivariable logistic regression.ResultsIn total, 3,320 respondents (16.6%) had a suspected risk of COPD but did not report receiving a diagnosis. This was projected to 105.3 million people (16.9% of urban adults). Relative to the controls, COPD-risk and COPD-diagnosed respondents had higher healthcare resource use, lower productivity, and lower health-related quality of life (HRQoL) (p < 0.05). Age, smoking, alcohol consumption, weight, exercise, comorbidities, gender, education, employment, and air pollution were associated with increased odds of COPD-risk relative to the controls (p < 0.05).ConclusionsA substantial group of individuals, undiagnosed, but with a risk of COPD, have impaired HRQoL, lower productivity, and elevated healthcare resource use. A range of sociodemographic factors are predictive of COPD risk, which may support targeted screening. Case-detection tools such as the LFQ may offer a convenient approach for identifying individuals for further definitive testing and appropriate treatment in China.
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Wang, Dehao, Pei Zhao, Yan Lv, Jing Ming, Ziqing Wang, Erpeng Yang, Yumeng Li, et al. "Proteomic-Based Platelet Activation-Associated Protein SELP May Be a Novel Biomarker for Coagulation and Prognostic in Essential Thrombocythemia." Journal of Clinical Medicine 12, no. 3 (January 30, 2023): 1078. http://dx.doi.org/10.3390/jcm12031078.
Abstract:
Abnormal platelet activation can lead to thrombosis in essential thrombocythemia (ET) and thus impact patient prognosis. Platelet activation-associated proteins are key molecules for platelet activation. However, it is unclear which proteins are most closely associated with the disease’s prognosis. To determine which platelet activation-related proteins can be employed as ET patient prognosis predictors, we used label-free quantification (LFQ) and parallel reaction monitoring (PRM) technology and first determined the serum proteomic expression levels and the differential proteins of ET patients. Then, based on the IPSET (International Prognostic Score for ET), the differential protein associated with the prognostic score was found. To investigate potential processes affecting prognosis, the connection of this protein with prognostic markers, such as thrombotic history, age, white blood cell count, coagulation factors, and inflammatory factors, were further examined. The levels of platelet activation-related proteins GPIbα, SELP, PF4, MMP1, and FLNA were significantly higher in ET patients, according to LFQ and PRM analyses (p < 0.01). Based on regression analysis of the IPSET prognostic score, it is suggested that the SELP level was positively correlated with the prognostic score and prognostic risk factor analysis (p < 0.05). Further regression analysis of SELP with coagulation factors showed that antithrombin (AT-III) was negatively correlated with SELP levels (p < 0.05). Further regression analysis of the inflammatory factors with AT-III and SELP revealed that IL-10, IL-12P70, and IL-31 were negatively correlated with AT-III and SELP (p < 0.01). Platelet activation pathway-related proteins are expressed more frequently in ET patients, and serum SELP may be a prognostic marker for these individuals by encouraging leukocyte increase and inflammatory factor expression and causing aberrant coagulation.
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Hanania, Nicola A., David M. Mannino, Barbara P. Yawn, Douglas W. Mapel, Fernando J. Martinez, James F. Donohue, Mark Kosinski, et al. "Predicting risk of airflow obstruction in primary care: Validation of the lung function questionnaire (LFQ)." Respiratory Medicine 104, no. 8 (August 2010): 1160–70. http://dx.doi.org/10.1016/j.rmed.2010.02.009.
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Bastidas, Alirio R., Eduardo Tuta-Quintero, José S. Arias, Diana Cufiño, Diana Moya, Daniel Martin, Faure Rodríguez, et al. "Comparison of the Diagnostic Performance of Five Clinical Questionnaires for Chronic Obstructive Pulmonary Disease." Canadian Respiratory Journal 2023 (November 24, 2023): 1–8. http://dx.doi.org/10.1155/2023/2821056.
