Changes In Molecular Composition Research Articles

Performance evaluation of aged asphalt rejuvenated with waste cooking oil on rheological and chemical characristics

Abstract This study investigates the influence of varying aging processes on the rheological behavior and microscopic features of bio-based recycled asphalt, focusing on the utilization of Waste Cooking Oil (WCO) as a rejuvenator. The research evaluates the rheological and fatigue characteristics of the modified binder, alongside a detailed microscopic analysis to determine the molecular composition changes in both aged and recycled asphalt. The incorporation of WCO was found to compromise rutting performance slightly, yet significantly enhance fatigue resistance and reduce susceptibility to low-temperature cracking. With the progression of aging, an increased dosage of WCO effectively mitigated the negative impacts, bringing the molecular composition and functional groups of the aged asphalt closer to that of the original material. Despite these improvements, a full restoration to the asphalt’s original properties remained elusive. These findings underscore the potential of waste bio-oil as a sustainable resource for enhancing the durability and environmental friendliness of asphalt pavements.

Going cresyl for plant cell imaging

The adventof fluorescent probesand the characterization of their photochemical properties in the past years allowed significant advances in the studies ofspatiotemporal cellular processes within complex and crowded systems.Dyesareindeedextremely useful tools forthe visualization ofcellular and subcellular structures present in living cells, as well asto studytheirdynamicand molecular composition or physiological changes. There are some areas of plant cell biology that have been more challenging to explore due to the physiology and organization of certain endomembrane compartments. In this study we characterize the labeling properties of cresyl violet as quick and inexpensive imaging agent for tracking endosomes, vacuole compartments which are usually very differentiated and categorized as more acidic as well as acidic plant compartments. Its photobleaching, labelling and cytotoxic properties are compared with other well-known and currently most used synthetic and molecular probes.

Research on loss rules of oil and gas in preserved shale cores after open air exposure

There is a large amount of oil and gas loss in traditional conventional core samples. Revealing the rules of oil and gas loss is of great significance for restore the pristine oil content and oil component in the shale. In this study, four preserved shale cores with different thermal maturity (Ro = 1.01–1.53%) and different total organic carbon content (TOC = 1.69–5.48 wt.%) were selected. The samples are obtained from the first member of the Qingshankou Formation in the Gulong Sag. Nuclear magnetic resonance (NMR) T1–T2 mapping and thermal desorption gas chromatography (TD–GC, at a constant temperature of 300°C for 3 min) were performed on the preserved cores and their replicas that were exposed in open air for different times, to study dynamic loss process and the molecular composition changes of shale oil. The results show that during exposure, shale experiences a large amount of oil loss, with a loss ratio of about 42%–78%, and the higher the maturity, the greater the loss ratio. The oil loss is mainly contributed by free oil, with a loss ratio as high as 88%. The adsorbed oil content, however, remains basically unchanged and has a good positive correlation with the TOC of shale. Once the cores were crushed, the gaseous hydrocarbon in oil was basically evaporated in just 5 min. After long-term storage, 90% of the C14- light hydrocarbon is lost, while the C14+ heavy hydrocarbon experiences basically no loss. Therefore, effective and timely analysis of preserved shales is extremely important. The oil content of uncrushed shale cores characterized by NMR T1–T2 mapping is much greater than that of the crushed sample measured by TD-GC, which means that NMR T1–T2 mapping can be important method to evaluate the original fluid saturation of shale.

Decreasing Photoreactivity and Concurrent Change in Dissolved Organic Matter Composition With Increasing Inland Water Residence Time

AbstractPhotochemical degradation of dissolved organic matter (DOM) has been the subject of numerous studies; however, its regulation along the inland water continuum is still unclear. We aimed to unravel the DOM photoreactivity and concurrent DOM compositional changes across 30 boreal aquatic ecosystems including peat waters, streams, rivers, and lakes distributed along a water residence time (WRT) gradient. Samples were subjected to a standardized exposure of simulated sunlight. We measured the apparent quantum yield (AQY), which corresponds to DOM photomineralization per photon absorbed, and the compositional change in DOM at bulk and individual compound levels in the original samples and after irradiation. AQY increased with the abundance of terrestrially derived DOM and decreased at higher WRT. Additionally, the photochemical changes in both DOM optical properties and molecular composition resembled changes along the natural boreal WRT gradient at low WRT (<3 years). Accordingly, mass spectrometry revealed that the abundance of photolabile and photoproduced molecules decreased with WRT along the boreal aquatic continuum. Our study highlights the tight link between DOM composition and DOM photodegradation. We suggest that photodegradation is an important driver of DOM composition change in waters with low WRT, where DOM is highly photoreactive.

