Pub Date : 2026-04-15Epub Date: 2026-01-21DOI: 10.1016/j.saa.2026.127509
Clara Barnés-Calle , Pere Gou , Elena Fulladosa , Frans W.J. van den Berg
Fourier transform infrared spectroscopy (FTIR) combined with Amide I band deconvolution has been used to investigate protein structural changes occurring during high moisture extrusion processing (HMEP). However, it is a sensitive, user-dependent technique that has sparked debate over its appropriate analytical approach. This paper aims to assess the suitability of FTIR Amide I band deconvolution to investigate protein structural changes in fava bean protein concentrate (FBPC) caused by temperature treatment and/or HMEP at different temperatures (110 °C, 135 °C and 165 °C), and to explore its relationship with the texturisation level of the obtained products. Influence of sample preparation and parameter selection during FTIR deconvolution procedure was also explored. To do so, FBPC was heated in a convection oven or subjected to HMEP at different temperatures (110, 135 or 165 °C), and Fourier self-deconvolution (FSD) and second derivative (SD) were explored as band-narrowing methods to analyse protein conformation from FTIR spectra. FTIR Amide I band deconvolution showed high sensitivity to sample preparation and parameter selection during FSD and SD analytical procedure. Results suggested that HMEP caused the denaturation of β-sheet forms present initially in FBPC, and an increase of other structures including intermolecular β-sheet and/or aggregates—probably due to the formation of new intermolecular bonds. Moreover, although higher temperature during HMEP enhanced fibre-like structure formation, texturisation level could not be directly related to the protein conformation of the final high moisture extrudates (HME), since no significant differences were observed between protein secondary structure of HME under the studied conditions.
傅里叶变换红外光谱（FTIR）结合酰胺I波段反褶积（Amide I band deconvolution）研究了高水分挤压加工（HMEP）过程中蛋白质结构的变化。然而，它是一种敏感的、依赖于用户的技术，引发了对其适当分析方法的争论。本文旨在评估FTIR酰胺I波段反卷积在不同温度（110°C、135°C和165°C）下温度处理和/或HMEP对蚕豆蛋白浓缩物（FBPC）蛋白质结构变化的适用性，并探讨其与所得产品织构水平的关系。探讨了样品制备和参数选择对反褶积过程的影响。为此，将FBPC在对流烤箱中加热或在不同温度（110、135或165℃）下进行HMEP，并探索傅里叶自反卷积（FSD）和二阶导数（SD）作为窄带方法来分析FTIR光谱中的蛋白质构象。FTIR酰胺I波段反褶积对FSD和SD分析过程中的样品制备和参数选择具有很高的敏感性。结果表明，HMEP引起了FBPC中最初存在的β-薄片形式的变性，并增加了其他结构，包括分子间β-薄片和/或聚集体，这可能是由于形成了新的分子间键。此外，尽管高温增强了纤维状结构的形成，但纹理化水平与最终高水分挤出物（HME）的蛋白质构象没有直接关系，因为在研究条件下，HME的蛋白质二级结构之间没有显著差异。
{"title":"Exploring the use of FTIR Amide I band deconvolution to investigate protein secondary structure and texturisation during high moisture extrusion","authors":"Clara Barnés-Calle , Pere Gou , Elena Fulladosa , Frans W.J. van den Berg","doi":"10.1016/j.saa.2026.127509","DOIUrl":"10.1016/j.saa.2026.127509","url":null,"abstract":"<div><div>Fourier transform infrared spectroscopy (FTIR) combined with Amide I band deconvolution has been used to investigate protein structural changes occurring during high moisture extrusion processing (HMEP). However, it is a sensitive, user-dependent technique that has sparked debate over its appropriate analytical approach. This paper aims to assess the suitability of FTIR Amide <em>I</em> band deconvolution to investigate protein structural changes in fava bean protein concentrate (FBPC) caused by temperature treatment and/or HMEP at different temperatures (110 °C, 135 °C and 165 °C), and to explore its relationship with the texturisation level of the obtained products. Influence of sample preparation and parameter selection during FTIR deconvolution procedure was also explored. To do so, FBPC was heated in a convection oven or subjected to HMEP at different temperatures (110, 135 or 165 °C), and Fourier self-deconvolution (FSD) and second derivative (SD) were explored as band-narrowing methods to analyse protein conformation from FTIR spectra. FTIR Amide I band deconvolution showed high sensitivity to sample preparation and parameter selection during FSD and SD analytical procedure. Results suggested that HMEP caused the denaturation of β-sheet forms present initially in FBPC, and an increase of other structures including intermolecular β-sheet and/or aggregates—probably due to the formation of new intermolecular bonds. Moreover, although higher temperature during HMEP enhanced fibre-like structure formation, texturisation level could not be directly related to the protein conformation of the final high moisture extrudates (HME), since no significant differences were observed between protein secondary structure of HME under the studied conditions.</div></div>","PeriodicalId":433,"journal":{"name":"Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy","volume":"351 ","pages":"Article 127509"},"PeriodicalIF":4.6,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146047562","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-04-15Epub Date: 2026-01-09DOI: 10.1016/j.saa.2026.127463
