ACS Publications最新文献

The renin-angiotensin system (RAS) is involved in kidney fibrosis. We previously identified six RAS-regulated proteins (RHOB, BST1, LYPA1, GLNA, TSP1, and LAMB2) that were increased in the urine of patients with kidney allograft fibrosis, compared to patients without fibrosis. We hypothesized that these urinary RAS-regulated proteins predicted primary outcomes in kidney transplant recipients enrolled in the largest RAS inhibitor randomized controlled trial. Urine excretion of 10 peptides corresponding to the six RAS-regulated proteins was quantified using parallel reaction monitoring mass spectrometry assays (normalized by urine creatinine) in a subset of patients in the trial. Machine learning models predicting outcomes based on urine peptide excretion rates were developed and evaluated. Urine samples (n = 111) from 56 patients were collected at 0, 6, 12, and 24 months. Twenty-four primary outcomes (doubling of serum creatinine, graft loss, or death) occurred in 17 patients. Logistic regression utilizing eight peptides of TSP1, BST1, LAMB2, LYPA1, and RHOB, from the last urine sample prior to outcomes, predicted a graft loss with an AUC of 0.78 (p = 0.00001). A random forest classifier utilizing BST1 and LYPA1 peptides predicted death with an AUC of 0.80 (p = 0.0016). Urine measurements of RAS-regulated proteins may predict outcomes in kidney transplant recipients, although further prospective studies are required.

Proteomics data-dependent acquisition data sets collected with high-resolution mass-spectrometry (MS) can achieve very high-quality results, but nearly every analysis yields results that are thresholded at some accepted false discovery rate, meaning that a substantial number of results are incorrect. For study conclusions that rely on a small number of peptide-spectrum matches being correct, it is thus important to examine at least some crucial spectra to ensure that they are not one of the incorrect identifications. We present Quetzal, a peptide fragment ion spectrum annotation tool to assist researchers in annotating and examining such spectra to ensure that they correctly support study conclusions. We describe how Quetzal annotates spectra using the new Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) mzPAF standard for fragment ion peak annotation, including the Python-based code, a web-service end point that provides annotation services, and a web-based application for annotating spectra and producing publication-quality figures. We illustrate its functionality with several annotated spectra of varying complexity. Quetzal provides easily accessible functionality that can assist in the effort to ensure and demonstrate that crucial spectra support study conclusions. Quetzal is publicly available at https://proteomecentral.proteomexchange.org/quetzal/.

Metabolic perturbations of the gut microbiome have been implicated in the pathogenesis of multiple human diseases, including type-2 diabetes (T2D). However, our understanding of the global metabolic alterations of the gut microbiota in T2D and their functional roles remains limited. To address this, we conducted a high-coverage metabolomics profiling analysis of serum samples from 1282 Chinese individuals with and without T2D. Among the 220 detected microbiota-associated compounds detected, 111 were significantly altered, forming a highly interactive regulatory network associated with T2D development. Pathway enrichment and correlation analyses revealed aberrant metabolic pathways, primarily including the activation of pyrimidine metabolism, unsaturated fatty acid biosynthesis, and diverse amino acid metabolisms such as Tryptophan metabolism, Lysine metabolism, and Branched-chain amino acid biosynthesis. A microbiota-dependent biomarker panel, comprising pipecolinic acid, methoxysalicylic acid, N-acetylhistamine, and 3-hydroxybutyrylcarnitine, was defined and validated with satisfactory sensitivity (>78%) for large-scale, population-based T2D screening. The functional role of a gut microbial product, N-acetylhistamine, was further elucidated in T2D progression through its inhibition of adenosine monophosphate-activated protein kinase phosphorylation. Overall, this study expands our understanding of gut microbiota-driven metabolic dysregulation in T2D and suggests that monitoring these metabolic changes could facilitate the diagnosis and treatment of T2D.