Transport mechanism of uranyl nitrate in nanopore of geopolymer with different Si/Al ratios: Molecular dynamics simulation

Geopolymer is an amorphous cementitious material produced by geopolymerization using minerals or industrial waste as the main raw material under the action of activators. It can be used for safe treatment of heavy metal and radioactive pollution. This study applied molecular dynamics simulation to investigate the transport behaviour of uranyl nitrate in nanochannel of geopolymer, and focused on the influence of changes in the Si/Al ratio of geopolymer on the adsorption and diffusion of ions and water molecules. The simulation results described by density distribution, radial distribution function (RDF), hydrogen bonding network structure, mean square displacement (MSD) and diffusion coefficient. The density distribution shows that geopolymer has the strongest adsorption capacity for UO22+, followed by NO3−, and finally H2O. The results also indicate that the changes in molecular composition of geopolymer have a significant impact on kinetic characteristics of UO22+, NO3− and H2O. As the Si/Al ratio decreases, the adsorption capacity of geopolymer shows an upward trend, with the most significant improvement in the adsorption of UO22+. In addition, when the Si/Al ratio reduces, the migration rate of UO22+ and NO3− slows down. It could hinder the diffusion of ions in nanopores of geopolymer. The work could optimize the preparation of geopolymer adsorbent, and reveal the transport mechanism of uranyl nitrate in nanopore of geopolymer with different Si/Al ratios at the atomic scale.

Study of the changes in molecular composition of high‒oleic palm oil (Coari × La Mé) before and after physical refining

High‒oleic palm oil (HOPO) is a lipid substrate rich in biologically valuable substances. However, standard physical refining procedures result in a medium‒to‒large‒scale loss of beneficial nutritional properties. This study reports, for the first time, on the primary phytochemicals contained in HOPO before and after physical refining and the antioxidant potential of HOPO and its refined fractions, including byproducts. The composition of these compounds was elucidated using attenuated total reflection‒Fourier Transform infrared spectroscopy and gas chromatography with flame ionization detection analysis. HOPO and HOPO distilled fatty acids (HOPO‒FAD) had the highest vitamin E (1,026.34 and 6,700.13 mg kg−1, respectively) and phenolic compounds (66.24 and 176.50 mg·GAE·kg−1, respectively) contents and showed the highest percentage DPPH• inhibition (77.85% and 97.19%, respectively). If valuable phytochemicals are preserved, HOPO and HOPO‒FAD may be promising sources of functional ingredients for use in the food, pharmaceutical, and nutraceutical industries.

The molecular composition of leaf lipids changes with seasonal gradients in temperature and light among deciduous and evergreen trees in a sub-humid ecosystem

Forest canopy structure is a fundamental ecosystem attribute affecting regional and global climate through primary production by CO2 drawdown and evapotranspirative feedback. Environmental changes in temperature and light affect leaf physiology and thus canopy functioning. Leaf physiological changes may be reflected in expressed chemical compounds (e.g., leaf lipid biomarkers), that offer opportunities to characterize and quantify climatic effects on plant canopies in the present and the past. To assess this possibility, we systematically investigated the lipids from leaves of deciduous angiosperm (Quercus buckleyi, April–October 2019) and evergreen gymnosperm (Juniperus ashei, April–October 2019 and January 2020) tree species at monthly sampling intervals over one growing season in a natural sub-humid ecosystem of central Texas. Fatty acid unsaturation in Q. buckleyi and J. ashei leaves was negatively correlated with air temperature. The average chain lengths of leaf wax n-alkanols of Q. buckleyi were strongly correlated with leaf area index (LAI) and absorbed photosynthetically active radiation (APAR) (r2 > 0.5). The stigmasterol/β-sitosterol ratio was correlated with light transmittance in the canopy of Q. buckleyi, with values of the sterol ratio three-fold higher in shaded leaves than in sparse canopies. The observed seasonal changes in leaf lipid molecular composition and chain-lengths might be related to their biosynthetic responses to temperature and light stresses. Finally, we developed multi-lipid regression models resolving seasonal differences in temperature, LAI, and APAR. We posit that the specific lipid biosynthetic responses to variations in temperature and light are a basis for reconstructing terrestrial paleoenvironmental changes.