Dandan Zhai , Jinfeng Liu , Jingyun Liu , Mingxing Li , Anqi Liu , Yu Yang , Zhenwei Zhang , Na Liu , Ming Hui , Peng Li
Ginsenosides, the principal bioactive constituents of American ginseng (Panax quinquefolius), require precise monitoring during column chromatography to ensure product quality. Conventional assays are time-consuming and unsuited for real-time process control, particularly for low-abundance compounds. Here, we present a rapid, non-destructive near-infrared (NIR) optical sensing system coupled with an Evolutionary Attention–based Long Short-Term Memory (EA-LSTM) model to predict ginsenoside concentrations dynamically. The approach exploits the high-speed acquisition and reproducibility of NIR spectra while leveraging EA-LSTM's temporal feature extraction and adaptive attention to focus on chemically informative elution segments. Offline spectra from eight elution batches, referenced by UPLC, enabled model training and validation, with high-frequency sampling simulated to mimic industrial deployment. The system demonstrated high accuracy (R2 = 0.9841, RPD = 7.94) and robustness under dynamic conditions (R2 = 0.9694, RPD = 5.72, response time = 0.34 ms), highlighting its potential for real-time, non-destructive monitoring and intelligent control in natural product purification.
{"title":"Real-time concentration prediction in column chromatography purification using NIR optical sensing and evolutionary attention-LSTM modeling","authors":"Dandan Zhai , Jinfeng Liu , Jingyun Liu , Mingxing Li , Anqi Liu , Yu Yang , Zhenwei Zhang , Na Liu , Ming Hui , Peng Li","doi":"10.1016/j.saa.2026.127463","DOIUrl":"10.1016/j.saa.2026.127463","url":null,"abstract":"<div><div>Ginsenosides, the principal bioactive constituents of American ginseng (<em>Panax quinquefolius</em>), require precise monitoring during column chromatography to ensure product quality. Conventional assays are time-consuming and unsuited for real-time process control, particularly for low-abundance compounds. Here, we present a rapid, non-destructive near-infrared (NIR) optical sensing system coupled with an Evolutionary Attention–based Long Short-Term Memory (EA-LSTM) model to predict ginsenoside concentrations dynamically. The approach exploits the high-speed acquisition and reproducibility of NIR spectra while leveraging EA-LSTM's temporal feature extraction and adaptive attention to focus on chemically informative elution segments. Offline spectra from eight elution batches, referenced by UPLC, enabled model training and validation, with high-frequency sampling simulated to mimic industrial deployment. The system demonstrated high accuracy (R<sup>2</sup> = 0.9841, RPD = 7.94) and robustness under dynamic conditions (R<sup>2</sup> = 0.9694, RPD = 5.72, response time = 0.34 ms), highlighting its potential for real-time, non-destructive monitoring and intelligent control in natural product purification.</div></div>","PeriodicalId":433,"journal":{"name":"Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy","volume":"351 ","pages":"Article 127463"},"PeriodicalIF":4.6,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146000206","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-04-15Epub Date: 2026-01-22DOI: 10.1016/j.saa.2026.127500
Feng-Ting Liu , Bang-Zhao Zhou , Jun-Ying Miao , Bao-Xiang Zhao , Zhao-Min Lin
Mitochondria is the primary organelle responsible for energy production, and their weakly alkaline microenvironment (pH ≈ 8) is closely linked to cellular metabolism and disease states. Mitochondrial acidification is closely associated with the pathogenesis of a spectrum of disorders, encompassing neurodegenerative syndromes, cardiovascular disorders and cancer. Therefore, monitoring mitochondrial pH fluctuations is crucial for deciphering cellular physiological processes. In this research, we constructed a novel pH fluorescent probe QAA based on amide-quinoline salt, featuring piperazine as the pH recognition site and quinoline salt as the mitochondrial targeting group. QAA exhibited excellent water solubility (PBS buffer) which could be well matched with the cell imaging conditions, appropriate pKa (8.0) and mitochondrial targeting. Fluorescence spectroscopy results indicated that QAA possessed high selectivity and sensitivity, with a linear response in pH range of 6.6 to 9.5. The recognition mechanism was confirmed by density functional theory (DFT) calculations and HNMR spectral. Crucially, QAA not only exhibited excellent photostability, low cytotoxicity and the ability to detect pH in cellular mitochondria, but also could be used for real water sample detection, achieving recovery rates ranging from 98.96% to 104.84%. QAA held practical potential as a mitochondrial pH indicator for studying physiology-related processes involving mitochondria.