Cell division in bacteria is initiated by constriction of the Z-ring comprising two essential proteins, FtsZ and FtsA. Though the essential function of the Z-ring in bacterial division has been established, the precise roles of FtsZ and FtsA in the constriction process remain elusive. Due to the minimal number of components, FtsZ/FtsA in cell wall-less bacteria is an ideal model system for obtaining mechanistic insights into Z-ring constriction in the absence of a cell wall synthesis machinery. In this study, we undertook a comparative analysis of FtsZ and FtsA protein sequences from 113 mycoplasma species and the corresponding sequences in cell-walled bacteria. We report a phylogenetically distinct group of 12 species that possess a putative membrane binding amphipathic helix at either the N- or C-terminal extensions of the globular FtsZ domain. Importantly, these FtsZs lack conservation of the conserved C-terminal peptide sequence. We experimentally prove that the proposed C-terminal amphipathic helix in Mycoplasma genitalium (M. genitalium) FtsZ exhibits membrane binding. Additionally, we identify a potential cholesterol recognition motif within the C-terminal amphipathic helix region of M. genitalium FtsZ. Our study catalogues the functional variations of membrane attachment by the FtsZ and FtsA system in cell wall-less mycoplasmas and provides a new perspective to dissect the role of FtsZ and FtsA in cell division.

Variation in parenting behavior is widespread across the animal kingdom, both within and between species. There are two ecotypes of the three-spined stickleback fish (Gasterosteus aculeatus) that exhibit dramatic differences in their paternal behavior. Males of the common ecotype are highly attentive fathers, tending to young from eggs to fry, while males of the white ecotype desert offspring as eggs. As the pituitary is a key regulator in the hypothalamic-pituitary-adrenal (HPA) axis and the hypothalamic-pituitary-gonadal (HPG) axis between the brain and body, its peptides may influence parenting behaviors. Here, we utilized matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) for high-throughput peptide analysis in single cells of pituitaries from both three-spined stickleback ecotypes. Peptide mass fingerprinting was performed using an in silico generated peptide library to identify detected prohormones. Differential analysis revealed POMC-derived peptides, MCH-derived peptides, and oxytocin as significantly different between the two ecotypes, with higher oxytocin levels in the common ecotype. Interestingly, these subtle chemical differences were not captured by Leiden clustering of the cellular phenotypes. These results call for further investigation of the neurochemical basis for parenting in sticklebacks.

Recent advances in numerically exact quantum dynamics methods have brought the dream of accurately modeling the dynamics of chemically complex open systems within reach. Path-integral-based methods, hierarchical equations of motion, and quantum analog simulators all require the spectral density (SD) of the environment to describe its effect on the system. Here, we focus on the decoherence dynamics of electronically excited species in solution in the common case where nonradiative electronic relaxation dominates and is much slower than electronic dephasing. We show that the computed relaxation rate is highly sensitive to the choice of SD representation─such as the Drude-Lorentz or Brownian modes─or strategy used to capture the main SD features, even when early-time dephasing dynamics remains robust. The key reason is that electronic relaxation is dominated by the resonant contribution from the high-frequency tails of the SD, which are orders of magnitude weaker than the main features of the SD and can vary significantly between strategies. This finding highlights an important, yet overlooked, numerical challenge: obtaining an accurate SD requires capturing its structure over several orders of magnitude to ensure correct decoherence dynamics at both early and late times. To address this, we provide a simple transformation that recovers the correct relaxation rates in quantum simulations constrained by algorithmic or physical limitations on the shape of the SD. Our findings enable a comparison of different numerically exact simulation methods and expand the capabilities of analog simulations of open quantum dynamics.

Histidine phosphorylation is a historically underexplored post-translational modification (PTM). Once deemed "elusive" due to its chemical lability, phosphohistidine (pHis) has recently come to light thanks to emerging chemical tools─including stable pHis analogs, pHis-specific antibodies, and tailored proteomics workflows─that enable its detection and functional analysis. Together, these innovations have led to a surge in the identification of pHis sites and raised awareness of their roles in both bacterial and mammalian systems. New assay systems have also facilitated the characterization of histidine kinases and phosphatases. This Review summarizes recent breakthroughs in pHis research tools, examines the limitations of current approaches, and outlines future tools needed to fully unravel the potential of histidine phosphorylation.