Unravelling host-pathogen interactions by biofilm infected human wound models

Approximately 80 % of persistent wound infections are affected by the presence of bacterial biofilms, resulting in a severe clinical challenge associated with prolonged healing periods, increased morbidity, and high healthcare costs. Unfortunately, in vitro models for wound infection research almost exclusively focus on early infection stages with planktonic bacteria. In this study, we present a new approach to emulate biofilm-infected human wounds by three-dimensional human in vitro systems. For this purpose, a matured biofilm consisting of the clinical key wound pathogen Pseudomonas aeruginosa was pre-cultivated on electrospun scaffolds allowing for non-destructive transfer of the matured biofilm to human in vitro wound models. We infected tissue-engineered human in vitro skin models as well as ex vivo human skin explants with the biofilm and analyzed structural tissue characteristics, biofilm growth behavior, and biofilm-tissue interactions. The structural development of biofilms in close proximity to the tissue, resulting in high bacterial burden and in vivo-like morphology, confirmed a manifest wound infection on all tested wound models, validating their applicability for general investigations of biofilm growth and structure. The extent of bacterial colonization of the wound bed, as well as the subsequent changes in molecular composition of skin tissue, were inherently linked to the characteristics of the underlying wound models including their viability and origin. Notably, the immune response observed in viable ex vivo and in vitro models was consistent with previous in vivo reports. While ex vivo models offered greater complexity and closer similarity to the in vivo conditions, in vitro models consistently demonstrated higher reproducibility. As a consequence, when focusing on direct biofilm-skin interactions, the viability of the wound models as well as their advantages and limitations should be aligned to the particular research question of future studies. Altogether, the novel model allows for a systematic investigation of host-pathogen interactions of bacterial biofilms and human wound tissue, also paving the way for development and predictive testing of novel therapeutics to combat biofilm-infected wounds.

Climate Warming-Driven Changes in the Molecular Composition of Soil Dissolved Organic Matter Across Depth: A Case Study on the Tibetan Plateau.

Dissolved organic matter (DOM) is critical for soil carbon sequestration in terrestrial ecosystems. DOM molecular composition varies with soil depth. However, the spatial heterogeneity of depth-dependent DOM in response to climate warming remains unclear, especially in alpine ecosystems. In this study, the DOM of alpine meadow soil samples was characterized comprehensively by using spectroscopy and mass spectrometry, and open-top chambers (OTCs) were employed to simulate warming. It was found that climate warming had the greatest impact on the upper layer (0-30 cm), followed by the lower layer (60-80 cm), while the middle layer (30-60 cm) was the most stable among the three soil layers. The reasons for the obvious changes in DOM in the upper and lower layers of soil were further explained based on biotic and abiotic factors. Specifically, soil nutrients (NH4+-N, NO3--N, TC, and TP) affected the molecular composition of DOM in layer L1 (0-15 cm), while pH affected layer L5 (60-80 cm). Gemmatimonadetes, Proteobacteria, and Actinobacteria played important roles in the composition of DOM in the L5 layer (60-80 cm), while the dominant fungal groups affecting the DOM composition increased in the L1 layer (0-15 cm) under warming. In summary, this research has contributed to a deeper understanding of depth-dependent changes in DOM molecular composition in alpine ecosystems.

Characterizing photochemical production carboxyl content of dissolved organic matters using absorbance spectroscopy combined with FT-ICR MS