{"title":"A novel amide-quinoline salt-based mitochondrial-targeted fluorescent probe for detecting pH in cells and water samples","authors":"Feng-Ting Liu , Bang-Zhao Zhou , Jun-Ying Miao , Bao-Xiang Zhao , Zhao-Min Lin","doi":"10.1016/j.saa.2026.127500","DOIUrl":"10.1016/j.saa.2026.127500","url":null,"abstract":"<div><div>Mitochondria is the primary organelle responsible for energy production, and their weakly alkaline microenvironment (pH ≈ 8) is closely linked to cellular metabolism and disease states. Mitochondrial acidification is closely associated with the pathogenesis of a spectrum of disorders, encompassing neurodegenerative syndromes, cardiovascular disorders and cancer. Therefore, monitoring mitochondrial pH fluctuations is crucial for deciphering cellular physiological processes. In this research, we constructed a novel pH fluorescent probe <strong>QAA</strong> based on amide-quinoline salt, featuring piperazine as the pH recognition site and quinoline salt as the mitochondrial targeting group. <strong>QAA</strong> exhibited excellent water solubility (PBS buffer) which could be well matched with the cell imaging conditions, appropriate p<em>K</em>a (8.0) and mitochondrial targeting. Fluorescence spectroscopy results indicated that <strong>QAA</strong> possessed high selectivity and sensitivity, with a linear response in pH range of 6.6 to 9.5. The recognition mechanism was confirmed by density functional theory (DFT) calculations and HNMR spectral. Crucially, <strong>QAA</strong> not only exhibited excellent photostability, low cytotoxicity and the ability to detect pH in cellular mitochondria, but also could be used for real water sample detection, achieving recovery rates ranging from 98.96% to 104.84%. <strong>QAA</strong> held practical potential as a mitochondrial pH indicator for studying physiology-related processes involving mitochondria.</div></div>","PeriodicalId":433,"journal":{"name":"Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy","volume":"351 ","pages":"Article 127500"},"PeriodicalIF":4.6,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146036111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-04-15Epub Date: 2026-01-13DOI: 10.1016/j.saa.2026.127470
Ziyi Wang , Keying Yang , Chen Yang , Bing Xue , Kaifu Ma , Zuonian Jin , Cailing Fan , Libo Jiang , Wei Shu
Drug-induced liver injury (DILI) disrupts hepatocellular homeostasis during the early phase. However, conventional detection methods often only become apparent after the injury has advanced. Cellular viscosity is a characteristic of the intracellular microenvironment, which regulates diffusion, membrane fluidity, organelle transport, and signaling, and can change rapidly under stress. As DILI can elicit mitochondrial dysfunction, endoplasmic reticulum stress, and lipid droplet remodeling, localized viscosity changes emerge early in the injury process. Here we report a near-infrared viscosity probe named WZY-1 based on a pyridinium-aryl molecular rotor. In high-viscosity media, the restriction of intramolecular rotation suppresses the twisted intramolecular charge transfer (TICT) and enhances the emission intensity. WZY-1 provides long-wavelength near-infrared emission with a large Stokes shift, maintains stable signals, shows tolerance to common ions and reactive species, and displays good biocompatibility. At the cellular level, WZY-1 can distinguish hepatocellular carcinoma cells from normal hepatic cells, and detect endogenous viscosity changes. In DILI models, it visualizes viscosity changes in cells, tissue, and live mice. Taken together, WZY-1 enables noninvasive, in situ, real-time readout of viscosity and supports early assessment of DILI across cellular, tissue, and animal levels.