Abstract:
Background. Chronic obstructive pulmonary disease (COPD) remains one of the most prevalent pathologies in the world and is among the leading causes of mortality and morbidity, partially due to underdiagnosis. The use of clinical questionnaires to identify high-risk individuals to take them to further diagnostic procedures has emerged as a strategy to address this problem. Objective. To compare the performance of the COULD IT BE COPD, CDQ, COPD-PS, LFQ, and PUMA questionnaires for COPD diagnosis. Methods. A cross-sectional study was carried out on subjects who underwent spirometry in the third-level center. Data were collected between January 2015 and March 2020. Bivariate analysis was performed between the study variables and the presence of COPD. The area under the receiver operating characteristics curve (AUC-ROC), sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), positive likelihood ratio (LR+), and negative likelihood ratio (LR−) for each questionnaire were calculated. The AUC-ROCs were compared with the DeLong test, considering a p value <0.05 statistically significant. Results. 681 subjects met the inclusion criteria and were taken to the final analysis. The prevalence of COPD was 27.5% (187/681). The mean age of the subjects was 65.9 years (SD ± 11.79); 46.3% (315/681) were female, and 83.6% (569/681) reported respiratory symptoms. Statistically significant relationship was found for COPD diagnosis with male sex, older age, respiratory symptoms, and exposure to wood smoke ( p value <0.05). The AUC-ROCs of the questionnaires were between 0.581 and 0.681. The COULD IT BE COPD questionnaire had a lower discriminatory capacity AUC-ROC of 0.581, concerning the other scores (DeLong test, p = 0.0002). Conclusion. The CDQ, COPD-PS, LFQ, PUMA, and COULD IT BE COPD questionnaires have acceptable performance for the diagnosis of COPD together with low sensitivity and specificity. Therefore, its use must be complemented with other diagnostic tests or techniques such as pulmonary function tests.
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Subramanian, Visalakshi H., Mukthapuram Lokesh, and A. K. Vijay Krishna Kumar. "Prevalence of risk for chronic obstructive pulmonary disease amongst carpenters using lung function questionnaire." International Journal Of Community Medicine And Public Health 10, no. 10 (September 30, 2023): 3737–40. http://dx.doi.org/10.18203/2394-6040.ijcmph20233108.
Abstract:
Background: An obstructive ventilatory pattern is a hallmark of chronic obstructive pulmonary disease (COPD), a slow-progressing respiratory condition that is frequently linked to cigarette use and can result in chronic respiratory failure. A case-finding tool called the lung function questionnaire (LFQ) is being created to help doctors choose which patients should undergo spirometry testing to confirm the presence of chronic obstructive pulmonary disease (COPD). Methods: Survey research study of 185 convenient sampling. Results: The results were obtained using lung function questionnaire. Statistical analysis shows that there is prevalence of risk for COPD amongst the carpenters. Conclusions: This study concludes that there is a risk of developing chronic obstructive pulmonary disease (COPD) in carpenters who are exposed to saw dust as more than half the samples have scored less than or equal to 18 which indicates the risk for COPD.
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Ribeiro, Apoena A., Flávia Purger, Jonas A. Rodrigues, Patrícia R. A. Oliveira, Adrian Lussi, Antonio Henrique Monteiro, Haimon D. L. Alves, Joaquim T. Assis, and Adalberto B. Vasconcellos. "Influence of Contact Points on the Performance of Caries Detection Methods in Approximal Surfaces of Primary Molars: An in vivo Study." Caries Research 49, no. 2 (2015): 99–108. http://dx.doi.org/10.1159/000368562.