Irradiation can significantly impact the structure, reactivity and environmental behavior of dissolved organic matter (DOM). The extent of these processes remains to be ascertained in more detail but the heterogeneity and site-specificity of DOM, and the lack of methods to characterize DOM at its environmentally-relevant concentrations make it a challenge. In this study, the differences of DOM response to photodegradation in four typical origins (i.e., surface water, sediment and intracellular and extracellular algal DOM) were tracked on the molecular-level using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS). Changes of the carboxyl and phenolic DOM moieties induced by irradiation were quantified by spectroscopic titrations, and the mechanism of functional groups affecting the changes of specific molecular composition was qualitatively proposed. The results demonstrated that intracellular algal organic matter (I-DOM) was most susceptible to photodegradation (ca. 63% DOM loss), then came extracellular algal organic matter (E-DOM) and surface water DOM (W-DOM) (ca. 15% DOM loss). Sediment DOM (S-DOM) was most resistant to irradiation, with a very small level of its mineralization. Lipids, lignin-like compounds and tannin-like compounds in I-DOM and E-DOM were relatively photo-labile. The photodegradation of lipids was related to the decarboxylation of carboxyl functional groups, while the photodegradation of tannin-like compounds was related to the rupture of phenolic functional groups. In comparison, the molecular composition of W-DOM and S-DOM was less affected by irradiation, which was also reflected in the fact that the carboxyl and phenolic functional groups were highly photo-resistant. This study showed that the photoactivity of DOM in surface water was closely related to the abundance of algae, so controlling the excessive reproduction of algae may have a positive effect on stability of quality and quantity of organic matter in surface water.

Application interval and concentration effect of gamma degraded chitosan on mulberry plant

Gamma radiation is one of the established tools to induce chain-scission of chitosan for low molecular weight chitosan preparation. The introduction of various radiation doses to chitosan powder produces degraded chitosan with various molecular ranges. They indicate different physicochemical and biological properties which are very important in product development. This study aimed to produce low molecular weight chitosan with an average molecular weight below 20 000 Da by exposing chitosan powder to gamma radiation at doses of 25, 50, 75 and 100 kGy. Then, to observe its growth-promoting activity on mulberry plants. The gamma-degraded chitosan was characterized by size exclusion chromatography-multi-angles laser light scattering (SEC-MALLS) and Fourier-Transform infrared (FTIR) to determine its weight-average molecular weight and molecular composition changes, respectively. After that, the gamma-degraded chitosan powder was dissolved in an acidic solution before spraying into mulberry. In the field, the mulberry plants were treated with 40, 80 and 100 ppm of degraded chitosan by foliar application. Each treatment consisted of 5 replicates of 2- 3 months-old mulberry plants which were randomly picked from the nursery. The control plants were treated with commercial growth promoter at concentration of 100 ppm which was applied weekly according to the farmer's practice. The study was carried out for 4.5 months at 2 different application intervals which were every two- and four-weeks’ time. The mulberry plants treated with 80 ppm and 100 ppm degraded chitosan every two- and four-weeks showed better results on an average number of leaves and fruit, respectively compared to control.

Integrating scRNA and bulk-RNA sequencing develops a cell senescence signature for analyzing tumor heterogeneity in clear cell renal cell carcinoma.

Cellular senescence (CS) plays a critical role in cancer development, including clear cell renal cell carcinoma (ccRCC). Traditional RNA sequencing cannot detect precise molecular composition changes within tumors. This study aimed to analyze cellular senescence's biochemical characteristics in ccRCC using single RNA sequencing (ScRNA-seq) and traditional RNA sequencing (Bulk RNA-seq). Researchers analyzed the biochemical characteristics of cellular senescence in ccRCC using ScRNA-seq and Bulk RNA-seq. They combined these approaches to identify differences between malignant and non-malignant phenotypes in ccRCC across three senescence-related pathways. Genes from these pathways were used to identify molecular subtypes associated with senescence, and a new risk model was constructed. The function of the gene DUSP1 in ccRCC was validated through biological experiments. The combined analysis of ScRNA-seq and Bulk RNA-seq revealed significant differences between malignant and non-malignant phenotypes in ccRCC across three senescence-related pathways. Researchers identified genes from these pathways to identify molecular subtypes associated with senescence, constructing a new risk model. Different subgroups showed significant differences in prognosis level, clinical stage and grade, immune infiltration, immunotherapy, and drug sensitivity. Senescence signature markers are practical biomarkers and predictors of molecular typing in ccRCC. Differences in prognosis level, clinical stage and grade, immune infiltration, immunotherapy, and drug sensitivity between different subgroups indicate that this approach could provide valuable insights into senescence-related treatment options and prognostic assessment for patients with ccRCC. The function of the gene DUSP1 in ccRCC was validated through biological experiments, confirming its feasibility as a novel biomarker for ccRCC. These findings suggest that targeted therapies based on senescence-related mechanisms could be an effective treatment option for ccRCC.