{"title":"A near-infrared viscosity probe for dynamic imaging of multilevel drug-induced liver injury","authors":"Ziyi Wang , Keying Yang , Chen Yang , Bing Xue , Kaifu Ma , Zuonian Jin , Cailing Fan , Libo Jiang , Wei Shu","doi":"10.1016/j.saa.2026.127470","DOIUrl":"10.1016/j.saa.2026.127470","url":null,"abstract":"<div><div>Drug-induced liver injury (DILI) disrupts hepatocellular homeostasis during the early phase. However, conventional detection methods often only become apparent after the injury has advanced. Cellular viscosity is a characteristic of the intracellular microenvironment, which regulates diffusion, membrane fluidity, organelle transport, and signaling, and can change rapidly under stress. As DILI can elicit mitochondrial dysfunction, endoplasmic reticulum stress, and lipid droplet remodeling, localized viscosity changes emerge early in the injury process. Here we report a near-infrared viscosity probe named <strong>WZY-1</strong> based on a pyridinium-aryl molecular rotor. In high-viscosity media, the restriction of intramolecular rotation suppresses the twisted intramolecular charge transfer (TICT) and enhances the emission intensity. <strong>WZY-1</strong> provides long-wavelength near-infrared emission with a large Stokes shift, maintains stable signals, shows tolerance to common ions and reactive species, and displays good biocompatibility. At the cellular level, <strong>WZY-1</strong> can distinguish hepatocellular carcinoma cells from normal hepatic cells, and detect endogenous viscosity changes. In DILI models, it visualizes viscosity changes in cells, tissue, and live mice. Taken together, <strong>WZY-1</strong> enables noninvasive, <em>in situ</em>, real-time readout of viscosity and supports early assessment of DILI across cellular, tissue, and animal levels.</div></div>","PeriodicalId":433,"journal":{"name":"Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy","volume":"351 ","pages":"Article 127470"},"PeriodicalIF":4.6,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146021229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Red wax seals were discovered at the Santi Quattro Coronati complex in Rome, within a staircase utilized as a domestic disposal pit in the late 15th or early 16th century. The four seals, recovered from three distinct stratigraphic units, were in a poor state of preservation. Over time, they underwent morphological and chemical transformations, resulting in the loss of the impressions they originally bore, along with the documents to which they were once affixed.
The composition and manufacturing techniques of wax seals changed over time, resulting in complex, multi-component materials. A multi-analytical approach was employed to investigate their composition and conservation state, incorporating Scanning Electron Microscopy (SEM) and Energy Dispersive X-ray Spectroscopy (EDS), X-ray Fluorescence (XRF) spectroscopy, Fiber Optic Reflectance Spectroscopy (FORS), Fourier-Transform Infrared spectroscopy (FTIR) in both micro-reflectance and Attenuated Total Reflectance (ATR) modes, and chemometric analysis. The study was exclusively performed on the archaeological samples recovered from the site under investigation. Consequently, the limited sample size precludes material classification as a primary objective. This study instead aims to advance knowledge of historical wax seal production materials and degradation processes, identifying key aging markers and assessing potential correlations between their conservation state and their respective stratigraphic contexts.
红色的蜡封是在罗马的Santi Quattro Coronati建筑群中发现的，在15世纪末或16世纪初，在一个楼梯内被用作家庭处理坑。从三个不同的地层单元中发现的四个封印，保存状况不佳。随着时间的推移，它们经历了形态和化学变化，导致它们最初所承载的印象以及它们曾经被贴在上面的文件的丢失。随着时间的推移，蜡封的成分和制造技术发生了变化，导致了复杂的、多组分的材料。采用扫描电子显微镜（SEM）、能量色散x射线能谱（EDS）、x射线荧光（XRF）光谱、光纤反射光谱（FORS）、微反射和衰减全反射（ATR）模式的傅里叶变换红外光谱（FTIR）和化学计量学分析等多种分析方法研究了它们的组成和守恒状态。这项研究完全是对从调查地点找到的考古样本进行的。因此，有限的样本量排除了将材料分类作为主要目标的可能性。相反，这项研究的目的是推进对历史蜡封生产材料和降解过程的了解，确定关键的老化标志，并评估其保存状态与各自地层背景之间的潜在相关性。
{"title":"Characterization of Seals from the Santi Quattro Coronati complex (Rome, Italy) with a focus on FTIR and chemometric analysis","authors":"Martina Franchi , Alessandro Ciccola , Matteo Taroni , Anna Candida Felici , Alessandro Nucara , Naurang Lal Saini , Luca Businaro , Lia Barelli , Simona Morretta , Alessia Cedola","doi":"10.1016/j.saa.2025.127413","DOIUrl":"10.1016/j.saa.2025.127413","url":null,"abstract":"<div><div>Red wax seals were discovered at the Santi Quattro Coronati complex in Rome, within a staircase utilized as a domestic disposal pit in the late 15th or early 16th century. The four seals, recovered from three distinct stratigraphic units, were in a poor state of preservation. Over time, they underwent morphological and chemical transformations, resulting in the loss of the impressions they originally bore, along with the documents to which they were once affixed.