Abstract:
This in vivo study aimed to evaluate the influence of contact points on the approximal caries detection in primary molars, by comparing the performance of the DIAGNOdent pen and visual-tactile examination after tooth separation to bitewing radiography (BW). A total of 112 children were examined and 33 children were selected. In three periods (a, b, and c), 209 approximal surfaces were examined: (a) examiner 1 performed visual-tactile examination using the Nyvad criteria (EX1); examiner 2 used DIAGNOdent pen (LF1) and took BW; (b) 1 week later, after tooth separation, examiner 1 performed the second visual-tactile examination (EX2) and examiner 2 used DIAGNOdent again (LF2); (c) after tooth exfoliation, surfaces were directly examined using DIAGNOdent (LF3). Teeth were examined by computed microtomography as a reference standard. Analyses were based on diagnostic thresholds: D1: D₀ = health, D1-D4 = disease; D2: D₀, D1 = health, D2-D4 = disease; D3: D₀-D2 = health, D3, D4 = disease. At D1, the highest sensitivity/specificity were observed for EX1 (1.00)/LF3 (0.68), respectively. At D2, the highest sensitivity/specificity were observed for LF3 (0.69)/BW (1.00), respectively. At D3, the highest sensitivity/specificity were observed for LF3 (0.78)/EX1, EX2 and BW (1.00). EX1 showed higher accuracy values than LF1, and EX2 showed similar values to LF2. We concluded that the visual-tactile examination showed better results in detecting sound surfaces and approximal caries lesions without tooth separation. However, the effectiveness of approximal caries lesion detection of both methods was increased by the absence of contact points. Therefore, regardless of the method of detection, orthodontic separating elastics should be used as a complementary tool for the diagnosis of approximal noncavitated lesions in primary molars.
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Ma, Yabo, Changzheng Du, Xianguo Xie, Yan Zhang, Chao Wang, Jinrui Xu, Guoliang Xia, and Yi Yang. "To explore the regulatory role of Wnt/P53/Caspase3 signal in mouse ovarian development based on LFQ proteomics." Journal of Proteomics 272 (February 2023): 104772. http://dx.doi.org/10.1016/j.jprot.2022.104772.
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Vakhrushev, I. V., S. E. Novikova, A. V. Tsvetkova, M. A. Pyatnitskiy, and K. N. Yarygin. "Comparative proteomic profiling of nuclear and cytosolic fractions from cell lines of different origin." Biomeditsinskaya Khimiya 64, no. 3 (2018): 233–40. http://dx.doi.org/10.18097/pbmc20186403233.
Abstract:
Proteomic analysis of the nuclear fraction is of great importance, since many cellular processes are initiated in the nucleus. Refinement and choice of experimental procedures for cell lysate fractionation and parameters for mass spectrometric detection and data processing continue to be of current interest. The mass spectrometry analysis presented here was tested on human cell lines derived from different tissues: HL-60 (peripheral blood); HepG2 (liver); EA.hy926 (vascular endothelium). High reproducibility of results and their consistency with biological properties of the objects under study were demonstrated. The use of cells of different types made it possible to reveal a set of 16 proteins whose LFQ-values allow for the discrimination between proteome fractions regardless of cell origin. Also, a set of 16 proteins is suggested which are associated with individual characteristics of cell lines regardless of cell fraction. These protein panels can serve as parameters to verify the proteomic analysis done was of sufficient quality, in particular as indicators of successful fractionation of cell or tissue lysate.
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Strasser, Lisa, Stefano Boi, Felipe Guapo, Nicholas Donohue, Niall Barron, Alana Rainbow-Fletcher, and Jonathan Bones. "Proteomic Landscape of Adeno-Associated Virus (AAV)-Producing HEK293 Cells." International Journal of Molecular Sciences 22, no. 21 (October 25, 2021): 11499. http://dx.doi.org/10.3390/ijms222111499.
Abstract:
Adeno-associated viral (AAV) vectors are widely used for gene therapy, providing treatment for diseases caused by absent or defective genes. Despite the success of gene therapy, AAV manufacturing is still challenging, with production yields being limited. With increased patient demand, improvements in host cell productivity through various engineering strategies will be necessary. Here, we study the host cell proteome of AAV5-producing HEK293 cells using reversed phase nano-liquid chromatography and tandem mass spectrometry (RPLC-MS/MS). Relative label-free quantitation (LFQ) was performed, allowing a comparison of transfected vs. untransfected cells. Gene ontology enrichment and pathway analysis revealed differential expression of proteins involved in fundamental cellular processes such as metabolism, proliferation, and cell death. Furthermore, changes in expression of proteins involved in endocytosis and lysosomal degradation were observed. Our data provides highly valuable insights into cellular mechanisms involved during recombinant AAV production by HEK293 cells, thus potentially enabling further improvements of gene therapy product manufacturing.