Loss of Selenium from Mollisol Paddy Wetlands of Cold Regions: Insights from Flow-through Reactor Experiments and Process-Based Modeling

Mollisols are critical agricultural resources for securing global food supply. Due to its health importance, selenium (Se) fate in the Mollisols attracts growing concerns. Land use change from conventional drylands to paddy wetlands impacts Se bioavailability in the vulnerable Mollisol agroecosystems. The underlying processes and mechanisms however remain elusive. Here, results of flow-through reactor experiments with paddy Mollisols from northern cold-region sites indicate that continuous flooding with surface water for 48 d induced redox zonation that facilitated the loss of Mollisol Se by up to 51%. Further process-based biogeochemical modeling suggests largest degradation rates of dissolved organic matter (DOM) in 30 cm deep Mollisols that contained the highest-level labile DOM and organic-bound Se. Electron shunting from degradation of Se-bearing DOM coupled to reductive dissolution of Se-adsorbed Fe oxides accounts mainly for Se(IV) release into the pore water. Consequent changes in DOM molecular composition make the reservoir of organic-bound Se vulnerable to flooding-induced redox zonation and likely enhance Se loss through destruction of thiolated Se and emission of gaseous Se from the Mollisol layer. This study highlights a neglected scenario where the speciation-driven loss of bioavailable Se from the paddy wetlands can be a significant consequence in the cold-region Mollisol agroecosystems.

Abstract 5561: Molecular imaging of calcification and soft tissue defines prognosis of DCIS to invasive breast cancer

Abstract Introduction: Ductal carcinoma in situ (DCIS) is a non-obligatory precursor to invasive breast cancer (IBC). Currently there are no reliable markers to indicate if DCIS will progress IBC after an initial treatment, or if it will remain as DCIS. Because of this uncertainty, standard treatment for DCIS includes surgery with or without radiotherapy. Breast microcalcifications are a common feature in the mammographic detection of DCIS and occur in around 80% of DCIS and 50% of IBC. Despite this, their potential role in the development of DCIS and with progression to IBC remains largely unexplored. The main aim of the study is to identify novel biomarkers for DCIS prognosis, based on chemical and molecular compositional changes of calcifications and their surrounding soft tissue in DCIS. Methods: Consecutive tissue section from 422 patients were analyzed using mid-infrared and Raman hyperspectral imaging and X-ray diffraction (XRD) and included (i) ‘DCIS controls’ (DCIS without recurrence) (n=193), (ii) ‘DCIS cases’ (DCIS which subsequently recurred as an invasive disease) (n=123), (iii) ‘synchronous DCIS with invasive cancer’ (n=44) and ‘benign’ (n=62) groups. Both parametrized and data mining approaches including cluster analysis, unsupervised and supervised multivariate statistical analysis and biomodelling based on leave-one-sample-out cross-validation were used to classify the data and develop DCIS prediction models. Results: Prediction modelling of 314 calcification and soft tissue spectral images from 170 patients (‘DCIS controls’=118 versus ‘DCIS cases’=52) showed an AUROC mean value of 0.85 in distinguishing DCIS that did not recur from DCIS that recurred as IBC. Prediction modelling of XRD data from 124 patients (‘DCIS controls’=67 versus ‘DCIS cases’=57) showed an AUROC mean value of 0.80. The calcification spectral features showed pathology specific changes in phosphate to carbonate ratio as well as changes in magnesium whitlockite content. The epithelial features showed changes in protein secondary structure and content indicating structural remodeling between the two groups. XRD parametrized data analysis corroborated these observations in terms of difference in whitlockite, as well as crystallinity/unit axis of the measured calcifications. The prediction models are currently being tested independently on the remaining sample data. Conclusion: Complementary chemical and molecular analysis of breast calcifications and soft tissue using spectroscopy and XRD imaging predicts the likely progression of DCIS to IBC. Subject to the ongoing validation of biomarkers, these approaches appear as promising DCIS risk assessment tools that can inform diagnosis, prognosis and treatment options. Citation Format: Jayakrupakar Nallala, Doriana Calabrese, Sarah Gosling, Esther Lips, Rachel Factor, Allison Hall, Sarah Pinder, Ihssane Bouybayoune, Elinor Sawyer, Lorraine King, Jeffrey Marks, Thomas Lynch, Donna Pinto, Jelle Wesseling, Shelley Hwang, Keith Rogers, Nick Stone, Grand Challenge PRECISION consortium. Molecular imaging of calcification and soft tissue defines prognosis of DCIS to invasive breast cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5561.