</div><div>The composition and manufacturing techniques of wax seals changed over time, resulting in complex, multi-component materials. A multi-analytical approach was employed to investigate their composition and conservation state, incorporating Scanning Electron Microscopy (SEM) and Energy Dispersive X-ray Spectroscopy (EDS), X-ray Fluorescence (XRF) spectroscopy, Fiber Optic Reflectance Spectroscopy (FORS), Fourier-Transform Infrared spectroscopy (FTIR) in both micro-reflectance and Attenuated Total Reflectance (ATR) modes, and chemometric analysis. The study was exclusively performed on the archaeological samples recovered from the site under investigation. Consequently, the limited sample size precludes material classification as a primary objective. This study instead aims to advance knowledge of historical wax seal production materials and degradation processes, identifying key aging markers and assessing potential correlations between their conservation state and their respective stratigraphic contexts.</div></div>","PeriodicalId":433,"journal":{"name":"Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy","volume":"351 ","pages":"Article 127413"},"PeriodicalIF":4.6,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146035685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
This research work reports synthesis of novel Mn/Ta codoped WO3, by simple and cost-effective method and then their properties were observed by various characterization techniques. Ultraviolet Visible spectroscopy has shown the bandgap tuning from 2.42 eV to 1.71 eV while XRD explained the reduction in average crystallite size from 63 nm to 47.7 nm. SEM and EDX analysis exposed the regularity and enhancement in morphology as well as elemental purity and compositions. The photoluminescence spectra confirmed the reduction in charges recombination rate by making codoped nanomaterials that is beneficial for photocatalytic removal of pollutants. However, these photocatalysts were used to perform the degradation of harmful agents of MB dye and Bruphen medicine and the efficiency of degradation is 91% and 90.6% respectively by Mn2%/Ta5%-WO3. The cyclic test confirmed the stability and reusability of nanomaterial used as potential photocatalyst. Mn/Ta-WO3 nanomaterials can be perfect candidates for wastewater treatments.
{"title":"Strategic novel Mn/Ta-WO3 nanomaterials for photocatalytic destruction of dual pollutants: Methylene blue dye and Bruphen medicine","authors":"Aqsa Ashraf , Ayesha Younas , Tahir Iqbal , Ayesha Mushtaq , Hassan Imam Rizvi , Jawza A. Almutairi , Samiah Alhabardi","doi":"10.1016/j.saa.2026.127493","DOIUrl":"10.1016/j.saa.2026.127493","url":null,"abstract":"<div><div>This research work reports synthesis of novel Mn/Ta codoped WO<sub>3</sub>, by simple and cost-effective method and then their properties were observed by various characterization techniques. Ultraviolet Visible spectroscopy has shown the bandgap tuning from 2.42 eV to 1.71 eV while XRD explained the reduction in average crystallite size from 63 nm to 47.7 nm. SEM and EDX analysis exposed the regularity and enhancement in morphology as well as elemental purity and compositions. The photoluminescence spectra confirmed the reduction in charges recombination rate by making codoped nanomaterials that is beneficial for photocatalytic removal of pollutants. However, these photocatalysts were used to perform the degradation of harmful agents of MB dye and Bruphen medicine and the efficiency of degradation is 91% and 90.6% respectively by Mn<sub>2%</sub>/Ta<sub>5%</sub>-WO<sub>3</sub>. The cyclic test confirmed the stability and reusability of nanomaterial used as potential photocatalyst. Mn/Ta-WO<sub>3</sub> nanomaterials can be perfect candidates for wastewater treatments.</div></div>","PeriodicalId":433,"journal":{"name":"Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy","volume":"351 ","pages":"Article 127493"},"PeriodicalIF":4.6,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146036077","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fourier transform infrared (FTIR) microspectroscopy is a rapid, label-free tool for microbial metabolic phenotyping. Here, we integrate synchrotron-based FTIR microspectroscopy with CRISPR-Cas9 editing to decipher the functional redundancy of lysine decarboxylases (LdcC1 and LdcC2) in probiotic Escherichia coli Nissle 1917. Under lysine stress, isogenic mutants (ΔldcC1, ΔldcC1ΔldcC2) exhibited distinct FTIR fingerprints. Spectral analysis revealed: (i) CH shifts (2950–2850 cm−1) indicating ΔldcC1-specific membrane remodeling; (ii) Amide I band profile alterations (∼1650 cm−1) suggesting protein structural perturbations; and (iii) a constitutive elevation in 1220–1260 cm−1 band area in the double mutant, revealing a basal state of metabolic frailty. Principal component analysis of second-derivative spectra revealed clear separation trends among strain phenotypes. We establish LdcC2 as a crucial functional complement, while LdcC1 uniquely contributes to membrane homeostasis. The compensatory stress response activated in the double mutant underscores metabolic redundancy as a cornerstone of intrinsic cellular robustness. Collectively, this work validates a CRISPR-FTIR phenomics platform that bridges targeted genetics with global biochemistry, offering a rapid alternative for functional genomics and metabolic engineering in microbes.