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Mergulhão, Naianny L. O. N., Laisa C. G. Bulhões, Valdemir C. Silva, Ilza F. B. Duarte, Irinaldo D. Basílio-Júnior, Johnnatan D. Freitas, Adeildo J. Oliveira, Marília O. F. Goulart, Círia V. Barbosa, and João X. Araújo-Júnior. "Insights from Syzygium aromaticum Essential Oil: Encapsulation, Characterization, and Antioxidant Activity." Pharmaceuticals 17, no. 5 (May 8, 2024): 599. http://dx.doi.org/10.3390/ph17050599.
Abstract:
Alginate encapsulates loaded with clove essential oil (CEO) were prepared by ionic gelation, with subsequent freeze-drying. The objective of the present work was to develop a product with the ability to protect CEO against its easy volatility and oxidation. The following techniques were used to characterize the formulations: eugenol release, degree of swelling, GC/MS, TGA/DSC, and SEM. The alginate solution (1.0%) containing different concentrations of CEO (LF1: 1.0%; LF2: 0.5%; LF3: 0.1%) was dropped into a 3.0% CaCl2 solution. After lyophilization, the encapsulated samples were wrinkled and rigid, with high encapsulation power (LF3: 76.9% ± 0.5). Three chemical components were identified: eugenol (the major one), caryophyllene, and humulene. The antioxidant power (LF1: DPPH IC50 18.1 µg mL−1) was consistent with the phenol content (LF1: 172.2 mg GAE g−1). The encapsulated ones were thermally stable, as shown by analysis of FTIR peaks, eugenol molecular structure was kept unaltered. The degree of swelling was 19.2% (PBS). The release of eugenol (92.5%) in the PBS solution was faster than in the acidic medium. It was concluded that the low-cost technology used allows the maintenance of the content and characteristics of CEO in the three concentrations tested, offering a basis for further research with essential oil encapsulates.
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Kramer, Michael H., Qiang Zhang, Robert W. Sprung, Petra Erdmann-Gilmore, Daniel R. George, Nichole M. Helton, Sharon E. Heath, et al. "Analysis of the Proteomes of Primary, De Novo Acute Myeloid Leukemia Cells from Adults." Blood 138, Supplement 1 (November 5, 2021): 3427. http://dx.doi.org/10.1182/blood-2021-148819.
Abstract:
Abstract Introduction: Proteins, despite being the primary effectors of cellular processes, are often studied only indirectly through analysis of the transcriptome. However, it is clear that the relationship between mRNA expression and protein expression is approximate at best. In Acute Myeloid Leukemia (AML), the genome and transcriptome have been thoroughly characterized, but the proteome has been less well studied. Here, we present a deep-scale study of the proteomes of 44 primary AML bone marrow samples representing a wide range of AML across the spectrum of cytogenetic risk, common mutations, and driver fusions. Methods: Bone marrow samples were collected at presentation from 44 adult patients with de novo AML as part of an institutional banking protocol, and buffy coat cells were immediately cryopreserved without further manipulation. Cryovials were thawed in the presence of the cell permeable serine protease inhibitor diisopropyl fluorophosphate (DFP) to inactivate the abundant neutrophil serine proteases (ELANE, CTSG, PRTN3, and PRSS57), and further processed for nano-liquid chromatography mass spectrometry in the presence of an extensive cocktail of protease inhibitors. Both label-free quantification (LFQ) and tandem-mass-tag (TMT) deep-scale proteomics were performed on these 44 patient samples, as well as 3 lineage-depleted bone marrow samples from healthy adult donors. Matching RNA-seq and exome sequencing data were available for the same samples as part of The Cancer Genome Atlas (TCGA) AML project. Results: 10,651 and 6,679 unique proteins were detected in the TMT and LFQ experiments, respectively. Correlations between measurements derived from the independent proteomic platforms (i.e. TMT and LFQ) is higher (mean Spearman correlation, 0.60, Figure 1A) than correlation between proteomic (TMT) and transcriptomic measurements from bulk RNA-seq data (Spearman 0.43, Figure 1B). Quality checks of the proteomic data strongly supported the reliability of quantification of protein measurements; for example, the mean ratio of beta globin protein (HBB) to alpha globin (HBA1) was 1.2 +/- 0.25 (Figure 1C), and several proteins known to be dysregulated by specific AML-initiating fusion proteins (for PML-RARA, HGF and RARA; for RUNX1-RUNX1T1, RUNX1T1; and for CBFB-MYH11, MYH11) were detected in the expected samples (Figure 1D). Globally, 1,364 proteins were differentially expressed in the AML samples (corrected p-value <0.05, fold change ≥ 1.5) compared to the lineage-depleted, healthy bone marrow samples. Globally overexpressed proteins were enriched for ribosomal RNA modification, mitochondrial protein import, nuclear export, and the mitochondrial electron transport chain, among others. These overexpressed proteins include 61 cell surface proteins that could potentially represent therapeutic targets (overexpressed on average in 82% of AML samples, range 25-97%). Globally downregulated proteins in AML samples were enriched for glycogen metabolism and protein groups associated with mature neutrophils (reflecting the expected maturation block in AML), among others. 