Seasonal Changes in Qualitative and Quantitative Characteristics of Humic Substances in Waters of Different Genesis: Membrane Technologies and Equilibrium Processes

Membrane filtration methods were applied in this study to research natural waters specification (and speciation). Lysimetric waters (soil waters) of background territories in different seasons are considered. Features of the change in molecular weights, elemental composition, and zeta potential of organic matter during fractionation from 8 μm to 100 kDa were found. The number of labile and non-labile speciation of some elements obtained by membrane filtration and ion-exchange separation methods were found and compared. The highest molecular weights of organic substances were found in summer samples of lysimetric waters (more than 100 kDa) with a predominance of the aromatic component in the IR spectra of the samples. Several maxima were also found in the molecular weight distribution, including the increase in autochthonous organic substances. The most stable negative zeta potential, as a stabilized colloid matter, are represented in summer (near -26 mV) and in autumn (near -22 mV) lysimetric water. A slight increase in metal ions bound into organic complexes is typical for summer and autumn samples.

Effects of Temperature, pH, and Salinity on Seed Germination of Acinos alpinus subsp. Meridionalis and FTIR Analysis of Molecular Composition Changes

This study aimed to determine the impact of three abiotic factors (Temperature, pH, and salinity) on the metabolic activities (macromolecules) and germination rate of Acinos alpinus subsp. Meridionalis (Satureja) seeds. In vitro, seed germination tests were performed in an aqueous medium. They were monitored as a function of time at different levels of temperature, NaCl concentration, and pH. The best germination rate (85.3%) was achieved at 15 °C and pH = 7. However, the germination was nil at a higher temperature (more than 25 °C), acidic pH (pH < 3.5), and higher NaCl concentration (more than >7.5 g L−1). Fourier transform infrared spectroscopy (FTIR) analysis showed an important variability of the chemical composition of germinated seeds. Indeed, the comparison of the absorbance peaks of chemical compounds in the treatments versus the control revealed significant differences in their concentrations and structures, which may justify why seeds fail to germinate under some extreme abiotic conditions. The results of this study are expected to serve as a guide for the protocols to be adopted in the ex situ conservation of this species.