{"title":"Deciphering functional redundancy of lysine decarboxylases in probiotic E. coli Nissle 1917 via an integrated CRISPR-FTIR phenomics platform","authors":"Yiqing Zhang , Mingyu Wu , Feng Geng , Yadi Wang , Junhong Lü","doi":"10.1016/j.saa.2026.127508","DOIUrl":"10.1016/j.saa.2026.127508","url":null,"abstract":"<div><div>Fourier transform infrared (FTIR) microspectroscopy is a rapid, label-free tool for microbial metabolic phenotyping. Here, we integrate synchrotron-based FTIR microspectroscopy with CRISPR-Cas9 editing to decipher the functional redundancy of lysine decarboxylases (LdcC1 and LdcC2) in probiotic <em>Escherichia coli</em> Nissle 1917. Under lysine stress, isogenic mutants (ΔldcC1, ΔldcC1ΔldcC2) exhibited distinct FTIR fingerprints. Spectral analysis revealed: (i) C<img>H shifts (2950–2850 cm<sup>−1</sup>) indicating ΔldcC1-specific membrane remodeling; (ii) Amide <em>I</em> band profile alterations (∼1650 cm<sup>−1</sup>) suggesting protein structural perturbations; and (iii) a constitutive elevation in 1220–1260 cm<sup>−1</sup> band area in the double mutant, revealing a basal state of metabolic frailty. Principal component analysis of second-derivative spectra revealed clear separation trends among strain phenotypes. We establish LdcC2 as a crucial functional complement, while LdcC1 uniquely contributes to membrane homeostasis. The compensatory stress response activated in the double mutant underscores metabolic redundancy as a cornerstone of intrinsic cellular robustness. Collectively, this work validates a CRISPR-FTIR phenomics platform that bridges targeted genetics with global biochemistry, offering a rapid alternative for functional genomics and metabolic engineering in microbes.</div></div>","PeriodicalId":433,"journal":{"name":"Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy","volume":"351 ","pages":"Article 127508"},"PeriodicalIF":4.6,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146036078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Effective feature selection is crucial for large-scale near-infrared (NIR) spectroscopy, yet existing algorithms face a trade-off between accuracy and efficiency. This trade-off arises from the search strategy: sequential methods are efficient but often lack generalization, while global methods capture feature interactions but incur high computational costs due to repeated retraining. To address these limitations, we propose Interval Retention Optimization (IRO), a framework that reformulates feature selection as a continuous allocation of retention rates across wavelength intervals. Guided by global importance measures and optimized with Bayesian search, IRO leverages a mask-based perturbation strategy to evaluate candidate subsets directly on a pre-trained model, thereby eliminating retraining and significantly boosting efficiency. Experimental results demonstrate that IRO can achieve improved prediction accuracy and computational efficiency, reducing RMSEP by up to 9.10 %, improving RMSECV and R2 by up to 5.51 % and 15.20 %, respectively, and accelerating computation by up to 87.54 %. These results highlight IRO as a scalable and practical solution for spectral feature selection in complex NIR applications.