771 of the 1364 differentially expressed proteins (56.5%) showed only minimal variability in mRNA expression levels (fold change of <1.1 between AML and normal marrow CD34 cell mRNA) that could not explain dysregulated protein expression. Several protein complexes likewise showed coordinated differential expression in the proteomic data, but no change in the transcriptome, including the THO complex (Figure 1E) and the phosphorylase kinase complex (Figure 1F), among others, indicating the presence of posttranscriptional regulation of the levels of many proteins in AML samples. Conclusion: We have created a deep-scale proteomic database from a set of well-characterized AML samples, allowing for a proteogenomic study of AML. We have identified many examples of post-transcriptional regulation of key metabolic pathways that may be relevant for better understanding AML cell metabolism and therapeutic vulnerabilities. Additional studies linking patterns of protein dysregulation with a variety of AML covariates are underway. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.
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Sagini, Micah N., Karel D. Klika, Agnes Hotz-Wagenblatt, Michael Zepp, and Martin R. Berger. "Lactosyl-sepharose binding proteins from pancreatic cancer cells show differential expression in primary and metastatic organs." Experimental Biology and Medicine 245, no. 7 (March 4, 2020): 631–43. http://dx.doi.org/10.1177/1535370220910691.
Abstract:
In normal cells, glycan binding proteins mediate various cellular processes upon recognition and binding to respective ligands. In tumor cells, these proteins have been associated with metastasis. Lactosyl-sepharose binding proteins (LSBPs) were isolated and identified in a workflow involving lactosyl affinity chromatography and label-free quantification mass spectrometry (LFQ MS). A binding study with monosaccharides was performed by microscale thermophoresis and nuclear magnetic resonance spectroscopy. Influence of galactose on LSBPs’ binding to the lactosyl resin was investigated by competitive affinity chromatography followed by LFQ MS. An analysis of amino acids with sugar binding motifs was searched using bioinformatics tools. The expression profiles of these proteins at the mRNA level, as determined by a chip array from a pancreatic ductal adenocarcinoma (PDAC) liver metastasis model, were used for evaluating their potential role in cancer progression. Proteomics data and their respective genes were analyzed by MaxQuant and Ingenuity Pathway Analysis. In total, 1295 LSBPs were isolated and identified from Suit2-007 human pancreatic adenocarcinoma cells. Interaction studies revealed that these proteins exhibit low to moderate affinity for monosaccharide sugars. Some of these LSBPs even showed reduced affinity after calcium depletion. Among the isolated proteins were annexins and galectins in addition to other families, with no history of binding lactosyl residues. A subset of LSBPs exhibited differential profiles in the pancreas, liver, and lung environments. These modulations may be related to tumor progression. In conclusion, we show that PDAC cells contain LSBPs, a subset of which binds galactose with calcium dependency. The differential expression of these proteins in a rat model highlights their value for diagnosis and as potential drug targets for PDAC therapy. Future work will be required to validate these findings in patient samples. Impact statement Interaction of glycan binding proteins with aberrantly expressed glycans in tumor environment is crucial for metastasis. Here, we established a work flow for investigating the presence of a subset of these proteins in PDAC cells, which bind to a lactosyl-sepharose resin. The resin had been designed to isolate proteins with lectin-like properties. The corresponding lactosyl-sepharose binding proteins (LSBPs) show affinity for galactose and other monosaccharides. A subset of the LSBPs shows also calcium dependency. The importance of these proteins is highlighted by their differential expression profiles in PDAC cells growing in primary (pancreas) and metastatic (liver and lung) organ sites. Based on their affinity for the lactosyl-resin and monosaccharides, LSBPs hold potential for PDAC diagnosis and as drug targets. This work has set the stage for further investigation of the occurrence and the role of LSBPs in patient samples using the newly established workflow.