Abstract P4-02-22: Breast microcalcification chemistry predicts DCIS prognosis

Abstract Introduction: Microcalcifications are a common feature in mammographic detection of ductal carcinoma in situ (DCIS), and occur in >80% of cases. Known to be present as type I (calcium oxalate-CaO) and type II (carbonated calcium hydroxyapatite-CHAP) microcalcifications, their association with DCIS and their role in the progression of DCIS to invasive breast cancer (IBC) remains unexplored. In an effort to understand the factors involved in DCIS prognosis, it is hypothesized that changes in the chemical composition of calcifications, in tandem with molecular changes in the surrounding soft tissue, will define patients with DCIS who will progress to develop IBC from those who remain with a stable DCIS phenotype. To this end, a novel label-free approach of hyperspectral imaging using mid-infrared (mid-IR) and Raman spectroscopy was used to probe calcification chemistry and molecular composition of the surrounding ductal and stromal soft tissue. The main aim of the work is to identify biomarkers for DCIS prognosis, based on chemical and molecular compositional changes of calcifications and the surrounding soft tissue. It is anticipated that the spectral biomarkers will provide patients and clinicians an informed risk assessment whether to undertake treatment for DCIS or to be placed under active surveillance. Methods: Tissue samples from 422 patient have been obtained and include (i) ‘pure DCIS’ (DCIS without recurrence) (n=193), (ii) ‘DCIS with invasive recurrence’ (DCIS from patients who subsequently were known to develop invasive disease) (n=123), (iii) ‘DCIS plus contemporaneous invasive cancer’ (n=44) and ‘benign’ (n=62) samples. Serial tissue sections were measured using mid-IR and Raman hyperspectral imaging approaches targeting the same calcification and soft tissue regions from specific DCIS ducts. Hyperspectral imaging data was initially pre-processed to digitally remove paraffin and unintended spectral interferences. The pre-processed data was subjected to cluster analysis followed by unsupervised and supervised machine learning classification models to identify spectral features associated with DCIS and its progression to IBC. Results: Cluster analysis based segmentation of hyperspectral images revealed histopathological features including calcifications, epithelium, necrotic areas, connective tissue and stroma. Spectra were extracted from each of the histopathological features using image coordinates, and biomodelling analysis was performed. Initial analysis of 314 calcification images from 170 patients with (i) ‘pure DCIS’ (n=118) and (ii) ‘DCIS with invasive recurrence’ (n=52) showed an area under the receiver operating characteristic (AUROC) mean value of 85% in distinguishing pure DCIS from DCIS that later recurred as IBC. The calcification features appeared to indicate pathology specific changes in phosphate and carbonate content as well as changes in magnesium whitlockite content. Similar analysis of the surrounding soft tissue spectral features showed an AUROC mean value of 85% (necrotic regions surrounding calcifications) and 76% (epithelium) respectively. The epithelial features showed changes in protein secondary structure and content, which together with the calcification changes indicate structural remodelling in DCIS that progresses to IBC, from those that do not. Perspectives: In the ongoing analyses of imaging data from 422 patients, it is anticipated that molecular/structural features from calcification and soft tissue imaging data will provide important cues in understanding DCIS prognosis and could be a promising way forward in determining management of DCIS risk and treatment underpinned by the identification of specific discriminatory spectral markers. Acknowledgments: This work was supported by Cancer Research UK and by KWF Kankerbestrijding (ref. C38317/A24043). Citation Format: Jayakrupakar Nallala, Doriana Calabrese, Sarah Gosling, Esther Lips, Rachel Factor, Allison Hall, Sarah E. Pinder, Ihssane Bouybayoune, Lorraine King, Jeffrey Marks, Thomas Lynch, Donna Pinto, Jelle Wesseling, E Shelley Hwang, Keith Rogers, Nick Stone. Breast microcalcification chemistry predicts DCIS prognosis [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P4-02-22.

Comprehensive evaluation and anti-inflammatory activity of “Zhi” polygonatum cyrtonema produced by the classical steaming approach

IntroductionPolygonati Rhizoma, known as “Huangjing”, was first documented in the well-known book Mingyi Bielu, written in the Chinese Han Dynasty. A "Nine-Steam-Nine-Bask" method is the best way to increase their tonic function by steaming and drying the raw rhizomes. This study was conducted with the primary objective of assessing "Zhi" P. cyrtonema qualitatively and quantitatively. Additionally, in vitro studies of the anti-inflammatory activity of "Zhi" P. cyrtonema revealed its pharmacodynamic effects and possible mechanisms of action. MethodsP. cyrtonema was steamed and dried nine times and subsequently subjected to hot water extraction and ethanol precipitation to obtain the desired P. cyrtonema polysaccharides (PCPs). Several approaches, including HPGPC-RID, NMR, and GC-MS, were used to evaluate the molecular weight, composition changes, and monosaccharide composition of PCPs during steaming. Multivariate data analysis, including PCA and HCA, was applied for the divergence analysis of "Zhi" P. cyrtonema. The anti-inflammatory effect of 4-Z PCPs on MH7A cells was evaluated using a cell viability assay. ELISA assays, DAPI staining, cell cycle assay, and scratching experiments revealed the potential mechanism. ResultsWith increasing steaming time, the color of the herb gradually changes from yellow to black and finally to dark black. In processed roots, the levels of polysaccharides decreased, while monosaccharides, such as galactose and glucose, increased. The high-molecular-weight polysaccharide was partially hydrolyzed, forming smaller polysaccharides, monosaccharides, and trace oligosaccharides. In the HPGPC profile, peak 1, with a retention time of 5.20 min and a molecular mass of 1140.51 kDa, can transform into peak 2 (6.10 min, 374.00 kDa) and peak 3 (9.71 min, 9.73 kDa). Using NMR analysis, it has been shown that 5-hydroxymethylfurfural (5-HMF), a toxic substance formed by the thermal degradation of saccharides, is present from the start of the fifth processed herb but is rare before 5-Z P. cyrtonema. The GC-MS analysis also revealed the presence of various monosaccharides, including mannose, galactose, glucose, fructose, rhamnose, arabinose, and galacturonic acid in "Zhi" P. cyrtonema. Using saccharides as variables, we were able to classify "Zhi" P. cyrtonema into four groups: fresh and 1-Z PCPs in groups A, 2-Z, 3-Z, 4-Z, 5-Z, 6-Z, 7-Z and 8-Z PCPs in group C, and 9-Z PCPs in group D. Results of the MH7A cell experiment indicate that 4-Z PCPs are more efficient than 0-Z and 9-Z PCP. After the fourth processing cycle, the differences between metabolic profiles became smaller. ConclusionsA combination of UV–Vis spectra, HPGPC-RID analysis, and NMR techniques were used in this study to achieve qualitative and quantitative analyses of "Zhi" PCPs, and we were able to make a comprehensive evaluation of "Zhi" P. cyrtonema. Meanwhile, using saccharides as variables by the HCA and PCA method, we were able to divide "Zhi" P. cyrtonema into four groups, namely fresh and 1-Z PCPs as group A, and 2-Z, 3-Z and 4-Z PCPs as group B, as well as 5-Z, 6-Z, 7-Z, 8-Z as group C, and 9-Z PCPs as group D. The anti-inflammatory activity studies indicated that the 4-Z PCPs better inhibited the growth of MH7A cells and induced apoptosis of synovial fibroblasts, suggesting that the 4-Z PCPs could be used as an anti-inflammatory reagent.

