Graph-Based Method for Calibration of High-Resolution Mass Spectra of Natural Organic Matter

Inaccuracies in ion detection and signal processing can undermine confidence in the molecular formula assignment of high-resolution mass spectrometry, which relies on precise matching of the mass-to-charge ratio (m/z). This study proposes a novel graph-based spectra calibration method, MSCMcalib, which implements coordinate transformation and pattern detection. MSCMcalib maps uncalibrated m/z data onto a modified 2D mass defect plot, facilitating the automatic calibration of detected lines, i.e., the calibration of uncalibrated peaks aligned with these lines. The “propagation” method is subsequently employed to accurately and automatically calibrate 605 m/z values across multiple lines, encompassing 98% of the m/z range. The calibrated m/z values divide the m/z range of the spectrum into multiple subintervals, with each subinterval undergoing a process of “scaling” calibration. The utilization of narrower partitions effectively mitigates divergence issues at both ends that arise from the polynomial fitting of errors against m/z. The effectiveness of MSCMcalib is validated through the calibration of SRFA data with m/z error ranges spanning from −10 to −6 ppm, resulting in an additional assignment of 11%–30% more molecular formulas compared to the quadratic fitting calibration

Combination of On-Chip Field Amplification and Bovine Serum Albumin Sweeping for Ultrasensitive Detection of Green Fluorescent Protein

We report a highly effective on-chip preconcentration method by combining field-amplified sample injection (FASI) and bovine serum albumin (BSA) sweeping for ultrasensitive detection of green fluorescent protein (GFP) on a simple cross-channel microchip device. With the formation of a stagnant sample/running buffer boundary by balancing the hydrodynamic flow and the electro-osmotic flow (EOF), GFP molecules can be continuously injected into the sample loading channel and stacked. We have also demonstrated that BSA is a very effective pseudo-stationary phase for sweeping concentration of proteins in comparison to the commonly used micelles. The combination of FASI and BSA sweeping yields a concentration factor of 3570 and a limit of detection of 8.4 pM for GFP. Using this method, we have separated GFP and GFP-insulin-like growth factor-I (GFP-IGF-I) fusion protein. The entire assay (GFP concentration, matrix elimination, and electrophoretic separation) can be completed within E. coli cells and the GFP content in single E. coli cells

Graph-Based Method for Calibration of High-Resolution Mass Spectra of Natural Organic Matter

Inaccuracies in ion detection and signal processing can undermine confidence in the molecular formula assignment of high-resolution mass spectrometry, which relies on precise matching of the mass-to-charge ratio (m/z). This study proposes a novel graph-based spectra calibration method, MSCMcalib, which implements coordinate transformation and pattern detection. MSCMcalib maps uncalibrated m/z data onto a modified 2D mass defect plot, facilitating the automatic calibration of detected lines, i.e., the calibration of uncalibrated peaks aligned with these lines. The “propagation” method is subsequently employed to accurately and automatically calibrate 605 m/z values across multiple lines, encompassing 98% of the m/z range. The calibrated m/z values divide the m/z range of the spectrum into multiple subintervals, with each subinterval undergoing a process of “scaling” calibration. The utilization of narrower partitions effectively mitigates divergence issues at both ends that arise from the polynomial fitting of errors against m/z. The effectiveness of MSCMcalib is validated through the calibration of SRFA data with m/z error ranges spanning from −10 to −6 ppm, resulting in an additional assignment of 11%–30% more molecular formulas compared to the quadratic fitting calibration

Combination of On-Chip Field Amplification and Bovine Serum Albumin Sweeping for Ultrasensitive Detection of Green Fluorescent Protein

We report a highly effective on-chip preconcentration method by combining field-amplified sample injection (FASI) and bovine serum albumin (BSA) sweeping for ultrasensitive detection of green fluorescent protein (GFP) on a simple cross-channel microchip device. With the formation of a stagnant sample/running buffer boundary by balancing the hydrodynamic flow and the electro-osmotic flow (EOF), GFP molecules can be continuously injected into the sample loading channel and stacked. We have also demonstrated that BSA is a very effective pseudo-stationary phase for sweeping concentration of proteins in comparison to the commonly used micelles. The combination of FASI and BSA sweeping yields a concentration factor of 3570 and a limit of detection of 8.4 pM for GFP. Using this method, we have separated GFP and GFP-insulin-like growth factor-I (GFP-IGF-I) fusion protein. The entire assay (GFP concentration, matrix elimination, and electrophoretic separation) can be completed within E. coli cells and the GFP content in single E. coli cells

Combination of On-Chip Field Amplification and Bovine Serum Albumin Sweeping for Ultrasensitive Detection of Green Fluorescent Protein

We report a highly effective on-chip preconcentration method by combining field-amplified sample injection (FASI) and bovine serum albumin (BSA) sweeping for ultrasensitive detection of green fluorescent protein (GFP) on a simple cross-channel microchip device. With the formation of a stagnant sample/running buffer boundary by balancing the hydrodynamic flow and the electro-osmotic flow (EOF), GFP molecules can be continuously injected into the sample loading channel and stacked. We have also demonstrated that BSA is a very effective pseudo-stationary phase for sweeping concentration of proteins in comparison to the commonly used micelles. The combination of FASI and BSA sweeping yields a concentration factor of 3570 and a limit of detection of 8.4 pM for GFP. Using this method, we have separated GFP and GFP-insulin-like growth factor-I (GFP-IGF-I) fusion protein. The entire assay (GFP concentration, matrix elimination, and electrophoretic separation) can be completed within E. coli cells and the GFP content in single E. coli cells