Luminescence thermometry is a remote temperature sensing technique that utilizes temperature-dependent luminescence properties. Lanthanide-doped materials with two thermally coupled emitting levels displaying a variation in luminescence intensity ratio (LIR) with temperature have been successfully explored to design sensitive luminescent thermometers. However, the low absorption strength of lanthanide parity-forbidden 4fⁿ → 4fⁿ transitions reduces the brightness. Also, this Boltzmann-type thermometer is only sensitive within a limited temperature range. To address these issues, we report here YV_1-xP_xO₄:Eu³⁺, Er³⁺ as a luminescent thermometer. This material utilizes the sensitized emission of Ln³⁺ by strong and broad vanadate charge transfer absorption and has a wide and tunable optimum temperature range by controlling the thermal quenching of Eu³⁺ emission through a variation of x. The new temperature probe offers a single material with multiple temperature-dependent luminescence properties, viz. the LIR of ²H_11/2/⁴S_3/2 emission of Er³⁺, the LIR of the integrated Er³⁺ and Eu³⁺ emission intensities, and the Eu³⁺ emission lifetime. Both micro- and nanocrystalline temperature probes are reported to achieve relative sensitivities (S_r) from ∼0.5%/K to over 5%/K in a wide temperature range of 300-873 K. To demonstrate practical applicability, the luminescent thermometer was applied to in situ chip temperature detection revealing temperature accuracies better than 1 K.

The stabilization mechanism of mesoporous silica (MS) of two different pore sizes (21 and 2.5 nm) on overloaded celecoxib (CEL) glass was investigated. Differential scanning calorimetry (DSC) measurements revealed the presence of three fractions with different molecular mobilities: free, intermediate, and rigid ones. The free fraction exhibited cold crystallization during DSC heating and was assumed to have almost the same properties as those of the bulk molecules. The rigid fraction did not exhibit either glass transition or cold crystallization behavior, which should be stabilized by interactions with the MS surface. The remaining molecules exhibited glass transition behavior without any tendency toward cold crystallization during heating, which is called the intermediate fraction. The molecular dynamics of each fraction was investigated by using broadband dielectric spectroscopy (BDS). While the intermediate and free fractions exhibited comparable mobility, the rigid fraction demonstrated pore-size-dependent behavior: enhanced and suppressed molecular mobility was observed for the rigid fraction confined in 21 and 2.5 nm-pores, respectively. Isothermal crystallization of CEL glass was investigated using DSC and BDS at 95 °C. The results revealed that the CEL glass mixed with MS with large pores exhibited slower crystallization compared to the CEL glass without MS, whereas accelerated crystallization was observed for the CEL mixed with a small amount of MS of small pores. The pore size of 21 nm was much larger than the cooperatively rearranging region (CRR) of the CEL glass, whereas the pore size of 2.5 nm was comparable to that. When the pore size was larger than that of the CRR, most of the loaded CEL molecules behaved as an intermediate fraction, presumably because the molecules could exchange inside and outside the pore. In contrast, the exchange was not likely to proceed when the pore size was comparable to or smaller than that of the CRR, leaving a large free fraction. This finding provides a deep understanding of the stabilization mechanism of overloaded pharmaceutical glass by using mesoporous materials.

Although amino acid (AA) metabolism is linked to tumor progression and could serve as an attractive intervention target, its association with neuroblastoma (NB) is unknown. Based on AA metabolism-related genes, we established three NB subtypes associated with distinct prognoses and specific functions, with C1 and C2 having better outcomes. The C1 displayed enhanced metabolic activity and recruited metabolism-associated cells. The C2 exhibited an activated immune microenvironment and was more vulnerable to immunotherapy. The C3, characterized by cell cycle peculiarity, possessed a dismal prognosis and high frequency of gene mutations and was susceptible to chemotherapy. Furthermore, single-cell RNA sequencing analysis revealed that the C3-associated Scissor+ cell subpopulation was characterized by notorious functional states and orchestrated an immunosuppressive microenvironment. Additionally, we identified that ALK and BIRC5 contributed to the shorter lifespan of C3 and their corresponding inhibitors were potential interventions. In conclusion, we identified three distinct subtypes of NB, which help us foster individualized therapeutic strategies to improve the prognosis of NB.