Genome-wide subcellular protein map for the flagellate parasite Trypanosoma brucei

Trypanosoma brucei is a model trypanosomatid, an important group of human, animal and plant unicellular parasites. Understanding their complex cell architecture and life cycle is challenging because, as with most eukaryotic microbes, ~50% of genome-encoded proteins have completely unknown functions. Here, using fluorescence microscopy and cell lines expressing endogenously tagged proteins, we mapped the subcellular localization of 89% of the T. brucei proteome, a resource we call TrypTag. We provide clues to function and define lineage-specific organelle adaptations for parasitism, mapping the ultraconserved cellular architecture of eukaryotes, including the first comprehensive ‘cartographic’ analysis of the eukaryotic flagellum, which is vital for morphogenesis and pathology. To demonstrate the power of this resource, we identify novel organelle subdomains and changes in molecular composition through the cell cycle. TrypTag is a transformative resource, important for hypothesis generation for both eukaryotic evolutionary molecular cell biology and fundamental parasite cell biology.

Shift in the Mode of Carbon Cycling Recorded by Biomarkers and Carbon Isotopic Compositions in the Yanchang Formation, Ordos Basin: Autotrophy vs Heterotrophy.

Organic-rich shales and mudstones have long been investigated regarding the control of source, environment, climate, etc. on the enrichment of organic carbon. However, little is documented about how autotrophy and heterotrophy influence organic carbon cycling/export. Here, we show molecular and carbon isotopic compositional changes of the shale or mudstone source rocks from the Chang 3 to 7 members of the Yanchang Formation. The Chang 7 member source rocks have higher quality (480-500 mg/g) and total organic carbon (TOC) (15.3% on average) than other member source rocks; the sterane/hopane ratio and the δ13C of organic carbon and kerogen decrease from the Chang 3 to 7 members, but Δδ ([average δ13C of n-C17 + n-C18] - [average δ13C of pristane + phytane]) increases, and no aryl isoprenoids and C40 aromatic carotenoids (e.g., isorenieratane) were observed. These low maturity biomarker features suggest that there were no water stratification, photic zone euxinia (PZE), and no obvious change in the organic matter source, and the water column is generally anoxic. A comparison of the δ13C of Pr and Ph with the δ13C of the n-C17 and n-C18 alkanes reveals a shift in the mode of carbon cycling/export (autotrophy versus heterotrophy) in the Yanchang Formation and that there was dominant heterotrophic bacterial activity or bacterial biomass in the Chang 7 member. The TOC spike in the Chang 7 member may result from boosted carbon cycling/export that improves organic carbon preservation than other members. Possible external forcings on the shift are abundant hydrothermal- or volcanic-derived metal salts as electron acceptors in the palaeowater, which is a reasonable explanation for enhanced heterotrophic bacterial activity. This finding improves our understanding of heterotrophic bacterial activity control on organic matter (OM) preservation and may be a significant supplement for understanding the ecological or environmental forcings in the Yanchang Formation, Ordos Basin.