Table1_Molecular Diagnosis and Prenatal Phenotype Analysis of Eight Fetuses With Ciliopathies.XLSX

Human ciliopathies are hereditary conditions caused by variants in ciliary-associated genes. Ciliopathies are often characterized by multiple system defects. However, it is not easy to make a definite diagnosis in the prenatal period only based on the imageology. In this report, eight new prenatal cases from five unrelated families diagnosed with ciliopathies were systematically examined. The clinical manifestations of these fetuses showed such prenatal diagnostic features as occipital encephalocele, and polydactyly and polycystic kidneys. Situs inversus caused by CPLANE1 variant was first reported. In Family 1 and Family 3, homozygous variants of CPLANE1 and NPHP4 caused by consanguineous marriage and uniparental disomy were detected by whole-exome sequencing, respectively. In Family 2, Family 4 and Family 5, compound heterozygotes of TMEM67 and DYNC2H1 including two novel missense variants and one novel nonsense variant were identified. The distribution of pathogenic missense variants along TMEM67 gene mainly clustered in the extracellular cysteine rich region, extracellular area with unknown structure, and the transmembrane regions. Genotype-phenotype relationship between CPLANE1 and TMEM67 genes was concluded. This report describes new clinical manifestations and novel variants in CPLANE1, TMEM67, NPHP4, and DYNC2H1.</p

Video_1_RETRACTED: Ppm1b Negatively Regulates 3-Bromopyruvate Induced Necroptosis in Breast Cancer Cells.avi

Up to 30% of breast cancer mortality is caused by cancer relapse despite primary clinical treatments due to distant metastases. Further research focusing on breast cancer mechanisms are needed for deeper understanding of disease prognosis. 3-bromopyruvate (3-BP), a glycolysis inhibitor, has been studied as one of the antitumor agents in recent years. In this report, we want to investigate the form of cell death induced by 3-BP and demonstrate the inhibitory effect of 3-BP on breast cancer cell proliferation and its mechanism in vivo and in vitro. We found that 3-BP could inhibit MDA-MB-231 and MCF-7 breast cancer cell proliferation, through energy metabolism inhibition. Further, necroptosis characters in MDA-MB-231 cells after 3-BP treatment were observed, which could be negatively regulated through Ppm1b by dephosphorylation of RIP3. In addition, 3-BP treatment in an MDA-MB-231 cell-transplanted mouse model showed a significant antitumor effect, which correlated with necroptosis-related protein Ppm1b. The findings demonstrate the potential for 3-BP in the treatment of breast cancer, providing impetus for further clinical studies.</p

Video_2_RETRACTED: Ppm1b Negatively Regulates 3-Bromopyruvate Induced Necroptosis in Breast Cancer Cells.avi

Up to 30% of breast cancer mortality is caused by cancer relapse despite primary clinical treatments due to distant metastases. Further research focusing on breast cancer mechanisms are needed for deeper understanding of disease prognosis. 3-bromopyruvate (3-BP), a glycolysis inhibitor, has been studied as one of the antitumor agents in recent years. In this report, we want to investigate the form of cell death induced by 3-BP and demonstrate the inhibitory effect of 3-BP on breast cancer cell proliferation and its mechanism in vivo and in vitro. We found that 3-BP could inhibit MDA-MB-231 and MCF-7 breast cancer cell proliferation, through energy metabolism inhibition. Further, necroptosis characters in MDA-MB-231 cells after 3-BP treatment were observed, which could be negatively regulated through Ppm1b by dephosphorylation of RIP3. In addition, 3-BP treatment in an MDA-MB-231 cell-transplanted mouse model showed a significant antitumor effect, which correlated with necroptosis-related protein Ppm1b. The findings demonstrate the potential for 3-BP in the treatment of breast cancer, providing impetus for further clinical studies.</p

Video_2_Ppm1b Negatively Regulates 3-Bromopyruvate Induced Necroptosis in Breast Cancer Cells.avi

Up to 30% of breast cancer mortality is caused by cancer relapse despite primary clinical treatments due to distant metastases. Further research focusing on breast cancer mechanisms are needed for deeper understanding of disease prognosis. 3-bromopyruvate (3-BP), a glycolysis inhibitor, has been studied as one of the antitumor agents in recent years. In this report, we want to investigate the form of cell death induced by 3-BP and demonstrate the inhibitory effect of 3-BP on breast cancer cell proliferation and its mechanism in vivo and in vitro. We found that 3-BP could inhibit MDA-MB-231 and MCF-7 breast cancer cell proliferation, through energy metabolism inhibition. Further, necroptosis characters in MDA-MB-231 cells after 3-BP treatment were observed, which could be negatively regulated through Ppm1b by dephosphorylation of RIP3. In addition, 3-BP treatment in an MDA-MB-231 cell-transplanted mouse model showed a significant antitumor effect, which correlated with necroptosis-related protein Ppm1b. The findings demonstrate the potential for 3-BP in the treatment of breast cancer, providing impetus for further clinical studies.</p