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Shettima, Abubakar, Intan Haslina Ishak, Benjamin Lau, Hadura Abu Hasan, Noorizan Miswan, and Nurulhasanah Othman. "Quantitative proteomics analysis of permethrin and temephos-resistant Ae. aegypti revealed diverse differentially expressed proteins associated with insecticide resistance from Penang Island, Malaysia." PLOS Neglected Tropical Diseases 17, no. 9 (September 18, 2023): e0011604. http://dx.doi.org/10.1371/journal.pntd.0011604.
Abstract:
Synthetic insecticides are the primary vector control method used globally. However, the widespread use of insecticides is a major cause of insecticide-resistance in mosquitoes. Hence, this study aimed at elucidating permethrin and temephos-resistant protein expression profiles in Ae. aegypti using quantitative proteomics. In this study, we evaluated the susceptibility of Ae. aegypti from Penang Island dengue hotspot and non-hotspot against 0.75% permethrin and 31.25 mg/l temephos using WHO bioassay method. Protein extracts from the mosquitoes were then analysed using LC–ESI–MS/MS for protein identification and quantification via label-free quantitative proteomics (LFQ). Next, Perseus 1.6.14.0 statistical software was used to perform differential protein expression analysis using ANOVA and Student’s t-test. The t-test selected proteins with≥2.0-fold change (FC) and ≥2 unique peptides for gene expression validation via qPCR. Finally, STRING software was used for functional ontology enrichment and protein-protein interactions (PPI). The WHO bioassay showed resistance with 28% and 53% mortalities in adult mosquitoes exposed to permethrin from the hotspot and non-hotspot areas. Meanwhile, the susceptibility of Ae. aegypti larvae revealed high resistance to temephos in hotspot and non-hotspot regions with 80% and 91% mortalities. The LFQ analyses revealed 501 and 557 (q-value <0.05) differentially expressed proteins in adults and larvae Ae. aegypti. The t-test showed 114 upregulated and 74 downregulated proteins in adult resistant versus laboratory strains exposed to permethrin. Meanwhile, 13 upregulated and 105 downregulated proteins were observed in larvae resistant versus laboratory strains exposed to temephos. The t-test revealed the upregulation of sodium/potassium-dependent ATPase β2 in adult permethrin resistant strain, H15 domain-containing protein, 60S ribosomal protein, and PB protein in larvae temephos resistant strain. The downregulation of troponin I, enolase phosphatase E1, glucosidase 2β was observed in adult permethrin resistant strain and tubulin β chain in larvae temephos resistant strain. Furthermore, the gene expression by qPCR revealed similar gene expression patterns in the above eight differentially expressed proteins. The PPI of differentially expressed proteins showed a p-value at <1.0 x 10−16 in permethrin and temephos resistant Ae. aegypti. Significantly enriched pathways in differentially expressed proteins revealed metabolic pathways, oxidative phosphorylation, carbon metabolism, biosynthesis of amino acids, glycolysis, and citrate cycle. In conclusion, this study has shown differentially expressed proteins and highlighted upregulated and downregulated proteins associated with insecticide resistance in Ae. aegypti. The validated differentially expressed proteins merit further investigation as a potential protein marker to monitor and predict insecticide resistance in field Ae. aegypti. The LC-MS/MS data were submitted into the MASSIVE database with identifier no: MSV000089259.