{"title":"Interval retention optimization (IRO): An efficient feature selection method for expanding spectral datasets","authors":"Yifan Cheng , Mengsheng Zhang , Chen Niu , Harse Sattar , Lianbo Guo","doi":"10.1016/j.saa.2026.127445","DOIUrl":"10.1016/j.saa.2026.127445","url":null,"abstract":"<div><div>Effective feature selection is crucial for large-scale near-infrared (NIR) spectroscopy, yet existing algorithms face a trade-off between accuracy and efficiency. This trade-off arises from the search strategy: sequential methods are efficient but often lack generalization, while global methods capture feature interactions but incur high computational costs due to repeated retraining. To address these limitations, we propose Interval Retention Optimization (IRO), a framework that reformulates feature selection as a continuous allocation of retention rates across wavelength intervals. Guided by global importance measures and optimized with Bayesian search, IRO leverages a mask-based perturbation strategy to evaluate candidate subsets directly on a pre-trained model, thereby eliminating retraining and significantly boosting efficiency. Experimental results demonstrate that IRO can achieve improved prediction accuracy and computational efficiency, reducing RMSEP by up to 9.10 %, improving RMSECV and <em>R</em><sup>2</sup> by up to 5.51 % and 15.20 %, respectively, and accelerating computation by up to 87.54 %. These results highlight IRO as a scalable and practical solution for spectral feature selection in complex NIR applications.</div></div>","PeriodicalId":433,"journal":{"name":"Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy","volume":"351 ","pages":"Article 127445"},"PeriodicalIF":4.6,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146013987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
More than 1.5 million annual deaths from invasive fungal infections underscore the demand for rapid and accurate diagnostics. Although single-cell Raman spectroscopy is a sensitive and label-free technique, its clinical translation is hindered by spectral inconsistencies between instruments. This work introduces a spectral transformer for instrument standardization (STIS), which replaces the localized linear approximations of traditional DS and PDS with a global self-attention mechanism. By encoding spectral position via embeddings and modeling full-range dependencies, STIS captures complex instrumental deviations without overfitting. Evaluated on Raman spectra from 47 clinical fungal strains, STIS markedly surpasses existing methods, raising the average correlation to 0.9897 and reducing the transfer error to 5.13%. Notably, consistent cross-device alignment is attained using only 10 standardization samples. With STIS calibration, slave instrument spectra achieve recognition accuracies of 95.74% (SVM) and 97.87% (CNN) on a held-out test set—An improvement exceeding 30% over uncalibrated data and clearly outperforming DS and PDS
{"title":"STIS: A novel approach for standardization of spectrometric instruments in fungal Raman spectroscopy","authors":"Hailong Feng, Mingyue Huang, Jing Liang, Xiaoxuan Xu, Bin Wang, Jing Xu","doi":"10.1016/j.saa.2026.127494","DOIUrl":"10.1016/j.saa.2026.127494","url":null,"abstract":"<div><div>More than 1.5 million annual deaths from invasive fungal infections underscore the demand for rapid and accurate diagnostics. Although single-cell Raman spectroscopy is a sensitive and label-free technique, its clinical translation is hindered by spectral inconsistencies between instruments. This work introduces a spectral transformer for instrument standardization (STIS), which replaces the localized linear approximations of traditional DS and PDS with a global self-attention mechanism. By encoding spectral position via embeddings and modeling full-range dependencies, STIS captures complex instrumental deviations without overfitting. Evaluated on Raman spectra from 47 clinical fungal strains, STIS markedly surpasses existing methods, raising the average correlation to 0.9897 and reducing the transfer error to 5.13%. Notably, consistent cross-device alignment is attained using only 10 standardization samples. With STIS calibration, slave instrument spectra achieve recognition accuracies of 95.74% (SVM) and 97.87% (CNN) on a held-out test set—An improvement exceeding 30% over uncalibrated data and clearly outperforming DS and PDS</div></div>","PeriodicalId":433,"journal":{"name":"Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy","volume":"351 ","pages":"Article 127494"},"PeriodicalIF":4.6,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146035684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-04-15Epub Date: 2026-01-22DOI: 10.1016/j.saa.2026.127506
Sughra Sarwar, Tahir Mehmood, Mudassir Iqbal
The natural characteristics of the infrared spectroscopic data are that it tends to distort the baseline, there is high-dimensionality and non-linear correlation that hinder reliable prediction of biochemical properties. To overcome these obstacles, this study introduces an integrated MARS–PLS2–Lasso framework that incorporates the effective baseline correction, non-linear regression, latent variable extraction, and sparse variable selection to promote the chemometric modeling accuracy and interpretability. Out of four baseline correction methods, viz. Asymmetric Least Squares (ALS), AirPLS, Polynomial fitting, and Wavelet baseline correction, the Wavelet method (sym8, Level 5) was found to be the most successful, in that it was able to represent local spectral variation with low-frequency noise. This technique achieved high predictive accuracy with RMSE = 0.2846–0.6857, MAE = 0.2371–0.5445 and MSE = 0.0810–0.4705 specifying both high model fit and minimal residual error across bacterial spectra. The Wavelet-corrected spectra revealed six key functional regions that contributed most significantly to bacterial differentiation: 720 cm−1 to 750 cm−1 (C–Cl stretching, CH bending), 1000 cm−1 to 1300 cm−1 (C–O stretching, esters, carboxylic acids), 1500 cm−1 to 1650 cm−1 (CC stretching), 1687 cm−1 to 1793 cm−1 (CO stretching, conjugated carbonyls), 2771 cm−1 to 3143 cm−1 (CH stretching, alkanes, alkenes), 3290 cm−1 to 3595 cm−1 (O–H and NH stretching ). Vibrational domains of interest are biochemical components of lipids, proteins, amides and polysaccharides that determine the structural integrity and metabolic activity of bacteria. The proposed MARS–PLS2–Lasso model leverages Multivariate Adaptive Regression Splines (MARS) to capture nonlinear relationships through adaptive basis functions, while Partial Least Squares (PLS2) extracts latent components that maximize covariance between spectral predictors and multiple bacterial responses. Lasso regularization adds sparsity to the model and reduces the complexity of the model, as well as penalizes less interesting basis functions, which overfit the model. Such a combination is used to provide a reasonable approximation of the parameter even in high-dimensional spectral data. In general, MARS–PLS2–Lasso provides a sound, interpretable, and chemically consistent way of high dimensional infrared spectral modeling. It is highly predictive, less noisy and has a more adequate manner of interpreting spectral–biochemical interactions, and thus, a bright way of bacteria modeling, spectral diagnostics and further use in bio-analytical spectroscopy.
