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Human skin provides both physical integrity and immunological protection from the external environment using functionally distinct layers, cell types and extracellular matrix. Despite its central role in human health and disease, the constituent proteins of skin have not been systematically characterized. Here, we combine advanced tissue dissection methods, flow cytometry and state-of-the-art proteomics to describe a spatially-resolved quantitative proteomic atlas of human skin. We quantify 10,701 proteins as a function of their spatial location and cellular origin. The resulting protein atlas and our initial data analyses demonstrate the value of proteomics for understanding cell-type diversity within the skin. We describe the quantitative distribution of structural proteins, known and previously undescribed proteins specific to cellular subsets and those with specialized immunological functions such as cytokines and chemokines. We anticipate that this proteomic atlas of human skin will become an essential community resource for basic and translational research ( https://skin.science/ ). The human skin is a highly complex organ comprising multiple tissue layers and diverse cell types. Here, the authors present a spatially-resolved quantitative proteomic atlas of the healthy human skin, characterizing the protein profiles of four skin layers and nine cell types.

The vast extent of the Amazon Basin has historically restricted the study of its tree communities to the local and regional scales. Here, we provide empirical data on the commonness, rarity, and richness of lowland tree species across the entire Amazon Basin and Guiana Shield (Amazonia), collected in 1170 tree plots in all major forest types. Extrapolations suggest that Amazonia harbors roughly 16,000 tree species, of which just 227 (1.4%) account for half of all trees. Most of these are habitat specialists and only dominant in one or two regions of the basin. We discuss some implications of the finding that a small group of species—less diverse than the North American tree flora—accounts for half of the world’s most diverse tree community.

Environmental DNA (eDNA) is increasingly used to noninvasively monitor aquatic animals in freshwater and coastal areas. However, the use of eDNA in the open ocean (hereafter referred to OceanDNA) is still limited because of the sparse distribution of eDNA in the open ocean. Small pelagic fish have a large biomass and are widely distributed in the open ocean. We tested the performance of two OceanDNA analysis methods—species-specific qPCR (quantitative polymerase chain reaction) and MiFish metabarcoding using universal primers—to determine the distribution of small pelagic fish in the open ocean. We focused on six small pelagic fish species ( Sardinops melanostictus , Engraulis japonicus , Scomber japonicus , Scomber australasicus , Trachurus japonicus , and Cololabis saira ) and selected the Kuroshio Extension area as a testbed, because distribution of the selected species is known to be influenced by the strong frontal structure. The results from OceanDNA methods were compared to those of net sampling to test for consistency. Then, we compared the detection performance in each target fish between the using of qPCR and MiFish methods. A positive correlation was evident between the qPCR and MiFish detection results. In the ranking of the species detection rates and spatial distribution estimations, comparable similarity was observed between results derived from the qPCR and MiFish methods. In contrast, the detection rate using the qPCR method was always higher than that of the MiFish method. Amplification bias on non-target DNA and low sample DNA quantity seemed to partially result in a lower detection rate for the MiFish method; the reason is still unclear. Considering the ability of MiFish to detect large numbers of species and the quantitative nature of qPCR, the combined usage of the two methods to monitor quantitative distribution of small pelagic fish species with information of fish community structures was recommended.

Proteins are major effectors and regulators of biological processes that can elicit multiple functions depending on their interaction with other proteins. The organization of proteins into macromolecular complexes and their quantitative distribution across these complexes is, therefore, of great biological and clinical significance. In this paper, we describe an integrated experimental and computational technique to quantify hundreds of protein complexes in a single operation. The method consists of size exclusion chromatography (SEC) to fractionate native protein complexes, SWATH/DIA mass spectrometry to precisely quantify the proteins in each SEC fraction, and the computational framework CCprofiler to detect and quantify protein complexes by error‐controlled, complex‐centric analysis using prior information from generic protein interaction maps. Our analysis of the HEK293 cell line proteome delineates 462 complexes composed of 2,127 protein subunits. The technique identifies novel sub‐complexes and assembly intermediates of central regulatory complexes while assessing the quantitative subunit distribution across them. We make the toolset CCprofiler freely accessible and provide a web platform, SECexplorer , for custom exploration of the HEK293 proteome modularity. Synopsis The study presents an integrated framework for targeted, complex‐centric analysis based on size exclusion chromatography (SEC) and SWATH/DIA mass spectrometry. The workflow facilitates the parallel detection of hundreds of protein complexes and their variants at high selectivity and under error‐control. The presented workflow is based on the concept of complex‐centric proteome profiling and combines size exclusion chromatography (SEC) with SWATH/DIA mass spectrometry. The implementation of the complex‐centric data analysis is supported by the computational framework CCprofiler . Application of the SEC‐SWATH‐MS workflow to HEK293 cells led the detection and quantification of subunit distribution of 462 distinct protein complexes containing 2,127 proteins and identified novel complex variants such as assembly intermediates. The interactive platform, SECexplorer is presented to support custom complex‐centric exploration of SEC‐SWATH‐MS datasets. Graphical Abstract The study presents an integrated framework for targeted, complex‐centric analysis based on size exclusion chromatography (SEC) and SWATH/DIA mass spectrometry. The workflow facilitates the parallel detection of hundreds of protein complexes and their variants at high selectivity and under error‐control.

Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) studies on trace element concentration and their spatial distribution in CaC 2 O 4 -matrix urinary stones are important but powerfully rely on matrix-matched external calibration. In this work, CaC 2 O 4 precipitate CaOx-1 which was doped with Mg, Cr, Mn, Fe, Co, Cu, Zn, and Sr was prepared by the homogeneous co-precipitation method. It had a homogeneous distribution of major (RSD of 0.46%) and trace elements (RSD of 1.83–6.92%) due to the negligible concentration difference compared with that prepared by the heterogeneous co-precipitation method. Based on this, an analytical method for quantitative determination of elemental concentration in CaC 2 O 4 -matrix samples was established using CaOx-1 as a calibration standard, and the accuracy of this method was assessed by calibrating the elemental concentration in another synthetic CaC 2 O 4 precipitate CaOx-2 with relative deviation ( D r ) from − 11.43% (Mn) to 9.76% (Mg). Finally, a methodology for quantitative imaging of Mg, Cr, Mn, Fe, Co, Cu, Zn, and Sr in urinary stones via LA-ICP-MS was developed. From the elemental distributional maps, an annular texture can be found for Mg, Cu, Zn, and Sr, which corresponds to the annular white and brown texture in the real urinary stone. A homogeneous distribution of Fe and low concentrations of Cr and Co were found throughout the stone, while Mn was highly concentrated in the margin of the stone. All these results demonstrate that quantitative distribution patterns of Mg, Cr, Mn, Fe, Co, Cu, Zn, and Sr can be obtained by LA-ICP-MS using CaOx-1 as a calibration standard, which can provide potential evidence for urological and other medical studies. Graphical Abstract

Antarctic krill, Euphausia superba, have a circumpolar distribution but are concentrated within the south-west Atlantic sector, where they support a unique food web and a commercial fishery. Within this sector, our first goal was to produce quantitative distribution maps of all six ontogenetic life stages of krill (eggs, nauplii plus metanauplii, calyptopes, furcilia, juveniles, and adults), based on a compilation of all available post 1970s data. Using these maps, we then examined firstly whether \"hotspots\" of egg production and early stage nursery occurred, and secondly whether the available habitat was partitioned between the successive life stages during the austral summer and autumn, when krill densities can be high. To address these questions, we compiled larval krill density records and extracted data spanning 41 years (1976-2016) from the existing KRILLBASE-abundance and KRILLBASE-length-frequency databases. Although adult males and females of spawning age were widely distributed, the distribution of eggs, nauplii and metanauplii indicates that spawning is most intense over the shelf and shelf slope. This contrasts with the distributions of calyptope and furcilia larvae, which were concentrated further offshore, mainly in the Southern Scotia Sea. Juveniles, however, were strongly concentrated over shelves along the Scotia Arc. Simple environmental analyses based on water depth and mean water temperature suggest that krill associate with different habitats over the course of their life cycle. From the early to late part of the austral season, juvenile distribution moves from ocean to shelf, opposite in direction to that for adults. Such habitat partitioning may reduce intraspecific competition for food, which has been suggested to occur when densities are exceptionally high during years of strong recruitment. It also prevents any potential cannibalism by adults on younger stages. Understanding the location of krill spawning and juvenile development in relation to potentially overlapping fishing activities is needed to protect the health of the south-west Atlantic sector ecosystem.