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Amorim, Aiala Vieira, Claudivan Feitosa de Lacerda, Carlos Farley Herbster Moura, and Enéas Gomes Filho. "Fruit size and quality of pineapples cv. Vitória in response to micronutrient doses and way of application and to soil covers." Revista Brasileira de Fruticultura 33, spe1 (October 2011): 505–10. http://dx.doi.org/10.1590/s0100-29452011000500068.
Abstract:
The objective of this study was to evaluate the effects of foundation and leaf fertilization with micronutrients on fruit size and quality of pineapple cv. Vitória under the environmental conditions of the Baixo Acaraú irrigated perimeter in Northern Ceará State, Brazil, under two covers (bagana and black plastic) of the sandy soil of low fertility. The experimental design was a randomized split blocks one with four levels of soil dressing and four levels of foliar fertilization, with five replications. Micronutrient soil dressing was studied as FTE-12 at doses of 0, 60, 120 and 180 kg ha-1. The four levels of foliar fertilization were: LF0 (without fertilizer), LF 1 (15 leaf fertilization, using the amount of 1158.75 g Fe ha-1, 844.65 g Mn ha-1, 391.5 g ha-1 Zn, 322.65 g ha-1 Cu and 216 g ha-1 B), LF2 (15 leaf fertilization, using twice the quantities of level LF1) and LF3 (15 leaf fertilization, using three times the amount of level LF1). At 13 months after planting the micropropagated plantlets was carried out the floral induction treatment and five months later the fruit harvest determining the following variables: fruit weight and median diameter, soluble solids content (SS) and titratable acidity (TA). Both fruit weight and diameter increased with increasing doses of micronutrients applied to the soil and to the leaves, of plants grown both on bagana soil cover and plastic mulch. On the other hand fruit pulp quality was little affected by the treatments studied. There were a small increase of SS contents for plants grown on bagana soil cover and a small decrease of titratable acidity for those grown on plastic mulch, in both cases just in response to micronutrient foliar application.
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Shah, Anup D., Robert J. A. Goode, Cheng Huang, David R. Powell, and Ralf B. Schittenhelm. "LFQ-Analyst: An Easy-To-Use Interactive Web Platform To Analyze and Visualize Label-Free Proteomics Data Preprocessed with MaxQuant." Journal of Proteome Research 19, no. 1 (October 28, 2019): 204–11. http://dx.doi.org/10.1021/acs.jproteome.9b00496.
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Morretta, Elva, Antonella D’Agostino, Elisabetta Cassese, Barbara Maglione, Antonello Petrella, Chiara Schiraldi, and Maria Chiara Monti. "Label-Free Quantitative Proteomics to Explore the Action Mechanism of the Pharmaceutical-Grade Triticum vulgare Extract in Speeding Up Keratinocyte Healing." Molecules 27, no. 3 (February 7, 2022): 1108. http://dx.doi.org/10.3390/molecules27031108.
Abstract:
Plant extracts have shown beneficial properties in terms of skin repair, promoting wound healing through a plethora of mechanisms. In particular, the poly-/oligosaccharidic aqueous extract of Triticum vulgare (TVE), as well as TVE-based products, shows interesting biological assets, hastening wound repair. Indeed, TVE acts in the treatment of tissue regeneration mainly on decubitus and venous leg ulcers. Moreover, on scratched monolayers, TVE prompts HaCat cell migration, correctly modulating the expression of metalloproteases toward a physiological matrix remodeling. Here, using the same HaCat-based in vitro scratch model, the TVE effect has been investigated thanks to an LFQ proteomic analysis of HaCat secretomes and immunoblotting. Indeed, the unbiased TVE effect on secreted proteins has not yet been fully understood, and it could be helpful to obtain a comprehensive picture of its bio-pharmacological profile. It has emerged that TVE treatment induces significant up-regulation of several proteins in the secretome (153 to be exact) whereas only a few were down-regulated (72 to be exact). Interestingly, many of the up-regulated proteins are implicated in promoting wound-healing-related processes, such as modulating cell–cell interaction and communication, cell proliferation and differentiation, and prompting cell adhesion and migration.