{"title":"Advanced spectral modeling for bacterial strains: A MARS–PLS2 approach with Lasso regularization and baseline optimization","authors":"Sughra Sarwar, Tahir Mehmood, Mudassir Iqbal","doi":"10.1016/j.saa.2026.127506","DOIUrl":"10.1016/j.saa.2026.127506","url":null,"abstract":"<div><div>The natural characteristics of the infrared spectroscopic data are that it tends to distort the baseline, there is high-dimensionality and non-linear correlation that hinder reliable prediction of biochemical properties. To overcome these obstacles, this study introduces an integrated MARS–PLS2–Lasso framework that incorporates the effective baseline correction, non-linear regression, latent variable extraction, and sparse variable selection to promote the chemometric modeling accuracy and interpretability. Out of four baseline correction methods, viz. Asymmetric Least Squares (ALS), AirPLS, Polynomial fitting, and Wavelet baseline correction, the Wavelet method (sym8, Level 5) was found to be the most successful, in that it was able to represent local spectral variation with low-frequency noise. This technique achieved high predictive accuracy with RMSE = 0.2846–0.6857, MAE = 0.2371–0.5445 and MSE = 0.0810–0.4705 specifying both high model fit and minimal residual error across bacterial spectra. The Wavelet-corrected spectra revealed six key functional regions that contributed most significantly to bacterial differentiation: 720<!--> <!-->cm<sup>−1</sup> to 750<!--> <!-->cm<sup>−1</sup> (C–Cl stretching, C<img>H bending), 1000<!--> <!-->cm<sup>−1</sup> to 1300<!--> <!-->cm<sup>−1</sup> (C–O stretching, esters, carboxylic acids), 1500<!--> <!-->cm<sup>−1</sup> to 1650<!--> <!-->cm<sup>−1</sup> (C<img>C stretching), 1687<!--> <!-->cm<sup>−1</sup> to 1793<!--> <!-->cm<sup>−1</sup> (C<img>O stretching, conjugated carbonyls), 2771<!--> <!-->cm<sup>−1</sup> to 3143<!--> <!-->cm<sup>−1</sup> (C<img>H stretching, alkanes, alkenes), 3290<!--> <!-->cm<sup>−1</sup> to 3595<!--> <!-->cm<sup>−1</sup> (O–H and N<img>H stretching ). Vibrational domains of interest are biochemical components of lipids, proteins, amides and polysaccharides that determine the structural integrity and metabolic activity of bacteria. The proposed MARS–PLS2–Lasso model leverages Multivariate Adaptive Regression Splines (MARS) to capture nonlinear relationships through adaptive basis functions, while Partial Least Squares (PLS2) extracts latent components that maximize covariance between spectral predictors and multiple bacterial responses. Lasso regularization adds sparsity to the model and reduces the complexity of the model, as well as penalizes less interesting basis functions, which overfit the model. Such a combination is used to provide a reasonable approximation of the parameter even in high-dimensional spectral data. In general, MARS–PLS2–Lasso provides a sound, interpretable, and chemically consistent way of high dimensional infrared spectral modeling. It is highly predictive, less noisy and has a more adequate manner of interpreting spectral–biochemical interactions, and thus, a bright way of bacteria modeling, spectral diagnostics and further use in bio-analytical spectroscopy.</div></div>","PeriodicalId":433,"journal":{"name":"Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy","volume":"351 ","pages":"Article 127506"},"PeriodicalIF":4.6,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146036096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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