Most catalytic, structural and regulatory functions of the cell are carried out by functional modules, typically complexes containing or consisting of proteins. The composition and abundance of these complexes and the quantitative distribution of specific proteins across different modules are therefore of major significance in basic and translational biology. However, detection and quantification of protein complexes on a proteome-wide scale is technically challenging. We have recently extended the targeted proteomics rationale to the level of native protein complex analysis (complex-centric proteome profiling). The complex-centric workflow described herein consists of size exclusion chromatography (SEC) to fractionate native protein complexes, data-independent acquisition mass spectrometry to precisely quantify the proteins in each SEC fraction based on a set of proteotypic peptides and targeted, complex-centric analysis where prior information from generic protein interaction maps is used to detect and quantify protein complexes with high selectivity and statistical error control via the computational framework CCprofiler ( https://github.com/CCprofiler/CCprofiler ). Complex-centric proteome profiling captures most proteins in complex-assembled state and reveals their organization into hundreds of complexes and complex variants observable in a given cellular state. The protocol is applicable to cultured cells and can potentially also be adapted to primary tissue and does not require any genetic engineering of the respective sample sources. At present, it requires ~8 d of wet-laboratory work, 15 d of mass spectrometry measurement time and 7 d of computational analysis. This protocol addresses the challenge of detecting and quantifying known protein complexes at the proteome level using SEC, DIA/SWATH mass spectrometry and a computational framework, CCprofiler.

Residue analyses on a grinding tool recovered at Grotta Paglicci sublayer 23A [32,614 ± 429 calibrated (cal) B.P.], Southern Italy, have demonstrated that early modern humans collected and processed various plants. The recording of starch grains attributable to Avena (oat) caryopses expands our information about the food plants used for producing flour in Europe during the Paleolithic and about the origins of a food tradition persisting up to the present in the Mediterranean basin. The quantitative distribution of the starch grains on the surface of the grinding stone furnished information about the tool handling, confirming its use as a pestlegrinder, as suggested by the wear-trace analysis. The particular state of preservation of the starch grains suggests the use of a thermal treatment before grinding, possibly to accelerate drying of the plants, making the following process easier and faster. The study clearly indicates that the exploitation of plant resources was very important for hunter–gatherer populations, to the point that the Early Gravettian inhabitants of Paglicci were able to process food plants and already possessed a wealth of knowledge that was to become widespread after the dawn of agriculture.

Breast cancer (BC) is the leading cause of cancer death among women worldwide, making the discovery and quantification of new biomarkers essential for improving diagnostic and preventive strategies to limit dissemination and improve prognosis. Essential trace metals such as Fe, Cu, and Zn may play critical roles in the pathophysiology of both benign and malignant breast tumors. However, due to the high metabolic activity and reduced element selectivity of cancer cells, also non-essential elements may be taken up and may even be implicated with disease progression. This study investigates the spatial distribution and concentrations of both essential and non-essential elements in breast tissues, assessing their potential for diagnostic applications. Laser ablation (LA)–inductively coupled plasma–mass spectrometry (ICP-MS) with a time-of-flight (ToF) mass analyzer (LA-ICP-ToF–MS) was used to inquire the distribution of almost all elements across the periodic table and their abundance in metastatic ( n  = 11), non-metastatic ( n  = 7), and healthy ( n  = 4) breast tissues. Quantification was achieved using gelatine-based standards for external calibration to quantitatively map various elements. Overall, the Fe, Cu, Zn, Sr, and Ba levels were significantly increased in tumor samples with Sr and Ba showing strong correlation, likely due to their similar chemistry. Comparison of calibrated LA-ICP-ToF–MS data with a histologic staining demonstrated the possibility to clearly differentiate between various tissue types and structures in breast tissues such as tumor niche and stroma. The levels of the studied elements were significantly higher in the tumor niche areas compared to the stroma, and for Fe, a significant accumulation was observed in the tumor niche areas from the metastatic patient group relative to the levels found in the same areas of the non-metastatic group. Graphical Abstract LA-ICP-ToF–MS was used to quantitatively map the biodistribution of essential and non-essential elements in metastatic and non-metastatic breast cancer tissues.

The distribution of biomolecules within cells changes upon aging and diseases. To quantitatively determine the spatial distribution of components inside cells, we built the user-friendly open-source 3D-cell-image analysis platform Cell Det ection and A nalysis of I ntensity L ounge (CellDetail). The algorithm within CellDetail is based on the concept of the dipole moment. CellDetail provides quantitative values for the distribution of the polarity proteins Cdc42 and Tubulin in young and aged hematopoietic stem cells (HSCs). Septin proteins form networks within cells that are critical for cell compartmentalization. We uncover a reduced level of organization of the Septin network within aged HSCs and within senescent human fibroblasts. Changes in the Septin network structure might therefore be a common feature of aging. The level of organization of the network of Septin proteins in aged HSCs can be restored to a youthful level by pharmacological attenuation of the activity of the small RhoGTPase Cdc42. Tools to determine the spatial distribution of components and their networks inside cells are not well developed. Here, authors provide the open-source 3D-cell-image analysis platform Cell Detection and Analysis of Intensity Lounge (CellDetail) for quantitative distribution analyses.